Starting phenix.real_space_refine on Sun Aug 9 23:49:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ynk_73210/08_2026/9ynk_73210.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ynk_73210/08_2026/9ynk_73210.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ynk_73210/08_2026/9ynk_73210.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ynk_73210/08_2026/9ynk_73210.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ynk_73210/08_2026/9ynk_73210.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ynk_73210/08_2026/9ynk_73210.map" } resolution = 3.42 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 3 9.91 5 Zn 4 6.06 5 P 15 5.49 5 S 224 5.16 5 C 24337 2.51 5 N 6503 2.21 5 O 6952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2081, 16280 Classifications: {'peptide': 2081} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 2016} Chain breaks: 22 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 687 Unresolved non-hydrogen angles: 882 Unresolved non-hydrogen dihedrals: 585 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'PHE:plan': 13, 'TYR:plan': 8, 'ASP:plan': 7, 'GLU:plan': 11, 'ASN:plan1': 16, 'ARG:plan': 7, 'HIS:plan': 5, 'GLN:plan1': 7, 'TRP:plan': 3} Unresolved non-hydrogen planarities: 362 Chain: "B" Number of atoms: 12410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1576, 12410 Classifications: {'peptide': 1576} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1531} Chain breaks: 16 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 481 Unresolved non-hydrogen angles: 626 Unresolved non-hydrogen dihedrals: 400 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'TYR:plan': 6, 'HIS:plan': 5, 'GLU:plan': 12, 'ASN:plan1': 8, 'ASP:plan': 6, 'ARG:plan': 4, 'PHE:plan': 8, 'TRP:plan': 2, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 259 Chain: "C" Number of atoms: 5780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 712, 5780 Classifications: {'peptide': 712} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 694} Chain breaks: 5 Chain: "D" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3413 Classifications: {'peptide': 416} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 404} Chain breaks: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 57 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15661 SG CYS A2562 79.177 56.532 82.038 1.00 25.83 S ATOM 15686 SG CYS A2565 80.287 60.113 82.304 1.00 28.09 S ATOM 28071 SG CYS B2562 70.820 83.752 71.389 1.00 34.19 S ATOM 28096 SG CYS B2565 73.961 84.666 69.444 1.00 34.88 S ATOM 33851 SG CYS C2562 83.628 78.482 47.520 1.00 69.67 S ATOM 33876 SG CYS C2565 86.847 76.962 48.840 1.00 59.37 S ATOM 37264 SG CYS D2562 92.319 52.982 56.699 1.00 54.27 S ATOM 37289 SG CYS D2565 93.116 53.929 60.351 1.00 52.30 S Time building chain proxies: 7.51, per 1000 atoms: 0.20 Number of scatterers: 38038 At special positions: 0 Unit cell: (147.96, 212.898, 205.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 3 19.99 S 224 16.00 P 15 15.00 O 6952 8.00 N 6503 7.00 C 24337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A2479 " - pdb=" SG CYS A2485 " distance=2.03 Simple disulfide: pdb=" SG CYS B2479 " - pdb=" SG CYS B2485 " distance=2.03 Simple disulfide: pdb=" SG CYS C2479 " - pdb=" SG CYS C2485 " distance=2.03 Simple disulfide: pdb=" SG CYS D2479 " - pdb=" SG CYS D2485 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.99 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2803 " pdb="ZN ZN A2803 " - pdb=" ND1 HIS A2587 " pdb="ZN ZN A2803 " - pdb=" NE2 HIS A2582 " pdb="ZN ZN A2803 " - pdb=" SG CYS A2562 " pdb="ZN ZN A2803 " - pdb=" SG CYS A2565 " pdb=" ZN B2802 " pdb="ZN ZN B2802 " - pdb=" NE2 HIS B2582 " pdb="ZN ZN B2802 " - pdb=" ND1 HIS B2587 " pdb="ZN ZN B2802 " - pdb=" SG CYS B2565 " pdb="ZN ZN B2802 " - pdb=" SG CYS B2562 " pdb=" ZN C2802 " pdb="ZN ZN C2802 " - pdb=" ND1 HIS C2587 " pdb="ZN ZN C2802 " - pdb=" NE2 HIS C2582 " pdb="ZN ZN C2802 " - pdb=" SG CYS C2565 " pdb="ZN ZN C2802 " - pdb=" SG CYS C2562 " pdb=" ZN D2802 " pdb="ZN ZN D2802 " - pdb=" ND1 HIS D2587 " pdb="ZN ZN D2802 " - pdb=" NE2 HIS D2582 " pdb="ZN ZN D2802 " - pdb=" SG CYS D2562 " pdb="ZN ZN D2802 " - pdb=" SG CYS D2565 " Number of angles added : 7 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9186 Finding SS restraints... Secondary structure from input PDB file: 269 helices and 20 sheets defined 75.2% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.741A pdb=" N ALA A 275 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 435 through 462 Processing helix chain 'A' and resid 465 through 485 Processing helix chain 'A' and resid 502 through 512 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 525 through 527 No H-bonds generated for 'chain 'A' and resid 525 through 527' Processing helix chain 'A' and resid 546 through 565 Processing helix chain 'A' and resid 567 through 576 Processing helix chain 'A' and resid 577 through 585 removed outlier: 4.097A pdb=" N MET A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 599 Processing helix chain 'A' and resid 602 through 610 removed outlier: 3.674A pdb=" N ILE A 610 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.726A pdb=" N ILE A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.917A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 657 removed outlier: 3.678A pdb=" N LEU A 651 " --> pdb=" O VAL A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 removed outlier: 4.271A pdb=" N ASP A 663 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 665 " --> pdb=" O ALA A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 719 Processing helix chain 'A' and resid 720 through 741 removed outlier: 3.874A pdb=" N VAL A 726 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 753 Processing helix chain 'A' and resid 757 through 767 Processing helix chain 'A' and resid 771 through 786 Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.604A pdb=" N ILE A 807 " --> pdb=" O TRP A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 820 removed outlier: 4.219A pdb=" N THR A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 829 Processing helix chain 'A' and resid 832 through 848 Processing helix chain 'A' and resid 856 through 875 removed outlier: 4.172A pdb=" N LEU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 3.995A pdb=" N ARG A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR A 888 " --> pdb=" O ARG A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 1000 Processing helix chain 'A' and resid 1027 through 1036 removed outlier: 3.915A pdb=" N ALA A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A1032 " --> pdb=" O ASP A1028 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1067 Processing helix chain 'A' and resid 1069 through 1084 removed outlier: 3.692A pdb=" N GLY A1075 " --> pdb=" O PRO A1071 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE A1084 " --> pdb=" O LEU A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1097 Processing helix chain 'A' and resid 1104 through 1125 Processing helix chain 'A' and resid 1174 through 1194 Processing helix chain 'A' and resid 1196 through 1211 removed outlier: 3.985A pdb=" N ASN A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN A1202 " --> pdb=" O LYS A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1222 removed outlier: 3.895A pdb=" N VAL A1215 " --> pdb=" O GLY A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1246 Processing helix chain 'A' and resid 1249 through 1258 Processing helix chain 'A' and resid 1259 through 1264 removed outlier: 4.497A pdb=" N PHE A1263 " --> pdb=" O HIS A1259 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1264 " --> pdb=" O LEU A1260 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1259 through 1264' Processing helix chain 'A' and resid 1267 through 1279 Processing helix chain 'A' and resid 1281 through 1286 Processing helix chain 'A' and resid 1289 through 1303 removed outlier: 4.114A pdb=" N VAL A1293 " --> pdb=" O SER A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1316 removed outlier: 3.931A pdb=" N LEU A1310 " --> pdb=" O HIS A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1343 removed outlier: 3.860A pdb=" N GLY A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU A1340 " --> pdb=" O ILE A1336 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASP A1341 " --> pdb=" O ASN A1337 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL A1342 " --> pdb=" O GLY A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1361 removed outlier: 3.548A pdb=" N LEU A1355 " --> pdb=" O SER A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1387 Processing helix chain 'A' and resid 1390 through 1401 removed outlier: 3.683A pdb=" N LYS A1396 " --> pdb=" O TYR A1392 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A1399 " --> pdb=" O ILE A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1412 removed outlier: 3.667A pdb=" N ILE A1406 " --> pdb=" O PRO A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1431 removed outlier: 3.729A pdb=" N ALA A1422 " --> pdb=" O GLU A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1461 Processing helix chain 'A' and resid 1475 through 1493 removed outlier: 4.732A pdb=" N ILE A1483 " --> pdb=" O VAL A1479 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N MET A1484 " --> pdb=" O THR A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1497 removed outlier: 3.606A pdb=" N ASP A1497 " --> pdb=" O PRO A1494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1494 through 1497' Processing helix chain 'A' and resid 1505 through 1520 Processing helix chain 'A' and resid 1526 through 1544 removed outlier: 3.739A pdb=" N SER A1532 " --> pdb=" O ALA A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1634 Proline residue: A1619 - end of helix removed outlier: 3.643A pdb=" N SER A1626 " --> pdb=" O GLN A1622 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A1627 " --> pdb=" O ALA A1623 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU A1628 " --> pdb=" O GLU A1624 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A1629 " --> pdb=" O PHE A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1638 Processing helix chain 'A' and resid 1643 through 1649 Processing helix chain 'A' and resid 1651 through 1664 removed outlier: 3.821A pdb=" N LYS A1662 " --> pdb=" O ASN A1658 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A1664 " --> pdb=" O THR A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1684 Processing helix chain 'A' and resid 1689 through 1705 Processing helix chain 'A' and resid 1741 through 1753 Processing helix chain 'A' and resid 1753 through 1765 Processing helix chain 'A' and resid 1767 through 1783 Processing helix chain 'A' and resid 1786 through 1799 Processing helix chain 'A' and resid 1802 through 1824 removed outlier: 3.595A pdb=" N THR A1824 " --> pdb=" O GLU A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1912 through 1917 Processing helix chain 'A' and resid 1917 through 1929 Processing helix chain 'A' and resid 1930 through 1932 No H-bonds generated for 'chain 'A' and resid 1930 through 1932' Processing helix chain 'A' and resid 1933 through 1940 Processing helix chain 'A' and resid 1950 through 1964 Processing helix chain 'A' and resid 1964 through 1970 Processing helix chain 'A' and resid 1972 through 1976 Processing helix chain 'A' and resid 1981 through 1997 Processing helix chain 'A' and resid 2002 through 2009 Processing helix chain 'A' and resid 2013 through 2024 removed outlier: 3.725A pdb=" N ILE A2017 " --> pdb=" O ASN A2013 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A2022 " --> pdb=" O ILE A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2026 through 2033 removed outlier: 4.312A pdb=" N TYR A2032 " --> pdb=" O PRO A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2052 removed outlier: 4.234A pdb=" N VAL A2037 " --> pdb=" O ARG A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2058 through 2066 Processing helix chain 'A' and resid 2069 through 2087 Processing helix chain 'A' and resid 2100 through 2116 Processing helix chain 'A' and resid 2119 through 2126 Processing helix chain 'A' and resid 2137 through 2145 Processing helix chain 'A' and resid 2166 through 2172 removed outlier: 3.507A pdb=" N GLU A2170 " --> pdb=" O ASN A2167 " (cutoff:3.500A) Processing helix chain 'A' and resid 2173 through 2184 Processing helix chain 'A' and resid 2192 through 2214 removed outlier: 4.393A pdb=" N GLU A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASP A2202 " --> pdb=" O GLN A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2218 through 2225 Processing helix chain 'A' and resid 2226 through 2248 Processing helix chain 'A' and resid 2288 through 2302 Processing helix chain 'A' and resid 2305 through 2331 Processing helix chain 'A' and resid 2332 through 2335 Processing helix chain 'A' and resid 2336 through 2343 Processing helix chain 'A' and resid 2343 through 2362 Processing helix chain 'A' and resid 2363 through 2371 removed outlier: 3.518A pdb=" N PHE A2369 " --> pdb=" O PHE A2366 " (cutoff:3.500A) Processing helix chain 'A' and resid 2372 through 2378 removed outlier: 3.959A pdb=" N TYR A2376 " --> pdb=" O PHE A2372 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2390 removed outlier: 3.776A pdb=" N LEU A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A2388 " --> pdb=" O VAL A2384 " (cutoff:3.500A) Processing helix chain 'A' and resid 2391 through 2416 Processing helix chain 'A' and resid 2417 through 2420 Processing helix chain 'A' and resid 2481 through 2496 Processing helix chain 'A' and resid 2499 through 2503 Processing helix chain 'A' and resid 2513 through 2528 Processing helix chain 'A' and resid 2531 through 2560 Processing helix chain 'A' and resid 2568 through 2573 removed outlier: 3.646A pdb=" N ASP A2573 " --> pdb=" O ASP A2570 " (cutoff:3.500A) Processing helix chain 'A' and resid 2578 through 2586 Processing helix chain 'A' and resid 2588 through 2602 Processing helix chain 'A' and resid 2603 through 2607 removed outlier: 3.563A pdb=" N TYR A2607 " --> pdb=" O PRO A2604 " (cutoff:3.500A) Processing helix chain 'A' and resid 2608 through 2621 Processing helix chain 'A' and resid 2631 through 2635 Processing helix chain 'B' and resid 611 through 626 Processing helix chain 'B' and resid 627 through 638 removed outlier: 4.214A pdb=" N LEU B 631 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 661 through 665 Processing helix chain 'B' and resid 709 through 719 Processing helix chain 'B' and resid 720 through 741 removed outlier: 4.166A pdb=" N VAL B 726 " --> pdb=" O ALA B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 756 removed outlier: 5.273A pdb=" N THR B 754 " --> pdb=" O ASN B 750 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN B 755 " --> pdb=" O GLN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 771 through 786 Processing helix chain 'B' and resid 812 through 820 removed outlier: 4.183A pdb=" N THR B 820 " --> pdb=" O TYR B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 829 removed outlier: 3.577A pdb=" N ARG B 824 " --> pdb=" O THR B 820 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET B 827 " --> pdb=" O SER B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 847 Processing helix chain 'B' and resid 856 through 875 removed outlier: 4.302A pdb=" N LEU B 860 " --> pdb=" O GLU B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.648A pdb=" N ARG B 887 " --> pdb=" O LEU B 883 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR B 888 " --> pdb=" O ARG B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 964 through 1000 Processing helix chain 'B' and resid 1027 through 1036 removed outlier: 3.626A pdb=" N ALA B1031 " --> pdb=" O ILE B1027 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B1032 " --> pdb=" O ASP B1028 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1067 Processing helix chain 'B' and resid 1069 through 1085 removed outlier: 3.730A pdb=" N GLY B1075 " --> pdb=" O PRO B1071 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE B1084 " --> pdb=" O LEU B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1097 Processing helix chain 'B' and resid 1102 through 1125 Processing helix chain 'B' and resid 1125 through 1130 removed outlier: 3.886A pdb=" N TRP B1129 " --> pdb=" O LYS B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1174 through 1194 Processing helix chain 'B' and resid 1196 through 1211 removed outlier: 3.894A pdb=" N ASN B1201 " --> pdb=" O LYS B1197 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN B1202 " --> pdb=" O LYS B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1222 removed outlier: 3.980A pdb=" N VAL B1215 " --> pdb=" O GLY B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1246 Processing helix chain 'B' and resid 1249 through 1258 Processing helix chain 'B' and resid 1259 through 1264 removed outlier: 3.536A pdb=" N LEU B1264 " --> pdb=" O ASN B1261 " (cutoff:3.500A) Processing helix chain 'B' and resid 1267 through 1279 Processing helix chain 'B' and resid 1281 through 1287 Processing helix chain 'B' and resid 1289 through 1303 removed outlier: 4.034A pdb=" N VAL B1293 " --> pdb=" O SER B1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 1306 through 1316 removed outlier: 4.101A pdb=" N LEU B1310 " --> pdb=" O HIS B1306 " (cutoff:3.500A) Processing helix chain 'B' and resid 1324 through 1338 Processing helix chain 'B' and resid 1351 through 1359 removed outlier: 3.643A pdb=" N LEU B1355 " --> pdb=" O SER B1351 " (cutoff:3.500A) Processing helix chain 'B' and resid 1372 through 1387 Processing helix chain 'B' and resid 1390 through 1401 removed outlier: 3.709A pdb=" N LYS B1396 " --> pdb=" O TYR B1392 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER B1399 " --> pdb=" O ILE B1395 " (cutoff:3.500A) Processing helix chain 'B' and resid 1402 through 1412 Processing helix chain 'B' and resid 1416 through 1431 removed outlier: 3.717A pdb=" N ALA B1422 " --> pdb=" O GLU B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1461 Processing helix chain 'B' and resid 1475 through 1493 removed outlier: 4.033A pdb=" N ILE B1483 " --> pdb=" O VAL B1479 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET B1484 " --> pdb=" O THR B1480 " (cutoff:3.500A) Processing helix chain 'B' and resid 1506 through 1520 removed outlier: 3.533A pdb=" N GLN B1514 " --> pdb=" O ILE B1510 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B1517 " --> pdb=" O LEU B1513 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR B1520 " --> pdb=" O ALA B1516 " (cutoff:3.500A) Processing helix chain 'B' and resid 1526 through 1542 removed outlier: 4.255A pdb=" N GLU B1542 " --> pdb=" O ARG B1538 " (cutoff:3.500A) Processing helix chain 'B' and resid 1599 through 1634 Proline residue: B1619 - end of helix removed outlier: 3.716A pdb=" N SER B1626 " --> pdb=" O GLN B1622 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B1627 " --> pdb=" O ALA B1623 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B1628 " --> pdb=" O GLU B1624 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B1629 " --> pdb=" O PHE B1625 " (cutoff:3.500A) Processing helix chain 'B' and resid 1635 through 1638 Processing helix chain 'B' and resid 1643 through 1649 Processing helix chain 'B' and resid 1651 through 1664 removed outlier: 3.874A pdb=" N LYS B1655 " --> pdb=" O ALA B1651 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS B1662 " --> pdb=" O ASN B1658 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET B1664 " --> pdb=" O THR B1660 " (cutoff:3.500A) Processing helix chain 'B' and resid 1667 through 1684 Processing helix chain 'B' and resid 1689 through 1705 Processing helix chain 'B' and resid 1741 through 1753 Processing helix chain 'B' and resid 1753 through 1765 Processing helix chain 'B' and resid 1767 through 1783 Processing helix chain 'B' and resid 1786 through 1799 Processing helix chain 'B' and resid 1802 through 1824 Processing helix chain 'B' and resid 1912 through 1917 Processing helix chain 'B' and resid 1917 through 1930 Processing helix chain 'B' and resid 1933 through 1943 removed outlier: 3.874A pdb=" N ARG B1941 " --> pdb=" O GLN B1937 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1964 Processing helix chain 'B' and resid 1964 through 1969 Processing helix chain 'B' and resid 1972 through 1977 removed outlier: 3.782A pdb=" N TYR B1976 " --> pdb=" O LEU B1972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1981 through 1997 Processing helix chain 'B' and resid 2002 through 2009 Processing helix chain 'B' and resid 2013 through 2024 removed outlier: 3.941A pdb=" N ILE B2017 " --> pdb=" O ASN B2013 " (cutoff:3.500A) Processing helix chain 'B' and resid 2026 through 2031 Processing helix chain 'B' and resid 2033 through 2052 removed outlier: 3.774A pdb=" N VAL B2037 " --> pdb=" O ARG B2033 " (cutoff:3.500A) Processing helix chain 'B' and resid 2058 through 2066 Processing helix chain 'B' and resid 2069 through 2087 removed outlier: 3.563A pdb=" N LEU B2073 " --> pdb=" O ARG B2069 " (cutoff:3.500A) Processing helix chain 'B' and resid 2100 through 2117 removed outlier: 3.778A pdb=" N ARG B2117 " --> pdb=" O HIS B2113 " (cutoff:3.500A) Processing helix chain 'B' and resid 2119 through 2126 Processing helix chain 'B' and resid 2137 through 2145 Processing helix chain 'B' and resid 2166 through 2172 removed outlier: 3.741A pdb=" N LEU B2172 " --> pdb=" O CYS B2169 " (cutoff:3.500A) Processing helix chain 'B' and resid 2173 through 2184 Processing helix chain 'B' and resid 2192 through 2216 removed outlier: 4.514A pdb=" N GLU B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASP B2202 " --> pdb=" O GLN B2198 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN B2215 " --> pdb=" O LYS B2211 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN B2216 " --> pdb=" O LYS B2212 " (cutoff:3.500A) Processing helix chain 'B' and resid 2216 through 2225 Processing helix chain 'B' and resid 2226 through 2248 Processing helix chain 'B' and resid 2288 through 2302 Processing helix chain 'B' and resid 2305 through 2331 Processing helix chain 'B' and resid 2336 through 2343 Processing helix chain 'B' and resid 2343 through 2362 Processing helix chain 'B' and resid 2363 through 2371 removed outlier: 3.700A pdb=" N PHE B2369 " --> pdb=" O PHE B2366 " (cutoff:3.500A) Processing helix chain 'B' and resid 2372 through 2378 removed outlier: 3.887A pdb=" N TYR B2376 " --> pdb=" O PHE B2372 " (cutoff:3.500A) Processing helix chain 'B' and resid 2378 through 2390 removed outlier: 3.527A pdb=" N LEU B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B2388 " --> pdb=" O VAL B2384 " (cutoff:3.500A) Processing helix chain 'B' and resid 2391 through 2416 Processing helix chain 'B' and resid 2417 through 2420 Processing helix chain 'B' and resid 2481 through 2496 Processing helix chain 'B' and resid 2498 through 2503 removed outlier: 4.220A pdb=" N GLY B2501 " --> pdb=" O GLY B2498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2513 through 2529 Processing helix chain 'B' and resid 2531 through 2561 removed outlier: 3.832A pdb=" N PHE B2537 " --> pdb=" O LEU B2533 " (cutoff:3.500A) Processing helix chain 'B' and resid 2568 through 2573 removed outlier: 3.957A pdb=" N ASP B2573 " --> pdb=" O ASP B2570 " (cutoff:3.500A) Processing helix chain 'B' and resid 2578 through 2586 Processing helix chain 'B' and resid 2588 through 2602 Processing helix chain 'B' and resid 2603 through 2607 Processing helix chain 'B' and resid 2608 through 2621 Processing helix chain 'C' and resid 1743 through 1753 removed outlier: 3.545A pdb=" N LEU C1749 " --> pdb=" O ILE C1745 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C1751 " --> pdb=" O CYS C1747 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU C1752 " --> pdb=" O LEU C1748 " (cutoff:3.500A) Processing helix chain 'C' and resid 1753 through 1765 Processing helix chain 'C' and resid 1767 through 1782 Processing helix chain 'C' and resid 1786 through 1799 removed outlier: 3.540A pdb=" N GLU C1799 " --> pdb=" O GLN C1795 " (cutoff:3.500A) Processing helix chain 'C' and resid 1802 through 1824 Processing helix chain 'C' and resid 1912 through 1929 removed outlier: 3.648A pdb=" N MET C1918 " --> pdb=" O ALA C1914 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C1919 " --> pdb=" O ILE C1915 " (cutoff:3.500A) Proline residue: C1920 - end of helix Processing helix chain 'C' and resid 1933 through 1940 Processing helix chain 'C' and resid 1950 through 1964 Processing helix chain 'C' and resid 1964 through 1970 Processing helix chain 'C' and resid 1972 through 1976 Processing helix chain 'C' and resid 1981 through 1997 removed outlier: 3.628A pdb=" N CYS C1996 " --> pdb=" O LEU C1992 " (cutoff:3.500A) Processing helix chain 'C' and resid 2002 through 2009 Processing helix chain 'C' and resid 2013 through 2024 removed outlier: 3.943A pdb=" N ILE C2017 " --> pdb=" O ASN C2013 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C2022 " --> pdb=" O ILE C2018 " (cutoff:3.500A) Processing helix chain 'C' and resid 2026 through 2031 Processing helix chain 'C' and resid 2033 through 2053 removed outlier: 3.972A pdb=" N VAL C2037 " --> pdb=" O ARG C2033 " (cutoff:3.500A) Processing helix chain 'C' and resid 2058 through 2066 Processing helix chain 'C' and resid 2069 through 2087 Processing helix chain 'C' and resid 2100 through 2116 Processing helix chain 'C' and resid 2119 through 2126 Processing helix chain 'C' and resid 2137 through 2145 Processing helix chain 'C' and resid 2166 through 2172 removed outlier: 3.515A pdb=" N TYR C2171 " --> pdb=" O ILE C2168 " (cutoff:3.500A) Processing helix chain 'C' and resid 2173 through 2184 Processing helix chain 'C' and resid 2192 through 2214 removed outlier: 4.519A pdb=" N GLU C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASP C2202 " --> pdb=" O GLN C2198 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG C2214 " --> pdb=" O GLN C2210 " (cutoff:3.500A) Processing helix chain 'C' and resid 2216 through 2225 Processing helix chain 'C' and resid 2226 through 2248 removed outlier: 3.586A pdb=" N GLY C2230 " --> pdb=" O ILE C2226 " (cutoff:3.500A) Processing helix chain 'C' and resid 2288 through 2302 Processing helix chain 'C' and resid 2305 through 2331 Processing helix chain 'C' and resid 2332 through 2335 removed outlier: 3.874A pdb=" N ARG C2335 " --> pdb=" O THR C2332 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2332 through 2335' Processing helix chain 'C' and resid 2336 through 2343 Processing helix chain 'C' and resid 2343 through 2362 Processing helix chain 'C' and resid 2363 through 2371 removed outlier: 3.570A pdb=" N PHE C2369 " --> pdb=" O PHE C2366 " (cutoff:3.500A) Processing helix chain 'C' and resid 2372 through 2378 removed outlier: 3.723A pdb=" N TYR C2376 " --> pdb=" O PHE C2372 " (cutoff:3.500A) Processing helix chain 'C' and resid 2379 through 2390 removed outlier: 3.690A pdb=" N VAL C2388 " --> pdb=" O VAL C2384 " (cutoff:3.500A) Processing helix chain 'C' and resid 2391 through 2416 Processing helix chain 'C' and resid 2417 through 2420 Processing helix chain 'C' and resid 2481 through 2496 Processing helix chain 'C' and resid 2499 through 2503 Processing helix chain 'C' and resid 2513 through 2528 Processing helix chain 'C' and resid 2531 through 2560 removed outlier: 3.933A pdb=" N PHE C2537 " --> pdb=" O LEU C2533 " (cutoff:3.500A) Processing helix chain 'C' and resid 2568 through 2572 removed outlier: 3.522A pdb=" N LYS C2571 " --> pdb=" O GLU C2568 " (cutoff:3.500A) Processing helix chain 'C' and resid 2578 through 2583 Processing helix chain 'C' and resid 2588 through 2602 Processing helix chain 'C' and resid 2603 through 2607 Processing helix chain 'C' and resid 2608 through 2621 Processing helix chain 'D' and resid 2166 through 2171 removed outlier: 3.562A pdb=" N TYR D2171 " --> pdb=" O ILE D2168 " (cutoff:3.500A) Processing helix chain 'D' and resid 2173 through 2184 Processing helix chain 'D' and resid 2192 through 2214 removed outlier: 4.194A pdb=" N GLU D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP D2202 " --> pdb=" O GLN D2198 " (cutoff:3.500A) Processing helix chain 'D' and resid 2216 through 2225 Processing helix chain 'D' and resid 2225 through 2248 removed outlier: 4.004A pdb=" N TRP D2229 " --> pdb=" O HIS D2225 " (cutoff:3.500A) Processing helix chain 'D' and resid 2288 through 2302 Processing helix chain 'D' and resid 2305 through 2331 Processing helix chain 'D' and resid 2332 through 2335 Processing helix chain 'D' and resid 2336 through 2343 Processing helix chain 'D' and resid 2343 through 2362 Processing helix chain 'D' and resid 2363 through 2371 removed outlier: 3.528A pdb=" N PHE D2366 " --> pdb=" O HIS D2363 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D2367 " --> pdb=" O GLU D2364 " (cutoff:3.500A) Processing helix chain 'D' and resid 2372 through 2378 removed outlier: 3.922A pdb=" N TYR D2376 " --> pdb=" O PHE D2372 " (cutoff:3.500A) Processing helix chain 'D' and resid 2378 through 2390 removed outlier: 3.532A pdb=" N LEU D2382 " --> pdb=" O GLU D2378 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL D2388 " --> pdb=" O VAL D2384 " (cutoff:3.500A) Processing helix chain 'D' and resid 2391 through 2416 Processing helix chain 'D' and resid 2417 through 2420 Processing helix chain 'D' and resid 2481 through 2496 Processing helix chain 'D' and resid 2499 through 2504 removed outlier: 4.204A pdb=" N VAL D2503 " --> pdb=" O GLY D2499 " (cutoff:3.500A) Processing helix chain 'D' and resid 2513 through 2528 Processing helix chain 'D' and resid 2531 through 2560 removed outlier: 3.833A pdb=" N PHE D2537 " --> pdb=" O LEU D2533 " (cutoff:3.500A) Processing helix chain 'D' and resid 2568 through 2573 removed outlier: 3.560A pdb=" N LYS D2571 " --> pdb=" O GLU D2568 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP D2573 " --> pdb=" O ASP D2570 " (cutoff:3.500A) Processing helix chain 'D' and resid 2578 through 2585 Processing helix chain 'D' and resid 2588 through 2602 Processing helix chain 'D' and resid 2603 through 2607 Processing helix chain 'D' and resid 2608 through 2620 Processing helix chain 'D' and resid 2631 through 2635 Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 151 removed outlier: 4.680A pdb=" N ARG A 148 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 130 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU A 123 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE A 14 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 217 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 161 through 164 removed outlier: 3.592A pdb=" N TYR A 162 " --> pdb=" O MET A 185 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL A 183 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 193 through 195 Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 307 Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 256 removed outlier: 4.176A pdb=" N PHE A 250 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 19.399A pdb=" N GLN A 260 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 14.486A pdb=" N THR A 419 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE A 262 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ILE A 417 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 389 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 10.840A pdb=" N SER A 400 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 15.491A pdb=" N VAL A 387 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 318 removed outlier: 6.202A pdb=" N ILE A 417 " --> pdb=" O LEU A 354 " (cutoff:3.500A) removed outlier: 11.824A pdb=" N SER A 356 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 16.179A pdb=" N LEU A 415 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 389 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 10.840A pdb=" N SER A 400 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 15.491A pdb=" N VAL A 387 " --> pdb=" O SER A 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 639 through 640 Processing sheet with id=AA8, first strand: chain 'A' and resid 667 through 671 Processing sheet with id=AA9, first strand: chain 'A' and resid 1318 through 1319 Processing sheet with id=AB1, first strand: chain 'A' and resid 2146 through 2152 Processing sheet with id=AB2, first strand: chain 'A' and resid 2422 through 2427 Processing sheet with id=AB3, first strand: chain 'B' and resid 639 through 640 Processing sheet with id=AB4, first strand: chain 'B' and resid 667 through 671 Processing sheet with id=AB5, first strand: chain 'B' and resid 1318 through 1319 Processing sheet with id=AB6, first strand: chain 'B' and resid 2146 through 2152 Processing sheet with id=AB7, first strand: chain 'B' and resid 2422 through 2427 Processing sheet with id=AB8, first strand: chain 'C' and resid 2146 through 2152 Processing sheet with id=AB9, first strand: chain 'C' and resid 2422 through 2427 Processing sheet with id=AC1, first strand: chain 'D' and resid 2146 through 2152 Processing sheet with id=AC2, first strand: chain 'D' and resid 2422 through 2427 2550 hydrogen bonds defined for protein. 7362 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.12 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12434 1.34 - 1.46: 6637 1.46 - 1.58: 19261 1.58 - 1.69: 21 1.69 - 1.81: 353 Bond restraints: 38706 Sorted by residual: bond pdb=" CG1 ILE B2213 " pdb=" CD1 ILE B2213 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.66e+00 bond pdb=" N SER A1965 " pdb=" CA SER A1965 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.31e+00 bond pdb=" C ASP B 790 " pdb=" N PRO B 791 " ideal model delta sigma weight residual 1.334 1.356 -0.022 2.34e-02 1.83e+03 8.88e-01 bond pdb=" CA GLN C1943 " pdb=" CB GLN C1943 " ideal model delta sigma weight residual 1.527 1.542 -0.015 1.61e-02 3.86e+03 8.67e-01 bond pdb=" C MET A 185 " pdb=" O MET A 185 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 8.20e-01 ... (remaining 38701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 51813 1.65 - 3.29: 469 3.29 - 4.94: 56 4.94 - 6.59: 16 6.59 - 8.24: 2 Bond angle restraints: 52356 Sorted by residual: angle pdb=" N VAL A 413 " pdb=" CA VAL A 413 " pdb=" C VAL A 413 " ideal model delta sigma weight residual 113.71 109.45 4.26 9.50e-01 1.11e+00 2.01e+01 angle pdb=" C ASP B1228 " pdb=" N GLU B1229 " pdb=" CA GLU B1229 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" N THR A1500 " pdb=" CA THR A1500 " pdb=" C THR A1500 " ideal model delta sigma weight residual 114.56 109.67 4.89 1.27e+00 6.20e-01 1.48e+01 angle pdb=" C LEU B 742 " pdb=" N ASP B 743 " pdb=" CA ASP B 743 " ideal model delta sigma weight residual 121.54 127.74 -6.20 1.91e+00 2.74e-01 1.05e+01 angle pdb=" C ASP B 854 " pdb=" N LYS B 855 " pdb=" CA LYS B 855 " ideal model delta sigma weight residual 121.54 127.27 -5.73 1.91e+00 2.74e-01 9.00e+00 ... (remaining 52351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 20795 17.86 - 35.73: 2195 35.73 - 53.59: 391 53.59 - 71.46: 75 71.46 - 89.32: 22 Dihedral angle restraints: 23478 sinusoidal: 9388 harmonic: 14090 Sorted by residual: dihedral pdb=" CA GLN A1098 " pdb=" C GLN A1098 " pdb=" N LEU A1099 " pdb=" CA LEU A1099 " ideal model delta harmonic sigma weight residual -180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA CYS C2479 " pdb=" CB CYS C2479 " pdb=" SG CYS C2479 " pdb=" SG CYS C2485 " ideal model delta sinusoidal sigma weight residual 79.00 8.58 70.42 1 2.00e+01 2.50e-03 1.60e+01 dihedral pdb=" CA CYS B2479 " pdb=" CB CYS B2479 " pdb=" SG CYS B2479 " pdb=" SG CYS B2485 " ideal model delta sinusoidal sigma weight residual 79.00 10.95 68.05 1 2.00e+01 2.50e-03 1.50e+01 ... (remaining 23475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3936 0.031 - 0.062: 1490 0.062 - 0.093: 453 0.093 - 0.124: 165 0.124 - 0.155: 5 Chirality restraints: 6049 Sorted by residual: chirality pdb=" CA ASP A1320 " pdb=" N ASP A1320 " pdb=" C ASP A1320 " pdb=" CB ASP A1320 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 chirality pdb=" CA ASP B 790 " pdb=" N ASP B 790 " pdb=" C ASP B 790 " pdb=" CB ASP B 790 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA ASP B1320 " pdb=" N ASP B1320 " pdb=" C ASP B1320 " pdb=" CB ASP B1320 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 6046 not shown) Planarity restraints: 6637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B1229 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.89e+00 pdb=" C GLU B1229 " 0.054 2.00e-02 2.50e+03 pdb=" O GLU B1229 " -0.020 2.00e-02 2.50e+03 pdb=" N LYS B1230 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A2305 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A2306 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A2306 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A2306 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C2305 " -0.032 5.00e-02 4.00e+02 4.90e-02 3.84e+00 pdb=" N PRO C2306 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO C2306 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO C2306 " -0.028 5.00e-02 4.00e+02 ... (remaining 6634 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3009 2.74 - 3.28: 38919 3.28 - 3.82: 63756 3.82 - 4.36: 71654 4.36 - 4.90: 127527 Nonbonded interactions: 304865 Sorted by model distance: nonbonded pdb=" OE2 GLU A1994 " pdb="CA CA A2804 " model vdw 2.202 2.510 nonbonded pdb=" OE2 GLU B1994 " pdb="CA CA B2803 " model vdw 2.225 2.510 nonbonded pdb=" OE1 GLU C1994 " pdb="CA CA C2803 " model vdw 2.296 2.510 nonbonded pdb=" O THR B2605 " pdb="CA CA B2803 " model vdw 2.318 2.510 nonbonded pdb=" O THR A2605 " pdb="CA CA A2804 " model vdw 2.376 2.510 ... (remaining 304860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 9.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 40.310 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.090 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 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 0.050 38726 Z= 0.143 Angle : 0.444 8.236 52371 Z= 0.243 Chirality : 0.038 0.155 6049 Planarity : 0.003 0.050 6637 Dihedral : 14.816 89.322 14280 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.02 % Allowed : 2.60 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.13), residues: 4687 helix: 2.27 (0.09), residues: 3199 sheet: -0.37 (0.33), residues: 248 loop : -0.40 (0.18), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D2186 TYR 0.014 0.001 TYR D2520 PHE 0.022 0.001 PHE A 519 TRP 0.010 0.001 TRP B2590 HIS 0.009 0.001 HIS C1932 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (38706) covalent geometry : angle 0.44145 / 0.24 (52356) SS BOND : bond 0.00328 / 0.17 ( 4) SS BOND : angle 0.76141 / 0.39 ( 8) hydrogen bonds : bond 0.10900 / 7.61 ( 2543) hydrogen bonds : angle 4.87796 / 3.47 ( 7362) metal coordination : bond 0.01101 / 0.83 ( 16) metal coordination : angle 3.72780 / 2.01 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 620 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 ARG cc_start: 0.7251 (mmt180) cc_final: 0.6967 (mtp85) REVERT: A 298 GLN cc_start: 0.7501 (mp10) cc_final: 0.7158 (mp10) REVERT: A 391 HIS cc_start: 0.6264 (t-90) cc_final: 0.5962 (t-90) REVERT: A 414 MET cc_start: 0.7189 (ppp) cc_final: 0.6800 (ppp) REVERT: A 509 MET cc_start: 0.7794 (mmp) cc_final: 0.7550 (mmt) REVERT: A 514 ILE cc_start: 0.8390 (tt) cc_final: 0.8089 (tt) REVERT: A 545 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7646 (mtm110) REVERT: A 546 TYR cc_start: 0.7943 (m-80) cc_final: 0.7545 (m-10) REVERT: A 564 GLN cc_start: 0.8512 (pp30) cc_final: 0.8054 (pp30) REVERT: A 577 ASN cc_start: 0.8041 (m-40) cc_final: 0.7813 (m-40) REVERT: A 625 ASN cc_start: 0.7538 (m110) cc_final: 0.7003 (m-40) REVERT: A 705 HIS cc_start: 0.8240 (m90) cc_final: 0.7948 (m90) REVERT: A 717 LYS cc_start: 0.8688 (ttmm) cc_final: 0.8434 (mttm) REVERT: A 992 MET cc_start: 0.8313 (mtt) cc_final: 0.8079 (mtt) REVERT: A 995 ILE cc_start: 0.8537 (tp) cc_final: 0.8301 (tp) REVERT: A 1124 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7039 (mm-30) REVERT: A 1279 MET cc_start: 0.8669 (ttp) cc_final: 0.8400 (ttt) REVERT: A 2616 GLN cc_start: 0.8483 (tp-100) cc_final: 0.8075 (tp40) REVERT: B 729 TYR cc_start: 0.8467 (t80) cc_final: 0.8219 (t80) REVERT: B 739 ARG cc_start: 0.7947 (mmm-85) cc_final: 0.7744 (mmm-85) REVERT: B 836 GLU cc_start: 0.8004 (tp30) cc_final: 0.7642 (tp30) REVERT: B 856 GLU cc_start: 0.7700 (tp30) cc_final: 0.7247 (mm-30) REVERT: B 1224 TYR cc_start: 0.7564 (p90) cc_final: 0.7172 (p90) REVERT: B 1279 MET cc_start: 0.8695 (ttp) cc_final: 0.8423 (ttp) REVERT: B 1294 GLN cc_start: 0.8405 (tt0) cc_final: 0.7908 (tt0) REVERT: B 1298 HIS cc_start: 0.8266 (t70) cc_final: 0.7938 (t-90) REVERT: B 1343 LEU cc_start: 0.8563 (mt) cc_final: 0.8224 (pp) REVERT: B 1811 TYR cc_start: 0.8045 (t80) cc_final: 0.7839 (t80) REVERT: B 2015 ILE cc_start: 0.8123 (mm) cc_final: 0.7915 (mm) REVERT: B 2031 LYS cc_start: 0.8364 (mmpt) cc_final: 0.8109 (mmpt) REVERT: B 2139 LEU cc_start: 0.7979 (mm) cc_final: 0.7720 (mp) REVERT: B 2158 MET cc_start: 0.8640 (mtm) cc_final: 0.8415 (mtm) REVERT: B 2296 LEU cc_start: 0.7969 (mt) cc_final: 0.7650 (mt) REVERT: B 2344 MET cc_start: 0.7465 (tpp) cc_final: 0.7151 (ttt) REVERT: B 2475 ILE cc_start: 0.8805 (mm) cc_final: 0.8423 (tp) REVERT: B 2616 GLN cc_start: 0.8510 (tp40) cc_final: 0.8242 (tp40) REVERT: B 2629 MET cc_start: 0.7692 (mmm) cc_final: 0.7354 (mmm) REVERT: C 1797 LEU cc_start: 0.8212 (mt) cc_final: 0.7997 (tp) REVERT: C 1806 PHE cc_start: 0.7870 (t80) cc_final: 0.7646 (t80) REVERT: C 1939 PHE cc_start: 0.8720 (t80) cc_final: 0.8148 (t80) REVERT: C 1988 ASN cc_start: 0.8428 (t0) cc_final: 0.8106 (t0) REVERT: C 2047 LEU cc_start: 0.7963 (tp) cc_final: 0.7758 (tp) REVERT: C 2071 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7679 (mmm160) REVERT: C 2189 GLN cc_start: 0.8096 (tt0) cc_final: 0.7734 (tt0) REVERT: C 2220 PHE cc_start: 0.7665 (t80) cc_final: 0.7439 (t80) REVERT: D 2310 LEU cc_start: 0.7793 (tp) cc_final: 0.7507 (mt) outliers start: 1 outliers final: 0 residues processed: 621 average time/residue: 0.2446 time to fit residues: 244.9307 Evaluate side-chains 440 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.1980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 0.7980 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A1261 ASN A1298 HIS A1786 ASN A2189 GLN A2198 GLN B1108 ASN B1283 HIS B1607 GLN B1788 GLN C1788 GLN C2160 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117329 restraints weight = 80500.669| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.71 r_work: 0.3199 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 38726 Z= 0.169 Angle : 0.488 9.467 52371 Z= 0.259 Chirality : 0.039 0.161 6049 Planarity : 0.003 0.050 6637 Dihedral : 5.497 81.877 5318 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.14 % Allowed : 7.47 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.13), residues: 4687 helix: 2.30 (0.09), residues: 3187 sheet: -0.20 (0.33), residues: 249 loop : -0.34 (0.19), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D2548 TYR 0.014 0.001 TYR D2520 PHE 0.020 0.001 PHE A1352 TRP 0.018 0.002 TRP B 697 HIS 0.006 0.001 HIS B2106 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (38706) covalent geometry : angle 0.48593 / 0.26 (52356) SS BOND : bond 0.00401 / 0.20 ( 4) SS BOND : angle 0.68792 / 0.36 ( 8) hydrogen bonds : bond 0.03877 / 2.71 ( 2543) hydrogen bonds : angle 4.22944 / 3.00 ( 7362) metal coordination : bond 0.01425 / 1.10 ( 16) metal coordination : angle 3.99689 / 2.13 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 469 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7639 (t0) cc_final: 0.7400 (t0) REVERT: A 293 ARG cc_start: 0.7140 (mmt180) cc_final: 0.6734 (mtp85) REVERT: A 298 GLN cc_start: 0.7328 (mp10) cc_final: 0.6975 (mp10) REVERT: A 391 HIS cc_start: 0.6060 (t-90) cc_final: 0.5791 (t-90) REVERT: A 414 MET cc_start: 0.6923 (ppp) cc_final: 0.6553 (ppp) REVERT: A 514 ILE cc_start: 0.8330 (tt) cc_final: 0.7885 (tp) REVERT: A 545 ARG cc_start: 0.8227 (mtm110) cc_final: 0.7887 (mtp-110) REVERT: A 564 GLN cc_start: 0.8332 (pp30) cc_final: 0.7879 (pp30) REVERT: A 625 ASN cc_start: 0.7486 (m110) cc_final: 0.6960 (m-40) REVERT: A 705 HIS cc_start: 0.7952 (m90) cc_final: 0.7465 (m90) REVERT: A 992 MET cc_start: 0.8107 (mtt) cc_final: 0.7859 (mtt) REVERT: A 995 ILE cc_start: 0.8451 (tp) cc_final: 0.8189 (tp) REVERT: A 1124 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6805 (mm-30) REVERT: A 1607 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7731 (mt0) REVERT: A 1918 MET cc_start: 0.8563 (mmm) cc_final: 0.8244 (mmm) REVERT: A 1972 LEU cc_start: 0.8279 (mt) cc_final: 0.7994 (mp) REVERT: A 2308 LEU cc_start: 0.7926 (tp) cc_final: 0.7690 (mp) REVERT: A 2309 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7574 (mp) REVERT: A 2616 GLN cc_start: 0.8216 (tp-100) cc_final: 0.7891 (tp40) REVERT: B 739 ARG cc_start: 0.7933 (mmm-85) cc_final: 0.7724 (mmm-85) REVERT: B 836 GLU cc_start: 0.7961 (tp30) cc_final: 0.7627 (tp30) REVERT: B 1067 HIS cc_start: 0.7769 (OUTLIER) cc_final: 0.7476 (t-90) REVERT: B 1129 TRP cc_start: 0.8369 (p-90) cc_final: 0.8127 (p-90) REVERT: B 1231 MET cc_start: 0.7209 (mmt) cc_final: 0.7003 (mmt) REVERT: B 1274 MET cc_start: 0.8526 (mmm) cc_final: 0.8193 (mmm) REVERT: B 1279 MET cc_start: 0.8649 (ttp) cc_final: 0.8413 (ttp) REVERT: B 1294 GLN cc_start: 0.8243 (tt0) cc_final: 0.7849 (tt0) REVERT: B 1298 HIS cc_start: 0.8319 (t70) cc_final: 0.8073 (t-90) REVERT: B 1342 VAL cc_start: 0.7922 (OUTLIER) cc_final: 0.7592 (m) REVERT: B 1811 TYR cc_start: 0.8094 (t80) cc_final: 0.7862 (t80) REVERT: B 2139 LEU cc_start: 0.7947 (mm) cc_final: 0.7703 (mp) REVERT: B 2296 LEU cc_start: 0.7791 (mt) cc_final: 0.7461 (mt) REVERT: B 2344 MET cc_start: 0.7253 (tpp) cc_final: 0.6842 (tmm) REVERT: B 2475 ILE cc_start: 0.8926 (mm) cc_final: 0.8560 (tp) REVERT: C 1797 LEU cc_start: 0.8226 (mt) cc_final: 0.7997 (tp) REVERT: C 1806 PHE cc_start: 0.7820 (t80) cc_final: 0.7555 (t80) REVERT: C 1980 LYS cc_start: 0.8614 (tttt) cc_final: 0.7874 (tptp) REVERT: C 1996 CYS cc_start: 0.7638 (m) cc_final: 0.6907 (p) REVERT: C 2071 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7685 (mmm160) REVERT: C 2189 GLN cc_start: 0.7863 (tt0) cc_final: 0.7596 (tt0) REVERT: C 2220 PHE cc_start: 0.7633 (t80) cc_final: 0.7114 (t80) REVERT: C 2475 ILE cc_start: 0.8804 (mm) cc_final: 0.8244 (tt) REVERT: D 2310 LEU cc_start: 0.7540 (tp) cc_final: 0.7253 (mt) REVERT: D 2559 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8433 (mmtt) outliers start: 46 outliers final: 27 residues processed: 494 average time/residue: 0.2262 time to fit residues: 182.8957 Evaluate side-chains 458 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 428 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2309 ILE Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1229 GLU Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 PHE Chi-restraints excluded: chain B residue 1615 HIS Chi-restraints excluded: chain B residue 1617 PHE Chi-restraints excluded: chain B residue 1632 LEU Chi-restraints excluded: chain B residue 1947 THR Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain C residue 1961 CYS Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2396 ILE Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 427 optimal weight: 2.9990 chunk 354 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 chunk 380 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 312 optimal weight: 0.0870 chunk 262 optimal weight: 2.9990 chunk 173 optimal weight: 0.0870 overall best weight: 1.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 461 ASN A 577 ASN A 582 GLN A1204 GLN A1298 HIS A2198 GLN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS B1607 GLN D2198 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.132099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116030 restraints weight = 82050.412| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.79 r_work: 0.3187 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 38726 Z= 0.165 Angle : 0.476 10.370 52371 Z= 0.253 Chirality : 0.039 0.153 6049 Planarity : 0.003 0.051 6637 Dihedral : 5.466 82.316 5318 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.17 % Allowed : 9.70 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.13), residues: 4687 helix: 2.29 (0.09), residues: 3189 sheet: -0.04 (0.34), residues: 247 loop : -0.37 (0.19), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1600 TYR 0.014 0.001 TYR D2520 PHE 0.022 0.001 PHE A1352 TRP 0.016 0.002 TRP B 697 HIS 0.005 0.001 HIS B2106 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (38706) covalent geometry : angle 0.47381 / 0.25 (52356) SS BOND : bond 0.00392 / 0.20 ( 4) SS BOND : angle 0.63749 / 0.34 ( 8) hydrogen bonds : bond 0.03762 / 2.63 ( 2543) hydrogen bonds : angle 4.15251 / 2.95 ( 7362) metal coordination : bond 0.01377 / 1.06 ( 16) metal coordination : angle 3.98553 / 2.13 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 450 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7701 (t0) cc_final: 0.7303 (t0) REVERT: A 293 ARG cc_start: 0.7130 (mmt180) cc_final: 0.6724 (mtp85) REVERT: A 298 GLN cc_start: 0.7377 (mp10) cc_final: 0.6992 (mp10) REVERT: A 391 HIS cc_start: 0.6060 (t-90) cc_final: 0.5851 (t-90) REVERT: A 414 MET cc_start: 0.6857 (ppp) cc_final: 0.6534 (ppp) REVERT: A 446 ASN cc_start: 0.7417 (t0) cc_final: 0.7216 (t0) REVERT: A 509 MET cc_start: 0.7997 (mmt) cc_final: 0.7561 (tpp) REVERT: A 514 ILE cc_start: 0.8097 (tt) cc_final: 0.7717 (tp) REVERT: A 545 ARG cc_start: 0.8292 (mtm110) cc_final: 0.8039 (mtm110) REVERT: A 564 GLN cc_start: 0.8341 (pp30) cc_final: 0.7877 (pp30) REVERT: A 585 ILE cc_start: 0.8611 (tp) cc_final: 0.8389 (tp) REVERT: A 625 ASN cc_start: 0.7490 (m110) cc_final: 0.6970 (m-40) REVERT: A 705 HIS cc_start: 0.7951 (m90) cc_final: 0.7400 (m90) REVERT: A 992 MET cc_start: 0.8127 (mtt) cc_final: 0.7868 (mtt) REVERT: A 995 ILE cc_start: 0.8453 (tp) cc_final: 0.8163 (tp) REVERT: A 1124 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6803 (mm-30) REVERT: A 1210 MET cc_start: 0.8108 (mmm) cc_final: 0.7803 (mmm) REVERT: A 1274 MET cc_start: 0.8253 (mmp) cc_final: 0.7990 (mmt) REVERT: A 1607 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7738 (mt0) REVERT: A 1972 LEU cc_start: 0.8288 (mt) cc_final: 0.7988 (mp) REVERT: A 2291 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.5951 (tt) REVERT: A 2309 ILE cc_start: 0.7762 (OUTLIER) cc_final: 0.7535 (mp) REVERT: A 2616 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7850 (tp40) REVERT: B 739 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7156 (mmm-85) REVERT: B 836 GLU cc_start: 0.7990 (tp30) cc_final: 0.7660 (tp30) REVERT: B 992 MET cc_start: 0.7826 (mtp) cc_final: 0.7587 (mtp) REVERT: B 1067 HIS cc_start: 0.7750 (OUTLIER) cc_final: 0.7473 (t-90) REVERT: B 1129 TRP cc_start: 0.8339 (p-90) cc_final: 0.8066 (p-90) REVERT: B 1274 MET cc_start: 0.8546 (mmm) cc_final: 0.8141 (mmm) REVERT: B 1279 MET cc_start: 0.8683 (ttp) cc_final: 0.8448 (ttp) REVERT: B 1294 GLN cc_start: 0.8257 (tt0) cc_final: 0.7853 (tt0) REVERT: B 1298 HIS cc_start: 0.8332 (t70) cc_final: 0.8078 (t-90) REVERT: B 1342 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7514 (m) REVERT: B 1343 LEU cc_start: 0.8624 (tp) cc_final: 0.8207 (tt) REVERT: B 2031 LYS cc_start: 0.8507 (mmpt) cc_final: 0.8139 (ptpt) REVERT: B 2139 LEU cc_start: 0.7947 (mm) cc_final: 0.7703 (mp) REVERT: B 2296 LEU cc_start: 0.7781 (mt) cc_final: 0.7445 (mt) REVERT: B 2344 MET cc_start: 0.7232 (tpp) cc_final: 0.6830 (tmm) REVERT: B 2475 ILE cc_start: 0.8921 (mm) cc_final: 0.8529 (tp) REVERT: C 1797 LEU cc_start: 0.8233 (mt) cc_final: 0.8000 (tp) REVERT: C 1806 PHE cc_start: 0.7749 (t80) cc_final: 0.7514 (t80) REVERT: C 2047 LEU cc_start: 0.8059 (tp) cc_final: 0.7855 (tp) REVERT: C 2189 GLN cc_start: 0.7892 (tt0) cc_final: 0.7600 (tt0) REVERT: C 2475 ILE cc_start: 0.8811 (mm) cc_final: 0.8250 (tt) REVERT: D 2310 LEU cc_start: 0.7521 (tp) cc_final: 0.7226 (mt) outliers start: 47 outliers final: 32 residues processed: 474 average time/residue: 0.2253 time to fit residues: 175.2001 Evaluate side-chains 459 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 423 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2309 ILE Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1229 GLU Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1297 VAL Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 PHE Chi-restraints excluded: chain B residue 1615 HIS Chi-restraints excluded: chain B residue 1617 PHE Chi-restraints excluded: chain B residue 1632 LEU Chi-restraints excluded: chain B residue 1947 THR Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2576 THR Chi-restraints excluded: chain C residue 1961 CYS Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2198 GLN Chi-restraints excluded: chain D residue 2242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 137 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 354 optimal weight: 0.6980 chunk 172 optimal weight: 0.7980 chunk 379 optimal weight: 0.0980 chunk 232 optimal weight: 2.9990 chunk 342 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 359 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN A1298 HIS A2189 GLN A2198 GLN ** B1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS B1818 GLN D2198 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.128279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113259 restraints weight = 84209.781| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.52 r_work: 0.3220 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 38726 Z= 0.114 Angle : 0.444 11.129 52371 Z= 0.236 Chirality : 0.037 0.147 6049 Planarity : 0.003 0.050 6637 Dihedral : 5.338 83.710 5318 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.39 % Allowed : 10.37 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.13), residues: 4687 helix: 2.38 (0.09), residues: 3195 sheet: 0.08 (0.34), residues: 247 loop : -0.33 (0.19), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2071 TYR 0.012 0.001 TYR D2520 PHE 0.021 0.001 PHE C1958 TRP 0.017 0.001 TRP B 697 HIS 0.004 0.000 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (38706) covalent geometry : angle 0.44236 / 0.24 (52356) SS BOND : bond 0.00193 / 0.10 ( 4) SS BOND : angle 0.55494 / 0.30 ( 8) hydrogen bonds : bond 0.03360 / 2.35 ( 2543) hydrogen bonds : angle 4.01334 / 2.84 ( 7362) metal coordination : bond 0.00760 / 0.55 ( 16) metal coordination : angle 3.28780 / 1.78 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 443 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7620 (t0) cc_final: 0.7171 (t0) REVERT: A 293 ARG cc_start: 0.7057 (mmt180) cc_final: 0.6684 (mtp85) REVERT: A 298 GLN cc_start: 0.7361 (mp10) cc_final: 0.6954 (mp10) REVERT: A 414 MET cc_start: 0.6856 (ppp) cc_final: 0.6557 (ppp) REVERT: A 446 ASN cc_start: 0.7428 (t0) cc_final: 0.7227 (t0) REVERT: A 545 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7927 (mtp-110) REVERT: A 564 GLN cc_start: 0.8338 (pp30) cc_final: 0.7863 (pp30) REVERT: A 585 ILE cc_start: 0.8708 (tp) cc_final: 0.8486 (tp) REVERT: A 625 ASN cc_start: 0.7478 (m110) cc_final: 0.6971 (m-40) REVERT: A 705 HIS cc_start: 0.7881 (m90) cc_final: 0.7423 (m90) REVERT: A 992 MET cc_start: 0.8037 (mtt) cc_final: 0.7780 (mtt) REVERT: A 995 ILE cc_start: 0.8481 (tp) cc_final: 0.8192 (tp) REVERT: A 1124 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6754 (mm-30) REVERT: A 1210 MET cc_start: 0.7994 (mmm) cc_final: 0.7713 (mmm) REVERT: A 1274 MET cc_start: 0.8194 (mmp) cc_final: 0.7909 (mmt) REVERT: A 1607 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7707 (mt0) REVERT: A 1972 LEU cc_start: 0.8250 (mt) cc_final: 0.7932 (mp) REVERT: A 2291 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6021 (tt) REVERT: A 2309 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7545 (mp) REVERT: A 2616 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7566 (tp-100) REVERT: B 782 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.7203 (ttp) REVERT: B 836 GLU cc_start: 0.7941 (tp30) cc_final: 0.7591 (tp30) REVERT: B 992 MET cc_start: 0.7761 (mtp) cc_final: 0.7541 (mtp) REVERT: B 1129 TRP cc_start: 0.8320 (p-90) cc_final: 0.8112 (p-90) REVERT: B 1224 TYR cc_start: 0.7669 (p90) cc_final: 0.7279 (p90) REVERT: B 1279 MET cc_start: 0.8636 (ttp) cc_final: 0.8411 (ttp) REVERT: B 1294 GLN cc_start: 0.8187 (tt0) cc_final: 0.7730 (tt0) REVERT: B 1298 HIS cc_start: 0.8264 (t70) cc_final: 0.8031 (t-90) REVERT: B 1342 VAL cc_start: 0.7846 (OUTLIER) cc_final: 0.7509 (m) REVERT: B 1343 LEU cc_start: 0.8637 (tp) cc_final: 0.8220 (tt) REVERT: B 2031 LYS cc_start: 0.8480 (mmpt) cc_final: 0.8119 (ptpt) REVERT: B 2085 LEU cc_start: 0.7450 (mp) cc_final: 0.7233 (mt) REVERT: B 2139 LEU cc_start: 0.7934 (mm) cc_final: 0.7633 (mt) REVERT: B 2296 LEU cc_start: 0.7836 (mt) cc_final: 0.7493 (mt) REVERT: B 2344 MET cc_start: 0.7205 (tpp) cc_final: 0.6810 (tmm) REVERT: B 2475 ILE cc_start: 0.8906 (mm) cc_final: 0.8510 (tp) REVERT: C 1797 LEU cc_start: 0.8179 (mt) cc_final: 0.7957 (tp) REVERT: C 1806 PHE cc_start: 0.7775 (t80) cc_final: 0.7553 (t80) REVERT: C 2189 GLN cc_start: 0.7818 (tt0) cc_final: 0.7524 (tt0) REVERT: D 2310 LEU cc_start: 0.7497 (tp) cc_final: 0.7240 (mt) outliers start: 56 outliers final: 35 residues processed: 472 average time/residue: 0.2221 time to fit residues: 172.3076 Evaluate side-chains 453 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 414 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 288 HIS Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2309 ILE Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain A residue 2479 CYS Chi-restraints excluded: chain A residue 2635 VAL Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1177 ASN Chi-restraints excluded: chain B residue 1229 GLU Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1297 VAL Chi-restraints excluded: chain B residue 1330 MET Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 PHE Chi-restraints excluded: chain B residue 1615 HIS Chi-restraints excluded: chain B residue 1632 LEU Chi-restraints excluded: chain B residue 1947 THR Chi-restraints excluded: chain B residue 2158 MET Chi-restraints excluded: chain B residue 2632 MET Chi-restraints excluded: chain C residue 1961 CYS Chi-restraints excluded: chain C residue 2308 LEU Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 270 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 133 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 276 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 409 optimal weight: 4.9990 chunk 382 optimal weight: 9.9990 chunk 290 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN A 582 GLN A1174 ASN A1298 HIS A2198 GLN ** B1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS C1944 ASN D2198 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.127991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.112880 restraints weight = 84354.729| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.61 r_work: 0.3204 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38726 Z= 0.138 Angle : 0.453 8.555 52371 Z= 0.240 Chirality : 0.038 0.146 6049 Planarity : 0.003 0.050 6637 Dihedral : 5.304 84.075 5318 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.69 % Allowed : 10.76 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.13), residues: 4687 helix: 2.38 (0.09), residues: 3195 sheet: 0.13 (0.35), residues: 247 loop : -0.31 (0.19), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1291 TYR 0.014 0.001 TYR D2520 PHE 0.029 0.001 PHE A 482 TRP 0.018 0.001 TRP B 697 HIS 0.004 0.001 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (38706) covalent geometry : angle 0.45061 / 0.24 (52356) SS BOND : bond 0.00325 / 0.16 ( 4) SS BOND : angle 0.69903 / 0.37 ( 8) hydrogen bonds : bond 0.03473 / 2.42 ( 2543) hydrogen bonds : angle 4.00013 / 2.84 ( 7362) metal coordination : bond 0.01101 / 0.84 ( 16) metal coordination : angle 3.65445 / 1.96 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 444 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7629 (t0) cc_final: 0.7135 (t0) REVERT: A 293 ARG cc_start: 0.7115 (mmt180) cc_final: 0.6733 (mtp85) REVERT: A 298 GLN cc_start: 0.7417 (mp10) cc_final: 0.7027 (mp10) REVERT: A 414 MET cc_start: 0.6873 (ppp) cc_final: 0.6528 (ppp) REVERT: A 478 ASP cc_start: 0.8000 (t0) cc_final: 0.7518 (t0) REVERT: A 545 ARG cc_start: 0.8202 (mtm110) cc_final: 0.7959 (mtm110) REVERT: A 564 GLN cc_start: 0.8340 (pp30) cc_final: 0.7853 (pp30) REVERT: A 585 ILE cc_start: 0.8767 (tp) cc_final: 0.8529 (tp) REVERT: A 625 ASN cc_start: 0.7482 (m110) cc_final: 0.6969 (m-40) REVERT: A 705 HIS cc_start: 0.7890 (m90) cc_final: 0.7417 (m90) REVERT: A 782 MET cc_start: 0.8289 (ttt) cc_final: 0.7985 (ttt) REVERT: A 992 MET cc_start: 0.8091 (mtt) cc_final: 0.7832 (mtt) REVERT: A 995 ILE cc_start: 0.8515 (tp) cc_final: 0.8239 (tp) REVERT: A 1124 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6787 (mm-30) REVERT: A 1210 MET cc_start: 0.8033 (mmm) cc_final: 0.7733 (mmm) REVERT: A 1274 MET cc_start: 0.8181 (mmp) cc_final: 0.7901 (mmt) REVERT: A 1607 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7703 (mt0) REVERT: A 2291 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.6030 (tt) REVERT: A 2309 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7532 (mp) REVERT: A 2616 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7577 (tp-100) REVERT: B 782 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7174 (ttp) REVERT: B 836 GLU cc_start: 0.7929 (tp30) cc_final: 0.7580 (tp30) REVERT: B 1224 TYR cc_start: 0.7572 (p90) cc_final: 0.7367 (p90) REVERT: B 1274 MET cc_start: 0.8543 (mmm) cc_final: 0.8145 (tpp) REVERT: B 1279 MET cc_start: 0.8643 (ttp) cc_final: 0.8412 (ttp) REVERT: B 1294 GLN cc_start: 0.8211 (tt0) cc_final: 0.7746 (tt0) REVERT: B 1298 HIS cc_start: 0.8291 (t70) cc_final: 0.8047 (t-90) REVERT: B 1343 LEU cc_start: 0.8634 (tp) cc_final: 0.8257 (tt) REVERT: B 2031 LYS cc_start: 0.8490 (mmpt) cc_final: 0.8128 (ptpt) REVERT: B 2139 LEU cc_start: 0.7940 (mm) cc_final: 0.7706 (mp) REVERT: B 2296 LEU cc_start: 0.7832 (mt) cc_final: 0.7477 (mt) REVERT: B 2344 MET cc_start: 0.7206 (tpp) cc_final: 0.6805 (tmm) REVERT: C 1797 LEU cc_start: 0.8193 (mt) cc_final: 0.7813 (tp) REVERT: C 1806 PHE cc_start: 0.7764 (t80) cc_final: 0.7510 (t80) REVERT: C 1814 MET cc_start: 0.8057 (mtt) cc_final: 0.7726 (mtp) REVERT: C 1980 LYS cc_start: 0.8599 (tttt) cc_final: 0.7933 (tptp) REVERT: C 2077 MET cc_start: 0.7871 (ttm) cc_final: 0.7622 (ttm) REVERT: C 2189 GLN cc_start: 0.7875 (tt0) cc_final: 0.7576 (tt0) REVERT: D 2310 LEU cc_start: 0.7484 (tp) cc_final: 0.7215 (mt) REVERT: D 2475 ILE cc_start: 0.8938 (mm) cc_final: 0.8669 (tp) outliers start: 68 outliers final: 40 residues processed: 477 average time/residue: 0.2519 time to fit residues: 196.4056 Evaluate side-chains 466 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 423 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1336 ILE Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2309 ILE Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain A residue 2479 CYS Chi-restraints excluded: chain A residue 2635 VAL Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1229 GLU Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1297 VAL Chi-restraints excluded: chain B residue 1330 MET Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 PHE Chi-restraints excluded: chain B residue 1615 HIS Chi-restraints excluded: chain B residue 1617 PHE Chi-restraints excluded: chain B residue 1632 LEU Chi-restraints excluded: chain B residue 1947 THR Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain C residue 1961 CYS Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2198 GLN Chi-restraints excluded: chain D residue 2227 SER Chi-restraints excluded: chain D residue 2242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 271 optimal weight: 10.0000 chunk 56 optimal weight: 0.0000 chunk 194 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 330 optimal weight: 1.9990 chunk 417 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 270 optimal weight: 9.9990 chunk 377 optimal weight: 3.9990 chunk 315 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A 577 ASN A 582 GLN A1298 HIS A2189 GLN ** B1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS D2198 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.127903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112588 restraints weight = 84490.619| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.65 r_work: 0.3193 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 38726 Z= 0.165 Angle : 0.475 11.705 52371 Z= 0.250 Chirality : 0.039 0.158 6049 Planarity : 0.003 0.050 6637 Dihedral : 5.363 83.738 5318 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.66 % Allowed : 11.86 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.13), residues: 4687 helix: 2.36 (0.09), residues: 3189 sheet: 0.11 (0.35), residues: 245 loop : -0.33 (0.19), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D2548 TYR 0.017 0.001 TYR C1794 PHE 0.034 0.001 PHE C2220 TRP 0.017 0.002 TRP B 697 HIS 0.004 0.001 HIS A2106 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (38706) covalent geometry : angle 0.47312 / 0.25 (52356) SS BOND : bond 0.00390 / 0.20 ( 4) SS BOND : angle 0.72446 / 0.39 ( 8) hydrogen bonds : bond 0.03621 / 2.53 ( 2543) hydrogen bonds : angle 4.03259 / 2.86 ( 7362) metal coordination : bond 0.01393 / 1.07 ( 16) metal coordination : angle 3.86664 / 2.07 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 443 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7658 (t0) cc_final: 0.7169 (t0) REVERT: A 293 ARG cc_start: 0.7134 (mmt180) cc_final: 0.6757 (mtp85) REVERT: A 298 GLN cc_start: 0.7426 (mp10) cc_final: 0.7035 (mp10) REVERT: A 414 MET cc_start: 0.6788 (ppp) cc_final: 0.6474 (ppp) REVERT: A 478 ASP cc_start: 0.7994 (t0) cc_final: 0.7512 (t0) REVERT: A 564 GLN cc_start: 0.8342 (pp30) cc_final: 0.7860 (pp30) REVERT: A 585 ILE cc_start: 0.8766 (tp) cc_final: 0.8545 (tp) REVERT: A 625 ASN cc_start: 0.7489 (m110) cc_final: 0.6980 (m-40) REVERT: A 705 HIS cc_start: 0.7892 (m90) cc_final: 0.7405 (m90) REVERT: A 782 MET cc_start: 0.8303 (ttt) cc_final: 0.7998 (ttt) REVERT: A 992 MET cc_start: 0.8127 (mtt) cc_final: 0.7862 (mtt) REVERT: A 995 ILE cc_start: 0.8494 (tp) cc_final: 0.8193 (tp) REVERT: A 1124 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6771 (mm-30) REVERT: A 1210 MET cc_start: 0.8079 (mmm) cc_final: 0.7811 (mtm) REVERT: A 1607 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7742 (mt0) REVERT: A 2291 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.5986 (tt) REVERT: A 2309 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7539 (mp) REVERT: A 2616 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7568 (tp-100) REVERT: B 782 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7173 (ttp) REVERT: B 836 GLU cc_start: 0.7923 (tp30) cc_final: 0.7584 (tp30) REVERT: B 1065 ILE cc_start: 0.7977 (mt) cc_final: 0.7757 (mt) REVERT: B 1224 TYR cc_start: 0.7738 (p90) cc_final: 0.7336 (p90) REVERT: B 1279 MET cc_start: 0.8660 (ttp) cc_final: 0.8433 (ttp) REVERT: B 1294 GLN cc_start: 0.8226 (tt0) cc_final: 0.7762 (tt0) REVERT: B 1298 HIS cc_start: 0.8316 (t70) cc_final: 0.8071 (t-90) REVERT: B 1343 LEU cc_start: 0.8640 (tp) cc_final: 0.8291 (tt) REVERT: B 2031 LYS cc_start: 0.8508 (mmpt) cc_final: 0.8125 (ptpt) REVERT: B 2139 LEU cc_start: 0.7955 (mm) cc_final: 0.7742 (mp) REVERT: B 2296 LEU cc_start: 0.7806 (mt) cc_final: 0.7440 (mt) REVERT: B 2344 MET cc_start: 0.7206 (tpp) cc_final: 0.6800 (tmm) REVERT: B 2475 ILE cc_start: 0.8924 (mm) cc_final: 0.8542 (tp) REVERT: C 1797 LEU cc_start: 0.8132 (mt) cc_final: 0.7891 (tp) REVERT: C 1980 LYS cc_start: 0.8608 (tttt) cc_final: 0.7945 (tptp) REVERT: C 1988 ASN cc_start: 0.8360 (t0) cc_final: 0.8096 (t0) REVERT: C 2077 MET cc_start: 0.7884 (ttm) cc_final: 0.7644 (ttm) REVERT: C 2189 GLN cc_start: 0.7886 (tt0) cc_final: 0.7581 (tt0) REVERT: D 2198 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7743 (mp-120) REVERT: D 2310 LEU cc_start: 0.7504 (tp) cc_final: 0.7226 (mt) outliers start: 67 outliers final: 42 residues processed: 479 average time/residue: 0.2213 time to fit residues: 174.1920 Evaluate side-chains 472 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 426 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 796 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2309 ILE Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain A residue 2479 CYS Chi-restraints excluded: chain A residue 2635 VAL Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1229 GLU Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 PHE Chi-restraints excluded: chain B residue 1615 HIS Chi-restraints excluded: chain B residue 1617 PHE Chi-restraints excluded: chain B residue 1632 LEU Chi-restraints excluded: chain B residue 1918 MET Chi-restraints excluded: chain B residue 1947 THR Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2576 THR Chi-restraints excluded: chain C residue 1961 CYS Chi-restraints excluded: chain C residue 2157 THR Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2198 GLN Chi-restraints excluded: chain D residue 2227 SER Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2479 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 241 optimal weight: 0.2980 chunk 339 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 392 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 467 optimal weight: 2.9990 chunk 272 optimal weight: 20.0000 chunk 232 optimal weight: 2.9990 chunk 343 optimal weight: 3.9990 chunk 398 optimal weight: 3.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN A 582 GLN A 751 GLN A1204 GLN A1298 HIS A2198 GLN A2216 ASN ** B1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS B1933 ASN B2106 HIS D2198 GLN D2235 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.126437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110969 restraints weight = 84994.699| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.56 r_work: 0.3150 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 38726 Z= 0.286 Angle : 0.567 10.397 52371 Z= 0.296 Chirality : 0.042 0.196 6049 Planarity : 0.004 0.051 6637 Dihedral : 5.695 80.990 5318 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.74 % Allowed : 12.87 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.13), residues: 4687 helix: 2.11 (0.09), residues: 3180 sheet: -0.09 (0.35), residues: 247 loop : -0.45 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1291 TYR 0.017 0.002 TYR B2352 PHE 0.052 0.002 PHE C2220 TRP 0.015 0.002 TRP B 697 HIS 0.007 0.001 HIS A2106 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.29 (38706) covalent geometry : angle 0.56463 / 0.30 (52356) SS BOND : bond 0.00979 / 0.49 ( 4) SS BOND : angle 1.03833 / 0.57 ( 8) hydrogen bonds : bond 0.04376 / 3.06 ( 2543) hydrogen bonds : angle 4.29549 / 3.05 ( 7362) metal coordination : bond 0.02786 / 2.15 ( 16) metal coordination : angle 4.75281 / 2.52 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 451 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7674 (t0) cc_final: 0.7207 (t0) REVERT: A 293 ARG cc_start: 0.7118 (mmt180) cc_final: 0.6749 (mtp85) REVERT: A 298 GLN cc_start: 0.7483 (mp10) cc_final: 0.7083 (mp10) REVERT: A 391 HIS cc_start: 0.6266 (t-90) cc_final: 0.5975 (t-90) REVERT: A 414 MET cc_start: 0.6794 (ppp) cc_final: 0.6440 (ppp) REVERT: A 478 ASP cc_start: 0.8017 (t0) cc_final: 0.7536 (t0) REVERT: A 564 GLN cc_start: 0.8313 (pp30) cc_final: 0.7764 (pp30) REVERT: A 625 ASN cc_start: 0.7523 (m110) cc_final: 0.7017 (m-40) REVERT: A 705 HIS cc_start: 0.7902 (m90) cc_final: 0.7330 (m90) REVERT: A 992 MET cc_start: 0.8161 (mtt) cc_final: 0.7893 (mtt) REVERT: A 995 ILE cc_start: 0.8499 (tp) cc_final: 0.8175 (tp) REVERT: A 1124 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6831 (mm-30) REVERT: A 1210 MET cc_start: 0.8239 (mmm) cc_final: 0.7772 (mmm) REVERT: A 1918 MET cc_start: 0.8561 (mmm) cc_final: 0.8238 (mmm) REVERT: A 2113 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7484 (t70) REVERT: A 2291 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.5943 (tt) REVERT: A 2309 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7602 (mp) REVERT: A 2616 GLN cc_start: 0.8230 (tp-100) cc_final: 0.7600 (tp-100) REVERT: B 836 GLU cc_start: 0.8012 (tp30) cc_final: 0.7671 (tp30) REVERT: B 1065 ILE cc_start: 0.8066 (mt) cc_final: 0.7847 (mt) REVERT: B 1224 TYR cc_start: 0.7705 (p90) cc_final: 0.7253 (p90) REVERT: B 1279 MET cc_start: 0.8728 (ttp) cc_final: 0.8498 (ttp) REVERT: B 1294 GLN cc_start: 0.8265 (tt0) cc_final: 0.7843 (tt0) REVERT: B 1298 HIS cc_start: 0.8383 (t70) cc_final: 0.8137 (t-90) REVERT: B 1343 LEU cc_start: 0.8626 (tp) cc_final: 0.8298 (tt) REVERT: B 1620 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7605 (mmm) REVERT: B 2031 LYS cc_start: 0.8532 (mmpt) cc_final: 0.8076 (ptpp) REVERT: B 2296 LEU cc_start: 0.7820 (mt) cc_final: 0.7432 (mt) REVERT: B 2344 MET cc_start: 0.7240 (tpp) cc_final: 0.6809 (tmm) REVERT: B 2475 ILE cc_start: 0.8969 (mm) cc_final: 0.8610 (tp) REVERT: C 1797 LEU cc_start: 0.8161 (mt) cc_final: 0.7908 (tp) REVERT: C 1806 PHE cc_start: 0.7918 (t80) cc_final: 0.7457 (t80) REVERT: C 1980 LYS cc_start: 0.8636 (tttt) cc_final: 0.8000 (tptp) REVERT: C 2077 MET cc_start: 0.7934 (ttm) cc_final: 0.7684 (ttm) REVERT: C 2189 GLN cc_start: 0.7998 (tt0) cc_final: 0.7706 (tt0) REVERT: D 2224 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7984 (ttp80) outliers start: 70 outliers final: 50 residues processed: 485 average time/residue: 0.2235 time to fit residues: 179.8945 Evaluate side-chains 485 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 431 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 582 GLN Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1286 ASN Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2299 ILE Chi-restraints excluded: chain A residue 2309 ILE Chi-restraints excluded: chain A residue 2310 LEU Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain A residue 2479 CYS Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1121 LEU Chi-restraints excluded: chain B residue 1229 GLU Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1297 VAL Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1615 HIS Chi-restraints excluded: chain B residue 1620 MET Chi-restraints excluded: chain B residue 1632 LEU Chi-restraints excluded: chain B residue 1918 MET Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2106 HIS Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2299 ILE Chi-restraints excluded: chain B residue 2576 THR Chi-restraints excluded: chain C residue 1951 LEU Chi-restraints excluded: chain C residue 1961 CYS Chi-restraints excluded: chain C residue 2157 THR Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2158 MET Chi-restraints excluded: chain D residue 2227 SER Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2475 ILE Chi-restraints excluded: chain D residue 2479 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 223 optimal weight: 3.9990 chunk 313 optimal weight: 0.9980 chunk 220 optimal weight: 0.9980 chunk 413 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 334 optimal weight: 2.9990 chunk 317 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 187 optimal weight: 0.6980 chunk 347 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN A 582 GLN A1298 HIS A2198 GLN ** B1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113531 restraints weight = 83813.439| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.59 r_work: 0.3202 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 38726 Z= 0.131 Angle : 0.474 11.546 52371 Z= 0.250 Chirality : 0.038 0.156 6049 Planarity : 0.003 0.050 6637 Dihedral : 5.503 82.325 5318 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.41 % Allowed : 13.67 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.13), residues: 4687 helix: 2.29 (0.09), residues: 3181 sheet: 0.05 (0.35), residues: 245 loop : -0.39 (0.19), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1291 TYR 0.013 0.001 TYR D2520 PHE 0.024 0.001 PHE A 471 TRP 0.020 0.002 TRP B 697 HIS 0.003 0.001 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (38706) covalent geometry : angle 0.47241 / 0.25 (52356) SS BOND : bond 0.00277 / 0.14 ( 4) SS BOND : angle 0.71134 / 0.39 ( 8) hydrogen bonds : bond 0.03575 / 2.50 ( 2543) hydrogen bonds : angle 4.06513 / 2.88 ( 7362) metal coordination : bond 0.00915 / 0.68 ( 16) metal coordination : angle 3.53398 / 1.91 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 428 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7671 (t0) cc_final: 0.7186 (t0) REVERT: A 293 ARG cc_start: 0.7120 (mmt180) cc_final: 0.6744 (mtp85) REVERT: A 298 GLN cc_start: 0.7370 (mp10) cc_final: 0.6962 (mp10) REVERT: A 414 MET cc_start: 0.6810 (ppp) cc_final: 0.6482 (ppp) REVERT: A 478 ASP cc_start: 0.7985 (t0) cc_final: 0.7505 (t0) REVERT: A 564 GLN cc_start: 0.8321 (pp30) cc_final: 0.7833 (pp30) REVERT: A 585 ILE cc_start: 0.8642 (tp) cc_final: 0.8430 (tp) REVERT: A 625 ASN cc_start: 0.7510 (m110) cc_final: 0.7010 (m-40) REVERT: A 705 HIS cc_start: 0.7874 (m90) cc_final: 0.7352 (m90) REVERT: A 782 MET cc_start: 0.8285 (ttt) cc_final: 0.7959 (ttt) REVERT: A 992 MET cc_start: 0.8077 (mtt) cc_final: 0.7815 (mtt) REVERT: A 995 ILE cc_start: 0.8478 (tp) cc_final: 0.8157 (tp) REVERT: A 1124 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6798 (mm-30) REVERT: A 1210 MET cc_start: 0.8090 (mmm) cc_final: 0.7647 (mtm) REVERT: A 2113 HIS cc_start: 0.7956 (OUTLIER) cc_final: 0.7407 (t70) REVERT: A 2291 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.5944 (tt) REVERT: A 2309 ILE cc_start: 0.7772 (OUTLIER) cc_final: 0.7539 (mp) REVERT: A 2616 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7554 (tp-100) REVERT: B 782 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7160 (ttp) REVERT: B 836 GLU cc_start: 0.7934 (tp30) cc_final: 0.7600 (tp30) REVERT: B 1065 ILE cc_start: 0.7945 (mt) cc_final: 0.7711 (mt) REVERT: B 1231 MET cc_start: 0.6995 (mmt) cc_final: 0.6749 (tpp) REVERT: B 1279 MET cc_start: 0.8685 (ttp) cc_final: 0.8452 (ttp) REVERT: B 1294 GLN cc_start: 0.8215 (tt0) cc_final: 0.7838 (tt0) REVERT: B 1298 HIS cc_start: 0.8325 (t70) cc_final: 0.8083 (t-90) REVERT: B 1343 LEU cc_start: 0.8597 (tp) cc_final: 0.8255 (tt) REVERT: B 2031 LYS cc_start: 0.8490 (mmpt) cc_final: 0.8107 (ptpt) REVERT: B 2139 LEU cc_start: 0.7865 (mm) cc_final: 0.7630 (mt) REVERT: B 2296 LEU cc_start: 0.7827 (mt) cc_final: 0.7445 (mt) REVERT: B 2344 MET cc_start: 0.7200 (tpp) cc_final: 0.6776 (tmm) REVERT: B 2475 ILE cc_start: 0.8924 (mm) cc_final: 0.8540 (tp) REVERT: C 1786 ASN cc_start: 0.7258 (t0) cc_final: 0.6929 (t0) REVERT: C 1797 LEU cc_start: 0.8136 (mt) cc_final: 0.7888 (tp) REVERT: C 1806 PHE cc_start: 0.7863 (t80) cc_final: 0.7559 (t80) REVERT: C 1980 LYS cc_start: 0.8601 (tttt) cc_final: 0.7943 (tptp) REVERT: C 2077 MET cc_start: 0.7861 (ttm) cc_final: 0.7608 (ttm) REVERT: D 2158 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8071 (tpp) REVERT: D 2198 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7837 (mp10) outliers start: 57 outliers final: 44 residues processed: 455 average time/residue: 0.2156 time to fit residues: 162.2176 Evaluate side-chains 462 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 412 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2309 ILE Chi-restraints excluded: chain A residue 2479 CYS Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1229 GLU Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1297 VAL Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 PHE Chi-restraints excluded: chain B residue 1600 ARG Chi-restraints excluded: chain B residue 1615 HIS Chi-restraints excluded: chain B residue 1617 PHE Chi-restraints excluded: chain B residue 1632 LEU Chi-restraints excluded: chain B residue 1947 THR Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2106 HIS Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2299 ILE Chi-restraints excluded: chain B residue 2632 MET Chi-restraints excluded: chain C residue 1961 CYS Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2158 MET Chi-restraints excluded: chain D residue 2198 GLN Chi-restraints excluded: chain D residue 2227 SER Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2475 ILE Chi-restraints excluded: chain D residue 2479 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 254 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 chunk 319 optimal weight: 3.9990 chunk 476 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN A1257 HIS A1298 HIS B1174 ASN ** B1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.124952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.109763 restraints weight = 86706.061| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.56 r_work: 0.3191 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 38726 Z= 0.172 Angle : 0.497 11.865 52371 Z= 0.260 Chirality : 0.039 0.184 6049 Planarity : 0.003 0.050 6637 Dihedral : 5.477 82.091 5318 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.49 % Allowed : 13.86 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.13), residues: 4687 helix: 2.28 (0.09), residues: 3177 sheet: -0.00 (0.35), residues: 247 loop : -0.38 (0.19), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1291 TYR 0.015 0.001 TYR D2520 PHE 0.050 0.001 PHE C2220 TRP 0.016 0.002 TRP B 697 HIS 0.004 0.001 HIS A2106 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (38706) covalent geometry : angle 0.49504 / 0.26 (52356) SS BOND : bond 0.00432 / 0.22 ( 4) SS BOND : angle 0.85402 / 0.46 ( 8) hydrogen bonds : bond 0.03751 / 2.62 ( 2543) hydrogen bonds : angle 4.09455 / 2.91 ( 7362) metal coordination : bond 0.01474 / 1.13 ( 16) metal coordination : angle 3.97498 / 2.13 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 430 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7615 (t0) cc_final: 0.7137 (t0) REVERT: A 293 ARG cc_start: 0.7069 (mmt180) cc_final: 0.6716 (mtp85) REVERT: A 298 GLN cc_start: 0.7405 (mp10) cc_final: 0.6996 (mp10) REVERT: A 414 MET cc_start: 0.6791 (ppp) cc_final: 0.6434 (ppp) REVERT: A 478 ASP cc_start: 0.7978 (t0) cc_final: 0.7503 (t0) REVERT: A 564 GLN cc_start: 0.8279 (pp30) cc_final: 0.7743 (pp30) REVERT: A 585 ILE cc_start: 0.8594 (tp) cc_final: 0.8371 (tp) REVERT: A 625 ASN cc_start: 0.7516 (m110) cc_final: 0.7022 (m-40) REVERT: A 705 HIS cc_start: 0.7878 (m90) cc_final: 0.7356 (m90) REVERT: A 782 MET cc_start: 0.8311 (ttt) cc_final: 0.7986 (ttt) REVERT: A 967 MET cc_start: 0.7864 (mmm) cc_final: 0.7659 (mmt) REVERT: A 992 MET cc_start: 0.8109 (mtt) cc_final: 0.7841 (mtt) REVERT: A 995 ILE cc_start: 0.8485 (tp) cc_final: 0.8163 (tp) REVERT: A 1124 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6813 (mm-30) REVERT: A 1210 MET cc_start: 0.8127 (mmm) cc_final: 0.7685 (mtm) REVERT: A 1408 ARG cc_start: 0.8013 (ttp-170) cc_final: 0.7757 (ttp-170) REVERT: A 2113 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7397 (t70) REVERT: A 2291 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5912 (tt) REVERT: A 2309 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7558 (mp) REVERT: A 2616 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7552 (tp-100) REVERT: B 782 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7181 (ttp) REVERT: B 836 GLU cc_start: 0.7930 (tp30) cc_final: 0.7597 (tp30) REVERT: B 1065 ILE cc_start: 0.7993 (mt) cc_final: 0.7758 (mt) REVERT: B 1224 TYR cc_start: 0.7842 (p90) cc_final: 0.7302 (p90) REVERT: B 1274 MET cc_start: 0.8543 (tpp) cc_final: 0.8317 (tpp) REVERT: B 1279 MET cc_start: 0.8672 (ttp) cc_final: 0.8454 (ttp) REVERT: B 1294 GLN cc_start: 0.8205 (tt0) cc_final: 0.7836 (tt0) REVERT: B 1298 HIS cc_start: 0.8316 (t70) cc_final: 0.8081 (t-90) REVERT: B 1343 LEU cc_start: 0.8611 (tp) cc_final: 0.8280 (tt) REVERT: B 1620 MET cc_start: 0.7594 (mmp) cc_final: 0.7325 (mmm) REVERT: B 1637 LEU cc_start: 0.7422 (mp) cc_final: 0.7043 (tp) REVERT: B 1681 MET cc_start: 0.8286 (tpp) cc_final: 0.7961 (ttt) REVERT: B 2031 LYS cc_start: 0.8472 (mmpt) cc_final: 0.8088 (ptpt) REVERT: B 2139 LEU cc_start: 0.7985 (mm) cc_final: 0.7757 (mt) REVERT: B 2296 LEU cc_start: 0.7836 (mt) cc_final: 0.7444 (mt) REVERT: B 2344 MET cc_start: 0.7231 (tpp) cc_final: 0.6777 (tmm) REVERT: B 2475 ILE cc_start: 0.8931 (mm) cc_final: 0.8553 (tp) REVERT: C 1786 ASN cc_start: 0.7232 (t0) cc_final: 0.6905 (t0) REVERT: C 1797 LEU cc_start: 0.8125 (mt) cc_final: 0.7879 (tp) REVERT: C 1806 PHE cc_start: 0.7882 (t80) cc_final: 0.7547 (t80) REVERT: C 1980 LYS cc_start: 0.8590 (tttt) cc_final: 0.7963 (tptp) REVERT: C 2017 ILE cc_start: 0.8611 (mm) cc_final: 0.8353 (mm) REVERT: C 2077 MET cc_start: 0.7884 (ttm) cc_final: 0.7624 (ttm) REVERT: C 2158 MET cc_start: 0.8809 (mtp) cc_final: 0.8543 (ttp) REVERT: C 2189 GLN cc_start: 0.7898 (tt0) cc_final: 0.7605 (tt0) REVERT: D 2158 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.8076 (tpp) REVERT: D 2198 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7811 (mp10) outliers start: 60 outliers final: 46 residues processed: 459 average time/residue: 0.2289 time to fit residues: 172.0793 Evaluate side-chains 471 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 419 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2309 ILE Chi-restraints excluded: chain A residue 2479 CYS Chi-restraints excluded: chain A residue 2635 VAL Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1229 GLU Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1297 VAL Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 PHE Chi-restraints excluded: chain B residue 1600 ARG Chi-restraints excluded: chain B residue 1615 HIS Chi-restraints excluded: chain B residue 1617 PHE Chi-restraints excluded: chain B residue 1632 LEU Chi-restraints excluded: chain B residue 1947 THR Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2106 HIS Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2158 MET Chi-restraints excluded: chain B residue 2632 MET Chi-restraints excluded: chain C residue 1961 CYS Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2158 MET Chi-restraints excluded: chain D residue 2198 GLN Chi-restraints excluded: chain D residue 2227 SER Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2310 LEU Chi-restraints excluded: chain D residue 2475 ILE Chi-restraints excluded: chain D residue 2479 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 451 optimal weight: 0.9980 chunk 2 optimal weight: 30.0000 chunk 419 optimal weight: 0.9980 chunk 279 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 442 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 429 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN A1298 HIS ** B1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2106 HIS C1944 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.125564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110465 restraints weight = 86238.841| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.42 r_work: 0.3211 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38726 Z= 0.126 Angle : 0.470 12.296 52371 Z= 0.246 Chirality : 0.038 0.155 6049 Planarity : 0.003 0.050 6637 Dihedral : 5.331 83.528 5318 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.39 % Allowed : 14.16 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.13), residues: 4687 helix: 2.37 (0.09), residues: 3185 sheet: 0.06 (0.35), residues: 247 loop : -0.33 (0.19), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1291 TYR 0.013 0.001 TYR B1224 PHE 0.026 0.001 PHE B2537 TRP 0.017 0.002 TRP B 697 HIS 0.004 0.001 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (38706) covalent geometry : angle 0.46874 / 0.25 (52356) SS BOND : bond 0.00223 / 0.11 ( 4) SS BOND : angle 0.66017 / 0.36 ( 8) hydrogen bonds : bond 0.03360 / 2.34 ( 2543) hydrogen bonds : angle 3.98416 / 2.82 ( 7362) metal coordination : bond 0.00855 / 0.63 ( 16) metal coordination : angle 3.50615 / 1.91 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9374 Ramachandran restraints generated. 4687 Oldfield, 0 Emsley, 4687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 430 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 ASP cc_start: 0.7656 (t0) cc_final: 0.7193 (t0) REVERT: A 293 ARG cc_start: 0.7096 (mmt180) cc_final: 0.6751 (mtp85) REVERT: A 298 GLN cc_start: 0.7380 (mp10) cc_final: 0.6962 (mp10) REVERT: A 414 MET cc_start: 0.6853 (ppp) cc_final: 0.6540 (ppp) REVERT: A 469 ARG cc_start: 0.8537 (tmm160) cc_final: 0.8334 (tmm-80) REVERT: A 478 ASP cc_start: 0.7977 (t0) cc_final: 0.7501 (t0) REVERT: A 564 GLN cc_start: 0.8301 (pp30) cc_final: 0.7799 (pp30) REVERT: A 585 ILE cc_start: 0.8631 (tp) cc_final: 0.8420 (tp) REVERT: A 625 ASN cc_start: 0.7513 (m110) cc_final: 0.7018 (m-40) REVERT: A 705 HIS cc_start: 0.7856 (m90) cc_final: 0.7421 (m90) REVERT: A 782 MET cc_start: 0.8291 (ttt) cc_final: 0.7975 (ttt) REVERT: A 967 MET cc_start: 0.7701 (mmm) cc_final: 0.7477 (mmt) REVERT: A 992 MET cc_start: 0.8066 (mtt) cc_final: 0.7815 (mtt) REVERT: A 995 ILE cc_start: 0.8499 (tp) cc_final: 0.8182 (tp) REVERT: A 1124 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6783 (mm-30) REVERT: A 1210 MET cc_start: 0.8026 (mmm) cc_final: 0.7595 (mmm) REVERT: A 1235 MET cc_start: 0.7780 (mmm) cc_final: 0.6959 (mmm) REVERT: A 2291 LEU cc_start: 0.6483 (OUTLIER) cc_final: 0.6024 (tt) REVERT: A 2309 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7565 (mp) REVERT: A 2616 GLN cc_start: 0.8245 (tp-100) cc_final: 0.7576 (tp-100) REVERT: B 710 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7655 (mmm-85) REVERT: B 782 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7197 (ttp) REVERT: B 836 GLU cc_start: 0.7926 (tp30) cc_final: 0.7603 (tp30) REVERT: B 1065 ILE cc_start: 0.7902 (mt) cc_final: 0.7653 (mt) REVERT: B 1224 TYR cc_start: 0.7808 (p90) cc_final: 0.7364 (p90) REVERT: B 1274 MET cc_start: 0.8490 (tpp) cc_final: 0.8257 (tpp) REVERT: B 1279 MET cc_start: 0.8638 (ttp) cc_final: 0.8414 (ttp) REVERT: B 1294 GLN cc_start: 0.8198 (tt0) cc_final: 0.7762 (tt0) REVERT: B 1298 HIS cc_start: 0.8311 (t70) cc_final: 0.8064 (t-90) REVERT: B 1343 LEU cc_start: 0.8622 (tp) cc_final: 0.8274 (tt) REVERT: B 1637 LEU cc_start: 0.7322 (mp) cc_final: 0.7066 (tp) REVERT: B 1646 ARG cc_start: 0.8494 (ttt90) cc_final: 0.8135 (ttt90) REVERT: B 1681 MET cc_start: 0.8243 (tpp) cc_final: 0.7916 (ttt) REVERT: B 2031 LYS cc_start: 0.8467 (mmpt) cc_final: 0.8103 (ptpt) REVERT: B 2139 LEU cc_start: 0.7972 (mm) cc_final: 0.7734 (mt) REVERT: B 2296 LEU cc_start: 0.7913 (mt) cc_final: 0.7511 (mt) REVERT: B 2344 MET cc_start: 0.7220 (tpp) cc_final: 0.6799 (tmm) REVERT: B 2475 ILE cc_start: 0.8946 (mm) cc_final: 0.8561 (tp) REVERT: B 2628 ARG cc_start: 0.7670 (tmm-80) cc_final: 0.7412 (ttp-170) REVERT: C 1786 ASN cc_start: 0.7169 (t0) cc_final: 0.6838 (t0) REVERT: C 1806 PHE cc_start: 0.7921 (t80) cc_final: 0.7641 (t80) REVERT: C 2017 ILE cc_start: 0.8526 (mm) cc_final: 0.8219 (mm) REVERT: C 2077 MET cc_start: 0.7853 (ttm) cc_final: 0.7591 (ttm) REVERT: D 2158 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8103 (tpp) REVERT: D 2198 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7763 (mp10) REVERT: D 2581 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7708 (tm-30) outliers start: 56 outliers final: 45 residues processed: 460 average time/residue: 0.2268 time to fit residues: 170.9888 Evaluate side-chains 473 residues out of total 4361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 423 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 785 MET Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 892 ILE Chi-restraints excluded: chain A residue 1255 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2309 ILE Chi-restraints excluded: chain A residue 2479 CYS Chi-restraints excluded: chain A residue 2635 VAL Chi-restraints excluded: chain B residue 617 THR Chi-restraints excluded: chain B residue 705 HIS Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 778 PHE Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1067 HIS Chi-restraints excluded: chain B residue 1229 GLU Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1297 VAL Chi-restraints excluded: chain B residue 1342 VAL Chi-restraints excluded: chain B residue 1352 PHE Chi-restraints excluded: chain B residue 1600 ARG Chi-restraints excluded: chain B residue 1615 HIS Chi-restraints excluded: chain B residue 1617 PHE Chi-restraints excluded: chain B residue 1632 LEU Chi-restraints excluded: chain B residue 1947 THR Chi-restraints excluded: chain B residue 2106 HIS Chi-restraints excluded: chain B residue 2158 MET Chi-restraints excluded: chain B residue 2299 ILE Chi-restraints excluded: chain B residue 2632 MET Chi-restraints excluded: chain C residue 1961 CYS Chi-restraints excluded: chain C residue 1973 LEU Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2158 MET Chi-restraints excluded: chain D residue 2198 GLN Chi-restraints excluded: chain D residue 2227 SER Chi-restraints excluded: chain D residue 2310 LEU Chi-restraints excluded: chain D residue 2475 ILE Chi-restraints excluded: chain D residue 2479 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 477 random chunks: chunk 321 optimal weight: 1.9990 chunk 263 optimal weight: 0.6980 chunk 209 optimal weight: 10.0000 chunk 409 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 385 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 350 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 577 ASN ** B1257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2106 HIS C1944 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.125518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110227 restraints weight = 86477.116| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.55 r_work: 0.3205 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38726 Z= 0.141 Angle : 0.482 12.418 52371 Z= 0.251 Chirality : 0.038 0.155 6049 Planarity : 0.003 0.050 6637 Dihedral : 5.314 83.954 5318 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.31 % Allowed : 14.48 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.13), residues: 4687 helix: 2.37 (0.09), residues: 3181 sheet: 0.07 (0.35), residues: 247 loop : -0.34 (0.19), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1291 TYR 0.016 0.001 TYR A 352 PHE 0.039 0.001 PHE C2220 TRP 0.015 0.002 TRP B 697 HIS 0.008 0.001 HIS B2106 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (38706) covalent geometry : angle 0.48023 / 0.25 (52356) SS BOND : bond 0.00302 / 0.15 ( 4) SS BOND : angle 0.72700 / 0.39 ( 8) hydrogen bonds : bond 0.03454 / 2.41 ( 2543) hydrogen bonds : angle 3.99265 / 2.83 ( 7362) metal coordination : bond 0.00981 / 0.74 ( 16) metal coordination : angle 3.75567 / 2.04 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8934.22 seconds wall clock time: 153 minutes 48.75 seconds (9228.75 seconds total)