Starting phenix.real_space_refine on Sun Aug 9 23:41:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ymz_73129/08_2026/9ymz_73129.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ymz_73129/08_2026/9ymz_73129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ymz_73129/08_2026/9ymz_73129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ymz_73129/08_2026/9ymz_73129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ymz_73129/08_2026/9ymz_73129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ymz_73129/08_2026/9ymz_73129.map" } resolution = 3.14 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= 0.004 sd= 0.010 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 15 5.49 5 S 236 5.16 5 C 24412 2.51 5 N 6451 2.21 5 O 6916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.06s 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: 38034 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 16945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2112, 16945 Classifications: {'peptide': 2112} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 2046} Chain breaks: 19 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 1, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "B" Number of atoms: 12417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1547, 12417 Classifications: {'peptide': 1547} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 1502} Chain breaks: 15 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 276 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'PHE:plan': 6, 'GLU:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 1, 'GLN:plan1': 5, 'HIS:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "C" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5107 Classifications: {'peptide': 625} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 608} Chain breaks: 7 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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' ZN': 1, 'ATP': 1, 'I3P': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" 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} Chain: "C" 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} 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 16326 SG CYS A2562 83.293 151.545 122.406 1.00 22.17 S ATOM 16351 SG CYS A2565 84.880 148.085 122.378 1.00 25.75 S ATOM 28743 SG CYS B2562 77.348 122.996 132.817 1.00 39.26 S ATOM 28768 SG CYS B2565 80.512 122.812 134.969 1.00 46.31 S ATOM 33850 SG CYS C2562 87.027 130.096 157.545 1.00 27.46 S ATOM 33875 SG CYS C2565 89.943 132.137 156.169 1.00 36.23 S ATOM 37263 SG CYS D2562 93.137 156.767 149.208 1.00 39.10 S ATOM 37288 SG CYS D2565 94.524 156.034 145.713 1.00 39.44 S Time building chain proxies: 7.19, per 1000 atoms: 0.19 Number of scatterers: 38034 At special positions: 0 Unit cell: (158.646, 204.678, 203.034, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 236 16.00 P 15 15.00 O 6916 8.00 N 6451 7.00 C 24412 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: 3.09 Conformation dependent library (CDL) restraints added in 1.7 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 A2565 " pdb="ZN ZN A2803 " - pdb=" SG CYS A2562 " 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=" NE2 HIS C2582 " pdb="ZN ZN C2802 " - pdb=" ND1 HIS C2587 " pdb="ZN ZN C2802 " - pdb=" SG CYS C2565 " pdb="ZN ZN C2802 " - pdb=" SG CYS C2562 " pdb=" ZN D2802 " pdb="ZN ZN D2802 " - pdb=" NE2 HIS D2582 " pdb="ZN ZN D2802 " - pdb=" ND1 HIS D2587 " pdb="ZN ZN D2802 " - pdb=" SG CYS D2565 " pdb="ZN ZN D2802 " - pdb=" SG CYS D2562 " Number of angles added : 5 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9026 Finding SS restraints... Secondary structure from input PDB file: 268 helices and 17 sheets defined 74.8% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.682A pdb=" N ALA A 275 " --> pdb=" O ALA A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 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 537 through 541 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 584 removed outlier: 4.104A pdb=" N MET A 581 " --> pdb=" O ASN A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 601 removed outlier: 3.903A pdb=" N ASN A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 610 Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.738A pdb=" N ILE A 615 " --> pdb=" O THR A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 removed outlier: 4.095A pdb=" N LEU A 631 " --> pdb=" O GLU A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 657 removed outlier: 3.607A pdb=" N LEU A 651 " --> pdb=" O VAL A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 665 removed outlier: 4.204A pdb=" N ASP A 663 " --> pdb=" O GLY A 660 " (cutoff:3.500A) removed outlier: 3.538A 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: 4.126A pdb=" N VAL A 726 " --> pdb=" O ALA A 722 " (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 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 812 through 829 removed outlier: 4.159A pdb=" N THR A 820 " --> pdb=" O TYR A 816 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER A 822 " --> pdb=" O SER A 818 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER A 823 " --> pdb=" O ILE A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 848 Processing helix chain 'A' and resid 856 through 875 removed outlier: 4.041A pdb=" N LEU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 894 removed outlier: 4.061A pdb=" N ARG A 887 " --> pdb=" O LEU A 883 " (cutoff:3.500A) removed outlier: 4.173A 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: 3.525A pdb=" N ALA A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1032 " --> pdb=" O ASP A1028 " (cutoff:3.500A) removed outlier: 3.779A 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: 3.753A 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 1102 through 1125 Processing helix chain 'A' and resid 1125 through 1130 removed outlier: 3.818A pdb=" N TRP A1129 " --> pdb=" O LYS A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1194 Processing helix chain 'A' and resid 1196 through 1211 removed outlier: 3.910A pdb=" N ASN A1201 " --> pdb=" O LYS A1197 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLN A1202 " --> pdb=" O LYS A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1222 removed outlier: 3.706A pdb=" N VAL A1215 " --> pdb=" O GLY A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1246 Processing helix chain 'A' and resid 1249 through 1258 Processing helix chain 'A' and resid 1259 through 1264 Processing helix chain 'A' and resid 1267 through 1279 Processing helix chain 'A' and resid 1281 through 1287 Processing helix chain 'A' and resid 1289 through 1303 removed outlier: 3.899A pdb=" N VAL A1293 " --> pdb=" O SER A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1317 removed outlier: 4.070A pdb=" N LEU A1310 " --> pdb=" O HIS A1306 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1339 removed outlier: 3.666A pdb=" N GLY A1339 " --> pdb=" O LEU A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1342 No H-bonds generated for 'chain 'A' and resid 1340 through 1342' Processing helix chain 'A' and resid 1351 through 1361 Processing helix chain 'A' and resid 1370 through 1387 Processing helix chain 'A' and resid 1390 through 1401 removed outlier: 3.532A pdb=" N LYS A1396 " --> pdb=" O TYR A1392 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER A1399 " --> pdb=" O ILE A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1412 removed outlier: 3.571A pdb=" N ILE A1406 " --> pdb=" O PRO A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1431 removed outlier: 3.981A 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 1474 through 1493 removed outlier: 4.254A pdb=" N ILE A1483 " --> pdb=" O VAL A1479 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET A1484 " --> pdb=" O THR A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1497 removed outlier: 4.026A 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: 3.881A pdb=" N ALA A1544 " --> pdb=" O LEU A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1634 Proline residue: A1619 - end of helix removed outlier: 3.672A pdb=" N SER A1626 " --> pdb=" O GLN A1622 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A1627 " --> pdb=" O ALA A1623 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A1628 " --> pdb=" O GLU A1624 " (cutoff:3.500A) removed outlier: 3.656A 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 1663 removed outlier: 3.802A pdb=" N LYS A1655 " --> pdb=" O ALA A1651 " (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 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 1969 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: 3.934A pdb=" N ILE A2017 " --> pdb=" O ASN A2013 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE A2022 " --> pdb=" O ILE A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2026 through 2033 removed outlier: 3.907A pdb=" N TYR A2032 " --> pdb=" O PRO A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2033 through 2052 removed outlier: 3.938A 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: 3.655A pdb=" N LEU A2172 " --> pdb=" O CYS A2169 " (cutoff:3.500A) Processing helix chain 'A' and resid 2173 through 2184 Processing helix chain 'A' and resid 2192 through 2214 removed outlier: 4.398A pdb=" N GLU A2201 " --> pdb=" O PHE A2197 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ASP A2202 " --> pdb=" O GLN A2198 " (cutoff:3.500A) Processing helix chain 'A' and resid 2216 through 2225 Processing helix chain 'A' and resid 2225 through 2248 removed outlier: 3.991A pdb=" N TRP A2229 " --> pdb=" O HIS A2225 " (cutoff:3.500A) Processing helix chain 'A' and resid 2288 through 2302 removed outlier: 3.525A pdb=" N TYR A2300 " --> pdb=" O LEU A2296 " (cutoff:3.500A) Processing helix chain 'A' and resid 2305 through 2331 Processing helix chain 'A' and resid 2332 through 2335 removed outlier: 3.672A pdb=" N ARG A2335 " --> pdb=" O THR A2332 " (cutoff:3.500A) No H-bonds generated for '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 Processing helix chain 'A' and resid 2372 through 2378 removed outlier: 3.892A pdb=" N TYR A2376 " --> pdb=" O PHE A2372 " (cutoff:3.500A) Processing helix chain 'A' and resid 2378 through 2390 removed outlier: 3.608A pdb=" N LEU A2382 " --> pdb=" O GLU A2378 " (cutoff:3.500A) removed outlier: 3.778A 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: 3.704A 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 Processing helix chain 'A' and resid 2608 through 2621 Processing helix chain 'A' and resid 2631 through 2635 Processing helix chain 'B' and resid 628 through 638 Processing helix chain 'B' and resid 645 through 657 Processing helix chain 'B' and resid 661 through 665 Processing helix chain 'B' and resid 728 through 741 Processing helix chain 'B' and resid 748 through 753 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 819 Processing helix chain 'B' and resid 820 through 829 removed outlier: 3.808A pdb=" N MET B 827 " --> pdb=" O SER B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 847 removed outlier: 3.671A pdb=" N MET B 835 " --> pdb=" O PHE B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 875 removed outlier: 4.278A pdb=" N LEU B 860 " --> pdb=" O GLU B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 894 removed outlier: 3.755A pdb=" N ARG B 887 " --> pdb=" O LEU B 883 " (cutoff:3.500A) removed outlier: 4.045A 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: 3.571A pdb=" N ALA B1032 " --> pdb=" O ASP B1028 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1066 Processing helix chain 'B' and resid 1069 through 1085 removed outlier: 3.608A 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 1103 through 1125 Processing helix chain 'B' and resid 1125 through 1130 removed outlier: 3.934A 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: 4.072A pdb=" N ASN B1201 " --> pdb=" O LYS B1197 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN B1202 " --> pdb=" O LYS B1198 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1222 removed outlier: 3.642A 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: 4.274A pdb=" N PHE B1263 " --> pdb=" O HIS B1259 " (cutoff:3.500A) Processing helix chain 'B' and resid 1267 through 1279 Processing helix chain 'B' and resid 1281 through 1287 removed outlier: 3.808A pdb=" N GLU B1287 " --> pdb=" O HIS B1283 " (cutoff:3.500A) Processing helix chain 'B' and resid 1289 through 1303 removed outlier: 3.975A pdb=" N VAL B1293 " --> pdb=" O SER B1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 1306 through 1317 removed outlier: 4.036A pdb=" N LEU B1310 " --> pdb=" O HIS B1306 " (cutoff:3.500A) Processing helix chain 'B' and resid 1324 through 1339 removed outlier: 3.742A pdb=" N GLY B1339 " --> pdb=" O LEU B1335 " (cutoff:3.500A) Processing helix chain 'B' and resid 1351 through 1359 removed outlier: 3.945A pdb=" N LEU B1355 " --> pdb=" O SER B1351 " (cutoff:3.500A) Processing helix chain 'B' and resid 1370 through 1387 Processing helix chain 'B' and resid 1390 through 1401 removed outlier: 3.758A pdb=" N LYS B1396 " --> pdb=" O TYR B1392 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER B1399 " --> pdb=" O ILE B1395 " (cutoff:3.500A) Processing helix chain 'B' and resid 1402 through 1412 removed outlier: 3.570A pdb=" N ILE B1406 " --> pdb=" O PRO B1402 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1431 removed outlier: 4.015A pdb=" N ALA B1422 " --> pdb=" O GLU B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 1446 through 1461 Processing helix chain 'B' and resid 1475 through 1493 removed outlier: 4.195A pdb=" N ILE B1483 " --> pdb=" O VAL B1479 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N MET B1484 " --> pdb=" O THR B1480 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1498 removed outlier: 3.750A pdb=" N ASP B1497 " --> pdb=" O PRO B1494 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN B1498 " --> pdb=" O PHE B1495 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1494 through 1498' Processing helix chain 'B' and resid 1505 through 1520 Processing helix chain 'B' and resid 1526 through 1541 removed outlier: 3.803A pdb=" N SER B1532 " --> pdb=" O ALA B1528 " (cutoff:3.500A) Processing helix chain 'B' and resid 1599 through 1634 Proline residue: B1619 - end of helix removed outlier: 3.548A pdb=" N SER B1626 " --> pdb=" O GLN B1622 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B1627 " --> pdb=" O ALA B1623 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B1628 " --> pdb=" O GLU B1624 " (cutoff:3.500A) removed outlier: 3.575A 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: 3.888A pdb=" N LYS B1655 " --> pdb=" O ALA B1651 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B1662 " --> pdb=" O ASN B1658 " (cutoff:3.500A) removed outlier: 3.775A 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 1929 Processing helix chain 'B' and resid 1930 through 1932 No H-bonds generated for 'chain 'B' and resid 1930 through 1932' Processing helix chain 'B' and resid 1933 through 1940 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: 3.740A pdb=" N TYR B1976 " --> pdb=" O LEU B1972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1981 through 1998 removed outlier: 4.668A pdb=" N GLY B1998 " --> pdb=" O GLU B1994 " (cutoff:3.500A) Processing helix chain 'B' and resid 2002 through 2009 Processing helix chain 'B' and resid 2013 through 2024 removed outlier: 3.844A 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: 3.732A 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 Processing helix chain 'B' and resid 2100 through 2116 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: 3.785A 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 2214 removed outlier: 4.453A pdb=" N GLU B2201 " --> pdb=" O PHE B2197 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASP B2202 " --> pdb=" O GLN B2198 " (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 2332 through 2335 removed outlier: 3.916A pdb=" N ARG B2335 " --> pdb=" O THR B2332 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2332 through 2335' 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: 3.541A pdb=" N SER B2368 " --> pdb=" O PHE B2365 " (cutoff:3.500A) Processing helix chain 'B' and resid 2372 through 2378 removed outlier: 3.925A pdb=" N TYR B2376 " --> pdb=" O PHE B2372 " (cutoff:3.500A) Processing helix chain 'B' and resid 2378 through 2390 removed outlier: 3.518A pdb=" N LEU B2382 " --> pdb=" O GLU B2378 " (cutoff:3.500A) removed outlier: 3.791A 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 2499 through 2503 Processing helix chain 'B' and resid 2513 through 2528 Processing helix chain 'B' and resid 2531 through 2560 Processing helix chain 'B' and resid 2568 through 2573 removed outlier: 3.720A pdb=" N ASP B2573 " --> pdb=" O ASP B2570 " (cutoff:3.500A) Processing helix chain 'B' and resid 2578 through 2585 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 2620 Processing helix chain 'C' and resid 1807 through 1821 Processing helix chain 'C' and resid 1918 through 1929 Processing helix chain 'C' and resid 1933 through 1940 Processing helix chain 'C' and resid 1951 through 1964 Processing helix chain 'C' and resid 1972 through 1976 Processing helix chain 'C' and resid 1981 through 1998 removed outlier: 3.643A pdb=" N CYS C1996 " --> pdb=" O LEU C1992 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY C1998 " --> pdb=" O GLU C1994 " (cutoff:3.500A) Processing helix chain 'C' and resid 2002 through 2009 Processing helix chain 'C' and resid 2013 through 2024 removed outlier: 4.015A pdb=" N ILE C2017 " --> pdb=" O ASN C2013 " (cutoff:3.500A) removed outlier: 3.569A 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 2052 removed outlier: 3.889A 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: 3.731A pdb=" N LEU C2172 " --> pdb=" O CYS C2169 " (cutoff:3.500A) Processing helix chain 'C' and resid 2173 through 2184 Processing helix chain 'C' and resid 2192 through 2214 removed outlier: 4.401A pdb=" N GLU C2201 " --> pdb=" O PHE C2197 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP C2202 " --> pdb=" O GLN C2198 " (cutoff:3.500A) removed outlier: 3.574A 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 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: 3.712A 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: 3.512A pdb=" N PHE C2369 " --> pdb=" O PHE C2366 " (cutoff:3.500A) Processing helix chain 'C' and resid 2372 through 2378 removed outlier: 3.799A pdb=" N TYR C2376 " --> pdb=" O PHE C2372 " (cutoff:3.500A) Processing helix chain 'C' and resid 2379 through 2390 removed outlier: 3.829A 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 Processing helix chain 'C' and resid 2568 through 2573 removed outlier: 4.030A pdb=" N ASP C2573 " --> pdb=" O ASP C2570 " (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 'C' and resid 2631 through 2635 Processing helix chain 'D' and resid 2166 through 2172 removed outlier: 3.629A pdb=" N LEU D2172 " --> pdb=" O CYS D2169 " (cutoff:3.500A) Processing helix chain 'D' and resid 2173 through 2184 Processing helix chain 'D' and resid 2192 through 2216 removed outlier: 4.331A pdb=" N GLU D2201 " --> pdb=" O PHE D2197 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASP D2202 " --> pdb=" O GLN D2198 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN D2215 " --> pdb=" O LYS D2211 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN D2216 " --> pdb=" O LYS D2212 " (cutoff:3.500A) Processing helix chain 'D' and resid 2218 through 2225 Processing helix chain 'D' and resid 2225 through 2248 removed outlier: 3.970A pdb=" N TRP D2229 " --> pdb=" O HIS D2225 " (cutoff:3.500A) Processing helix chain 'D' and resid 2288 through 2303 Processing helix chain 'D' and resid 2305 through 2331 Processing helix chain 'D' and resid 2332 through 2335 removed outlier: 3.709A pdb=" N ARG D2335 " --> pdb=" O THR D2332 " (cutoff:3.500A) No H-bonds generated for '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: 3.510A pdb=" N PHE D2366 " --> pdb=" O HIS D2363 " (cutoff:3.500A) Processing helix chain 'D' and resid 2372 through 2378 removed outlier: 3.852A pdb=" N TYR D2376 " --> pdb=" O PHE D2372 " (cutoff:3.500A) Processing helix chain 'D' and resid 2378 through 2390 removed outlier: 3.876A 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 2498 through 2503 removed outlier: 4.362A pdb=" N GLY D2501 " --> pdb=" O GLY D2498 " (cutoff:3.500A) Processing helix chain 'D' and resid 2513 through 2528 Processing helix chain 'D' and resid 2531 through 2560 Processing helix chain 'D' and resid 2568 through 2573 removed outlier: 3.538A pdb=" N LYS D2571 " --> pdb=" O GLU D2568 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP D2573 " --> pdb=" O ASP D2570 " (cutoff:3.500A) Processing helix chain 'D' and resid 2578 through 2586 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 removed outlier: 3.551A pdb=" N VAL D2635 " --> pdb=" O MET D2632 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 152 removed outlier: 4.660A pdb=" N ARG A 148 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LEU A 123 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE A 14 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 182 " --> pdb=" O TRP A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 4.359A pdb=" N GLU A 208 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 244 removed outlier: 13.865A pdb=" N VAL A 240 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N CYS A 253 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU A 242 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE A 250 " --> pdb=" O ARG A 265 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 260 through 265 current: chain 'A' and resid 305 through 307 removed outlier: 5.383A pdb=" N PHE A 305 " --> pdb=" O LEU A 314 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 352 through 357 current: chain 'A' and resid 386 through 391 removed outlier: 15.690A pdb=" N VAL A 387 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N SER A 400 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU A 389 " --> pdb=" O VAL A 398 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 639 through 640 Processing sheet with id=AA5, first strand: chain 'A' and resid 667 through 671 Processing sheet with id=AA6, first strand: chain 'A' and resid 801 through 803 removed outlier: 3.795A pdb=" N LEU A1100 " --> pdb=" O ARG A 802 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1318 through 1319 Processing sheet with id=AA8, first strand: chain 'A' and resid 2146 through 2152 Processing sheet with id=AA9, first strand: chain 'A' and resid 2422 through 2427 Processing sheet with id=AB1, first strand: chain 'B' and resid 639 through 640 removed outlier: 3.567A pdb=" N SER B 640 " --> pdb=" O THR B 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 667 through 671 Processing sheet with id=AB3, first strand: chain 'B' and resid 2146 through 2152 Processing sheet with id=AB4, first strand: chain 'B' and resid 2422 through 2427 Processing sheet with id=AB5, first strand: chain 'C' and resid 2146 through 2152 Processing sheet with id=AB6, first strand: chain 'C' and resid 2422 through 2427 Processing sheet with id=AB7, first strand: chain 'D' and resid 2146 through 2152 Processing sheet with id=AB8, first strand: chain 'D' and resid 2422 through 2427 2481 hydrogen bonds defined for protein. 7128 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: 10.13 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12292 1.34 - 1.46: 4980 1.46 - 1.57: 21084 1.57 - 1.69: 21 1.69 - 1.81: 368 Bond restraints: 38745 Sorted by residual: bond pdb=" CB ASP B 743 " pdb=" CG ASP B 743 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CA ASP B 743 " pdb=" CB ASP B 743 " ideal model delta sigma weight residual 1.530 1.547 -0.017 1.69e-02 3.50e+03 9.60e-01 bond pdb=" CA ASP A1320 " pdb=" CB ASP A1320 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.61e-02 3.86e+03 9.59e-01 bond pdb=" C ASP B 790 " pdb=" N PRO B 791 " ideal model delta sigma weight residual 1.334 1.356 -0.023 2.34e-02 1.83e+03 9.30e-01 bond pdb=" N ASP A1320 " pdb=" CA ASP A1320 " ideal model delta sigma weight residual 1.460 1.473 -0.014 1.42e-02 4.96e+03 9.12e-01 ... (remaining 38740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 51782 1.53 - 3.07: 527 3.07 - 4.60: 56 4.60 - 6.14: 22 6.14 - 7.67: 4 Bond angle restraints: 52391 Sorted by residual: angle pdb=" C LEU B 742 " pdb=" N ASP B 743 " pdb=" CA ASP B 743 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.54e+00 angle pdb=" C GLN B 745 " pdb=" N TYR B 746 " pdb=" CA TYR B 746 " ideal model delta sigma weight residual 121.54 127.09 -5.55 1.91e+00 2.74e-01 8.43e+00 angle pdb=" C ALA B1319 " pdb=" N ASP B1320 " pdb=" CA ASP B1320 " ideal model delta sigma weight residual 122.46 126.11 -3.65 1.41e+00 5.03e-01 6.69e+00 angle pdb=" CA ASP B 743 " pdb=" CB ASP B 743 " pdb=" CG ASP B 743 " ideal model delta sigma weight residual 112.60 115.18 -2.58 1.00e+00 1.00e+00 6.65e+00 angle pdb=" N PRO A1070 " pdb=" CA PRO A1070 " pdb=" C PRO A1070 " ideal model delta sigma weight residual 110.70 113.77 -3.07 1.22e+00 6.72e-01 6.34e+00 ... (remaining 52386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 20798 17.71 - 35.42: 2232 35.42 - 53.13: 359 53.13 - 70.83: 77 70.83 - 88.54: 27 Dihedral angle restraints: 23493 sinusoidal: 9637 harmonic: 13856 Sorted by residual: dihedral pdb=" CA ARG B 789 " pdb=" C ARG B 789 " pdb=" N ASP B 790 " pdb=" CA ASP B 790 " ideal model delta harmonic sigma weight residual -180.00 -156.44 -23.56 0 5.00e+00 4.00e-02 2.22e+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 7.07 71.93 1 2.00e+01 2.50e-03 1.66e+01 dihedral pdb=" CA CYS D2479 " pdb=" CB CYS D2479 " pdb=" SG CYS D2479 " pdb=" SG CYS D2485 " ideal model delta sinusoidal sigma weight residual 79.00 7.86 71.14 1 2.00e+01 2.50e-03 1.62e+01 ... (remaining 23490 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 4113 0.032 - 0.064: 1345 0.064 - 0.097: 430 0.097 - 0.129: 119 0.129 - 0.161: 9 Chirality restraints: 6016 Sorted by residual: 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 2.35 0.16 2.00e-01 2.50e+01 6.48e-01 chirality pdb=" CB VAL A 846 " pdb=" CA VAL A 846 " pdb=" CG1 VAL A 846 " pdb=" CG2 VAL A 846 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.15 2.00e-01 2.50e+01 5.97e-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 2.36 0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 6013 not shown) Planarity restraints: 6609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 746 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.22e+00 pdb=" C TYR B 746 " -0.040 2.00e-02 2.50e+03 pdb=" O TYR B 746 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU B 747 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A2305 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.22e+00 pdb=" N PRO A2306 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A2306 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A2306 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A1222 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A1223 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A1223 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1223 " 0.028 5.00e-02 4.00e+02 ... (remaining 6606 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 16751 2.96 - 3.44: 40712 3.44 - 3.93: 63290 3.93 - 4.41: 73115 4.41 - 4.90: 118367 Nonbonded interactions: 312235 Sorted by model distance: nonbonded pdb=" O LEU B 742 " pdb=" OD1 ASP B 743 " model vdw 2.473 3.040 nonbonded pdb=" O ALA A1319 " pdb=" OD1 ASP A1320 " model vdw 2.500 3.040 nonbonded pdb=" O ALA B1319 " pdb=" OD1 ASP B1320 " model vdw 2.537 3.040 nonbonded pdb=" O TYR A 226 " pdb=" OG SER A 227 " model vdw 2.553 3.040 nonbonded pdb=" O ASN D2194 " pdb=" OE1 GLN D2198 " model vdw 2.554 3.040 ... (remaining 312230 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: 13.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 0.880 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 38.430 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 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 : 0.002 0.036 38765 Z= 0.108 Angle : 0.428 7.669 52404 Z= 0.237 Chirality : 0.037 0.161 6016 Planarity : 0.003 0.051 6609 Dihedral : 14.688 88.543 14455 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.32 (0.13), residues: 4606 helix: 2.37 (0.09), residues: 3088 sheet: -0.49 (0.32), residues: 262 loop : -0.07 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 744 TYR 0.013 0.001 TYR A1811 PHE 0.012 0.001 PHE B1245 TRP 0.012 0.001 TRP A1448 HIS 0.008 0.001 HIS C2591 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (38745) covalent geometry : angle 0.42632 / 0.24 (52391) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 0.37542 / 0.19 ( 8) hydrogen bonds : bond 0.10715 / 7.05 ( 2481) hydrogen bonds : angle 4.78642 / 3.35 ( 7128) metal coordination : bond 0.00696 / 0.42 ( 16) metal coordination : angle 3.94363 / 2.05 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 684 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8036 (m-40) cc_final: 0.7014 (p0) REVERT: A 117 TYR cc_start: 0.7104 (m-80) cc_final: 0.6901 (m-80) REVERT: A 129 ASN cc_start: 0.8384 (t0) cc_final: 0.8094 (t0) REVERT: A 175 ASN cc_start: 0.8159 (m-40) cc_final: 0.7857 (t0) REVERT: A 259 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8251 (tptt) REVERT: A 423 LYS cc_start: 0.7365 (ttpt) cc_final: 0.6863 (tptt) REVERT: A 466 GLN cc_start: 0.7765 (tt0) cc_final: 0.6939 (tm-30) REVERT: A 470 ARG cc_start: 0.8027 (mtm110) cc_final: 0.6970 (mtm-85) REVERT: A 485 ASP cc_start: 0.8128 (t0) cc_final: 0.7560 (t70) REVERT: A 581 MET cc_start: 0.8426 (mtp) cc_final: 0.8181 (mtm) REVERT: A 1129 TRP cc_start: 0.8177 (p-90) cc_final: 0.7796 (p-90) REVERT: A 1130 VAL cc_start: 0.8369 (t) cc_final: 0.8099 (m) REVERT: A 1174 ASN cc_start: 0.6834 (t0) cc_final: 0.6522 (m-40) REVERT: A 1177 ASN cc_start: 0.8615 (m-40) cc_final: 0.8271 (m-40) REVERT: A 1180 ARG cc_start: 0.8542 (ttp-110) cc_final: 0.8225 (mtm110) REVERT: A 1187 ILE cc_start: 0.9149 (mm) cc_final: 0.8916 (mt) REVERT: A 1290 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7526 (tm-30) REVERT: A 1291 ARG cc_start: 0.8499 (ttp-110) cc_final: 0.8299 (ttp-110) REVERT: A 1392 TYR cc_start: 0.8309 (t80) cc_final: 0.8069 (t80) REVERT: A 1438 MET cc_start: 0.6323 (ptm) cc_final: 0.5982 (ptp) REVERT: A 1767 ASN cc_start: 0.8211 (t0) cc_final: 0.7970 (t0) REVERT: A 1918 MET cc_start: 0.8787 (mmm) cc_final: 0.8559 (mmm) REVERT: A 2121 LEU cc_start: 0.8787 (mm) cc_final: 0.8384 (mp) REVERT: A 2292 VAL cc_start: 0.7621 (t) cc_final: 0.7350 (p) REVERT: A 2302 ILE cc_start: 0.8330 (pt) cc_final: 0.8103 (mp) REVERT: B 638 CYS cc_start: 0.6391 (m) cc_final: 0.6102 (m) REVERT: B 696 TYR cc_start: 0.8343 (m-80) cc_final: 0.7897 (m-80) REVERT: B 747 LEU cc_start: 0.8407 (tp) cc_final: 0.8022 (tp) REVERT: B 1260 LEU cc_start: 0.8132 (tp) cc_final: 0.7886 (tp) REVERT: B 1294 GLN cc_start: 0.8402 (tt0) cc_final: 0.7966 (tp-100) REVERT: B 1359 MET cc_start: 0.8354 (mtm) cc_final: 0.8090 (mtp) REVERT: B 1398 ASN cc_start: 0.8614 (m-40) cc_final: 0.8376 (m-40) REVERT: B 1454 PHE cc_start: 0.8152 (m-10) cc_final: 0.7921 (m-10) REVERT: B 1653 MET cc_start: 0.7989 (tpp) cc_final: 0.7662 (mpp) REVERT: B 1934 ARG cc_start: 0.7711 (ttm-80) cc_final: 0.7327 (tpt-90) REVERT: B 1976 TYR cc_start: 0.8146 (m-80) cc_final: 0.7691 (m-80) REVERT: B 2071 ARG cc_start: 0.7526 (tpm170) cc_final: 0.7153 (tpp-160) REVERT: B 2079 ASN cc_start: 0.7720 (m-40) cc_final: 0.7486 (m-40) REVERT: B 2357 MET cc_start: 0.8621 (mtp) cc_final: 0.8385 (mtt) REVERT: C 1921 ILE cc_start: 0.8015 (mt) cc_final: 0.7762 (mt) REVERT: C 2037 VAL cc_start: 0.7662 (t) cc_final: 0.7444 (p) REVERT: C 2082 ASN cc_start: 0.7694 (m-40) cc_final: 0.7486 (m-40) REVERT: C 2103 ASP cc_start: 0.7695 (m-30) cc_final: 0.7401 (t0) REVERT: C 2154 HIS cc_start: 0.7586 (t70) cc_final: 0.7228 (t70) REVERT: C 2344 MET cc_start: 0.8059 (tpp) cc_final: 0.7813 (mmm) REVERT: C 2423 MET cc_start: 0.8617 (mmm) cc_final: 0.8389 (mmt) REVERT: C 2621 LYS cc_start: 0.8607 (mtpp) cc_final: 0.8258 (mptt) REVERT: D 2153 ARG cc_start: 0.6532 (mmm-85) cc_final: 0.6283 (mmt180) REVERT: D 2158 MET cc_start: 0.8361 (mtp) cc_final: 0.8060 (mtm) REVERT: D 2629 MET cc_start: 0.8131 (mmt) cc_final: 0.7768 (mmt) outliers start: 0 outliers final: 0 residues processed: 684 average time/residue: 0.2328 time to fit residues: 252.6896 Evaluate side-chains 489 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 432 optimal weight: 0.0170 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 0.0060 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.0970 overall best weight: 0.3832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A1298 HIS A2383 ASN B 847 ASN B1249 ASN B1283 HIS B1658 ASN ** B1746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1786 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1795 GLN B1796 GLN B1981 ASN B2013 ASN B2329 ASN C1818 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.091686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075266 restraints weight = 97441.626| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.14 r_work: 0.3095 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 38765 Z= 0.103 Angle : 0.440 7.297 52404 Z= 0.236 Chirality : 0.037 0.162 6016 Planarity : 0.003 0.050 6609 Dihedral : 5.578 86.526 5246 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.82 % Allowed : 6.49 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.54 (0.13), residues: 4606 helix: 2.50 (0.09), residues: 3092 sheet: -0.43 (0.31), residues: 275 loop : 0.11 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1769 TYR 0.017 0.001 TYR A 256 PHE 0.011 0.001 PHE B1245 TRP 0.011 0.001 TRP D2590 HIS 0.006 0.001 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (38745) covalent geometry : angle 0.43847 / 0.24 (52391) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 0.37185 / 0.20 ( 8) hydrogen bonds : bond 0.03406 / 2.27 ( 2481) hydrogen bonds : angle 4.08092 / 2.87 ( 7128) metal coordination : bond 0.00668 / 0.39 ( 16) metal coordination : angle 3.38357 / 1.73 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 502 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7966 (m-40) cc_final: 0.6966 (p0) REVERT: A 117 TYR cc_start: 0.6847 (m-80) cc_final: 0.6631 (m-80) REVERT: A 129 ASN cc_start: 0.8339 (t0) cc_final: 0.8039 (t0) REVERT: A 175 ASN cc_start: 0.8065 (m-40) cc_final: 0.7823 (t0) REVERT: A 259 LYS cc_start: 0.8495 (ttpt) cc_final: 0.8197 (tptt) REVERT: A 423 LYS cc_start: 0.7268 (ttpt) cc_final: 0.6743 (tptp) REVERT: A 466 GLN cc_start: 0.7746 (tt0) cc_final: 0.6911 (tm-30) REVERT: A 470 ARG cc_start: 0.7848 (mtm110) cc_final: 0.6900 (mtm-85) REVERT: A 485 ASP cc_start: 0.7851 (t0) cc_final: 0.7242 (t70) REVERT: A 581 MET cc_start: 0.8498 (mtp) cc_final: 0.8295 (mtm) REVERT: A 1129 TRP cc_start: 0.8123 (p-90) cc_final: 0.7744 (p-90) REVERT: A 1130 VAL cc_start: 0.8348 (t) cc_final: 0.8056 (m) REVERT: A 1180 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7951 (mtm110) REVERT: A 1290 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7399 (tm-30) REVERT: A 1298 HIS cc_start: 0.7866 (OUTLIER) cc_final: 0.7495 (t-90) REVERT: A 1453 ASN cc_start: 0.7218 (t0) cc_final: 0.6919 (t0) REVERT: A 1681 MET cc_start: 0.8269 (mtp) cc_final: 0.7877 (mtp) REVERT: A 1767 ASN cc_start: 0.8054 (t0) cc_final: 0.7838 (t0) REVERT: A 2069 ARG cc_start: 0.7121 (mmm-85) cc_final: 0.6760 (mmm-85) REVERT: A 2077 MET cc_start: 0.8485 (ttp) cc_final: 0.8101 (ptp) REVERT: A 2121 LEU cc_start: 0.8693 (mm) cc_final: 0.8375 (mp) REVERT: B 638 CYS cc_start: 0.6390 (m) cc_final: 0.6021 (m) REVERT: B 669 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8189 (mmtm) REVERT: B 747 LEU cc_start: 0.8183 (tp) cc_final: 0.7876 (tp) REVERT: B 821 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7235 (t70) REVERT: B 1290 GLU cc_start: 0.7577 (tm-30) cc_final: 0.7352 (tm-30) REVERT: B 1392 TYR cc_start: 0.7338 (t80) cc_final: 0.7112 (t80) REVERT: B 1398 ASN cc_start: 0.8742 (m-40) cc_final: 0.8399 (m-40) REVERT: B 1934 ARG cc_start: 0.7684 (ttm-80) cc_final: 0.7410 (tpt-90) REVERT: B 1976 TYR cc_start: 0.8157 (m-80) cc_final: 0.7799 (m-80) REVERT: B 2079 ASN cc_start: 0.7712 (m-40) cc_final: 0.7498 (m-40) REVERT: B 2624 ASP cc_start: 0.8170 (m-30) cc_final: 0.7832 (m-30) REVERT: C 1921 ILE cc_start: 0.7709 (mt) cc_final: 0.7446 (mt) REVERT: C 2082 ASN cc_start: 0.7633 (m-40) cc_final: 0.7429 (m-40) REVERT: C 2103 ASP cc_start: 0.7519 (m-30) cc_final: 0.7263 (t0) REVERT: C 2154 HIS cc_start: 0.7507 (t70) cc_final: 0.7176 (t70) REVERT: C 2423 MET cc_start: 0.8476 (mmm) cc_final: 0.8220 (mmt) REVERT: C 2621 LYS cc_start: 0.8462 (mtpp) cc_final: 0.8177 (mptt) REVERT: D 2153 ARG cc_start: 0.6332 (mmm-85) cc_final: 0.6072 (mmt180) REVERT: D 2158 MET cc_start: 0.8217 (mtp) cc_final: 0.7878 (mtm) REVERT: D 2629 MET cc_start: 0.8011 (mmt) cc_final: 0.7548 (mmt) outliers start: 34 outliers final: 22 residues processed: 517 average time/residue: 0.2271 time to fit residues: 187.8503 Evaluate side-chains 483 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 459 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 1298 HIS Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2299 ILE Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1249 ASN Chi-restraints excluded: chain B residue 1283 HIS Chi-restraints excluded: chain B residue 1298 HIS Chi-restraints excluded: chain C residue 2077 MET Chi-restraints excluded: chain C residue 2178 CYS Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain C residue 2589 MET Chi-restraints excluded: chain D residue 2186 ARG Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2308 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 302 optimal weight: 0.5980 chunk 421 optimal weight: 0.9980 chunk 93 optimal weight: 9.9990 chunk 344 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 427 optimal weight: 4.9990 chunk 354 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A1298 HIS A2383 ASN B1283 HIS B1286 ASN B1658 ASN B1944 ASN B1981 ASN D2616 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.090044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.073495 restraints weight = 97539.257| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.14 r_work: 0.3043 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 38765 Z= 0.185 Angle : 0.484 7.802 52404 Z= 0.257 Chirality : 0.039 0.164 6016 Planarity : 0.003 0.051 6609 Dihedral : 5.738 88.251 5246 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.32 % Allowed : 7.62 % Favored : 91.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.37 (0.13), residues: 4606 helix: 2.37 (0.09), residues: 3096 sheet: -0.55 (0.31), residues: 283 loop : 0.06 (0.19), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1291 TYR 0.015 0.001 TYR A2352 PHE 0.020 0.002 PHE A1451 TRP 0.012 0.002 TRP D2590 HIS 0.010 0.001 HIS A1298 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (38745) covalent geometry : angle 0.48173 / 0.26 (52391) SS BOND : bond 0.00522 / 0.26 ( 4) SS BOND : angle 0.38775 / 0.20 ( 8) hydrogen bonds : bond 0.04015 / 2.70 ( 2481) hydrogen bonds : angle 4.17500 / 2.94 ( 7128) metal coordination : bond 0.00914 / 0.51 ( 16) metal coordination : angle 4.66707 / 2.39 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 480 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8058 (m-40) cc_final: 0.7002 (p0) REVERT: A 117 TYR cc_start: 0.7168 (m-80) cc_final: 0.6749 (m-80) REVERT: A 124 LEU cc_start: 0.8809 (tt) cc_final: 0.8609 (tp) REVERT: A 129 ASN cc_start: 0.8399 (t0) cc_final: 0.8056 (t0) REVERT: A 175 ASN cc_start: 0.8249 (m-40) cc_final: 0.7815 (t0) REVERT: A 259 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8236 (tptt) REVERT: A 423 LYS cc_start: 0.7460 (ttpt) cc_final: 0.6906 (tptp) REVERT: A 466 GLN cc_start: 0.7871 (tt0) cc_final: 0.6937 (tm-30) REVERT: A 470 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7134 (mtm-85) REVERT: A 485 ASP cc_start: 0.8171 (t0) cc_final: 0.7544 (t70) REVERT: A 1130 VAL cc_start: 0.8379 (t) cc_final: 0.8045 (m) REVERT: A 1290 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7909 (tm-30) REVERT: A 1453 ASN cc_start: 0.7330 (t0) cc_final: 0.7005 (t0) REVERT: A 1664 MET cc_start: 0.8104 (mtm) cc_final: 0.7880 (ttm) REVERT: A 1681 MET cc_start: 0.8522 (mtp) cc_final: 0.8145 (mtp) REVERT: A 1767 ASN cc_start: 0.8282 (t0) cc_final: 0.7998 (t0) REVERT: A 2069 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7138 (mmm-85) REVERT: A 2077 MET cc_start: 0.8665 (ttp) cc_final: 0.8284 (ptp) REVERT: A 2121 LEU cc_start: 0.8668 (mm) cc_final: 0.8362 (mp) REVERT: A 2344 MET cc_start: 0.8094 (mmm) cc_final: 0.7823 (mpp) REVERT: B 638 CYS cc_start: 0.6617 (m) cc_final: 0.6220 (m) REVERT: B 669 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8160 (mmtt) REVERT: B 747 LEU cc_start: 0.8259 (tp) cc_final: 0.7910 (tp) REVERT: B 1934 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7625 (tpt-90) REVERT: B 1976 TYR cc_start: 0.8393 (m-80) cc_final: 0.8010 (m-80) REVERT: B 2076 VAL cc_start: 0.7817 (p) cc_final: 0.7561 (m) REVERT: B 2079 ASN cc_start: 0.7798 (m-40) cc_final: 0.7582 (m-40) REVERT: B 2158 MET cc_start: 0.8752 (mtp) cc_final: 0.8499 (mmm) REVERT: C 1921 ILE cc_start: 0.7886 (mt) cc_final: 0.7638 (mt) REVERT: C 1957 GLN cc_start: 0.7136 (tm-30) cc_final: 0.6567 (tt0) REVERT: C 2103 ASP cc_start: 0.7793 (m-30) cc_final: 0.7464 (t0) REVERT: C 2154 HIS cc_start: 0.7746 (t70) cc_final: 0.7425 (t70) REVERT: C 2423 MET cc_start: 0.8583 (mmm) cc_final: 0.8281 (mmt) REVERT: C 2621 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8195 (mptt) REVERT: D 2153 ARG cc_start: 0.6749 (mmm-85) cc_final: 0.6503 (mmt180) REVERT: D 2158 MET cc_start: 0.8376 (mtp) cc_final: 0.8022 (mtm) REVERT: D 2629 MET cc_start: 0.8293 (mmt) cc_final: 0.7876 (mmt) outliers start: 55 outliers final: 37 residues processed: 508 average time/residue: 0.2177 time to fit residues: 179.0881 Evaluate side-chains 488 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 451 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 1326 LYS Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1283 HIS Chi-restraints excluded: chain B residue 1298 HIS Chi-restraints excluded: chain B residue 1336 ILE Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1689 VAL Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1953 CYS Chi-restraints excluded: chain B residue 2077 MET Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain C residue 2077 MET Chi-restraints excluded: chain C residue 2178 CYS Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2589 MET Chi-restraints excluded: chain D residue 2178 CYS Chi-restraints excluded: chain D residue 2186 ARG Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2308 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 403 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 335 optimal weight: 0.8980 chunk 86 optimal weight: 0.5980 chunk 232 optimal weight: 0.9990 chunk 289 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 329 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A2383 ASN B 750 ASN B 847 ASN ** B1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS B1658 ASN B1944 ASN B1981 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.090856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.074379 restraints weight = 97152.458| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.13 r_work: 0.3067 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 38765 Z= 0.124 Angle : 0.444 6.918 52404 Z= 0.238 Chirality : 0.038 0.162 6016 Planarity : 0.003 0.051 6609 Dihedral : 5.633 89.156 5246 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.20 % Allowed : 9.18 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.46 (0.13), residues: 4606 helix: 2.45 (0.09), residues: 3098 sheet: -0.48 (0.31), residues: 285 loop : 0.07 (0.19), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1769 TYR 0.013 0.001 TYR A1811 PHE 0.015 0.001 PHE A 444 TRP 0.012 0.001 TRP D2590 HIS 0.004 0.001 HIS C2591 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (38745) covalent geometry : angle 0.44240 / 0.24 (52391) SS BOND : bond 0.00281 / 0.14 ( 4) SS BOND : angle 0.31993 / 0.17 ( 8) hydrogen bonds : bond 0.03570 / 2.40 ( 2481) hydrogen bonds : angle 4.05782 / 2.86 ( 7128) metal coordination : bond 0.00674 / 0.38 ( 16) metal coordination : angle 3.85278 / 2.00 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 466 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7976 (m-40) cc_final: 0.6942 (p0) REVERT: A 117 TYR cc_start: 0.6909 (m-80) cc_final: 0.6467 (m-80) REVERT: A 129 ASN cc_start: 0.8321 (t0) cc_final: 0.7947 (t0) REVERT: A 175 ASN cc_start: 0.8135 (m-40) cc_final: 0.7679 (t0) REVERT: A 259 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8218 (tptt) REVERT: A 423 LYS cc_start: 0.7296 (ttpt) cc_final: 0.6746 (tptp) REVERT: A 466 GLN cc_start: 0.7691 (tt0) cc_final: 0.6795 (tm-30) REVERT: A 470 ARG cc_start: 0.7872 (mtm110) cc_final: 0.6881 (mtm-85) REVERT: A 485 ASP cc_start: 0.7866 (t0) cc_final: 0.7236 (t70) REVERT: A 1056 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8339 (m) REVERT: A 1453 ASN cc_start: 0.7337 (t0) cc_final: 0.7016 (t0) REVERT: A 1664 MET cc_start: 0.7965 (mtm) cc_final: 0.7758 (ttm) REVERT: A 1767 ASN cc_start: 0.8071 (t0) cc_final: 0.7848 (t0) REVERT: A 2069 ARG cc_start: 0.7227 (mmm-85) cc_final: 0.6912 (mmm-85) REVERT: A 2077 MET cc_start: 0.8467 (ttp) cc_final: 0.8112 (ptp) REVERT: A 2121 LEU cc_start: 0.8701 (mm) cc_final: 0.8383 (mp) REVERT: A 2291 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6298 (mt) REVERT: A 2292 VAL cc_start: 0.7750 (t) cc_final: 0.7406 (p) REVERT: A 2344 MET cc_start: 0.7871 (mmm) cc_final: 0.7633 (mpp) REVERT: B 638 CYS cc_start: 0.6406 (m) cc_final: 0.5975 (m) REVERT: B 669 LYS cc_start: 0.8569 (mmtp) cc_final: 0.8188 (mmtt) REVERT: B 1332 MET cc_start: 0.8851 (mmm) cc_final: 0.8613 (mmm) REVERT: B 1398 ASN cc_start: 0.8763 (m-40) cc_final: 0.8458 (m-40) REVERT: B 1934 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7411 (tpt-90) REVERT: B 1976 TYR cc_start: 0.8196 (m-80) cc_final: 0.7810 (m-80) REVERT: B 2079 ASN cc_start: 0.7713 (m-40) cc_final: 0.7488 (m-40) REVERT: B 2224 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7171 (ttp80) REVERT: B 2624 ASP cc_start: 0.8232 (m-30) cc_final: 0.7912 (m-30) REVERT: C 1921 ILE cc_start: 0.7747 (mt) cc_final: 0.7499 (mt) REVERT: C 1957 GLN cc_start: 0.6923 (tm-30) cc_final: 0.6509 (tt0) REVERT: C 2103 ASP cc_start: 0.7541 (m-30) cc_final: 0.7275 (t0) REVERT: C 2154 HIS cc_start: 0.7491 (t70) cc_final: 0.7190 (t70) REVERT: C 2423 MET cc_start: 0.8482 (mmm) cc_final: 0.8221 (mmt) REVERT: D 2158 MET cc_start: 0.8221 (mtp) cc_final: 0.7881 (mtm) REVERT: D 2629 MET cc_start: 0.8019 (mmt) cc_final: 0.7574 (mmt) outliers start: 50 outliers final: 38 residues processed: 489 average time/residue: 0.2279 time to fit residues: 179.4367 Evaluate side-chains 493 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 453 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1326 LYS Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1283 HIS Chi-restraints excluded: chain B residue 1298 HIS Chi-restraints excluded: chain B residue 1317 VAL Chi-restraints excluded: chain B residue 1336 ILE Chi-restraints excluded: chain B residue 1391 VAL Chi-restraints excluded: chain B residue 1416 ILE Chi-restraints excluded: chain B residue 1689 VAL Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1953 CYS Chi-restraints excluded: chain B residue 2077 MET Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain C residue 1810 LEU Chi-restraints excluded: chain C residue 1960 ASP Chi-restraints excluded: chain C residue 2077 MET Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain C residue 2589 MET Chi-restraints excluded: chain D residue 2178 CYS Chi-restraints excluded: chain D residue 2186 ARG Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2308 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 224 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 358 optimal weight: 1.9990 chunk 405 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 318 optimal weight: 5.9990 chunk 241 optimal weight: 0.0770 chunk 27 optimal weight: 6.9990 chunk 255 optimal weight: 2.9990 chunk 400 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A2383 ASN B1098 GLN ** B1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS B1658 ASN ** B1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1818 GLN B1944 ASN B1981 ASN B2329 ASN D2616 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.089649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.073438 restraints weight = 97346.892| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.12 r_work: 0.3037 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 38765 Z= 0.239 Angle : 0.516 7.592 52404 Z= 0.272 Chirality : 0.041 0.174 6016 Planarity : 0.004 0.052 6609 Dihedral : 5.873 86.295 5246 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.75 % Allowed : 9.71 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.19 (0.13), residues: 4606 helix: 2.24 (0.09), residues: 3103 sheet: -0.56 (0.30), residues: 283 loop : -0.06 (0.19), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1769 TYR 0.016 0.002 TYR A2352 PHE 0.023 0.002 PHE A1451 TRP 0.013 0.002 TRP C2229 HIS 0.012 0.001 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.24 (38745) covalent geometry : angle 0.51419 / 0.27 (52391) SS BOND : bond 0.00708 / 0.36 ( 4) SS BOND : angle 0.29415 / 0.15 ( 8) hydrogen bonds : bond 0.04289 / 2.90 ( 2481) hydrogen bonds : angle 4.22953 / 2.98 ( 7128) metal coordination : bond 0.01148 / 0.63 ( 16) metal coordination : angle 4.80116 / 2.48 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 466 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8024 (m-40) cc_final: 0.6994 (p0) REVERT: A 117 TYR cc_start: 0.7262 (m-80) cc_final: 0.6795 (m-80) REVERT: A 129 ASN cc_start: 0.8370 (t0) cc_final: 0.7999 (t0) REVERT: A 175 ASN cc_start: 0.8265 (m-40) cc_final: 0.7784 (t0) REVERT: A 259 LYS cc_start: 0.8611 (ttpt) cc_final: 0.8255 (tptt) REVERT: A 423 LYS cc_start: 0.7501 (ttpt) cc_final: 0.6936 (tptp) REVERT: A 466 GLN cc_start: 0.7813 (tt0) cc_final: 0.6969 (tm-30) REVERT: A 470 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7134 (mtm-85) REVERT: A 485 ASP cc_start: 0.8212 (t0) cc_final: 0.7595 (t70) REVERT: A 655 PHE cc_start: 0.8604 (m-80) cc_final: 0.8228 (m-80) REVERT: A 1438 MET cc_start: 0.6346 (ptm) cc_final: 0.6055 (ptp) REVERT: A 1453 ASN cc_start: 0.7368 (t0) cc_final: 0.7025 (t0) REVERT: A 1664 MET cc_start: 0.8075 (mtm) cc_final: 0.7813 (ttm) REVERT: A 1767 ASN cc_start: 0.8312 (t0) cc_final: 0.8008 (t0) REVERT: A 2069 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7238 (mmm-85) REVERT: A 2077 MET cc_start: 0.8682 (ttp) cc_final: 0.8330 (ptp) REVERT: A 2121 LEU cc_start: 0.8678 (mm) cc_final: 0.8402 (mp) REVERT: A 2291 LEU cc_start: 0.6551 (OUTLIER) cc_final: 0.6244 (mt) REVERT: A 2292 VAL cc_start: 0.7705 (t) cc_final: 0.7338 (p) REVERT: A 2344 MET cc_start: 0.8042 (mmm) cc_final: 0.7629 (mpp) REVERT: B 638 CYS cc_start: 0.6451 (m) cc_final: 0.5994 (m) REVERT: B 669 LYS cc_start: 0.8545 (mmtp) cc_final: 0.8134 (mmtt) REVERT: B 751 GLN cc_start: 0.8135 (pt0) cc_final: 0.7736 (tt0) REVERT: B 1332 MET cc_start: 0.9013 (mmm) cc_final: 0.8704 (mmm) REVERT: B 1934 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7658 (tpt-90) REVERT: B 1976 TYR cc_start: 0.8370 (m-80) cc_final: 0.8010 (m-80) REVERT: B 2079 ASN cc_start: 0.7863 (m-40) cc_final: 0.7637 (m-40) REVERT: B 2224 ARG cc_start: 0.7838 (ttp80) cc_final: 0.7446 (ttp80) REVERT: C 1921 ILE cc_start: 0.7869 (mt) cc_final: 0.7640 (mt) REVERT: C 1957 GLN cc_start: 0.7062 (tm-30) cc_final: 0.6638 (tt0) REVERT: C 2103 ASP cc_start: 0.7808 (m-30) cc_final: 0.7501 (t0) REVERT: C 2154 HIS cc_start: 0.7712 (t70) cc_final: 0.7380 (t70) REVERT: C 2423 MET cc_start: 0.8600 (mmm) cc_final: 0.8283 (mmt) REVERT: D 2158 MET cc_start: 0.8377 (mtp) cc_final: 0.7960 (mtm) REVERT: D 2629 MET cc_start: 0.8288 (mmt) cc_final: 0.7860 (mmt) outliers start: 73 outliers final: 53 residues processed: 504 average time/residue: 0.2200 time to fit residues: 180.3382 Evaluate side-chains 505 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 451 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1326 LYS Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1946 LYS Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1298 HIS Chi-restraints excluded: chain B residue 1317 VAL Chi-restraints excluded: chain B residue 1336 ILE Chi-restraints excluded: chain B residue 1391 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1689 VAL Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1953 CYS Chi-restraints excluded: chain B residue 2005 THR Chi-restraints excluded: chain B residue 2077 MET Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2479 CYS Chi-restraints excluded: chain B residue 2513 LEU Chi-restraints excluded: chain C residue 1960 ASP Chi-restraints excluded: chain C residue 2178 CYS Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2571 LYS Chi-restraints excluded: chain C residue 2583 ILE Chi-restraints excluded: chain C residue 2589 MET Chi-restraints excluded: chain D residue 2178 CYS Chi-restraints excluded: chain D residue 2186 ARG Chi-restraints excluded: chain D residue 2201 GLU Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2308 LEU Chi-restraints excluded: chain D residue 2475 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 105 optimal weight: 0.9980 chunk 452 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 450 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 164 HIS A 247 GLN A2383 ASN A2552 GLN ** B1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS B1286 ASN B1658 ASN B1944 ASN B1981 ASN B2329 ASN D2616 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.090099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.073818 restraints weight = 97401.567| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.11 r_work: 0.3048 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38765 Z= 0.174 Angle : 0.483 9.059 52404 Z= 0.256 Chirality : 0.039 0.174 6016 Planarity : 0.003 0.052 6609 Dihedral : 5.832 86.929 5246 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.71 % Allowed : 10.38 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.25 (0.13), residues: 4606 helix: 2.29 (0.09), residues: 3098 sheet: -0.58 (0.30), residues: 283 loop : -0.03 (0.19), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2071 TYR 0.025 0.001 TYR A1392 PHE 0.026 0.001 PHE A1451 TRP 0.013 0.001 TRP D2590 HIS 0.007 0.001 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (38745) covalent geometry : angle 0.48156 / 0.26 (52391) SS BOND : bond 0.00473 / 0.24 ( 4) SS BOND : angle 0.28330 / 0.15 ( 8) hydrogen bonds : bond 0.03969 / 2.68 ( 2481) hydrogen bonds : angle 4.16536 / 2.94 ( 7128) metal coordination : bond 0.00890 / 0.49 ( 16) metal coordination : angle 4.41704 / 2.30 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 457 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8007 (m-40) cc_final: 0.6969 (p0) REVERT: A 117 TYR cc_start: 0.7240 (m-80) cc_final: 0.6782 (m-80) REVERT: A 129 ASN cc_start: 0.8357 (t0) cc_final: 0.7993 (t0) REVERT: A 259 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8275 (tptt) REVERT: A 423 LYS cc_start: 0.7479 (ttpt) cc_final: 0.6909 (tptp) REVERT: A 466 GLN cc_start: 0.7798 (tt0) cc_final: 0.6907 (tm-30) REVERT: A 470 ARG cc_start: 0.8102 (mtm110) cc_final: 0.7156 (mtm-85) REVERT: A 485 ASP cc_start: 0.8195 (t0) cc_final: 0.7575 (t70) REVERT: A 1056 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8413 (m) REVERT: A 1294 GLN cc_start: 0.8443 (tt0) cc_final: 0.8142 (mt0) REVERT: A 1438 MET cc_start: 0.6325 (ptm) cc_final: 0.6037 (ptp) REVERT: A 1453 ASN cc_start: 0.7312 (t0) cc_final: 0.6991 (t0) REVERT: A 1664 MET cc_start: 0.8056 (mtm) cc_final: 0.7792 (ttm) REVERT: A 1767 ASN cc_start: 0.8283 (t0) cc_final: 0.7979 (t0) REVERT: A 2069 ARG cc_start: 0.7613 (mmm-85) cc_final: 0.7286 (mmm-85) REVERT: A 2077 MET cc_start: 0.8658 (ttp) cc_final: 0.8295 (ptp) REVERT: A 2291 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.6198 (mt) REVERT: A 2292 VAL cc_start: 0.7659 (t) cc_final: 0.7322 (p) REVERT: A 2344 MET cc_start: 0.8019 (mmm) cc_final: 0.7609 (mpp) REVERT: A 2348 TYR cc_start: 0.8613 (t80) cc_final: 0.8362 (t80) REVERT: B 638 CYS cc_start: 0.6367 (m) cc_final: 0.5963 (m) REVERT: B 669 LYS cc_start: 0.8548 (mmtp) cc_final: 0.8126 (mmtt) REVERT: B 751 GLN cc_start: 0.8126 (pt0) cc_final: 0.7757 (tt0) REVERT: B 1282 TYR cc_start: 0.8679 (t80) cc_final: 0.8401 (t80) REVERT: B 1332 MET cc_start: 0.9042 (mmm) cc_final: 0.8698 (mmm) REVERT: B 1398 ASN cc_start: 0.8839 (m-40) cc_final: 0.8528 (m-40) REVERT: B 1934 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7639 (tpt-90) REVERT: B 1976 TYR cc_start: 0.8370 (m-80) cc_final: 0.8017 (m-80) REVERT: B 2079 ASN cc_start: 0.7803 (m-40) cc_final: 0.7576 (m-40) REVERT: B 2224 ARG cc_start: 0.7833 (ttp80) cc_final: 0.7446 (ttp80) REVERT: C 1921 ILE cc_start: 0.7875 (mt) cc_final: 0.7647 (mt) REVERT: C 2103 ASP cc_start: 0.7801 (m-30) cc_final: 0.7481 (t0) REVERT: C 2154 HIS cc_start: 0.7749 (t70) cc_final: 0.7414 (t70) REVERT: C 2423 MET cc_start: 0.8597 (mmm) cc_final: 0.8290 (mmt) REVERT: D 2158 MET cc_start: 0.8349 (mtp) cc_final: 0.7935 (mtm) REVERT: D 2308 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7887 (mp) REVERT: D 2629 MET cc_start: 0.8274 (mmt) cc_final: 0.7863 (mmt) outliers start: 71 outliers final: 55 residues processed: 496 average time/residue: 0.2225 time to fit residues: 178.6011 Evaluate side-chains 504 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 446 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1326 LYS Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2299 ILE Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1283 HIS Chi-restraints excluded: chain B residue 1298 HIS Chi-restraints excluded: chain B residue 1317 VAL Chi-restraints excluded: chain B residue 1336 ILE Chi-restraints excluded: chain B residue 1354 ILE Chi-restraints excluded: chain B residue 1391 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1689 VAL Chi-restraints excluded: chain B residue 1748 LEU Chi-restraints excluded: chain B residue 1765 THR Chi-restraints excluded: chain B residue 1944 ASN Chi-restraints excluded: chain B residue 1953 CYS Chi-restraints excluded: chain B residue 2005 THR Chi-restraints excluded: chain B residue 2077 MET Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2513 LEU Chi-restraints excluded: chain C residue 1960 ASP Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2479 CYS Chi-restraints excluded: chain D residue 2178 CYS Chi-restraints excluded: chain D residue 2186 ARG Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2308 LEU Chi-restraints excluded: chain D residue 2475 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 434 optimal weight: 0.3980 chunk 185 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 461 optimal weight: 0.9990 chunk 271 optimal weight: 0.9990 chunk 235 optimal weight: 0.5980 chunk 354 optimal weight: 0.8980 chunk 324 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 287 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A2383 ASN B1098 GLN ** B1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1658 ASN ** B1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1818 GLN B1981 ASN D2616 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.090944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.074963 restraints weight = 97223.166| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.00 r_work: 0.3087 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38765 Z= 0.116 Angle : 0.450 7.530 52404 Z= 0.241 Chirality : 0.038 0.211 6016 Planarity : 0.003 0.052 6609 Dihedral : 5.671 88.835 5246 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.47 % Allowed : 11.11 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.44 (0.13), residues: 4606 helix: 2.44 (0.09), residues: 3091 sheet: -0.52 (0.31), residues: 281 loop : 0.03 (0.19), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2071 TYR 0.013 0.001 TYR A1811 PHE 0.028 0.001 PHE A1451 TRP 0.012 0.001 TRP D2590 HIS 0.013 0.001 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (38745) covalent geometry : angle 0.44855 / 0.24 (52391) SS BOND : bond 0.00222 / 0.11 ( 4) SS BOND : angle 0.32694 / 0.18 ( 8) hydrogen bonds : bond 0.03535 / 2.38 ( 2481) hydrogen bonds : angle 4.04194 / 2.85 ( 7128) metal coordination : bond 0.00671 / 0.38 ( 16) metal coordination : angle 3.70338 / 1.94 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 460 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.7988 (m-40) cc_final: 0.6958 (p0) REVERT: A 117 TYR cc_start: 0.7150 (m-80) cc_final: 0.6722 (m-80) REVERT: A 129 ASN cc_start: 0.8351 (t0) cc_final: 0.7992 (t0) REVERT: A 259 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8258 (tptt) REVERT: A 293 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.5744 (ttp-170) REVERT: A 423 LYS cc_start: 0.7398 (ttpt) cc_final: 0.6812 (tptp) REVERT: A 466 GLN cc_start: 0.7713 (tt0) cc_final: 0.6842 (tm-30) REVERT: A 470 ARG cc_start: 0.8024 (mtm110) cc_final: 0.7123 (mtm-85) REVERT: A 485 ASP cc_start: 0.8117 (t0) cc_final: 0.7491 (t70) REVERT: A 655 PHE cc_start: 0.8564 (m-80) cc_final: 0.8192 (m-80) REVERT: A 1056 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8465 (m) REVERT: A 1294 GLN cc_start: 0.8376 (tt0) cc_final: 0.8074 (mt0) REVERT: A 1453 ASN cc_start: 0.7376 (t0) cc_final: 0.7064 (t0) REVERT: A 1767 ASN cc_start: 0.8234 (t0) cc_final: 0.7940 (t0) REVERT: A 2069 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.7242 (mmm-85) REVERT: A 2077 MET cc_start: 0.8616 (ttp) cc_final: 0.8237 (ptp) REVERT: A 2291 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6348 (mt) REVERT: B 669 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8136 (mmtt) REVERT: B 751 GLN cc_start: 0.8089 (pt0) cc_final: 0.6885 (tt0) REVERT: B 825 ASN cc_start: 0.7602 (m-40) cc_final: 0.7318 (m-40) REVERT: B 1282 TYR cc_start: 0.8616 (t80) cc_final: 0.8385 (t80) REVERT: B 1332 MET cc_start: 0.9008 (mmm) cc_final: 0.8659 (mmm) REVERT: B 1392 TYR cc_start: 0.7592 (t80) cc_final: 0.7332 (t80) REVERT: B 1398 ASN cc_start: 0.8786 (m-40) cc_final: 0.8466 (m-40) REVERT: B 1653 MET cc_start: 0.7979 (mmm) cc_final: 0.7600 (mpp) REVERT: B 1934 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7629 (tpt-90) REVERT: B 1976 TYR cc_start: 0.8328 (m-80) cc_final: 0.7985 (m-80) REVERT: B 2031 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8068 (ptpp) REVERT: B 2079 ASN cc_start: 0.7791 (m-40) cc_final: 0.7562 (m-40) REVERT: B 2224 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7420 (ttp80) REVERT: B 2292 VAL cc_start: 0.7541 (t) cc_final: 0.7301 (p) REVERT: C 1921 ILE cc_start: 0.7830 (mt) cc_final: 0.7592 (mt) REVERT: C 2103 ASP cc_start: 0.7780 (m-30) cc_final: 0.7467 (t0) REVERT: C 2154 HIS cc_start: 0.7710 (t70) cc_final: 0.7374 (t70) REVERT: C 2423 MET cc_start: 0.8589 (mmm) cc_final: 0.8319 (mmt) REVERT: D 2158 MET cc_start: 0.8282 (mtp) cc_final: 0.7896 (mtm) REVERT: D 2213 ILE cc_start: 0.8779 (tt) cc_final: 0.8532 (pt) outliers start: 61 outliers final: 42 residues processed: 498 average time/residue: 0.2205 time to fit residues: 178.0777 Evaluate side-chains 492 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 447 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1326 LYS Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 2006 CYS Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2299 ILE Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1298 HIS Chi-restraints excluded: chain B residue 1317 VAL Chi-restraints excluded: chain B residue 1336 ILE Chi-restraints excluded: chain B residue 1391 VAL Chi-restraints excluded: chain B residue 1953 CYS Chi-restraints excluded: chain B residue 2077 MET Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2479 CYS Chi-restraints excluded: chain C residue 1960 ASP Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2479 CYS Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2186 ARG Chi-restraints excluded: chain D residue 2475 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 242 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 376 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 311 optimal weight: 4.9990 chunk 353 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 372 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 705 HIS A2383 ASN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS B1658 ASN ** B1788 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1981 ASN D2616 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.090555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.074513 restraints weight = 97115.218| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.03 r_work: 0.3072 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38765 Z= 0.149 Angle : 0.469 7.758 52404 Z= 0.250 Chirality : 0.039 0.175 6016 Planarity : 0.003 0.051 6609 Dihedral : 5.676 87.803 5246 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.59 % Allowed : 11.25 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.39 (0.13), residues: 4606 helix: 2.40 (0.09), residues: 3092 sheet: -0.52 (0.31), residues: 281 loop : 0.03 (0.19), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2071 TYR 0.017 0.001 TYR A1109 PHE 0.022 0.001 PHE B1426 TRP 0.012 0.001 TRP D2590 HIS 0.007 0.001 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (38745) covalent geometry : angle 0.46760 / 0.25 (52391) SS BOND : bond 0.00369 / 0.19 ( 4) SS BOND : angle 0.39134 / 0.21 ( 8) hydrogen bonds : bond 0.03719 / 2.51 ( 2481) hydrogen bonds : angle 4.06744 / 2.87 ( 7128) metal coordination : bond 0.00781 / 0.44 ( 16) metal coordination : angle 4.30950 / 2.25 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 456 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8007 (m-40) cc_final: 0.6977 (p0) REVERT: A 117 TYR cc_start: 0.7202 (m-80) cc_final: 0.6766 (m-80) REVERT: A 129 ASN cc_start: 0.8338 (t0) cc_final: 0.7980 (t0) REVERT: A 259 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8285 (tptt) REVERT: A 293 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.5771 (ttp-170) REVERT: A 423 LYS cc_start: 0.7434 (ttpt) cc_final: 0.6843 (tptp) REVERT: A 466 GLN cc_start: 0.7727 (tt0) cc_final: 0.6862 (tm-30) REVERT: A 470 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7151 (mtm-85) REVERT: A 485 ASP cc_start: 0.8168 (t0) cc_final: 0.7543 (t70) REVERT: A 655 PHE cc_start: 0.8608 (m-80) cc_final: 0.8239 (m-80) REVERT: A 1056 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8433 (m) REVERT: A 1453 ASN cc_start: 0.7355 (t0) cc_final: 0.7036 (t0) REVERT: A 1767 ASN cc_start: 0.8242 (t0) cc_final: 0.7950 (t0) REVERT: A 2069 ARG cc_start: 0.7598 (mmm-85) cc_final: 0.7298 (mmm-85) REVERT: A 2077 MET cc_start: 0.8648 (ttp) cc_final: 0.8279 (ptp) REVERT: A 2291 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6329 (mt) REVERT: A 2344 MET cc_start: 0.7967 (mmm) cc_final: 0.7463 (mpp) REVERT: B 669 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8151 (mmtt) REVERT: B 751 GLN cc_start: 0.8022 (pt0) cc_final: 0.7691 (tt0) REVERT: B 825 ASN cc_start: 0.7577 (m-40) cc_final: 0.7348 (m-40) REVERT: B 1653 MET cc_start: 0.8008 (mmm) cc_final: 0.7650 (mpp) REVERT: B 1934 ARG cc_start: 0.8013 (ttm-80) cc_final: 0.7645 (tpt-90) REVERT: B 1940 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8397 (mt) REVERT: B 1976 TYR cc_start: 0.8345 (m-80) cc_final: 0.7995 (m-80) REVERT: B 2059 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7557 (tm-30) REVERT: B 2079 ASN cc_start: 0.7802 (m-40) cc_final: 0.7574 (m-40) REVERT: B 2224 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7411 (ttp80) REVERT: B 2292 VAL cc_start: 0.7542 (t) cc_final: 0.7285 (p) REVERT: C 1921 ILE cc_start: 0.7857 (mt) cc_final: 0.7620 (mt) REVERT: C 2103 ASP cc_start: 0.7799 (m-30) cc_final: 0.7498 (t0) REVERT: C 2154 HIS cc_start: 0.7741 (t70) cc_final: 0.7394 (t70) REVERT: C 2423 MET cc_start: 0.8619 (mmm) cc_final: 0.8350 (mmt) REVERT: D 2158 MET cc_start: 0.8312 (mtp) cc_final: 0.7912 (mtm) outliers start: 66 outliers final: 51 residues processed: 495 average time/residue: 0.2281 time to fit residues: 183.0841 Evaluate side-chains 502 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 447 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1326 LYS Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1033 GLN Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1283 HIS Chi-restraints excluded: chain B residue 1298 HIS Chi-restraints excluded: chain B residue 1317 VAL Chi-restraints excluded: chain B residue 1391 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1689 VAL Chi-restraints excluded: chain B residue 1765 THR Chi-restraints excluded: chain B residue 1940 LEU Chi-restraints excluded: chain B residue 1953 CYS Chi-restraints excluded: chain B residue 2077 MET Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2479 CYS Chi-restraints excluded: chain C residue 1960 ASP Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2178 CYS Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2479 CYS Chi-restraints excluded: chain C residue 2571 LYS Chi-restraints excluded: chain D residue 2178 CYS Chi-restraints excluded: chain D residue 2186 ARG Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2475 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 437 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 417 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 294 optimal weight: 3.9990 chunk 389 optimal weight: 0.9980 chunk 398 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 705 HIS A2383 ASN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1257 HIS B1658 ASN B1944 ASN B1981 ASN D2616 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.090846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.074814 restraints weight = 97713.727| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.03 r_work: 0.3078 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38765 Z= 0.133 Angle : 0.466 8.601 52404 Z= 0.248 Chirality : 0.038 0.167 6016 Planarity : 0.003 0.051 6609 Dihedral : 5.646 86.640 5246 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.66 % Allowed : 11.30 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.41 (0.13), residues: 4606 helix: 2.42 (0.09), residues: 3097 sheet: -0.50 (0.31), residues: 281 loop : 0.02 (0.19), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 829 TYR 0.036 0.001 TYR A1392 PHE 0.024 0.001 PHE D2537 TRP 0.016 0.001 TRP D2590 HIS 0.027 0.001 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (38745) covalent geometry : angle 0.46425 / 0.25 (52391) SS BOND : bond 0.00305 / 0.15 ( 4) SS BOND : angle 0.56914 / 0.30 ( 8) hydrogen bonds : bond 0.03614 / 2.43 ( 2481) hydrogen bonds : angle 4.04301 / 2.85 ( 7128) metal coordination : bond 0.00706 / 0.40 ( 16) metal coordination : angle 4.06986 / 2.14 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 447 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8003 (m-40) cc_final: 0.6964 (p0) REVERT: A 117 TYR cc_start: 0.7196 (m-80) cc_final: 0.6732 (m-80) REVERT: A 129 ASN cc_start: 0.8322 (t0) cc_final: 0.7966 (t0) REVERT: A 259 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8294 (tptt) REVERT: A 293 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.5795 (ttp-170) REVERT: A 423 LYS cc_start: 0.7423 (ttpt) cc_final: 0.6831 (tptp) REVERT: A 466 GLN cc_start: 0.7694 (tt0) cc_final: 0.6853 (tm-30) REVERT: A 470 ARG cc_start: 0.8036 (mtm110) cc_final: 0.7173 (mtm-85) REVERT: A 485 ASP cc_start: 0.8156 (t0) cc_final: 0.7508 (t70) REVERT: A 1056 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8451 (m) REVERT: A 1294 GLN cc_start: 0.8353 (tt0) cc_final: 0.8000 (mt0) REVERT: A 1453 ASN cc_start: 0.7315 (t0) cc_final: 0.7003 (t0) REVERT: A 1767 ASN cc_start: 0.8221 (t0) cc_final: 0.7952 (t0) REVERT: A 2069 ARG cc_start: 0.7610 (mmm-85) cc_final: 0.7315 (mmm-85) REVERT: A 2077 MET cc_start: 0.8635 (ttp) cc_final: 0.8261 (ptp) REVERT: A 2291 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6282 (mt) REVERT: A 2292 VAL cc_start: 0.7738 (t) cc_final: 0.7419 (p) REVERT: A 2344 MET cc_start: 0.7978 (mmm) cc_final: 0.7437 (mpp) REVERT: B 669 LYS cc_start: 0.8556 (mmtp) cc_final: 0.7893 (mmtt) REVERT: B 696 TYR cc_start: 0.8235 (m-80) cc_final: 0.7522 (m-80) REVERT: B 751 GLN cc_start: 0.8041 (pt0) cc_final: 0.7690 (tt0) REVERT: B 825 ASN cc_start: 0.7600 (m-40) cc_final: 0.7320 (m-40) REVERT: B 1332 MET cc_start: 0.8987 (mmm) cc_final: 0.8783 (mmm) REVERT: B 1392 TYR cc_start: 0.7584 (t80) cc_final: 0.7359 (t80) REVERT: B 1653 MET cc_start: 0.7983 (mmm) cc_final: 0.7695 (mpp) REVERT: B 1934 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7663 (tpt-90) REVERT: B 1940 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8392 (mt) REVERT: B 1976 TYR cc_start: 0.8361 (m-80) cc_final: 0.8008 (m-80) REVERT: B 2031 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8075 (ptpp) REVERT: B 2079 ASN cc_start: 0.7801 (m-40) cc_final: 0.7564 (m-40) REVERT: B 2224 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7450 (ttp80) REVERT: C 1921 ILE cc_start: 0.7837 (mt) cc_final: 0.7600 (mt) REVERT: C 2103 ASP cc_start: 0.7787 (m-30) cc_final: 0.7474 (t0) REVERT: C 2154 HIS cc_start: 0.7747 (t70) cc_final: 0.7399 (t70) REVERT: C 2423 MET cc_start: 0.8611 (mmm) cc_final: 0.8348 (mmt) REVERT: D 2158 MET cc_start: 0.8295 (mtp) cc_final: 0.7962 (mtm) REVERT: D 2202 ASP cc_start: 0.8336 (t0) cc_final: 0.8125 (t0) REVERT: D 2213 ILE cc_start: 0.8749 (tt) cc_final: 0.8525 (pt) outliers start: 69 outliers final: 55 residues processed: 489 average time/residue: 0.2378 time to fit residues: 188.0464 Evaluate side-chains 502 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 443 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1326 LYS Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1344 ILE Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 1975 LEU Chi-restraints excluded: chain A residue 2006 CYS Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1033 GLN Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1298 HIS Chi-restraints excluded: chain B residue 1317 VAL Chi-restraints excluded: chain B residue 1354 ILE Chi-restraints excluded: chain B residue 1391 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1658 ASN Chi-restraints excluded: chain B residue 1689 VAL Chi-restraints excluded: chain B residue 1765 THR Chi-restraints excluded: chain B residue 1940 LEU Chi-restraints excluded: chain B residue 1953 CYS Chi-restraints excluded: chain B residue 2077 MET Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2479 CYS Chi-restraints excluded: chain C residue 1960 ASP Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2178 CYS Chi-restraints excluded: chain C residue 2299 ILE Chi-restraints excluded: chain C residue 2479 CYS Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain C residue 2571 LYS Chi-restraints excluded: chain D residue 2178 CYS Chi-restraints excluded: chain D residue 2186 ARG Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2475 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 147 optimal weight: 2.9990 chunk 447 optimal weight: 0.9990 chunk 467 optimal weight: 0.9990 chunk 241 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 374 optimal weight: 7.9990 chunk 369 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 391 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A2383 ASN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS B1658 ASN B1944 ASN B1981 ASN D2616 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.090903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074472 restraints weight = 97211.724| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.07 r_work: 0.3072 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 38765 Z= 0.135 Angle : 0.469 9.143 52404 Z= 0.249 Chirality : 0.038 0.170 6016 Planarity : 0.003 0.051 6609 Dihedral : 5.628 87.070 5246 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.56 % Allowed : 11.51 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.41 (0.13), residues: 4606 helix: 2.41 (0.09), residues: 3100 sheet: -0.53 (0.31), residues: 281 loop : 0.03 (0.19), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 829 TYR 0.038 0.001 TYR A1392 PHE 0.035 0.001 PHE A1451 TRP 0.012 0.001 TRP D2590 HIS 0.008 0.001 HIS B1659 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (38745) covalent geometry : angle 0.46753 / 0.25 (52391) SS BOND : bond 0.00310 / 0.16 ( 4) SS BOND : angle 0.56961 / 0.30 ( 8) hydrogen bonds : bond 0.03608 / 2.43 ( 2481) hydrogen bonds : angle 4.04131 / 2.84 ( 7128) metal coordination : bond 0.00727 / 0.41 ( 16) metal coordination : angle 4.15121 / 2.19 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9212 Ramachandran restraints generated. 4606 Oldfield, 0 Emsley, 4606 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 448 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ASN cc_start: 0.8005 (m-40) cc_final: 0.6957 (p0) REVERT: A 117 TYR cc_start: 0.7189 (m-80) cc_final: 0.6683 (m-80) REVERT: A 129 ASN cc_start: 0.8315 (t0) cc_final: 0.7959 (t0) REVERT: A 259 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8282 (tptt) REVERT: A 293 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.5792 (ttp-170) REVERT: A 423 LYS cc_start: 0.7425 (ttpt) cc_final: 0.6827 (tptp) REVERT: A 466 GLN cc_start: 0.7693 (tt0) cc_final: 0.6853 (tm-30) REVERT: A 470 ARG cc_start: 0.8043 (mtm110) cc_final: 0.7173 (mtm-85) REVERT: A 485 ASP cc_start: 0.8139 (t0) cc_final: 0.7516 (t70) REVERT: A 1056 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8454 (m) REVERT: A 1294 GLN cc_start: 0.8382 (tt0) cc_final: 0.8001 (mt0) REVERT: A 1453 ASN cc_start: 0.7326 (t0) cc_final: 0.7025 (t0) REVERT: A 1767 ASN cc_start: 0.8224 (t0) cc_final: 0.7950 (t0) REVERT: A 2069 ARG cc_start: 0.7618 (mmm-85) cc_final: 0.7322 (mmm-85) REVERT: A 2077 MET cc_start: 0.8651 (ttp) cc_final: 0.8270 (ptp) REVERT: A 2291 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.6292 (mt) REVERT: A 2292 VAL cc_start: 0.7758 (t) cc_final: 0.7460 (p) REVERT: A 2344 MET cc_start: 0.7985 (mmm) cc_final: 0.7448 (mpp) REVERT: B 669 LYS cc_start: 0.8557 (mmtp) cc_final: 0.7898 (mmtt) REVERT: B 696 TYR cc_start: 0.8229 (m-80) cc_final: 0.7525 (m-80) REVERT: B 751 GLN cc_start: 0.8051 (pt0) cc_final: 0.7740 (tt0) REVERT: B 825 ASN cc_start: 0.7570 (m-40) cc_final: 0.7290 (m-40) REVERT: B 1653 MET cc_start: 0.8030 (mmm) cc_final: 0.7682 (mpp) REVERT: B 1934 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7674 (tpt-90) REVERT: B 1940 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8409 (mt) REVERT: B 1976 TYR cc_start: 0.8373 (m-80) cc_final: 0.8021 (m-80) REVERT: B 2059 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7551 (tm-30) REVERT: B 2079 ASN cc_start: 0.7816 (m-40) cc_final: 0.7578 (m-40) REVERT: B 2224 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7422 (ttp80) REVERT: C 1921 ILE cc_start: 0.7834 (mt) cc_final: 0.7598 (mt) REVERT: C 2103 ASP cc_start: 0.7805 (m-30) cc_final: 0.7491 (t0) REVERT: C 2154 HIS cc_start: 0.7740 (t70) cc_final: 0.7393 (t70) REVERT: C 2423 MET cc_start: 0.8622 (mmm) cc_final: 0.8359 (mmt) REVERT: D 2158 MET cc_start: 0.8299 (mtp) cc_final: 0.7971 (mtm) REVERT: D 2213 ILE cc_start: 0.8781 (tt) cc_final: 0.8544 (pt) outliers start: 65 outliers final: 54 residues processed: 487 average time/residue: 0.2178 time to fit residues: 173.5586 Evaluate side-chains 504 residues out of total 4287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 446 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 714 GLN Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 1000 PHE Chi-restraints excluded: chain A residue 1056 THR Chi-restraints excluded: chain A residue 1066 MET Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1181 ILE Chi-restraints excluded: chain A residue 1265 THR Chi-restraints excluded: chain A residue 1326 LYS Chi-restraints excluded: chain A residue 1332 MET Chi-restraints excluded: chain A residue 1447 ILE Chi-restraints excluded: chain A residue 1610 VAL Chi-restraints excluded: chain A residue 2006 CYS Chi-restraints excluded: chain A residue 2113 HIS Chi-restraints excluded: chain A residue 2291 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2317 CYS Chi-restraints excluded: chain A residue 2576 THR Chi-restraints excluded: chain B residue 728 THR Chi-restraints excluded: chain B residue 782 MET Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 821 ASP Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1260 LEU Chi-restraints excluded: chain B residue 1262 LEU Chi-restraints excluded: chain B residue 1283 HIS Chi-restraints excluded: chain B residue 1298 HIS Chi-restraints excluded: chain B residue 1317 VAL Chi-restraints excluded: chain B residue 1336 ILE Chi-restraints excluded: chain B residue 1391 VAL Chi-restraints excluded: chain B residue 1455 LEU Chi-restraints excluded: chain B residue 1658 ASN Chi-restraints excluded: chain B residue 1689 VAL Chi-restraints excluded: chain B residue 1765 THR Chi-restraints excluded: chain B residue 1940 LEU Chi-restraints excluded: chain B residue 1953 CYS Chi-restraints excluded: chain B residue 2077 MET Chi-restraints excluded: chain B residue 2113 HIS Chi-restraints excluded: chain B residue 2479 CYS Chi-restraints excluded: chain C residue 1960 ASP Chi-restraints excluded: chain C residue 2015 ILE Chi-restraints excluded: chain C residue 2178 CYS Chi-restraints excluded: chain C residue 2479 CYS Chi-restraints excluded: chain C residue 2556 GLU Chi-restraints excluded: chain D residue 2178 CYS Chi-restraints excluded: chain D residue 2186 ARG Chi-restraints excluded: chain D residue 2242 LEU Chi-restraints excluded: chain D residue 2475 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 67 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 367 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 317 optimal weight: 4.9990 chunk 366 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 chunk 123 optimal weight: 10.0000 chunk 441 optimal weight: 5.9990 chunk 349 optimal weight: 6.9990 overall best weight: 1.8062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 247 GLN A 705 HIS A2383 ASN ** B1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1283 HIS B1658 ASN B1788 GLN B1818 GLN B1944 ASN B1981 ASN B2329 ASN D2616 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.089728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.073660 restraints weight = 97529.647| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.07 r_work: 0.3042 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 38765 Z= 0.222 Angle : 0.530 11.349 52404 Z= 0.278 Chirality : 0.041 0.175 6016 Planarity : 0.004 0.051 6609 Dihedral : 5.849 87.550 5246 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.51 % Allowed : 11.75 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: 2.20 (0.13), residues: 4606 helix: 2.26 (0.09), residues: 3102 sheet: -0.63 (0.31), residues: 281 loop : -0.07 (0.19), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2071 TYR 0.037 0.002 TYR A1392 PHE 0.021 0.002 PHE C2563 TRP 0.015 0.002 TRP D2590 HIS 0.032 0.001 HIS B1283 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.22 (38745) covalent geometry : angle 0.52807 / 0.28 (52391) SS BOND : bond 0.00660 / 0.33 ( 4) SS BOND : angle 0.57647 / 0.30 ( 8) hydrogen bonds : bond 0.04210 / 2.85 ( 2481) hydrogen bonds : angle 4.20732 / 2.96 ( 7128) metal coordination : bond 0.01108 / 0.60 ( 16) metal coordination : angle 4.98703 / 2.59 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10553.51 seconds wall clock time: 180 minutes 47.51 seconds (10847.51 seconds total)