Starting phenix.real_space_refine on Sat Mar 7 12:12:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yxx_14368/03_2026/7yxx_14368.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yxx_14368/03_2026/7yxx_14368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yxx_14368/03_2026/7yxx_14368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yxx_14368/03_2026/7yxx_14368.map" model { file = "/net/cci-nas-00/data/ceres_data/7yxx_14368/03_2026/7yxx_14368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yxx_14368/03_2026/7yxx_14368.cif" } resolution = 3.3 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= 0.001 sd= 0.034 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: 4 Type Number sf(0) Gaussians S 288 5.16 5 C 27121 2.51 5 N 7259 2.21 5 O 7689 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42357 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 14155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1754, 14144 Classifications: {'peptide': 1754} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1685} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 1754, 14144 Classifications: {'peptide': 1754} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1685} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 14438 Chain: "B" Number of atoms: 14155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1754, 14144 Classifications: {'peptide': 1754} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1685} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 1754, 14144 Classifications: {'peptide': 1754} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1685} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 14438 Chain: "C" Number of atoms: 14047 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1741, 14036 Classifications: {'peptide': 1741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1672} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Conformer: "B" Number of residues, atoms: 1741, 14036 Classifications: {'peptide': 1741} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 68, 'TRANS': 1672} Chain breaks: 16 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 bond proxies already assigned to first conformer: 14328 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A1745 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG A1745 " occ=0.40 residue: pdb=" N AARG B1745 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG B1745 " occ=0.40 residue: pdb=" N AARG C1745 " occ=0.60 ... (20 atoms not shown) pdb=" NH2BARG C1745 " occ=0.40 Time building chain proxies: 17.06, per 1000 atoms: 0.40 Number of scatterers: 42357 At special positions: 0 Unit cell: (152.256, 213.824, 222.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 288 16.00 O 7689 8.00 N 7259 7.00 C 27121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 3.2 seconds 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10002 Finding SS restraints... Secondary structure from input PDB file: 267 helices and 28 sheets defined 67.4% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 325 through 345 Processing helix chain 'A' and resid 347 through 365 Processing helix chain 'A' and resid 384 through 394 removed outlier: 3.540A pdb=" N ASN A 393 " --> pdb=" O TRP A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.672A pdb=" N ARG A 401 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP A 402 " --> pdb=" O ILE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 423 removed outlier: 3.550A pdb=" N LYS A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 437 Processing helix chain 'A' and resid 442 through 457 removed outlier: 3.646A pdb=" N VAL A 446 " --> pdb=" O HIS A 442 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 479 removed outlier: 3.626A pdb=" N ASN A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 497 removed outlier: 3.639A pdb=" N ALA A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 516 removed outlier: 4.056A pdb=" N LYS A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 539 removed outlier: 3.967A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 560 removed outlier: 3.962A pdb=" N GLN A 550 " --> pdb=" O THR A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 580 removed outlier: 3.848A pdb=" N LYS A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 576 " --> pdb=" O GLN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 removed outlier: 4.224A pdb=" N ASN A 604 " --> pdb=" O HIS A 600 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASN A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 631 removed outlier: 3.668A pdb=" N GLU A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 665 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 690 through 705 removed outlier: 3.917A pdb=" N ARG A 694 " --> pdb=" O TYR A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 723 removed outlier: 3.546A pdb=" N PHE A 720 " --> pdb=" O ASN A 716 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 751 removed outlier: 3.848A pdb=" N LYS A 738 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS A 739 " --> pdb=" O ASN A 735 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 780 removed outlier: 3.866A pdb=" N TRP A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 799 removed outlier: 3.795A pdb=" N ASN A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 831 removed outlier: 4.052A pdb=" N THR A 829 " --> pdb=" O ALA A 825 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N CYS A 831 " --> pdb=" O TYR A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 866 removed outlier: 3.756A pdb=" N GLU A 859 " --> pdb=" O THR A 855 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS A 864 " --> pdb=" O TYR A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1031 removed outlier: 3.860A pdb=" N LEU A1021 " --> pdb=" O TYR A1017 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A1023 " --> pdb=" O SER A1019 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER A1029 " --> pdb=" O ALA A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1046 removed outlier: 3.890A pdb=" N ARG A1037 " --> pdb=" O MET A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1066 removed outlier: 3.509A pdb=" N ARG A1058 " --> pdb=" O ILE A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1084 through 1100 removed outlier: 3.950A pdb=" N VAL A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A1089 " --> pdb=" O ALA A1085 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1121 removed outlier: 4.442A pdb=" N PHE A1115 " --> pdb=" O SER A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1121 through 1132 Processing helix chain 'A' and resid 1133 through 1136 removed outlier: 4.269A pdb=" N LEU A1136 " --> pdb=" O ASN A1133 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1133 through 1136' Processing helix chain 'A' and resid 1140 through 1164 removed outlier: 3.657A pdb=" N LYS A1153 " --> pdb=" O LEU A1149 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A1157 " --> pdb=" O LYS A1153 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR A1164 " --> pdb=" O THR A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1250 removed outlier: 3.701A pdb=" N ILE A1239 " --> pdb=" O ASP A1235 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A1241 " --> pdb=" O CYS A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1252 No H-bonds generated for 'chain 'A' and resid 1251 through 1252' Processing helix chain 'A' and resid 1253 through 1257 Processing helix chain 'A' and resid 1261 through 1269 removed outlier: 3.783A pdb=" N THR A1265 " --> pdb=" O ASN A1261 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A1268 " --> pdb=" O ILE A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1299 removed outlier: 3.802A pdb=" N ALA A1288 " --> pdb=" O VAL A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1307 removed outlier: 3.578A pdb=" N ALA A1305 " --> pdb=" O THR A1301 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1306 " --> pdb=" O ALA A1302 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1301 through 1307' Processing helix chain 'A' and resid 1313 through 1321 Processing helix chain 'A' and resid 1326 through 1342 removed outlier: 3.547A pdb=" N MET A1339 " --> pdb=" O GLN A1335 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1359 Processing helix chain 'A' and resid 1364 through 1369 removed outlier: 3.886A pdb=" N ALA A1369 " --> pdb=" O ALA A1365 " (cutoff:3.500A) Processing helix chain 'A' and resid 1370 through 1373 removed outlier: 4.072A pdb=" N GLY A1373 " --> pdb=" O LYS A1370 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1370 through 1373' Processing helix chain 'A' and resid 1374 through 1389 Processing helix chain 'A' and resid 1396 through 1417 Processing helix chain 'A' and resid 1423 through 1439 removed outlier: 3.802A pdb=" N LEU A1427 " --> pdb=" O GLU A1423 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A1439 " --> pdb=" O LYS A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1465 Processing helix chain 'A' and resid 1469 through 1479 removed outlier: 3.825A pdb=" N VAL A1473 " --> pdb=" O PRO A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1510 Processing helix chain 'A' and resid 1512 through 1528 removed outlier: 4.815A pdb=" N GLN A1518 " --> pdb=" O ARG A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1578 removed outlier: 4.606A pdb=" N VAL A1571 " --> pdb=" O TYR A1567 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A1577 " --> pdb=" O GLN A1573 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A1578 " --> pdb=" O GLN A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1587 Processing helix chain 'A' and resid 1633 through 1657 Processing helix chain 'A' and resid 1664 through 1671 Processing helix chain 'A' and resid 1685 through 1704 Processing helix chain 'A' and resid 1708 through 1714 Processing helix chain 'A' and resid 1749 through 1760 removed outlier: 3.651A pdb=" N GLN A1756 " --> pdb=" O ASP A1752 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR A1757 " --> pdb=" O SER A1753 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A1758 " --> pdb=" O LEU A1754 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1768 Processing helix chain 'A' and resid 1825 through 1827 No H-bonds generated for 'chain 'A' and resid 1825 through 1827' Processing helix chain 'A' and resid 1828 through 1837 Processing helix chain 'A' and resid 1912 through 1920 Processing helix chain 'A' and resid 1988 through 2005 removed outlier: 3.567A pdb=" N MET A2003 " --> pdb=" O MET A1999 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A2004 " --> pdb=" O HIS A2000 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A2005 " --> pdb=" O ASN A2001 " (cutoff:3.500A) Processing helix chain 'A' and resid 2006 through 2019 Processing helix chain 'A' and resid 2020 through 2025 removed outlier: 3.918A pdb=" N ASN A2025 " --> pdb=" O VAL A2022 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2055 removed outlier: 3.526A pdb=" N PHE A2053 " --> pdb=" O ALA A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2060 through 2065 Processing helix chain 'A' and resid 2067 through 2079 removed outlier: 3.529A pdb=" N ILE A2076 " --> pdb=" O ASP A2072 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A2077 " --> pdb=" O ALA A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2081 through 2093 removed outlier: 3.685A pdb=" N ARG A2085 " --> pdb=" O SER A2081 " (cutoff:3.500A) Processing helix chain 'A' and resid 2098 through 2105 Processing helix chain 'A' and resid 2109 through 2127 Processing helix chain 'A' and resid 2151 through 2163 removed outlier: 3.530A pdb=" N LEU A2163 " --> pdb=" O ALA A2159 " (cutoff:3.500A) Processing helix chain 'A' and resid 2167 through 2171 Processing helix chain 'A' and resid 2175 through 2187 removed outlier: 3.502A pdb=" N PHE A2179 " --> pdb=" O LEU A2175 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A2182 " --> pdb=" O TYR A2178 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2199 Processing helix chain 'A' and resid 2200 through 2208 Processing helix chain 'A' and resid 2225 through 2238 Processing helix chain 'A' and resid 2241 through 2245 removed outlier: 3.871A pdb=" N MET A2245 " --> pdb=" O SER A2242 " (cutoff:3.500A) Processing helix chain 'A' and resid 2272 through 2280 removed outlier: 3.942A pdb=" N ILE A2278 " --> pdb=" O ASN A2274 " (cutoff:3.500A) Processing helix chain 'A' and resid 2283 through 2292 removed outlier: 3.541A pdb=" N LYS A2287 " --> pdb=" O THR A2283 " (cutoff:3.500A) Processing helix chain 'A' and resid 2296 through 2308 removed outlier: 4.159A pdb=" N VAL A2300 " --> pdb=" O SER A2296 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A2301 " --> pdb=" O GLU A2297 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP A2308 " --> pdb=" O ARG A2304 " (cutoff:3.500A) Processing helix chain 'A' and resid 2310 through 2327 Processing helix chain 'A' and resid 2329 through 2332 Processing helix chain 'A' and resid 2333 through 2345 Processing helix chain 'A' and resid 2350 through 2360 Processing helix chain 'A' and resid 2368 through 2376 Processing helix chain 'A' and resid 2380 through 2398 removed outlier: 3.531A pdb=" N ALA A2384 " --> pdb=" O TYR A2380 " (cutoff:3.500A) Processing helix chain 'A' and resid 2399 through 2404 Processing helix chain 'A' and resid 2408 through 2428 removed outlier: 3.539A pdb=" N LYS A2412 " --> pdb=" O ASN A2408 " (cutoff:3.500A) Processing helix chain 'A' and resid 2461 through 2474 removed outlier: 3.502A pdb=" N GLU A2472 " --> pdb=" O ALA A2468 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A2473 " --> pdb=" O LYS A2469 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 345 removed outlier: 3.526A pdb=" N LYS B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 Processing helix chain 'B' and resid 382 through 394 removed outlier: 3.825A pdb=" N MET B 386 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 403 removed outlier: 4.499A pdb=" N ASP B 402 " --> pdb=" O ILE B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 423 removed outlier: 3.546A pdb=" N VAL B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 416 " --> pdb=" O LYS B 412 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 423 " --> pdb=" O PHE B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 436 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 442 through 457 Processing helix chain 'B' and resid 458 through 460 No H-bonds generated for 'chain 'B' and resid 458 through 460' Processing helix chain 'B' and resid 461 through 479 removed outlier: 3.672A pdb=" N HIS B 467 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 497 Processing helix chain 'B' and resid 502 through 516 removed outlier: 4.117A pdb=" N LYS B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 509 " --> pdb=" O HIS B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 539 removed outlier: 3.706A pdb=" N LEU B 527 " --> pdb=" O ASP B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.515A pdb=" N LEU B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 580 Processing helix chain 'B' and resid 599 through 609 removed outlier: 3.940A pdb=" N ILE B 603 " --> pdb=" O ARG B 599 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN B 604 " --> pdb=" O HIS B 600 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN B 609 " --> pdb=" O GLN B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 630 removed outlier: 3.724A pdb=" N GLU B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 623 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 626 " --> pdb=" O THR B 622 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 665 Processing helix chain 'B' and resid 673 through 682 removed outlier: 4.162A pdb=" N GLN B 679 " --> pdb=" O PRO B 675 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 680 " --> pdb=" O GLN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 705 removed outlier: 3.896A pdb=" N ARG B 694 " --> pdb=" O TYR B 690 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET B 705 " --> pdb=" O TYR B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 723 removed outlier: 4.347A pdb=" N GLU B 721 " --> pdb=" O LYS B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 752 removed outlier: 3.752A pdb=" N LYS B 738 " --> pdb=" O GLU B 734 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS B 739 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG B 750 " --> pdb=" O ALA B 746 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 751 " --> pdb=" O VAL B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 780 removed outlier: 3.792A pdb=" N TRP B 775 " --> pdb=" O LEU B 771 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG B 776 " --> pdb=" O ASP B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 798 Processing helix chain 'B' and resid 807 through 831 removed outlier: 3.866A pdb=" N THR B 829 " --> pdb=" O ALA B 825 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU B 830 " --> pdb=" O SER B 826 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N CYS B 831 " --> pdb=" O TYR B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 866 removed outlier: 3.598A pdb=" N ALA B 847 " --> pdb=" O ALA B 843 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 848 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 859 " --> pdb=" O THR B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 1015 through 1031 removed outlier: 3.803A pdb=" N LEU B1021 " --> pdb=" O TYR B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1046 removed outlier: 4.534A pdb=" N ARG B1037 " --> pdb=" O MET B1033 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1065 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1085 through 1100 removed outlier: 4.120A pdb=" N LEU B1089 " --> pdb=" O ALA B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1121 removed outlier: 4.552A pdb=" N PHE B1115 " --> pdb=" O SER B1111 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B1121 " --> pdb=" O PHE B1117 " (cutoff:3.500A) Processing helix chain 'B' and resid 1121 through 1132 removed outlier: 3.593A pdb=" N LEU B1127 " --> pdb=" O LEU B1123 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B1130 " --> pdb=" O VAL B1126 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1163 removed outlier: 3.675A pdb=" N ARG B1145 " --> pdb=" O MET B1141 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU B1157 " --> pdb=" O LYS B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1235 through 1252 removed outlier: 3.508A pdb=" N ILE B1239 " --> pdb=" O ASP B1235 " (cutoff:3.500A) Processing helix chain 'B' and resid 1253 through 1257 Processing helix chain 'B' and resid 1262 through 1269 removed outlier: 3.657A pdb=" N LYS B1266 " --> pdb=" O GLU B1262 " (cutoff:3.500A) Processing helix chain 'B' and resid 1280 through 1299 removed outlier: 3.573A pdb=" N LEU B1289 " --> pdb=" O CYS B1285 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B1298 " --> pdb=" O LEU B1294 " (cutoff:3.500A) Processing helix chain 'B' and resid 1301 through 1309 removed outlier: 3.751A pdb=" N ALA B1305 " --> pdb=" O THR B1301 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU B1306 " --> pdb=" O ALA B1302 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LYS B1308 " --> pdb=" O ASP B1304 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU B1309 " --> pdb=" O ALA B1305 " (cutoff:3.500A) Processing helix chain 'B' and resid 1313 through 1319 Processing helix chain 'B' and resid 1325 through 1342 removed outlier: 3.643A pdb=" N ARG B1329 " --> pdb=" O SER B1325 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU B1334 " --> pdb=" O GLN B1330 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B1335 " --> pdb=" O VAL B1331 " (cutoff:3.500A) Processing helix chain 'B' and resid 1347 through 1358 Processing helix chain 'B' and resid 1364 through 1369 Processing helix chain 'B' and resid 1372 through 1389 removed outlier: 4.241A pdb=" N THR B1377 " --> pdb=" O GLY B1373 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B1378 " --> pdb=" O ASP B1374 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B1379 " --> pdb=" O TYR B1375 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN B1384 " --> pdb=" O ARG B1380 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B1387 " --> pdb=" O LEU B1383 " (cutoff:3.500A) Processing helix chain 'B' and resid 1397 through 1417 removed outlier: 3.522A pdb=" N ASN B1401 " --> pdb=" O GLU B1397 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE B1410 " --> pdb=" O TRP B1406 " (cutoff:3.500A) Processing helix chain 'B' and resid 1423 through 1438 removed outlier: 3.504A pdb=" N LEU B1427 " --> pdb=" O GLU B1423 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU B1436 " --> pdb=" O GLY B1432 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1448 Processing helix chain 'B' and resid 1457 through 1466 Processing helix chain 'B' and resid 1469 through 1479 Processing helix chain 'B' and resid 1494 through 1510 removed outlier: 3.676A pdb=" N ILE B1498 " --> pdb=" O SER B1494 " (cutoff:3.500A) Processing helix chain 'B' and resid 1512 through 1527 removed outlier: 3.805A pdb=" N LEU B1516 " --> pdb=" O CYS B1512 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B1518 " --> pdb=" O ARG B1514 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1578 removed outlier: 3.947A pdb=" N ASN B1569 " --> pdb=" O THR B1565 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B1571 " --> pdb=" O TYR B1567 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET B1577 " --> pdb=" O GLN B1573 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE B1578 " --> pdb=" O GLN B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1578 through 1587 removed outlier: 3.503A pdb=" N LEU B1586 " --> pdb=" O ARG B1582 " (cutoff:3.500A) Processing helix chain 'B' and resid 1633 through 1657 removed outlier: 3.740A pdb=" N ILE B1650 " --> pdb=" O HIS B1646 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B1656 " --> pdb=" O GLY B1652 " (cutoff:3.500A) Processing helix chain 'B' and resid 1664 through 1671 Processing helix chain 'B' and resid 1685 through 1704 Processing helix chain 'B' and resid 1708 through 1714 Processing helix chain 'B' and resid 1749 through 1760 removed outlier: 3.843A pdb=" N TYR B1757 " --> pdb=" O SER B1753 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL B1758 " --> pdb=" O LEU B1754 " (cutoff:3.500A) Processing helix chain 'B' and resid 1764 through 1768 Processing helix chain 'B' and resid 1825 through 1827 No H-bonds generated for 'chain 'B' and resid 1825 through 1827' Processing helix chain 'B' and resid 1828 through 1837 Processing helix chain 'B' and resid 1912 through 1920 removed outlier: 4.018A pdb=" N MET B1916 " --> pdb=" O ASP B1912 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS B1917 " --> pdb=" O ASP B1913 " (cutoff:3.500A) Processing helix chain 'B' and resid 1962 through 1966 Processing helix chain 'B' and resid 1988 through 2005 removed outlier: 3.518A pdb=" N TYR B2005 " --> pdb=" O ASN B2001 " (cutoff:3.500A) Processing helix chain 'B' and resid 2006 through 2019 Processing helix chain 'B' and resid 2034 through 2055 Processing helix chain 'B' and resid 2066 through 2079 removed outlier: 3.961A pdb=" N TRP B2070 " --> pdb=" O SER B2066 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B2077 " --> pdb=" O ALA B2073 " (cutoff:3.500A) Processing helix chain 'B' and resid 2081 through 2093 removed outlier: 3.645A pdb=" N ALA B2089 " --> pdb=" O ARG B2085 " (cutoff:3.500A) Processing helix chain 'B' and resid 2098 through 2105 Processing helix chain 'B' and resid 2109 through 2127 Processing helix chain 'B' and resid 2151 through 2163 Processing helix chain 'B' and resid 2167 through 2171 Processing helix chain 'B' and resid 2175 through 2188 removed outlier: 4.227A pdb=" N PHE B2182 " --> pdb=" O TYR B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2199 Processing helix chain 'B' and resid 2200 through 2208 Processing helix chain 'B' and resid 2225 through 2238 removed outlier: 3.576A pdb=" N SER B2230 " --> pdb=" O GLY B2226 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B2238 " --> pdb=" O GLN B2234 " (cutoff:3.500A) Processing helix chain 'B' and resid 2272 through 2280 removed outlier: 3.535A pdb=" N ILE B2278 " --> pdb=" O ASN B2274 " (cutoff:3.500A) Processing helix chain 'B' and resid 2283 through 2292 removed outlier: 3.563A pdb=" N ILE B2290 " --> pdb=" O VAL B2286 " (cutoff:3.500A) Processing helix chain 'B' and resid 2297 through 2307 Processing helix chain 'B' and resid 2310 through 2327 Processing helix chain 'B' and resid 2333 through 2345 removed outlier: 3.828A pdb=" N GLN B2342 " --> pdb=" O ASP B2338 " (cutoff:3.500A) Processing helix chain 'B' and resid 2350 through 2360 removed outlier: 3.522A pdb=" N ALA B2358 " --> pdb=" O ARG B2354 " (cutoff:3.500A) Processing helix chain 'B' and resid 2368 through 2376 removed outlier: 3.655A pdb=" N GLN B2374 " --> pdb=" O PHE B2370 " (cutoff:3.500A) Processing helix chain 'B' and resid 2380 through 2396 removed outlier: 4.073A pdb=" N ALA B2384 " --> pdb=" O TYR B2380 " (cutoff:3.500A) Processing helix chain 'B' and resid 2398 through 2406 removed outlier: 3.556A pdb=" N ILE B2404 " --> pdb=" O VAL B2400 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B2405 " --> pdb=" O ALA B2401 " (cutoff:3.500A) Processing helix chain 'B' and resid 2409 through 2426 Processing helix chain 'B' and resid 2460 through 2471 Processing helix chain 'C' and resid 325 through 345 removed outlier: 3.537A pdb=" N LYS C 329 " --> pdb=" O GLU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 365 Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.666A pdb=" N MET C 386 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 401 Processing helix chain 'C' and resid 402 through 405 removed outlier: 3.582A pdb=" N HIS C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 402 through 405' Processing helix chain 'C' and resid 406 through 422 removed outlier: 4.159A pdb=" N LYS C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE C 416 " --> pdb=" O LYS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 436 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 442 through 457 Processing helix chain 'C' and resid 458 through 460 No H-bonds generated for 'chain 'C' and resid 458 through 460' Processing helix chain 'C' and resid 461 through 479 removed outlier: 3.562A pdb=" N HIS C 467 " --> pdb=" O GLU C 463 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 498 Processing helix chain 'C' and resid 503 through 516 Processing helix chain 'C' and resid 521 through 539 removed outlier: 4.169A pdb=" N ASP C 526 " --> pdb=" O VAL C 522 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU C 527 " --> pdb=" O ASP C 523 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 559 Processing helix chain 'C' and resid 565 through 580 removed outlier: 3.554A pdb=" N LYS C 571 " --> pdb=" O ILE C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 606 removed outlier: 4.101A pdb=" N ILE C 603 " --> pdb=" O ARG C 599 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN C 604 " --> pdb=" O HIS C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 631 removed outlier: 3.504A pdb=" N MET C 624 " --> pdb=" O LEU C 620 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER C 626 " --> pdb=" O THR C 622 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET C 627 " --> pdb=" O TYR C 623 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 665 Processing helix chain 'C' and resid 673 through 683 removed outlier: 4.174A pdb=" N GLN C 679 " --> pdb=" O PRO C 675 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 680 " --> pdb=" O GLN C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 705 removed outlier: 3.782A pdb=" N ARG C 694 " --> pdb=" O TYR C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 723 removed outlier: 3.661A pdb=" N ASP C 718 " --> pdb=" O ASP C 714 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE C 720 " --> pdb=" O ASN C 716 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU C 721 " --> pdb=" O LYS C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 751 removed outlier: 3.580A pdb=" N LYS C 738 " --> pdb=" O GLU C 734 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS C 739 " --> pdb=" O ASN C 735 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU C 751 " --> pdb=" O VAL C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 780 removed outlier: 3.941A pdb=" N TRP C 775 " --> pdb=" O LEU C 771 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ARG C 776 " --> pdb=" O ASP C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 798 Processing helix chain 'C' and resid 807 through 831 removed outlier: 3.601A pdb=" N THR C 829 " --> pdb=" O ALA C 825 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU C 830 " --> pdb=" O SER C 826 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS C 831 " --> pdb=" O TYR C 827 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 866 removed outlier: 3.804A pdb=" N GLU C 859 " --> pdb=" O THR C 855 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 862 " --> pdb=" O ARG C 858 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 863 " --> pdb=" O GLU C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1032 removed outlier: 3.791A pdb=" N LEU C1021 " --> pdb=" O TYR C1017 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C1023 " --> pdb=" O SER C1019 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1033 through 1046 removed outlier: 4.137A pdb=" N ARG C1037 " --> pdb=" O MET C1033 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C1045 " --> pdb=" O ARG C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1066 removed outlier: 3.720A pdb=" N ILE C1054 " --> pdb=" O ASP C1050 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU C1055 " --> pdb=" O SER C1051 " (cutoff:3.500A) Processing helix chain 'C' and resid 1077 through 1081 Processing helix chain 'C' and resid 1084 through 1100 removed outlier: 3.983A pdb=" N VAL C1088 " --> pdb=" O SER C1084 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU C1089 " --> pdb=" O ALA C1085 " (cutoff:3.500A) Processing helix chain 'C' and resid 1111 through 1121 removed outlier: 4.392A pdb=" N PHE C1115 " --> pdb=" O SER C1111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C1121 " --> pdb=" O PHE C1117 " (cutoff:3.500A) Processing helix chain 'C' and resid 1121 through 1131 removed outlier: 3.564A pdb=" N LEU C1127 " --> pdb=" O LEU C1123 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C1130 " --> pdb=" O VAL C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1164 removed outlier: 3.593A pdb=" N LEU C1157 " --> pdb=" O LYS C1153 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TYR C1164 " --> pdb=" O THR C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1235 through 1251 removed outlier: 3.776A pdb=" N ILE C1239 " --> pdb=" O ASP C1235 " (cutoff:3.500A) Processing helix chain 'C' and resid 1253 through 1257 Processing helix chain 'C' and resid 1262 through 1269 removed outlier: 3.714A pdb=" N LYS C1266 " --> pdb=" O GLU C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1280 through 1299 removed outlier: 3.627A pdb=" N MET C1292 " --> pdb=" O ALA C1288 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C1293 " --> pdb=" O LEU C1289 " (cutoff:3.500A) Processing helix chain 'C' and resid 1301 through 1307 removed outlier: 3.595A pdb=" N SER C1307 " --> pdb=" O LEU C1303 " (cutoff:3.500A) Processing helix chain 'C' and resid 1313 through 1321 Processing helix chain 'C' and resid 1326 through 1342 Processing helix chain 'C' and resid 1348 through 1360 removed outlier: 3.622A pdb=" N PHE C1352 " --> pdb=" O ARG C1348 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C1360 " --> pdb=" O LEU C1356 " (cutoff:3.500A) Processing helix chain 'C' and resid 1363 through 1369 removed outlier: 3.924A pdb=" N ALA C1369 " --> pdb=" O ALA C1365 " (cutoff:3.500A) Processing helix chain 'C' and resid 1372 through 1389 removed outlier: 3.544A pdb=" N LEU C1378 " --> pdb=" O ASP C1374 " (cutoff:3.500A) Processing helix chain 'C' and resid 1396 through 1417 removed outlier: 3.629A pdb=" N ASN C1402 " --> pdb=" O VAL C1398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C1403 " --> pdb=" O LEU C1399 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C1410 " --> pdb=" O TRP C1406 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C1414 " --> pdb=" O ILE C1410 " (cutoff:3.500A) Processing helix chain 'C' and resid 1423 through 1439 removed outlier: 3.544A pdb=" N LEU C1427 " --> pdb=" O GLU C1423 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C1436 " --> pdb=" O GLY C1432 " (cutoff:3.500A) Processing helix chain 'C' and resid 1457 through 1465 Processing helix chain 'C' and resid 1469 through 1479 removed outlier: 3.556A pdb=" N VAL C1473 " --> pdb=" O PRO C1469 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1510 removed outlier: 3.664A pdb=" N PHE C1502 " --> pdb=" O ILE C1498 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C1504 " --> pdb=" O ALA C1500 " (cutoff:3.500A) Processing helix chain 'C' and resid 1512 through 1528 removed outlier: 3.813A pdb=" N GLN C1518 " --> pdb=" O ARG C1514 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1578 removed outlier: 3.794A pdb=" N VAL C1571 " --> pdb=" O TYR C1567 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET C1577 " --> pdb=" O GLN C1573 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE C1578 " --> pdb=" O GLN C1574 " (cutoff:3.500A) Processing helix chain 'C' and resid 1578 through 1587 Processing helix chain 'C' and resid 1633 through 1657 removed outlier: 3.553A pdb=" N ILE C1650 " --> pdb=" O HIS C1646 " (cutoff:3.500A) Processing helix chain 'C' and resid 1664 through 1671 removed outlier: 3.509A pdb=" N TRP C1668 " --> pdb=" O PRO C1664 " (cutoff:3.500A) Processing helix chain 'C' and resid 1685 through 1704 removed outlier: 3.642A pdb=" N PHE C1689 " --> pdb=" O ASP C1685 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1714 Processing helix chain 'C' and resid 1749 through 1760 removed outlier: 3.875A pdb=" N TYR C1757 " --> pdb=" O SER C1753 " (cutoff:3.500A) Processing helix chain 'C' and resid 1764 through 1768 Processing helix chain 'C' and resid 1828 through 1837 Processing helix chain 'C' and resid 1912 through 1920 removed outlier: 3.665A pdb=" N MET C1916 " --> pdb=" O ASP C1912 " (cutoff:3.500A) Processing helix chain 'C' and resid 1988 through 2005 removed outlier: 3.541A pdb=" N MET C2003 " --> pdb=" O MET C1999 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C2004 " --> pdb=" O HIS C2000 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C2005 " --> pdb=" O ASN C2001 " (cutoff:3.500A) Processing helix chain 'C' and resid 2006 through 2019 Processing helix chain 'C' and resid 2020 through 2024 Processing helix chain 'C' and resid 2034 through 2055 Processing helix chain 'C' and resid 2060 through 2065 Processing helix chain 'C' and resid 2067 through 2079 removed outlier: 3.761A pdb=" N LEU C2077 " --> pdb=" O ALA C2073 " (cutoff:3.500A) Processing helix chain 'C' and resid 2081 through 2093 removed outlier: 3.711A pdb=" N ARG C2085 " --> pdb=" O SER C2081 " (cutoff:3.500A) Processing helix chain 'C' and resid 2098 through 2105 Processing helix chain 'C' and resid 2109 through 2127 Processing helix chain 'C' and resid 2151 through 2162 Processing helix chain 'C' and resid 2163 through 2165 No H-bonds generated for 'chain 'C' and resid 2163 through 2165' Processing helix chain 'C' and resid 2166 through 2171 Processing helix chain 'C' and resid 2175 through 2187 removed outlier: 3.943A pdb=" N LEU C2181 " --> pdb=" O GLN C2177 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE C2182 " --> pdb=" O TYR C2178 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR C2185 " --> pdb=" O LEU C2181 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2199 removed outlier: 3.924A pdb=" N LYS C2193 " --> pdb=" O GLY C2189 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C2195 " --> pdb=" O ALA C2191 " (cutoff:3.500A) Processing helix chain 'C' and resid 2200 through 2208 removed outlier: 3.705A pdb=" N LEU C2207 " --> pdb=" O ALA C2203 " (cutoff:3.500A) Processing helix chain 'C' and resid 2225 through 2237 removed outlier: 3.719A pdb=" N SER C2230 " --> pdb=" O GLY C2226 " (cutoff:3.500A) Processing helix chain 'C' and resid 2241 through 2245 removed outlier: 3.845A pdb=" N MET C2245 " --> pdb=" O SER C2242 " (cutoff:3.500A) Processing helix chain 'C' and resid 2272 through 2280 Processing helix chain 'C' and resid 2283 through 2292 removed outlier: 3.508A pdb=" N LYS C2287 " --> pdb=" O THR C2283 " (cutoff:3.500A) Processing helix chain 'C' and resid 2297 through 2307 removed outlier: 3.672A pdb=" N LYS C2301 " --> pdb=" O GLU C2297 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU C2302 " --> pdb=" O GLU C2298 " (cutoff:3.500A) Processing helix chain 'C' and resid 2310 through 2327 Processing helix chain 'C' and resid 2329 through 2331 No H-bonds generated for 'chain 'C' and resid 2329 through 2331' Processing helix chain 'C' and resid 2332 through 2345 removed outlier: 4.076A pdb=" N TYR C2336 " --> pdb=" O GLU C2332 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN C2342 " --> pdb=" O ASP C2338 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE C2343 " --> pdb=" O LEU C2339 " (cutoff:3.500A) Processing helix chain 'C' and resid 2350 through 2360 Processing helix chain 'C' and resid 2368 through 2377 removed outlier: 3.602A pdb=" N ILE C2373 " --> pdb=" O LEU C2369 " (cutoff:3.500A) Processing helix chain 'C' and resid 2380 through 2398 removed outlier: 3.828A pdb=" N ALA C2384 " --> pdb=" O TYR C2380 " (cutoff:3.500A) Processing helix chain 'C' and resid 2398 through 2406 Processing helix chain 'C' and resid 2408 through 2428 removed outlier: 3.632A pdb=" N TRP C2417 " --> pdb=" O ARG C2413 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU C2420 " --> pdb=" O THR C2416 " (cutoff:3.500A) Processing helix chain 'C' and resid 2461 through 2474 removed outlier: 3.924A pdb=" N MET C2465 " --> pdb=" O HIS C2461 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C2472 " --> pdb=" O ALA C2468 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C2473 " --> pdb=" O LYS C2469 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 754 through 755 Processing sheet with id=AA2, first strand: chain 'A' and resid 1558 through 1559 removed outlier: 6.401A pdb=" N GLY A1558 " --> pdb=" O TYR A1662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1672 through 1673 Processing sheet with id=AA4, first strand: chain 'A' and resid 1730 through 1737 removed outlier: 6.751A pdb=" N SER A1717 " --> pdb=" O LYS A1787 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1740 through 1742 removed outlier: 5.905A pdb=" N LEU A1740 " --> pdb=" O GLN A1796 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR A1949 " --> pdb=" O LEU A1797 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A1869 " --> pdb=" O TYR A1949 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU A1951 " --> pdb=" O GLY A1867 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY A1867 " --> pdb=" O LEU A1951 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR A1953 " --> pdb=" O LEU A1865 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A1865 " --> pdb=" O TYR A1953 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG A1955 " --> pdb=" O TYR A1863 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR A1863 " --> pdb=" O ARG A1955 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1740 through 1742 removed outlier: 5.905A pdb=" N LEU A1740 " --> pdb=" O GLN A1796 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR A1949 " --> pdb=" O LEU A1797 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A1869 " --> pdb=" O TYR A1949 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU A1951 " --> pdb=" O GLY A1867 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLY A1867 " --> pdb=" O LEU A1951 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR A1953 " --> pdb=" O LEU A1865 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU A1865 " --> pdb=" O TYR A1953 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG A1955 " --> pdb=" O TYR A1863 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TYR A1863 " --> pdb=" O ARG A1955 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A1866 " --> pdb=" O ILE A1885 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1769 through 1771 removed outlier: 3.514A pdb=" N LYS A1776 " --> pdb=" O CYS A1771 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1800 through 1803 Processing sheet with id=AA9, first strand: chain 'A' and resid 1924 through 1931 removed outlier: 3.699A pdb=" N ASP A1931 " --> pdb=" O ARG A1936 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 754 through 755 removed outlier: 3.579A pdb=" N VAL B 755 " --> pdb=" O MET B 762 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1558 through 1559 removed outlier: 6.080A pdb=" N GLY B1558 " --> pdb=" O TYR B1662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 1672 through 1673 Processing sheet with id=AB4, first strand: chain 'B' and resid 1730 through 1737 removed outlier: 6.787A pdb=" N SER B1717 " --> pdb=" O LYS B1787 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1739 through 1743 removed outlier: 6.183A pdb=" N LEU B1740 " --> pdb=" O GLN B1796 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B1798 " --> pdb=" O LEU B1740 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL B1742 " --> pdb=" O LYS B1798 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR B1949 " --> pdb=" O LEU B1797 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B1869 " --> pdb=" O TYR B1949 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B1951 " --> pdb=" O GLY B1867 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY B1867 " --> pdb=" O LEU B1951 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR B1953 " --> pdb=" O LEU B1865 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B1865 " --> pdb=" O TYR B1953 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG B1955 " --> pdb=" O TYR B1863 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR B1863 " --> pdb=" O ARG B1955 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1739 through 1743 removed outlier: 6.183A pdb=" N LEU B1740 " --> pdb=" O GLN B1796 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B1798 " --> pdb=" O LEU B1740 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N VAL B1742 " --> pdb=" O LYS B1798 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR B1949 " --> pdb=" O LEU B1797 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B1869 " --> pdb=" O TYR B1949 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B1951 " --> pdb=" O GLY B1867 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY B1867 " --> pdb=" O LEU B1951 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR B1953 " --> pdb=" O LEU B1865 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU B1865 " --> pdb=" O TYR B1953 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG B1955 " --> pdb=" O TYR B1863 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR B1863 " --> pdb=" O ARG B1955 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B1866 " --> pdb=" O ILE B1885 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1769 through 1771 removed outlier: 3.659A pdb=" N LYS B1776 " --> pdb=" O CYS B1771 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1800 through 1803 Processing sheet with id=AB9, first strand: chain 'B' and resid 1924 through 1931 Processing sheet with id=AC1, first strand: chain 'C' and resid 754 through 755 removed outlier: 3.700A pdb=" N VAL C 755 " --> pdb=" O MET C 762 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1558 through 1559 removed outlier: 6.640A pdb=" N GLY C1558 " --> pdb=" O TYR C1662 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 1672 through 1673 Processing sheet with id=AC4, first strand: chain 'C' and resid 1730 through 1737 removed outlier: 7.076A pdb=" N SER C1717 " --> pdb=" O LYS C1787 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C1780 " --> pdb=" O LEU C1763 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1740 through 1742 removed outlier: 6.309A pdb=" N LEU C1740 " --> pdb=" O GLN C1796 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N TYR C1949 " --> pdb=" O LEU C1797 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP C1946 " --> pdb=" O SER C1872 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER C1872 " --> pdb=" O TRP C1946 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA C1948 " --> pdb=" O VAL C1870 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C1870 " --> pdb=" O ALA C1948 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C1950 " --> pdb=" O VAL C1868 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL C1868 " --> pdb=" O ILE C1950 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE C1952 " --> pdb=" O VAL C1866 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR C1863 " --> pdb=" O LEU C1822 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU C1822 " --> pdb=" O TYR C1863 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1740 through 1742 removed outlier: 6.309A pdb=" N LEU C1740 " --> pdb=" O GLN C1796 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N TYR C1949 " --> pdb=" O LEU C1797 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP C1946 " --> pdb=" O SER C1872 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER C1872 " --> pdb=" O TRP C1946 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA C1948 " --> pdb=" O VAL C1870 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL C1870 " --> pdb=" O ALA C1948 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE C1950 " --> pdb=" O VAL C1868 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL C1868 " --> pdb=" O ILE C1950 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N PHE C1952 " --> pdb=" O VAL C1866 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C1866 " --> pdb=" O ILE C1885 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1769 through 1771 removed outlier: 3.617A pdb=" N LYS C1776 " --> pdb=" O CYS C1771 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1800 through 1803 Processing sheet with id=AC9, first strand: chain 'C' and resid 1924 through 1931 Processing sheet with id=AD1, first strand: chain 'C' and resid 2239 through 2240 2416 hydrogen bonds defined for protein. 7086 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: 11.26 Time building geometry restraints manager: 4.97 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: 13801 1.34 - 1.46: 8890 1.46 - 1.58: 20159 1.58 - 1.70: 0 1.70 - 1.81: 426 Bond restraints: 43276 Sorted by residual: bond pdb=" N ARG C 544 " pdb=" CA ARG C 544 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.26e-02 6.30e+03 7.78e+00 bond pdb=" N ASP A 543 " pdb=" CA ASP A 543 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.19e-02 7.06e+03 7.45e+00 bond pdb=" N THR B 546 " pdb=" CA THR B 546 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.00e+00 bond pdb=" N ARG B 544 " pdb=" CA ARG B 544 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.23e-02 6.61e+03 6.80e+00 bond pdb=" N THR C 546 " pdb=" CA THR C 546 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.57e+00 ... (remaining 43271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 57554 2.08 - 4.15: 847 4.15 - 6.23: 118 6.23 - 8.30: 15 8.30 - 10.38: 4 Bond angle restraints: 58538 Sorted by residual: angle pdb=" N TYR A2402 " pdb=" CA TYR A2402 " pdb=" C TYR A2402 " ideal model delta sigma weight residual 114.62 107.17 7.45 1.14e+00 7.69e-01 4.27e+01 angle pdb=" N ILE C2404 " pdb=" CA ILE C2404 " pdb=" C ILE C2404 " ideal model delta sigma weight residual 111.81 107.16 4.65 8.60e-01 1.35e+00 2.92e+01 angle pdb=" C ASP C1902 " pdb=" CA ASP C1902 " pdb=" CB ASP C1902 " ideal model delta sigma weight residual 116.54 110.37 6.17 1.15e+00 7.56e-01 2.88e+01 angle pdb=" C PHE A1258 " pdb=" N SER A1259 " pdb=" CA SER A1259 " ideal model delta sigma weight residual 121.48 131.86 -10.38 2.04e+00 2.40e-01 2.59e+01 angle pdb=" N ALA B2358 " pdb=" CA ALA B2358 " pdb=" C ALA B2358 " ideal model delta sigma weight residual 114.75 108.70 6.05 1.26e+00 6.30e-01 2.30e+01 ... (remaining 58533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 23567 17.71 - 35.41: 2026 35.41 - 53.12: 344 53.12 - 70.83: 99 70.83 - 88.54: 26 Dihedral angle restraints: 26062 sinusoidal: 10653 harmonic: 15409 Sorted by residual: dihedral pdb=" CA ILE B2362 " pdb=" C ILE B2362 " pdb=" N PRO B2363 " pdb=" CA PRO B2363 " ideal model delta harmonic sigma weight residual -180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLU C1444 " pdb=" C GLU C1444 " pdb=" N LYS C1445 " pdb=" CA LYS C1445 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA GLU A2170 " pdb=" C GLU A2170 " pdb=" N HIS A2171 " pdb=" CA HIS A2171 " ideal model delta harmonic sigma weight residual -180.00 -158.28 -21.72 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 26059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 4800 0.041 - 0.082: 1361 0.082 - 0.124: 278 0.124 - 0.165: 22 0.165 - 0.206: 8 Chirality restraints: 6469 Sorted by residual: chirality pdb=" CB ILE C1299 " pdb=" CA ILE C1299 " pdb=" CG1 ILE C1299 " pdb=" CG2 ILE C1299 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB ILE B1299 " pdb=" CA ILE B1299 " pdb=" CG1 ILE B1299 " pdb=" CG2 ILE B1299 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.73e-01 chirality pdb=" CA ARG A 803 " pdb=" N ARG A 803 " pdb=" C ARG A 803 " pdb=" CB ARG A 803 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 6466 not shown) Planarity restraints: 7485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 541 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.09e+01 pdb=" C SER A 541 " 0.057 2.00e-02 2.50e+03 pdb=" O SER A 541 " -0.022 2.00e-02 2.50e+03 pdb=" N GLN A 542 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A2034 " 0.051 5.00e-02 4.00e+02 7.68e-02 9.45e+00 pdb=" N PRO A2035 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO A2035 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A2035 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 541 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.06e+00 pdb=" C SER B 541 " -0.049 2.00e-02 2.50e+03 pdb=" O SER B 541 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN B 542 " 0.016 2.00e-02 2.50e+03 ... (remaining 7482 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3137 2.74 - 3.28: 45538 3.28 - 3.82: 71463 3.82 - 4.36: 87259 4.36 - 4.90: 143025 Nonbonded interactions: 350422 Sorted by model distance: nonbonded pdb=" O VAL B2160 " pdb=" OH TYR B2178 " model vdw 2.196 3.040 nonbonded pdb=" NZ LYS A1811 " pdb=" O TRP A1945 " model vdw 2.198 3.120 nonbonded pdb=" O LYS A1446 " pdb=" ND2 ASN A1515 " model vdw 2.203 3.120 nonbonded pdb=" NH2 ARG B2304 " pdb=" OE1 GLN B2342 " model vdw 2.206 3.120 nonbonded pdb=" O GLN C2324 " pdb=" OG SER C2328 " model vdw 2.206 3.040 ... (remaining 350417 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 321 through 1744 or resid 1746 through 2428 or resid 2460 \ through 2475)) selection = (chain 'B' and (resid 321 through 1744 or resid 1746 through 2428 or resid 2460 \ through 2475)) selection = (chain 'C' and (resid 321 through 1744 or resid 1746 through 2475)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 8.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.710 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 50.860 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43276 Z= 0.158 Angle : 0.627 10.379 58538 Z= 0.363 Chirality : 0.039 0.206 6469 Planarity : 0.004 0.077 7485 Dihedral : 14.011 88.536 16060 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.13 % Favored : 94.68 % Rotamer: Outliers : 0.26 % Allowed : 0.32 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.12), residues: 5156 helix: -0.17 (0.09), residues: 3161 sheet: 0.36 (0.33), residues: 275 loop : -1.52 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1665 TYR 0.019 0.001 TYR C2329 PHE 0.023 0.001 PHE A1651 TRP 0.044 0.001 TRP B 565 HIS 0.006 0.001 HIS B2032 Details of bonding type rmsd covalent geometry : bond 0.00319 (43276) covalent geometry : angle 0.62705 (58538) hydrogen bonds : bond 0.26072 ( 2392) hydrogen bonds : angle 8.05557 ( 7086) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 254 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6157 (OUTLIER) cc_final: 0.5121 (pm20) REVERT: A 663 PHE cc_start: 0.9225 (t80) cc_final: 0.8984 (t80) REVERT: A 700 TRP cc_start: 0.9454 (t60) cc_final: 0.9092 (t60) REVERT: A 705 MET cc_start: 0.8424 (mpp) cc_final: 0.7977 (mpp) REVERT: A 785 ILE cc_start: 0.8715 (mm) cc_final: 0.8364 (mm) REVERT: A 1718 PHE cc_start: 0.8442 (m-80) cc_final: 0.7926 (m-80) REVERT: A 1934 MET cc_start: 0.6119 (tpt) cc_final: 0.5684 (tpp) REVERT: A 1937 MET cc_start: 0.6913 (mmp) cc_final: 0.6573 (tpt) REVERT: B 705 MET cc_start: -0.0218 (ptt) cc_final: -0.0502 (ppp) REVERT: B 1044 MET cc_start: 0.1935 (ptt) cc_final: 0.1024 (ptp) REVERT: B 1047 MET cc_start: 0.4508 (ppp) cc_final: 0.4243 (ppp) REVERT: B 1916 MET cc_start: 0.6744 (mpp) cc_final: 0.6176 (mpp) REVERT: C 525 MET cc_start: -0.1284 (ptm) cc_final: -0.1509 (ptm) REVERT: C 627 MET cc_start: 0.0168 (mtt) cc_final: -0.0456 (ptt) REVERT: C 1116 HIS cc_start: 0.8871 (m-70) cc_final: 0.8575 (m-70) REVERT: C 1339 MET cc_start: 0.8014 (ptt) cc_final: 0.7676 (ppp) outliers start: 12 outliers final: 6 residues processed: 266 average time/residue: 0.2291 time to fit residues: 103.6335 Evaluate side-chains 197 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 190 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 548 LYS Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain C residue 545 ASP Chi-restraints excluded: chain C residue 1356 LEU Chi-restraints excluded: chain C residue 1357 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 394 optimal weight: 50.0000 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 0.6980 chunk 523 optimal weight: 9.9990 chunk 497 optimal weight: 0.6980 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 0.6980 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 0.0040 chunk 223 optimal weight: 9.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 405 HIS A 406 GLN A 607 GLN A 650 HIS ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 GLN B1330 GLN ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1472 ASN B1684 HIS B2011 GLN B2080 HIS ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN C1371 HIS ** C2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.140473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.106118 restraints weight = 299934.026| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 6.47 r_work: 0.3340 rms_B_bonded: 6.15 restraints_weight: 2.0000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43276 Z= 0.148 Angle : 0.685 14.594 58538 Z= 0.354 Chirality : 0.041 0.221 6469 Planarity : 0.005 0.083 7485 Dihedral : 5.025 73.494 5709 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.23 % Favored : 94.60 % Rotamer: Outliers : 0.37 % Allowed : 4.22 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.12), residues: 5156 helix: 0.50 (0.09), residues: 3265 sheet: 0.37 (0.32), residues: 262 loop : -1.51 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 742 TYR 0.025 0.001 TYR A1268 PHE 0.032 0.002 PHE C1336 TRP 0.034 0.001 TRP A 435 HIS 0.007 0.001 HIS A1747 Details of bonding type rmsd covalent geometry : bond 0.00302 (43276) covalent geometry : angle 0.68503 (58538) hydrogen bonds : bond 0.05476 ( 2392) hydrogen bonds : angle 5.12986 ( 7086) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 210 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6234 (OUTLIER) cc_final: 0.5243 (pm20) REVERT: A 570 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7791 (pp) REVERT: A 663 PHE cc_start: 0.9457 (t80) cc_final: 0.9249 (t80) REVERT: A 680 ILE cc_start: 0.8121 (pt) cc_final: 0.7824 (pt) REVERT: A 700 TRP cc_start: 0.9407 (t60) cc_final: 0.9005 (t60) REVERT: A 705 MET cc_start: 0.8472 (mpp) cc_final: 0.7964 (mpp) REVERT: A 763 MET cc_start: -0.2594 (tmm) cc_final: -0.5568 (ptm) REVERT: A 850 MET cc_start: 0.8554 (mpp) cc_final: 0.8105 (mmm) REVERT: A 1031 LEU cc_start: 0.8256 (tp) cc_final: 0.7992 (pt) REVERT: A 1577 MET cc_start: 0.7739 (mmm) cc_final: 0.7227 (tmm) REVERT: A 1718 PHE cc_start: 0.8445 (m-80) cc_final: 0.7788 (m-80) REVERT: A 1934 MET cc_start: 0.6103 (tpt) cc_final: 0.5803 (tpp) REVERT: B 392 GLN cc_start: 0.0037 (OUTLIER) cc_final: -0.0293 (mp-120) REVERT: B 705 MET cc_start: 0.1028 (ptt) cc_final: 0.0561 (ppp) REVERT: B 1033 MET cc_start: 0.7061 (pmm) cc_final: 0.6714 (pmm) REVERT: B 1044 MET cc_start: 0.2358 (ptt) cc_final: 0.1431 (ptt) REVERT: B 1047 MET cc_start: 0.4595 (ppp) cc_final: 0.4318 (ppp) REVERT: B 1141 MET cc_start: 0.5548 (tpt) cc_final: 0.5173 (tpt) REVERT: B 1916 MET cc_start: 0.6215 (mpp) cc_final: 0.5976 (mpp) REVERT: B 1937 MET cc_start: 0.0901 (tpt) cc_final: 0.0696 (tpt) REVERT: B 2007 MET cc_start: 0.8781 (tmm) cc_final: 0.8521 (tmm) REVERT: C 1033 MET cc_start: 0.8588 (tpp) cc_final: 0.8362 (mmm) REVERT: C 1339 MET cc_start: 0.8353 (ptt) cc_final: 0.8062 (ppp) REVERT: C 1353 PHE cc_start: 0.8333 (m-80) cc_final: 0.8117 (m-80) REVERT: C 1354 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8837 (mp) REVERT: C 1926 MET cc_start: 0.6218 (ppp) cc_final: 0.5417 (tmm) outliers start: 17 outliers final: 8 residues processed: 221 average time/residue: 0.2240 time to fit residues: 85.9011 Evaluate side-chains 205 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1812 PHE Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 1812 PHE Chi-restraints excluded: chain C residue 1354 ILE Chi-restraints excluded: chain C residue 1356 LEU Chi-restraints excluded: chain C residue 1647 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 45 optimal weight: 9.9990 chunk 516 optimal weight: 2.9990 chunk 412 optimal weight: 5.9990 chunk 396 optimal weight: 8.9990 chunk 381 optimal weight: 50.0000 chunk 517 optimal weight: 0.8980 chunk 438 optimal weight: 0.2980 chunk 493 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 462 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN A1116 HIS ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1457 ASN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 GLN B1064 HIS ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 405 HIS C 406 GLN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1134 ASN C1330 GLN C1574 GLN C2221 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.138591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.104182 restraints weight = 317160.918| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 6.29 r_work: 0.3268 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 43276 Z= 0.199 Angle : 0.672 12.092 58538 Z= 0.340 Chirality : 0.042 0.182 6469 Planarity : 0.005 0.065 7485 Dihedral : 4.905 69.088 5698 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 0.58 % Allowed : 5.93 % Favored : 93.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 5156 helix: 0.59 (0.09), residues: 3280 sheet: 0.26 (0.32), residues: 264 loop : -1.52 (0.16), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 788 TYR 0.024 0.002 TYR C2329 PHE 0.029 0.002 PHE C1336 TRP 0.025 0.002 TRP B 565 HIS 0.007 0.001 HIS A1646 Details of bonding type rmsd covalent geometry : bond 0.00452 (43276) covalent geometry : angle 0.67154 (58538) hydrogen bonds : bond 0.04373 ( 2392) hydrogen bonds : angle 4.77999 ( 7086) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6316 (OUTLIER) cc_final: 0.5487 (pm20) REVERT: A 570 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7737 (pp) REVERT: A 624 MET cc_start: 0.7422 (mmm) cc_final: 0.7164 (mmm) REVERT: A 663 PHE cc_start: 0.9449 (t80) cc_final: 0.9173 (t80) REVERT: A 700 TRP cc_start: 0.9374 (t60) cc_final: 0.9004 (t60) REVERT: A 850 MET cc_start: 0.8575 (mpp) cc_final: 0.8013 (mpp) REVERT: A 1577 MET cc_start: 0.7908 (mmm) cc_final: 0.7501 (tmm) REVERT: A 1718 PHE cc_start: 0.8567 (m-80) cc_final: 0.7987 (m-80) REVERT: B 392 GLN cc_start: 0.0235 (OUTLIER) cc_final: -0.0135 (mp-120) REVERT: B 705 MET cc_start: 0.1035 (ptt) cc_final: -0.0176 (ppp) REVERT: B 1044 MET cc_start: 0.2655 (ptt) cc_final: 0.1827 (ptp) REVERT: B 1047 MET cc_start: 0.4737 (ppp) cc_final: 0.4499 (ppp) REVERT: B 1100 MET cc_start: 0.4360 (ppp) cc_final: 0.3965 (ptt) REVERT: B 1916 MET cc_start: 0.6437 (mpp) cc_final: 0.6133 (mpp) REVERT: C 1100 MET cc_start: 0.6683 (ppp) cc_final: 0.6010 (ptp) REVERT: C 1339 MET cc_start: 0.8401 (ptt) cc_final: 0.7951 (ppp) REVERT: C 1345 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.7133 (ptt) REVERT: C 1353 PHE cc_start: 0.8352 (m-80) cc_final: 0.8053 (m-80) REVERT: C 1354 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8757 (mp) REVERT: C 1926 MET cc_start: 0.6115 (ppp) cc_final: 0.5386 (tmm) REVERT: C 1999 MET cc_start: 0.8832 (mmt) cc_final: 0.8608 (mmm) outliers start: 27 outliers final: 13 residues processed: 217 average time/residue: 0.2093 time to fit residues: 80.9104 Evaluate side-chains 207 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 545 ASP Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1812 PHE Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 2055 THR Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 1245 ILE Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1354 ILE Chi-restraints excluded: chain C residue 1356 LEU Chi-restraints excluded: chain C residue 1647 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 350 optimal weight: 50.0000 chunk 110 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 252 optimal weight: 20.0000 chunk 243 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 232 optimal weight: 20.0000 chunk 475 optimal weight: 40.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1335 GLN B1430 HIS ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.137876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.103314 restraints weight = 279981.180| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 6.94 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 43276 Z= 0.243 Angle : 0.678 17.929 58538 Z= 0.343 Chirality : 0.042 0.175 6469 Planarity : 0.005 0.063 7485 Dihedral : 4.955 67.195 5698 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.85 % Favored : 94.02 % Rotamer: Outliers : 0.76 % Allowed : 7.47 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.12), residues: 5156 helix: 0.57 (0.09), residues: 3286 sheet: 0.15 (0.31), residues: 264 loop : -1.51 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 788 TYR 0.021 0.002 TYR A1375 PHE 0.024 0.002 PHE C1336 TRP 0.025 0.002 TRP C 512 HIS 0.035 0.002 HIS A1116 Details of bonding type rmsd covalent geometry : bond 0.00555 (43276) covalent geometry : angle 0.67779 (58538) hydrogen bonds : bond 0.04015 ( 2392) hydrogen bonds : angle 4.72514 ( 7086) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.5614 (pm20) REVERT: A 570 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7658 (pp) REVERT: A 663 PHE cc_start: 0.9231 (t80) cc_final: 0.8961 (t80) REVERT: A 700 TRP cc_start: 0.9397 (t60) cc_final: 0.9007 (t60) REVERT: A 763 MET cc_start: -0.2245 (tmm) cc_final: -0.5231 (ptm) REVERT: A 850 MET cc_start: 0.8325 (mpp) cc_final: 0.7809 (mpp) REVERT: A 1577 MET cc_start: 0.7584 (mmm) cc_final: 0.7258 (tmm) REVERT: A 1718 PHE cc_start: 0.8645 (m-80) cc_final: 0.8091 (m-80) REVERT: A 1933 MET cc_start: 0.2454 (pmm) cc_final: 0.2034 (mtm) REVERT: B 392 GLN cc_start: -0.0270 (OUTLIER) cc_final: -0.0809 (mp-120) REVERT: B 705 MET cc_start: -0.0041 (ptt) cc_final: -0.1052 (ppp) REVERT: B 1044 MET cc_start: 0.2579 (ptt) cc_final: 0.1854 (ptt) REVERT: B 1047 MET cc_start: 0.4521 (ppp) cc_final: 0.4271 (ppp) REVERT: B 1100 MET cc_start: 0.4194 (ppp) cc_final: 0.3816 (ptt) REVERT: B 1910 MET cc_start: -0.2732 (tpp) cc_final: -0.3449 (tpt) REVERT: C 503 MET cc_start: 0.3625 (tmm) cc_final: 0.3400 (mmp) REVERT: C 1100 MET cc_start: 0.6782 (ppp) cc_final: 0.6022 (ptp) REVERT: C 1254 LEU cc_start: 0.5138 (OUTLIER) cc_final: 0.4618 (mp) REVERT: C 1339 MET cc_start: 0.8452 (ptt) cc_final: 0.8006 (ppp) REVERT: C 1345 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7168 (ptt) REVERT: C 1353 PHE cc_start: 0.8160 (m-80) cc_final: 0.7853 (m-80) REVERT: C 1926 MET cc_start: 0.5726 (ppp) cc_final: 0.5242 (tmm) REVERT: C 2188 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8434 (mp) outliers start: 35 outliers final: 17 residues processed: 217 average time/residue: 0.2141 time to fit residues: 82.9671 Evaluate side-chains 211 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1812 PHE Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 2055 THR Chi-restraints excluded: chain B residue 2245 MET Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 338 MET Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1245 ILE Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1356 LEU Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 2188 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 316 optimal weight: 0.8980 chunk 393 optimal weight: 20.0000 chunk 317 optimal weight: 0.6980 chunk 33 optimal weight: 6.9990 chunk 511 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 373 optimal weight: 4.9990 chunk 251 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 chunk 309 optimal weight: 5.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1116 HIS ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.138972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.104625 restraints weight = 285694.471| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 6.94 r_work: 0.3269 rms_B_bonded: 6.32 restraints_weight: 2.0000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 43276 Z= 0.171 Angle : 0.633 14.461 58538 Z= 0.318 Chirality : 0.040 0.269 6469 Planarity : 0.004 0.062 7485 Dihedral : 4.749 63.527 5696 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.77 % Favored : 94.13 % Rotamer: Outliers : 0.71 % Allowed : 8.38 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 5156 helix: 0.73 (0.09), residues: 3282 sheet: 0.15 (0.31), residues: 264 loop : -1.44 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.020 0.001 TYR A 623 PHE 0.023 0.002 PHE C1336 TRP 0.030 0.001 TRP C 512 HIS 0.006 0.001 HIS B1322 Details of bonding type rmsd covalent geometry : bond 0.00387 (43276) covalent geometry : angle 0.63318 (58538) hydrogen bonds : bond 0.03635 ( 2392) hydrogen bonds : angle 4.54717 ( 7086) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6370 (OUTLIER) cc_final: 0.5702 (pm20) REVERT: A 570 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7758 (pp) REVERT: A 663 PHE cc_start: 0.9454 (t80) cc_final: 0.9220 (t80) REVERT: A 700 TRP cc_start: 0.9336 (t60) cc_final: 0.9015 (t60) REVERT: A 763 MET cc_start: -0.1967 (tmm) cc_final: -0.4973 (ptm) REVERT: A 850 MET cc_start: 0.8611 (mpp) cc_final: 0.8246 (mpp) REVERT: A 1718 PHE cc_start: 0.8469 (m-80) cc_final: 0.7687 (m-80) REVERT: A 1735 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8227 (pm20) REVERT: A 1933 MET cc_start: 0.2500 (pmm) cc_final: 0.2085 (mtm) REVERT: B 392 GLN cc_start: 0.0208 (OUTLIER) cc_final: -0.0145 (mp-120) REVERT: B 705 MET cc_start: 0.1301 (ptt) cc_final: 0.0164 (ppp) REVERT: B 1044 MET cc_start: 0.2664 (ptt) cc_final: 0.1871 (ptt) REVERT: B 1047 MET cc_start: 0.4768 (ppp) cc_final: 0.4522 (ppp) REVERT: B 1100 MET cc_start: 0.4240 (ppp) cc_final: 0.3918 (ptt) REVERT: B 1141 MET cc_start: 0.5448 (tpt) cc_final: 0.4977 (tpt) REVERT: B 1824 MET cc_start: 0.7139 (tpp) cc_final: 0.4946 (mtp) REVERT: C 1100 MET cc_start: 0.6538 (ppp) cc_final: 0.5882 (ptp) REVERT: C 1254 LEU cc_start: 0.5282 (OUTLIER) cc_final: 0.4594 (mp) REVERT: C 1316 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6259 (tt) REVERT: C 1339 MET cc_start: 0.8426 (ptt) cc_final: 0.8026 (ppp) REVERT: C 1345 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7115 (ptt) REVERT: C 1353 PHE cc_start: 0.8201 (m-80) cc_final: 0.7915 (m-80) REVERT: C 1577 MET cc_start: 0.6432 (tpp) cc_final: 0.6166 (tpp) REVERT: C 1926 MET cc_start: 0.6514 (ppp) cc_final: 0.5742 (tmm) outliers start: 33 outliers final: 15 residues processed: 209 average time/residue: 0.2111 time to fit residues: 78.6504 Evaluate side-chains 210 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1812 PHE Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1316 ILE Chi-restraints excluded: chain B residue 2245 MET Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1643 VAL Chi-restraints excluded: chain C residue 1647 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 29 optimal weight: 5.9990 chunk 382 optimal weight: 9.9990 chunk 399 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 273 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 193 optimal weight: 0.7980 chunk 343 optimal weight: 0.7980 chunk 477 optimal weight: 8.9990 chunk 246 optimal weight: 20.0000 chunk 436 optimal weight: 0.0770 overall best weight: 3.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.138247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.106852 restraints weight = 365229.711| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 9.98 r_work: 0.3171 rms_B_bonded: 7.13 restraints_weight: 2.0000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 43276 Z= 0.223 Angle : 0.663 13.271 58538 Z= 0.333 Chirality : 0.041 0.221 6469 Planarity : 0.005 0.062 7485 Dihedral : 4.760 62.178 5694 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.16 % Favored : 93.72 % Rotamer: Outliers : 0.65 % Allowed : 8.94 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.12), residues: 5156 helix: 0.71 (0.09), residues: 3285 sheet: 0.15 (0.32), residues: 263 loop : -1.45 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C2113 TYR 0.021 0.002 TYR A 623 PHE 0.024 0.002 PHE C1468 TRP 0.022 0.001 TRP C 512 HIS 0.034 0.001 HIS A1116 Details of bonding type rmsd covalent geometry : bond 0.00511 (43276) covalent geometry : angle 0.66265 (58538) hydrogen bonds : bond 0.03679 ( 2392) hydrogen bonds : angle 4.57671 ( 7086) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.5933 (pm20) REVERT: A 570 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7728 (pp) REVERT: A 663 PHE cc_start: 0.9457 (t80) cc_final: 0.9242 (t80) REVERT: A 700 TRP cc_start: 0.9365 (t60) cc_final: 0.9047 (t60) REVERT: A 705 MET cc_start: 0.8507 (mpp) cc_final: 0.7918 (mpp) REVERT: A 763 MET cc_start: -0.1844 (tmm) cc_final: -0.4880 (ptm) REVERT: A 850 MET cc_start: 0.8671 (mpp) cc_final: 0.8377 (mpp) REVERT: A 1718 PHE cc_start: 0.8640 (m-80) cc_final: 0.8129 (m-80) REVERT: A 1933 MET cc_start: 0.2312 (pmm) cc_final: 0.2020 (mtm) REVERT: B 392 GLN cc_start: 0.0145 (OUTLIER) cc_final: -0.0221 (mp-120) REVERT: B 705 MET cc_start: 0.1304 (ptt) cc_final: 0.0175 (ppp) REVERT: B 1044 MET cc_start: 0.2764 (ptt) cc_final: 0.2026 (ptt) REVERT: B 1047 MET cc_start: 0.4852 (ppp) cc_final: 0.4577 (ppp) REVERT: B 1100 MET cc_start: 0.4406 (ppp) cc_final: 0.4122 (ptt) REVERT: C 1047 MET cc_start: -0.1993 (tpt) cc_final: -0.2281 (tpt) REVERT: C 1100 MET cc_start: 0.6504 (ppp) cc_final: 0.6032 (ptp) REVERT: C 1254 LEU cc_start: 0.5234 (OUTLIER) cc_final: 0.4415 (mt) REVERT: C 1316 ILE cc_start: 0.6901 (OUTLIER) cc_final: 0.6132 (tt) REVERT: C 1339 MET cc_start: 0.8525 (ptt) cc_final: 0.8084 (ppp) REVERT: C 1345 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7132 (ptt) REVERT: C 1353 PHE cc_start: 0.8323 (m-80) cc_final: 0.8005 (m-80) REVERT: C 1577 MET cc_start: 0.6568 (tpp) cc_final: 0.6304 (tpp) REVERT: C 1926 MET cc_start: 0.6499 (ppp) cc_final: 0.5701 (tmm) outliers start: 30 outliers final: 18 residues processed: 210 average time/residue: 0.2192 time to fit residues: 81.8758 Evaluate side-chains 210 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1116 HIS Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1812 PHE Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1290 GLU Chi-restraints excluded: chain B residue 2055 THR Chi-restraints excluded: chain B residue 2245 MET Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1245 ILE Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1643 VAL Chi-restraints excluded: chain C residue 1647 LEU Chi-restraints excluded: chain C residue 1709 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 110 optimal weight: 7.9990 chunk 382 optimal weight: 0.5980 chunk 282 optimal weight: 50.0000 chunk 386 optimal weight: 7.9990 chunk 521 optimal weight: 2.9990 chunk 435 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 492 optimal weight: 0.7980 chunk 120 optimal weight: 0.0070 chunk 442 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.0400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 HIS ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2221 GLN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.139372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.109881 restraints weight = 340476.580| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 8.76 r_work: 0.3278 rms_B_bonded: 6.77 restraints_weight: 2.0000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43276 Z= 0.121 Angle : 0.605 12.553 58538 Z= 0.302 Chirality : 0.039 0.219 6469 Planarity : 0.004 0.062 7485 Dihedral : 4.612 60.822 5694 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 0.61 % Allowed : 9.39 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.12), residues: 5156 helix: 0.91 (0.09), residues: 3285 sheet: 0.20 (0.32), residues: 263 loop : -1.39 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.020 0.001 TYR A 623 PHE 0.023 0.001 PHE C1336 TRP 0.037 0.001 TRP C 512 HIS 0.014 0.001 HIS C1116 Details of bonding type rmsd covalent geometry : bond 0.00270 (43276) covalent geometry : angle 0.60464 (58538) hydrogen bonds : bond 0.03294 ( 2392) hydrogen bonds : angle 4.37137 ( 7086) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6629 (OUTLIER) cc_final: 0.5947 (pm20) REVERT: A 570 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7723 (pp) REVERT: A 663 PHE cc_start: 0.9451 (t80) cc_final: 0.9208 (t80) REVERT: A 700 TRP cc_start: 0.9359 (t60) cc_final: 0.9030 (t60) REVERT: A 705 MET cc_start: 0.8431 (mpp) cc_final: 0.7812 (mpp) REVERT: A 763 MET cc_start: -0.1946 (tmm) cc_final: -0.4884 (ptm) REVERT: A 1116 HIS cc_start: 0.8403 (m-70) cc_final: 0.8028 (t-90) REVERT: A 1718 PHE cc_start: 0.8625 (m-80) cc_final: 0.8097 (m-80) REVERT: A 1933 MET cc_start: 0.2313 (pmm) cc_final: 0.2063 (mtm) REVERT: B 392 GLN cc_start: 0.0121 (OUTLIER) cc_final: -0.0260 (mp-120) REVERT: B 705 MET cc_start: 0.0969 (ptt) cc_final: -0.0135 (ppp) REVERT: B 1044 MET cc_start: 0.2793 (ptt) cc_final: 0.2040 (ptt) REVERT: B 1047 MET cc_start: 0.4804 (ppp) cc_final: 0.4408 (ppp) REVERT: B 1100 MET cc_start: 0.4371 (ppp) cc_final: 0.4113 (ptt) REVERT: C 1100 MET cc_start: 0.6503 (ppp) cc_final: 0.6043 (ptp) REVERT: C 1254 LEU cc_start: 0.5324 (OUTLIER) cc_final: 0.4582 (mp) REVERT: C 1316 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6454 (tt) REVERT: C 1345 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7068 (ptt) REVERT: C 1353 PHE cc_start: 0.8184 (m-80) cc_final: 0.7896 (m-80) REVERT: C 1577 MET cc_start: 0.6570 (tpp) cc_final: 0.6319 (tpp) REVERT: C 1926 MET cc_start: 0.6481 (ppp) cc_final: 0.5705 (tmm) outliers start: 28 outliers final: 14 residues processed: 211 average time/residue: 0.2196 time to fit residues: 82.1502 Evaluate side-chains 209 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 1290 GLU Chi-restraints excluded: chain B residue 2245 MET Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1643 VAL Chi-restraints excluded: chain C residue 1647 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 521 optimal weight: 0.4980 chunk 301 optimal weight: 0.5980 chunk 264 optimal weight: 0.7980 chunk 402 optimal weight: 5.9990 chunk 336 optimal weight: 0.7980 chunk 410 optimal weight: 0.0870 chunk 25 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 420 optimal weight: 1.9990 chunk 226 optimal weight: 9.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 862 ASN ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 605 GLN ** C1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1335 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.139833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.110410 restraints weight = 348789.194| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 8.59 r_work: 0.3284 rms_B_bonded: 6.69 restraints_weight: 2.0000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 43276 Z= 0.109 Angle : 0.604 16.200 58538 Z= 0.299 Chirality : 0.039 0.213 6469 Planarity : 0.004 0.064 7485 Dihedral : 4.468 60.296 5694 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.09 % Favored : 94.83 % Rotamer: Outliers : 0.56 % Allowed : 9.74 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.12), residues: 5156 helix: 1.06 (0.09), residues: 3277 sheet: 0.24 (0.31), residues: 263 loop : -1.35 (0.16), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1041 TYR 0.018 0.001 TYR A2222 PHE 0.022 0.001 PHE B1689 TRP 0.047 0.001 TRP A 476 HIS 0.007 0.001 HIS C1116 Details of bonding type rmsd covalent geometry : bond 0.00234 (43276) covalent geometry : angle 0.60447 (58538) hydrogen bonds : bond 0.03137 ( 2392) hydrogen bonds : angle 4.26793 ( 7086) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.5997 (pm20) REVERT: A 570 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7671 (pp) REVERT: A 663 PHE cc_start: 0.9451 (t80) cc_final: 0.9214 (t80) REVERT: A 700 TRP cc_start: 0.9329 (t60) cc_final: 0.8923 (t60) REVERT: A 705 MET cc_start: 0.8446 (mpp) cc_final: 0.7900 (mpp) REVERT: A 763 MET cc_start: -0.1937 (tmm) cc_final: -0.4892 (ptm) REVERT: A 850 MET cc_start: 0.8460 (mpp) cc_final: 0.8010 (mpp) REVERT: A 1116 HIS cc_start: 0.8462 (m-70) cc_final: 0.8083 (t-90) REVERT: A 1687 LEU cc_start: 0.8510 (mm) cc_final: 0.8301 (tp) REVERT: A 1718 PHE cc_start: 0.8541 (m-80) cc_final: 0.8024 (m-80) REVERT: A 1933 MET cc_start: 0.2333 (pmm) cc_final: 0.2123 (mtm) REVERT: B 392 GLN cc_start: 0.0170 (OUTLIER) cc_final: -0.0183 (mp-120) REVERT: B 705 MET cc_start: 0.0974 (ptt) cc_final: 0.0658 (ppp) REVERT: B 1044 MET cc_start: 0.2852 (ptt) cc_final: 0.2086 (ptt) REVERT: B 1047 MET cc_start: 0.5015 (ppp) cc_final: 0.4576 (ppp) REVERT: B 1100 MET cc_start: 0.4467 (ppp) cc_final: 0.4231 (ptt) REVERT: B 1162 ILE cc_start: 0.6393 (tp) cc_final: 0.6098 (pt) REVERT: B 1577 MET cc_start: 0.6464 (mmm) cc_final: 0.5244 (tpp) REVERT: B 1933 MET cc_start: 0.3710 (tpt) cc_final: 0.3416 (ppp) REVERT: C 1100 MET cc_start: 0.6570 (ppp) cc_final: 0.6140 (ptp) REVERT: C 1254 LEU cc_start: 0.5349 (OUTLIER) cc_final: 0.4550 (mp) REVERT: C 1316 ILE cc_start: 0.6969 (OUTLIER) cc_final: 0.6597 (tt) REVERT: C 1345 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6906 (ptt) REVERT: C 1353 PHE cc_start: 0.8157 (m-80) cc_final: 0.7941 (m-80) REVERT: C 1926 MET cc_start: 0.6448 (ppp) cc_final: 0.5607 (tmm) outliers start: 26 outliers final: 14 residues processed: 209 average time/residue: 0.2135 time to fit residues: 78.8459 Evaluate side-chains 208 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 1290 GLU Chi-restraints excluded: chain B residue 2245 MET Chi-restraints excluded: chain B residue 2299 THR Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1335 GLN Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1647 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 79 optimal weight: 6.9990 chunk 263 optimal weight: 0.8980 chunk 487 optimal weight: 1.9990 chunk 416 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 521 optimal weight: 0.9990 chunk 447 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 518 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 440 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 ASN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.139601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.109041 restraints weight = 328480.385| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 7.31 r_work: 0.3308 rms_B_bonded: 6.03 restraints_weight: 2.0000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43276 Z= 0.119 Angle : 0.602 13.652 58538 Z= 0.299 Chirality : 0.039 0.206 6469 Planarity : 0.004 0.064 7485 Dihedral : 4.431 60.465 5694 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.11 % Favored : 94.83 % Rotamer: Outliers : 0.43 % Allowed : 9.96 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.12), residues: 5156 helix: 1.11 (0.09), residues: 3270 sheet: 0.28 (0.32), residues: 258 loop : -1.35 (0.16), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.016 0.001 TYR A2222 PHE 0.036 0.001 PHE C1336 TRP 0.043 0.001 TRP C 512 HIS 0.006 0.001 HIS C1116 Details of bonding type rmsd covalent geometry : bond 0.00265 (43276) covalent geometry : angle 0.60219 (58538) hydrogen bonds : bond 0.03130 ( 2392) hydrogen bonds : angle 4.24645 ( 7086) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 2.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6754 (OUTLIER) cc_final: 0.6102 (pm20) REVERT: A 570 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7627 (pp) REVERT: A 663 PHE cc_start: 0.9435 (t80) cc_final: 0.9192 (t80) REVERT: A 700 TRP cc_start: 0.9327 (t60) cc_final: 0.8922 (t60) REVERT: A 705 MET cc_start: 0.8473 (mpp) cc_final: 0.7923 (mpp) REVERT: A 763 MET cc_start: -0.1900 (tmm) cc_final: -0.4892 (ptm) REVERT: A 850 MET cc_start: 0.8449 (mpp) cc_final: 0.8071 (mpp) REVERT: A 1116 HIS cc_start: 0.8492 (m-70) cc_final: 0.8120 (t-90) REVERT: A 1577 MET cc_start: 0.8080 (mmm) cc_final: 0.7603 (tpp) REVERT: A 1687 LEU cc_start: 0.8541 (mm) cc_final: 0.8337 (tp) REVERT: A 1718 PHE cc_start: 0.8537 (m-80) cc_final: 0.8006 (m-80) REVERT: B 392 GLN cc_start: 0.0144 (OUTLIER) cc_final: -0.0218 (mp-120) REVERT: B 705 MET cc_start: 0.0813 (ptt) cc_final: 0.0524 (ppp) REVERT: B 737 MET cc_start: -0.5580 (mmt) cc_final: -0.5963 (mmt) REVERT: B 1044 MET cc_start: 0.2837 (ptt) cc_final: 0.2113 (ptt) REVERT: B 1047 MET cc_start: 0.5071 (ppp) cc_final: 0.4606 (ppp) REVERT: B 1100 MET cc_start: 0.4479 (ppp) cc_final: 0.4260 (ptt) REVERT: B 1162 ILE cc_start: 0.6382 (tp) cc_final: 0.6105 (pt) REVERT: B 1577 MET cc_start: 0.6508 (mmm) cc_final: 0.5304 (tpp) REVERT: B 1933 MET cc_start: 0.3557 (tpt) cc_final: 0.3314 (ppp) REVERT: C 1100 MET cc_start: 0.6632 (ppp) cc_final: 0.6231 (ptp) REVERT: C 1254 LEU cc_start: 0.5354 (OUTLIER) cc_final: 0.4588 (mp) REVERT: C 1316 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6620 (tt) REVERT: C 1345 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6923 (ptt) REVERT: C 1577 MET cc_start: 0.6295 (tpp) cc_final: 0.5980 (tpp) REVERT: C 1926 MET cc_start: 0.6434 (ppp) cc_final: 0.5591 (tmm) outliers start: 20 outliers final: 14 residues processed: 202 average time/residue: 0.2174 time to fit residues: 77.8873 Evaluate side-chains 206 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 1290 GLU Chi-restraints excluded: chain B residue 2055 THR Chi-restraints excluded: chain B residue 2245 MET Chi-restraints excluded: chain B residue 2299 THR Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1647 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 169 optimal weight: 0.0980 chunk 462 optimal weight: 0.7980 chunk 461 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 341 optimal weight: 6.9990 chunk 351 optimal weight: 7.9990 chunk 510 optimal weight: 2.9990 chunk 347 optimal weight: 4.9990 chunk 340 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.139080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.107065 restraints weight = 311888.242| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 8.05 r_work: 0.3248 rms_B_bonded: 6.32 restraints_weight: 2.0000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 43276 Z= 0.150 Angle : 0.627 13.396 58538 Z= 0.311 Chirality : 0.040 0.300 6469 Planarity : 0.004 0.063 7485 Dihedral : 4.451 60.520 5694 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.28 % Favored : 94.66 % Rotamer: Outliers : 0.48 % Allowed : 10.06 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.12), residues: 5156 helix: 1.09 (0.09), residues: 3271 sheet: 0.38 (0.32), residues: 252 loop : -1.37 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 742 TYR 0.017 0.001 TYR A2222 PHE 0.022 0.001 PHE B1689 TRP 0.047 0.001 TRP C 512 HIS 0.006 0.001 HIS C1116 Details of bonding type rmsd covalent geometry : bond 0.00342 (43276) covalent geometry : angle 0.62712 (58538) hydrogen bonds : bond 0.03197 ( 2392) hydrogen bonds : angle 4.28175 ( 7086) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10312 Ramachandran restraints generated. 5156 Oldfield, 0 Emsley, 5156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 GLN cc_start: 0.6836 (OUTLIER) cc_final: 0.6244 (pm20) REVERT: A 570 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7655 (pp) REVERT: A 663 PHE cc_start: 0.9424 (t80) cc_final: 0.9193 (t80) REVERT: A 700 TRP cc_start: 0.9296 (t60) cc_final: 0.8902 (t60) REVERT: A 705 MET cc_start: 0.8473 (mpp) cc_final: 0.7944 (mpp) REVERT: A 763 MET cc_start: -0.1874 (tmm) cc_final: -0.4828 (ptm) REVERT: A 850 MET cc_start: 0.8430 (mpp) cc_final: 0.8027 (mpp) REVERT: A 1116 HIS cc_start: 0.8472 (m-70) cc_final: 0.8107 (t-90) REVERT: A 1718 PHE cc_start: 0.8569 (m-80) cc_final: 0.8048 (m-80) REVERT: A 1933 MET cc_start: 0.3525 (mtm) cc_final: 0.2656 (mtt) REVERT: B 392 GLN cc_start: 0.0253 (OUTLIER) cc_final: -0.0061 (mp-120) REVERT: B 705 MET cc_start: 0.1280 (ptt) cc_final: 0.0923 (ppp) REVERT: B 737 MET cc_start: -0.5492 (mmt) cc_final: -0.5846 (mmt) REVERT: B 1044 MET cc_start: 0.2747 (ptt) cc_final: 0.2030 (ptt) REVERT: B 1047 MET cc_start: 0.5319 (ppp) cc_final: 0.4828 (ppp) REVERT: B 1100 MET cc_start: 0.4573 (ppp) cc_final: 0.4352 (ptt) REVERT: B 1577 MET cc_start: 0.6490 (mmm) cc_final: 0.5245 (tpp) REVERT: B 1933 MET cc_start: 0.3539 (tpt) cc_final: 0.3283 (ppp) REVERT: C 1100 MET cc_start: 0.6608 (ppp) cc_final: 0.6234 (ptp) REVERT: C 1254 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.4616 (mt) REVERT: C 1316 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6630 (tt) REVERT: C 1345 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6850 (ptt) REVERT: C 1577 MET cc_start: 0.6357 (tpp) cc_final: 0.6059 (tpp) REVERT: C 1824 MET cc_start: 0.7017 (tmm) cc_final: 0.5290 (pmm) REVERT: C 1926 MET cc_start: 0.6472 (ppp) cc_final: 0.5593 (tmm) outliers start: 22 outliers final: 16 residues processed: 200 average time/residue: 0.2041 time to fit residues: 72.6475 Evaluate side-chains 206 residues out of total 4665 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 GLN Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 1338 LEU Chi-restraints excluded: chain A residue 1568 MET Chi-restraints excluded: chain A residue 1735 GLU Chi-restraints excluded: chain A residue 1934 MET Chi-restraints excluded: chain A residue 1937 MET Chi-restraints excluded: chain B residue 392 GLN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 1290 GLU Chi-restraints excluded: chain B residue 2055 THR Chi-restraints excluded: chain B residue 2245 MET Chi-restraints excluded: chain B residue 2299 THR Chi-restraints excluded: chain B residue 2362 ILE Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1254 LEU Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1316 ILE Chi-restraints excluded: chain C residue 1345 MET Chi-restraints excluded: chain C residue 1647 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 61 optimal weight: 6.9990 chunk 98 optimal weight: 30.0000 chunk 453 optimal weight: 10.0000 chunk 373 optimal weight: 8.9990 chunk 272 optimal weight: 7.9990 chunk 455 optimal weight: 10.0000 chunk 153 optimal weight: 0.4980 chunk 55 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 314 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 610 HIS ** A1261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1994 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2221 GLN ** C 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.137042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.104643 restraints weight = 296892.287| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 7.75 r_work: 0.3211 rms_B_bonded: 6.22 restraints_weight: 2.0000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 43276 Z= 0.312 Angle : 0.749 13.097 58538 Z= 0.375 Chirality : 0.044 0.232 6469 Planarity : 0.005 0.064 7485 Dihedral : 4.836 61.911 5694 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.16 % Favored : 93.78 % Rotamer: Outliers : 0.50 % Allowed : 10.06 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 5156 helix: 0.74 (0.09), residues: 3283 sheet: 0.17 (0.32), residues: 258 loop : -1.46 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C2113 TYR 0.026 0.002 TYR C2285 PHE 0.034 0.002 PHE C1468 TRP 0.047 0.002 TRP C 512 HIS 0.012 0.002 HIS B 516 Details of bonding type rmsd covalent geometry : bond 0.00710 (43276) covalent geometry : angle 0.74880 (58538) hydrogen bonds : bond 0.03847 ( 2392) hydrogen bonds : angle 4.61288 ( 7086) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17250.94 seconds wall clock time: 293 minutes 41.22 seconds (17621.22 seconds total)