Starting phenix.real_space_refine on Sat Mar 23 19:44:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r04_14219/03_2024/7r04_14219_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r04_14219/03_2024/7r04_14219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r04_14219/03_2024/7r04_14219.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r04_14219/03_2024/7r04_14219.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r04_14219/03_2024/7r04_14219_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r04_14219/03_2024/7r04_14219_trim_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.002 sd= 0.998 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2176 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 236 5.16 5 C 23263 2.51 5 N 6109 2.21 5 O 6639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A GLU 716": "OE1" <-> "OE2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A GLU 1495": "OE1" <-> "OE2" Residue "A TYR 1927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B GLU 540": "OE1" <-> "OE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B GLU 924": "OE1" <-> "OE2" Residue "B GLU 1320": "OE1" <-> "OE2" Residue "B PHE 1791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1898": "OE1" <-> "OE2" Residue "B GLU 1919": "OE1" <-> "OE2" Residue "B GLU 2306": "OE1" <-> "OE2" Residue "B GLU 2336": "OE1" <-> "OE2" Residue "B PHE 2685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2706": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 36250 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 18523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2326, 18523 Classifications: {'peptide': 2326} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 91, 'TRANS': 2234} Chain breaks: 13 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 17695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2229, 17695 Classifications: {'peptide': 2229} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 86, 'TRANS': 2142} Chain breaks: 16 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 18.22, per 1000 atoms: 0.50 Number of scatterers: 36250 At special positions: 0 Unit cell: (141.772, 173.512, 329.038, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 236 16.00 P 3 15.00 O 6639 8.00 N 6109 7.00 C 23263 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 - 3.50 Amino acid : False - 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: 13.84 Conformation dependent library (CDL) restraints added in 6.0 seconds 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 223 helices and 8 sheets defined 66.5% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.21 Creating SS restraints... Processing helix chain 'A' and resid 6 through 23 removed outlier: 5.184A pdb=" N GLN A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU A 21 " --> pdb=" O PHE A 17 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 33 through 49 removed outlier: 3.866A pdb=" N TYR A 49 " --> pdb=" O ASN A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 67 Processing helix chain 'A' and resid 73 through 95 Processing helix chain 'A' and resid 107 through 119 Proline residue: A 115 - end of helix Processing helix chain 'A' and resid 128 through 162 removed outlier: 7.021A pdb=" N GLU A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LEU A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASN A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ASN A 151 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 182 removed outlier: 4.664A pdb=" N GLU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N TYR A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 206 through 226 removed outlier: 3.836A pdb=" N ALA A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRP A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 240 through 257 removed outlier: 4.058A pdb=" N LYS A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 249 " --> pdb=" O CYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 276 removed outlier: 3.754A pdb=" N ALA A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Proline residue: A 268 - end of helix Processing helix chain 'A' and resid 278 through 284 removed outlier: 4.305A pdb=" N GLN A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 307 removed outlier: 5.907A pdb=" N ASP A 301 " --> pdb=" O LEU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 331 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 351 through 357 removed outlier: 4.616A pdb=" N LEU A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 Processing helix chain 'A' and resid 392 through 398 removed outlier: 4.002A pdb=" N CYS A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 430 through 433 No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 437 through 451 removed outlier: 3.555A pdb=" N GLY A 444 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 521 through 533 removed outlier: 4.240A pdb=" N LEU A 532 " --> pdb=" O GLY A 528 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 552 Processing helix chain 'A' and resid 557 through 561 Processing helix chain 'A' and resid 566 through 587 Processing helix chain 'A' and resid 593 through 614 removed outlier: 3.752A pdb=" N GLU A 602 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 694 removed outlier: 3.545A pdb=" N GLU A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 720 removed outlier: 4.852A pdb=" N ARG A 711 " --> pdb=" O MET A 707 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 747 Processing helix chain 'A' and resid 752 through 764 Processing helix chain 'A' and resid 771 through 792 Processing helix chain 'A' and resid 831 through 850 removed outlier: 5.373A pdb=" N GLY A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 902 Processing helix chain 'A' and resid 910 through 923 removed outlier: 3.522A pdb=" N GLY A 922 " --> pdb=" O LYS A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 944 Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 955 through 974 removed outlier: 3.756A pdb=" N ALA A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 983 No H-bonds generated for 'chain 'A' and resid 980 through 983' Processing helix chain 'A' and resid 989 through 1000 Processing helix chain 'A' and resid 1006 through 1024 Processing helix chain 'A' and resid 1034 through 1048 removed outlier: 4.064A pdb=" N ASP A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP A1048 " --> pdb=" O TYR A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1079 removed outlier: 3.833A pdb=" N GLU A1074 " --> pdb=" O GLN A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1095 through 1118 Processing helix chain 'A' and resid 1135 through 1155 Processing helix chain 'A' and resid 1161 through 1164 No H-bonds generated for 'chain 'A' and resid 1161 through 1164' Processing helix chain 'A' and resid 1173 through 1187 removed outlier: 4.437A pdb=" N THR A1184 " --> pdb=" O MET A1180 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1213 Processing helix chain 'A' and resid 1222 through 1230 removed outlier: 3.545A pdb=" N ASN A1229 " --> pdb=" O MET A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1233 through 1249 removed outlier: 5.401A pdb=" N ASP A1237 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE A1247 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP A1248 " --> pdb=" O THR A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1267 removed outlier: 4.279A pdb=" N GLU A1266 " --> pdb=" O SER A1262 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1292 Processing helix chain 'A' and resid 1294 through 1315 Proline residue: A1303 - end of helix removed outlier: 3.628A pdb=" N VAL A1308 " --> pdb=" O LEU A1304 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A1312 " --> pdb=" O VAL A1308 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1355 removed outlier: 5.131A pdb=" N SER A1355 " --> pdb=" O ILE A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1375 removed outlier: 3.616A pdb=" N VAL A1371 " --> pdb=" O CYS A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1380 through 1391 removed outlier: 3.628A pdb=" N VAL A1384 " --> pdb=" O SER A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1398 Processing helix chain 'A' and resid 1400 through 1403 No H-bonds generated for 'chain 'A' and resid 1400 through 1403' Processing helix chain 'A' and resid 1412 through 1429 Processing helix chain 'A' and resid 1441 through 1462 removed outlier: 3.607A pdb=" N ASP A1445 " --> pdb=" O PRO A1442 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A1451 " --> pdb=" O LYS A1448 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP A1452 " --> pdb=" O SER A1449 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A1453 " --> pdb=" O ASN A1450 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1461 " --> pdb=" O PHE A1458 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA A1462 " --> pdb=" O LEU A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1480 through 1502 removed outlier: 3.665A pdb=" N ASN A1493 " --> pdb=" O LEU A1489 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N GLU A1495 " --> pdb=" O TRP A1491 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS A1496 " --> pdb=" O ASN A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1525 Processing helix chain 'A' and resid 1545 through 1554 Processing helix chain 'A' and resid 1561 through 1569 Processing helix chain 'A' and resid 1596 through 1610 Processing helix chain 'A' and resid 1629 through 1631 No H-bonds generated for 'chain 'A' and resid 1629 through 1631' Processing helix chain 'A' and resid 1635 through 1642 removed outlier: 3.880A pdb=" N TRP A1641 " --> pdb=" O PHE A1637 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N PHE A1642 " --> pdb=" O LEU A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1647 through 1651 Processing helix chain 'A' and resid 1663 through 1671 Processing helix chain 'A' and resid 1675 through 1677 No H-bonds generated for 'chain 'A' and resid 1675 through 1677' Processing helix chain 'A' and resid 1691 through 1696 removed outlier: 4.064A pdb=" N ALA A1695 " --> pdb=" O PRO A1691 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU A1696 " --> pdb=" O GLY A1692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1691 through 1696' Processing helix chain 'A' and resid 1707 through 1711 Processing helix chain 'A' and resid 1764 through 1766 No H-bonds generated for 'chain 'A' and resid 1764 through 1766' Processing helix chain 'A' and resid 1796 through 1813 removed outlier: 3.770A pdb=" N ILE A1806 " --> pdb=" O SER A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1826 through 1828 No H-bonds generated for 'chain 'A' and resid 1826 through 1828' Processing helix chain 'A' and resid 1830 through 1842 removed outlier: 3.699A pdb=" N ASN A1840 " --> pdb=" O ILE A1836 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A1842 " --> pdb=" O LEU A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1862 Processing helix chain 'A' and resid 1884 through 1897 Processing helix chain 'A' and resid 1902 through 1913 Processing helix chain 'A' and resid 1918 through 1928 Processing helix chain 'A' and resid 1931 through 1938 removed outlier: 4.029A pdb=" N VAL A1936 " --> pdb=" O SER A1933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1944 through 1963 Processing helix chain 'A' and resid 1968 through 1981 removed outlier: 4.105A pdb=" N TRP A1976 " --> pdb=" O GLN A1972 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A1977 " --> pdb=" O ALA A1973 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN A1981 " --> pdb=" O GLY A1977 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 1998 Processing helix chain 'A' and resid 2005 through 2019 removed outlier: 3.800A pdb=" N VAL A2015 " --> pdb=" O ALA A2011 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A2016 " --> pdb=" O ASP A2012 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2041 removed outlier: 3.916A pdb=" N THR A2040 " --> pdb=" O ILE A2036 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS A2041 " --> pdb=" O ILE A2037 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2066 removed outlier: 4.121A pdb=" N ASP A2055 " --> pdb=" O LEU A2052 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA A2061 " --> pdb=" O ALA A2058 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A2066 " --> pdb=" O TYR A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2075 through 2089 Proline residue: A2080 - end of helix Processing helix chain 'A' and resid 2095 through 2114 removed outlier: 3.543A pdb=" N LEU A2112 " --> pdb=" O ILE A2108 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS A2113 " --> pdb=" O ILE A2109 " (cutoff:3.500A) Processing helix chain 'A' and resid 2122 through 2135 removed outlier: 3.965A pdb=" N GLN A2126 " --> pdb=" O GLU A2122 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A2127 " --> pdb=" O GLU A2123 " (cutoff:3.500A) Processing helix chain 'A' and resid 2138 through 2144 Processing helix chain 'A' and resid 2152 through 2158 removed outlier: 3.834A pdb=" N ALA A2156 " --> pdb=" O ALA A2152 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE A2157 " --> pdb=" O ALA A2153 " (cutoff:3.500A) Processing helix chain 'A' and resid 2181 through 2195 Processing helix chain 'A' and resid 2205 through 2216 removed outlier: 3.692A pdb=" N GLU A2210 " --> pdb=" O ASP A2206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A2211 " --> pdb=" O GLN A2207 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A2212 " --> pdb=" O TRP A2208 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A2214 " --> pdb=" O GLU A2210 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE A2215 " --> pdb=" O LEU A2211 " (cutoff:3.500A) Processing helix chain 'A' and resid 2223 through 2234 Processing helix chain 'A' and resid 2240 through 2259 removed outlier: 4.092A pdb=" N LYS A2259 " --> pdb=" O GLU A2255 " (cutoff:3.500A) Processing helix chain 'A' and resid 2264 through 2283 Proline residue: A2282 - end of helix Processing helix chain 'A' and resid 2289 through 2304 removed outlier: 4.597A pdb=" N LEU A2294 " --> pdb=" O HIS A2291 " (cutoff:3.500A) Processing helix chain 'A' and resid 2307 through 2326 removed outlier: 3.645A pdb=" N THR A2314 " --> pdb=" O TYR A2310 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA A2315 " --> pdb=" O SER A2311 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2332 No H-bonds generated for 'chain 'A' and resid 2329 through 2332' Processing helix chain 'A' and resid 2335 through 2357 Proline residue: A2345 - end of helix removed outlier: 5.168A pdb=" N TRP A2348 " --> pdb=" O ASN A2344 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N HIS A2349 " --> pdb=" O PRO A2345 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS A2350 " --> pdb=" O LEU A2346 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A2352 " --> pdb=" O TRP A2348 " (cutoff:3.500A) Processing helix chain 'A' and resid 2365 through 2378 removed outlier: 4.498A pdb=" N LYS A2375 " --> pdb=" O GLY A2371 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLY A2376 " --> pdb=" O HIS A2372 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR A2377 " --> pdb=" O LEU A2373 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG A2378 " --> pdb=" O LEU A2374 " (cutoff:3.500A) Processing helix chain 'A' and resid 2382 through 2402 Processing helix chain 'A' and resid 2415 through 2420 Processing helix chain 'A' and resid 2592 through 2608 removed outlier: 3.505A pdb=" N LEU A2605 " --> pdb=" O VAL A2601 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A2606 " --> pdb=" O LEU A2602 " (cutoff:3.500A) Processing helix chain 'A' and resid 2612 through 2628 removed outlier: 3.580A pdb=" N VAL A2627 " --> pdb=" O ALA A2623 " (cutoff:3.500A) Processing helix chain 'A' and resid 2633 through 2650 removed outlier: 3.999A pdb=" N HIS A2637 " --> pdb=" O PRO A2634 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN A2638 " --> pdb=" O VAL A2635 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A2639 " --> pdb=" O VAL A2636 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP A2641 " --> pdb=" O ASN A2638 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER A2642 " --> pdb=" O LEU A2639 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A2644 " --> pdb=" O ASP A2641 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A2645 " --> pdb=" O SER A2642 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A2650 " --> pdb=" O LEU A2647 " (cutoff:3.500A) Processing helix chain 'A' and resid 2654 through 2669 Proline residue: A2659 - end of helix Processing helix chain 'A' and resid 2674 through 2676 No H-bonds generated for 'chain 'A' and resid 2674 through 2676' Processing helix chain 'A' and resid 2679 through 2684 removed outlier: 3.752A pdb=" N LEU A2682 " --> pdb=" O THR A2679 " (cutoff:3.500A) Processing helix chain 'A' and resid 2707 through 2721 Processing helix chain 'B' and resid 6 through 23 Proline residue: B 22 - end of helix Processing helix chain 'B' and resid 33 through 49 removed outlier: 3.573A pdb=" N GLU B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 73 through 97 Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 114 through 125 removed outlier: 6.651A pdb=" N CYS B 124 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 151 through 159 Processing helix chain 'B' and resid 172 through 182 removed outlier: 3.931A pdb=" N GLU B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU B 179 " --> pdb=" O HIS B 175 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 Processing helix chain 'B' and resid 206 through 224 Processing helix chain 'B' and resid 228 through 236 removed outlier: 3.633A pdb=" N TYR B 235 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN B 236 " --> pdb=" O THR B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 256 Processing helix chain 'B' and resid 260 through 276 Proline residue: B 268 - end of helix Processing helix chain 'B' and resid 279 through 284 removed outlier: 3.862A pdb=" N ILE B 284 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 308 removed outlier: 4.023A pdb=" N LYS B 296 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 333 removed outlier: 3.656A pdb=" N THR B 332 " --> pdb=" O CYS B 328 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N TYR B 333 " --> pdb=" O LYS B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 349 removed outlier: 4.113A pdb=" N VAL B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLN B 347 " --> pdb=" O PHE B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 392 through 398 removed outlier: 4.147A pdb=" N CYS B 397 " --> pdb=" O HIS B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 437 through 451 Processing helix chain 'B' and resid 488 through 502 Processing helix chain 'B' and resid 521 through 533 Processing helix chain 'B' and resid 539 through 552 Processing helix chain 'B' and resid 557 through 561 Processing helix chain 'B' and resid 567 through 587 Processing helix chain 'B' and resid 591 through 614 removed outlier: 4.168A pdb=" N THR B 594 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 695 Processing helix chain 'B' and resid 700 through 720 removed outlier: 3.809A pdb=" N ARG B 711 " --> pdb=" O MET B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 731 No H-bonds generated for 'chain 'B' and resid 729 through 731' Processing helix chain 'B' and resid 735 through 746 removed outlier: 4.828A pdb=" N ASN B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 765 Processing helix chain 'B' and resid 771 through 792 Processing helix chain 'B' and resid 831 through 849 removed outlier: 5.023A pdb=" N GLY B 849 " --> pdb=" O CYS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 906 removed outlier: 5.690A pdb=" N HIS B 906 " --> pdb=" O MET B 902 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 922 removed outlier: 3.945A pdb=" N GLN B 912 " --> pdb=" O LYS B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 944 Processing helix chain 'B' and resid 955 through 972 Processing helix chain 'B' and resid 980 through 985 removed outlier: 4.196A pdb=" N GLN B 985 " --> pdb=" O GLU B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1002 Processing helix chain 'B' and resid 1006 through 1024 Processing helix chain 'B' and resid 1035 through 1047 Processing helix chain 'B' and resid 1062 through 1079 removed outlier: 3.769A pdb=" N SER B1078 " --> pdb=" O GLU B1074 " (cutoff:3.500A) Processing helix chain 'B' and resid 1095 through 1118 Processing helix chain 'B' and resid 1135 through 1155 removed outlier: 3.526A pdb=" N LEU B1147 " --> pdb=" O HIS B1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1169 removed outlier: 3.880A pdb=" N ILE B1165 " --> pdb=" O LEU B1161 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY B1166 " --> pdb=" O MET B1162 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU B1167 " --> pdb=" O HIS B1163 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY B1168 " --> pdb=" O SER B1164 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR B1169 " --> pdb=" O ILE B1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1161 through 1169' Processing helix chain 'B' and resid 1173 through 1188 Processing helix chain 'B' and resid 1222 through 1228 Processing helix chain 'B' and resid 1233 through 1248 removed outlier: 4.479A pdb=" N ASP B1237 " --> pdb=" O SER B1234 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA B1240 " --> pdb=" O ASP B1237 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B1243 " --> pdb=" O ALA B1240 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL B1244 " --> pdb=" O ARG B1241 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B1245 " --> pdb=" O VAL B1242 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE B1247 " --> pdb=" O VAL B1244 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B1248 " --> pdb=" O THR B1245 " (cutoff:3.500A) Processing helix chain 'B' and resid 1253 through 1266 Processing helix chain 'B' and resid 1280 through 1309 removed outlier: 6.257A pdb=" N THR B1295 " --> pdb=" O VAL B1291 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N TYR B1296 " --> pdb=" O TYR B1292 " (cutoff:3.500A) Proline residue: B1303 - end of helix removed outlier: 3.520A pdb=" N ILE B1307 " --> pdb=" O PRO B1303 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B1308 " --> pdb=" O LEU B1304 " (cutoff:3.500A) Processing helix chain 'B' and resid 1332 through 1354 removed outlier: 4.518A pdb=" N SER B1354 " --> pdb=" O ILE B1350 " (cutoff:3.500A) Processing helix chain 'B' and resid 1359 through 1375 removed outlier: 3.574A pdb=" N GLN B1374 " --> pdb=" O GLN B1370 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG B1375 " --> pdb=" O VAL B1371 " (cutoff:3.500A) Processing helix chain 'B' and resid 1380 through 1391 removed outlier: 3.618A pdb=" N VAL B1384 " --> pdb=" O SER B1380 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B1391 " --> pdb=" O ALA B1387 " (cutoff:3.500A) Processing helix chain 'B' and resid 1393 through 1398 Processing helix chain 'B' and resid 1412 through 1430 removed outlier: 3.540A pdb=" N LEU B1420 " --> pdb=" O ARG B1416 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B1423 " --> pdb=" O LYS B1419 " (cutoff:3.500A) Processing helix chain 'B' and resid 1441 through 1449 removed outlier: 4.024A pdb=" N ASP B1445 " --> pdb=" O PRO B1442 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS B1448 " --> pdb=" O ASP B1445 " (cutoff:3.500A) Processing helix chain 'B' and resid 1451 through 1461 removed outlier: 3.531A pdb=" N ILE B1461 " --> pdb=" O PHE B1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 1488 through 1491 No H-bonds generated for 'chain 'B' and resid 1488 through 1491' Processing helix chain 'B' and resid 1514 through 1524 removed outlier: 5.217A pdb=" N THR B1520 " --> pdb=" O ASP B1516 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU B1521 " --> pdb=" O LYS B1517 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B1522 " --> pdb=" O MET B1518 " (cutoff:3.500A) Processing helix chain 'B' and resid 1568 through 1570 No H-bonds generated for 'chain 'B' and resid 1568 through 1570' Processing helix chain 'B' and resid 1589 through 1591 No H-bonds generated for 'chain 'B' and resid 1589 through 1591' Processing helix chain 'B' and resid 1596 through 1613 removed outlier: 3.863A pdb=" N LYS B1611 " --> pdb=" O LEU B1607 " (cutoff:3.500A) Proline residue: B1612 - end of helix Processing helix chain 'B' and resid 1629 through 1631 No H-bonds generated for 'chain 'B' and resid 1629 through 1631' Processing helix chain 'B' and resid 1635 through 1642 removed outlier: 3.548A pdb=" N LYS B1640 " --> pdb=" O ASP B1636 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TRP B1641 " --> pdb=" O PHE B1637 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE B1642 " --> pdb=" O LEU B1638 " (cutoff:3.500A) Processing helix chain 'B' and resid 1647 through 1651 Processing helix chain 'B' and resid 1663 through 1671 Processing helix chain 'B' and resid 1675 through 1677 No H-bonds generated for 'chain 'B' and resid 1675 through 1677' Processing helix chain 'B' and resid 1694 through 1696 No H-bonds generated for 'chain 'B' and resid 1694 through 1696' Processing helix chain 'B' and resid 1707 through 1711 Processing helix chain 'B' and resid 1796 through 1814 removed outlier: 3.708A pdb=" N LEU B1812 " --> pdb=" O THR B1808 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B1813 " --> pdb=" O ARG B1809 " (cutoff:3.500A) Processing helix chain 'B' and resid 1830 through 1841 Processing helix chain 'B' and resid 1846 through 1863 removed outlier: 3.547A pdb=" N ASN B1854 " --> pdb=" O SER B1850 " (cutoff:3.500A) Processing helix chain 'B' and resid 1884 through 1897 Processing helix chain 'B' and resid 1902 through 1914 removed outlier: 4.023A pdb=" N GLU B1907 " --> pdb=" O LEU B1903 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B1914 " --> pdb=" O ILE B1910 " (cutoff:3.500A) Processing helix chain 'B' and resid 1918 through 1928 removed outlier: 3.770A pdb=" N LEU B1923 " --> pdb=" O GLU B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1931 through 1938 removed outlier: 3.840A pdb=" N VAL B1936 " --> pdb=" O SER B1933 " (cutoff:3.500A) Processing helix chain 'B' and resid 1945 through 1963 Processing helix chain 'B' and resid 1968 through 1974 Processing helix chain 'B' and resid 1976 through 1979 No H-bonds generated for 'chain 'B' and resid 1976 through 1979' Processing helix chain 'B' and resid 1985 through 1998 removed outlier: 3.781A pdb=" N SER B1992 " --> pdb=" O VAL B1988 " (cutoff:3.500A) Processing helix chain 'B' and resid 2005 through 2020 removed outlier: 4.020A pdb=" N VAL B2015 " --> pdb=" O ALA B2011 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA B2016 " --> pdb=" O ASP B2012 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY B2020 " --> pdb=" O ALA B2016 " (cutoff:3.500A) Processing helix chain 'B' and resid 2023 through 2041 removed outlier: 3.962A pdb=" N THR B2040 " --> pdb=" O ILE B2036 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N CYS B2041 " --> pdb=" O ILE B2037 " (cutoff:3.500A) Processing helix chain 'B' and resid 2052 through 2066 removed outlier: 4.366A pdb=" N ASP B2055 " --> pdb=" O LEU B2052 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP B2056 " --> pdb=" O MET B2053 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE B2059 " --> pdb=" O ASP B2056 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU B2060 " --> pdb=" O ILE B2057 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B2066 " --> pdb=" O TYR B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2079 through 2089 Processing helix chain 'B' and resid 2095 through 2113 Processing helix chain 'B' and resid 2122 through 2135 Processing helix chain 'B' and resid 2138 through 2143 Processing helix chain 'B' and resid 2152 through 2157 removed outlier: 3.892A pdb=" N PHE B2157 " --> pdb=" O ALA B2153 " (cutoff:3.500A) Processing helix chain 'B' and resid 2178 through 2198 removed outlier: 4.469A pdb=" N ASP B2198 " --> pdb=" O ALA B2194 " (cutoff:3.500A) Processing helix chain 'B' and resid 2204 through 2216 removed outlier: 3.811A pdb=" N PHE B2215 " --> pdb=" O LEU B2211 " (cutoff:3.500A) Processing helix chain 'B' and resid 2224 through 2234 Processing helix chain 'B' and resid 2240 through 2259 Processing helix chain 'B' and resid 2264 through 2280 Processing helix chain 'B' and resid 2289 through 2304 removed outlier: 4.585A pdb=" N LEU B2294 " --> pdb=" O HIS B2291 " (cutoff:3.500A) Processing helix chain 'B' and resid 2307 through 2326 Processing helix chain 'B' and resid 2335 through 2342 removed outlier: 3.808A pdb=" N PHE B2339 " --> pdb=" O PRO B2335 " (cutoff:3.500A) Processing helix chain 'B' and resid 2347 through 2357 Processing helix chain 'B' and resid 2365 through 2378 removed outlier: 4.471A pdb=" N LYS B2375 " --> pdb=" O GLY B2371 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY B2376 " --> pdb=" O HIS B2372 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR B2377 " --> pdb=" O LEU B2373 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG B2378 " --> pdb=" O LEU B2374 " (cutoff:3.500A) Processing helix chain 'B' and resid 2382 through 2402 Processing helix chain 'B' and resid 2413 through 2422 removed outlier: 4.254A pdb=" N ALA B2416 " --> pdb=" O GLN B2413 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B2417 " --> pdb=" O SER B2414 " (cutoff:3.500A) Processing helix chain 'B' and resid 2592 through 2608 removed outlier: 3.505A pdb=" N LEU B2602 " --> pdb=" O LEU B2598 " (cutoff:3.500A) Processing helix chain 'B' and resid 2612 through 2628 removed outlier: 3.872A pdb=" N GLU B2624 " --> pdb=" O GLU B2620 " (cutoff:3.500A) Processing helix chain 'B' and resid 2633 through 2636 Processing helix chain 'B' and resid 2638 through 2650 removed outlier: 5.601A pdb=" N SER B2642 " --> pdb=" O LEU B2639 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS B2643 " --> pdb=" O LEU B2640 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE B2644 " --> pdb=" O ASP B2641 " (cutoff:3.500A) Processing helix chain 'B' and resid 2654 through 2669 Proline residue: B2659 - end of helix Processing helix chain 'B' and resid 2674 through 2676 No H-bonds generated for 'chain 'B' and resid 2674 through 2676' Processing helix chain 'B' and resid 2681 through 2683 No H-bonds generated for 'chain 'B' and resid 2681 through 2683' Processing helix chain 'B' and resid 2707 through 2721 Processing sheet with id= A, first strand: chain 'A' and resid 1584 through 1588 removed outlier: 6.981A pdb=" N GLU A1619 " --> pdb=" O PHE A1585 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N TYR A1587 " --> pdb=" O GLU A1619 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL A1621 " --> pdb=" O TYR A1587 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE A1620 " --> pdb=" O SER A1654 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A1656 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A1622 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ILE A1658 " --> pdb=" O VAL A1622 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1717 through 1719 Processing sheet with id= C, first strand: chain 'A' and resid 1730 through 1732 removed outlier: 4.208A pdb=" N THR A1790 " --> pdb=" O LEU A1725 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1749 through 1751 Processing sheet with id= E, first strand: chain 'B' and resid 1572 through 1574 removed outlier: 7.607A pdb=" N ILE B1620 " --> pdb=" O SER B1654 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B1656 " --> pdb=" O ILE B1620 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL B1622 " --> pdb=" O VAL B1656 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE B1658 " --> pdb=" O VAL B1622 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1717 through 1719 Processing sheet with id= G, first strand: chain 'B' and resid 1730 through 1732 removed outlier: 4.619A pdb=" N THR B1790 " --> pdb=" O LEU B1725 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN B1777 " --> pdb=" O ASP B1774 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR B1779 " --> pdb=" O LEU B1772 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU B1772 " --> pdb=" O THR B1779 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 1749 through 1751 2003 hydrogen bonds defined for protein. 5511 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: 16.65 Time building geometry restraints manager: 14.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 11649 1.35 - 1.50: 9703 1.50 - 1.65: 15276 1.65 - 1.79: 162 1.79 - 1.94: 198 Bond restraints: 36988 Sorted by residual: bond pdb=" PG GSP A2901 " pdb=" S1G GSP A2901 " ideal model delta sigma weight residual 1.700 1.943 -0.243 2.00e-02 2.50e+03 1.47e+02 bond pdb=" CA SER A1540 " pdb=" CB SER A1540 " ideal model delta sigma weight residual 1.530 1.471 0.059 1.54e-02 4.22e+03 1.45e+01 bond pdb=" C ARG B1441 " pdb=" N PRO B1442 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.19e-02 7.06e+03 1.25e+01 bond pdb=" CA SER A1545 " pdb=" CB SER A1545 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.56e-02 4.11e+03 1.22e+01 bond pdb=" C PRO A1527 " pdb=" O PRO A1527 " ideal model delta sigma weight residual 1.240 1.205 0.036 1.12e-02 7.97e+03 1.03e+01 ... (remaining 36983 not shown) Histogram of bond angle deviations from ideal: 91.99 - 100.74: 62 100.74 - 109.49: 3757 109.49 - 118.24: 25527 118.24 - 126.99: 20323 126.99 - 135.73: 478 Bond angle restraints: 50147 Sorted by residual: angle pdb=" N PRO A1527 " pdb=" CA PRO A1527 " pdb=" C PRO A1527 " ideal model delta sigma weight residual 110.70 98.15 12.55 1.22e+00 6.72e-01 1.06e+02 angle pdb=" N LYS A1517 " pdb=" CA LYS A1517 " pdb=" C LYS A1517 " ideal model delta sigma weight residual 111.28 104.73 6.55 1.09e+00 8.42e-01 3.61e+01 angle pdb=" C ASN A1542 " pdb=" CA ASN A1542 " pdb=" CB ASN A1542 " ideal model delta sigma weight residual 110.37 120.13 -9.76 1.64e+00 3.72e-01 3.55e+01 angle pdb=" C PRO A1514 " pdb=" CA PRO A1514 " pdb=" CB PRO A1514 " ideal model delta sigma weight residual 113.06 104.03 9.03 1.59e+00 3.96e-01 3.23e+01 angle pdb=" N LYS A1062 " pdb=" CA LYS A1062 " pdb=" C LYS A1062 " ideal model delta sigma weight residual 111.71 105.34 6.37 1.15e+00 7.56e-01 3.07e+01 ... (remaining 50142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.97: 21735 29.97 - 59.94: 608 59.94 - 89.91: 62 89.91 - 119.89: 2 119.89 - 149.86: 1 Dihedral angle restraints: 22408 sinusoidal: 8972 harmonic: 13436 Sorted by residual: dihedral pdb=" CA ASP B2705 " pdb=" C ASP B2705 " pdb=" N TYR B2706 " pdb=" CA TYR B2706 " ideal model delta harmonic sigma weight residual 180.00 -140.45 -39.55 0 5.00e+00 4.00e-02 6.26e+01 dihedral pdb=" CA ASP B1248 " pdb=" C ASP B1248 " pdb=" N SER B1249 " pdb=" CA SER B1249 " ideal model delta harmonic sigma weight residual 180.00 -146.48 -33.52 0 5.00e+00 4.00e-02 4.49e+01 dihedral pdb=" O3B GSP A2901 " pdb=" O3A GSP A2901 " pdb=" PB GSP A2901 " pdb=" PA GSP A2901 " ideal model delta sinusoidal sigma weight residual 93.55 -56.31 149.86 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 22405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 5001 0.072 - 0.143: 768 0.143 - 0.215: 72 0.215 - 0.287: 19 0.287 - 0.358: 9 Chirality restraints: 5869 Sorted by residual: chirality pdb=" CB ILE B 237 " pdb=" CA ILE B 237 " pdb=" CG1 ILE B 237 " pdb=" CG2 ILE B 237 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA VAL A1061 " pdb=" N VAL A1061 " pdb=" C VAL A1061 " pdb=" CB VAL A1061 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA TYR A 235 " pdb=" N TYR A 235 " pdb=" C TYR A 235 " pdb=" CB TYR A 235 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 5866 not shown) Planarity restraints: 6299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B2705 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C ASP B2705 " 0.077 2.00e-02 2.50e+03 pdb=" O ASP B2705 " -0.029 2.00e-02 2.50e+03 pdb=" N TYR B2706 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1048 " -0.027 2.00e-02 2.50e+03 2.50e-02 1.57e+01 pdb=" CG TRP B1048 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP B1048 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP B1048 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1048 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B1048 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B1048 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1048 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1048 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP B1048 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A2633 " -0.059 5.00e-02 4.00e+02 9.05e-02 1.31e+01 pdb=" N PRO A2634 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO A2634 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A2634 " -0.050 5.00e-02 4.00e+02 ... (remaining 6296 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3487 2.74 - 3.28: 39168 3.28 - 3.82: 62430 3.82 - 4.36: 72970 4.36 - 4.90: 119213 Nonbonded interactions: 297268 Sorted by model distance: nonbonded pdb=" O MET A2010 " pdb=" OG1 THR A2013 " model vdw 2.201 2.440 nonbonded pdb=" O MET A2064 " pdb=" OG SER A2068 " model vdw 2.206 2.440 nonbonded pdb=" NH2 ARG A 385 " pdb=" O LEU A 423 " model vdw 2.219 2.520 nonbonded pdb=" O LEU A1340 " pdb=" OG1 THR A1343 " model vdw 2.230 2.440 nonbonded pdb=" OH TYR B 80 " pdb=" OE2 GLU B 133 " model vdw 2.247 2.440 ... (remaining 297263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 1050 or (resid 1061 through 1062 and (name N or \ name CA or name C or name O or name CB )) or resid 1063 through 1190 or resid 12 \ 20 through 1224 or (resid 1225 and (name N or name CA or name C or name O or nam \ e CB or name CG or name SD )) or resid 1226 through 1228 or (resid 1229 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1230 through 1262 or ( \ resid 1263 and (name N or name CA or name C or name O or name CB )) or resid 126 \ 4 through 1273 or (resid 1274 and (name N or name CA or name C or name O or name \ CB )) or resid 1275 through 1373 or (resid 1374 and (name N or name CA or name \ C or name O or name CB )) or resid 1375 through 1464 or resid 1487 or (resid 148 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 1489 through \ 1492 or (resid 1493 and (name N or name CA or name C or name O or name CB )) or \ resid 1494 or (resid 1495 through 1496 and (name N or name CA or name C or name \ O or name CB )) or resid 1497 through 1501 or resid 1513 through 1514 or (resid \ 1515 and (name N or name CA or name C or name O or name CB )) or resid 1516 thr \ ough 1520 or (resid 1521 through 1523 and (name N or name CA or name C or name O \ or name CB )) or resid 1524 through 1525 or (resid 1567 and (name N or name CA \ or name C or name O or name CB )) or resid 1568 or (resid 1569 and (name N or na \ me CA or name C or name O or name CB )) or resid 1570 through 1816 or resid 1829 \ through 2723)) selection = (chain 'B' and (resid 5 through 1271 or (resid 1272 and (name N or name CA or na \ me C or name O or name CB )) or resid 1273 through 1332 or (resid 1333 and (name \ N or name CA or name C or name O or name CB )) or resid 1334 through 2723)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 29.620 Check model and map are aligned: 0.540 Set scattering table: 0.310 Process input model: 94.710 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.180 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.006 0.243 36988 Z= 0.382 Angle : 1.024 15.113 50147 Z= 0.558 Chirality : 0.054 0.358 5869 Planarity : 0.007 0.090 6299 Dihedral : 13.988 149.857 13614 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 0.27 % Allowed : 0.64 % Favored : 99.09 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 4493 helix: -0.06 (0.09), residues: 3005 sheet: -0.74 (0.44), residues: 114 loop : -0.89 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP B1048 HIS 0.008 0.001 HIS A1922 PHE 0.040 0.003 PHE B1993 TYR 0.029 0.002 TYR A1659 ARG 0.009 0.001 ARG B 764 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 250 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 775 GLU cc_start: 0.8261 (tp30) cc_final: 0.7814 (tp30) REVERT: A 1342 MET cc_start: 0.8758 (tpp) cc_final: 0.8415 (tpp) REVERT: A 1440 MET cc_start: 0.8750 (mmp) cc_final: 0.8308 (mmm) REVERT: A 1518 MET cc_start: 0.9327 (ppp) cc_final: 0.8972 (ppp) REVERT: A 1816 ASP cc_start: 0.8212 (p0) cc_final: 0.7981 (p0) REVERT: A 1968 TYR cc_start: 0.7861 (t80) cc_final: 0.7347 (t80) REVERT: A 1972 GLN cc_start: 0.8275 (mt0) cc_final: 0.7978 (mt0) REVERT: A 2012 ASP cc_start: 0.8510 (m-30) cc_final: 0.8244 (t70) REVERT: A 2192 MET cc_start: 0.8671 (ttt) cc_final: 0.7658 (tpp) REVERT: A 2196 MET cc_start: 0.4581 (mmm) cc_final: 0.3345 (mmm) REVERT: A 2295 PHE cc_start: 0.8806 (t80) cc_final: 0.8565 (t80) REVERT: A 2296 TRP cc_start: 0.7741 (m100) cc_final: 0.6528 (m100) REVERT: A 2310 TYR cc_start: 0.8716 (t80) cc_final: 0.8416 (t80) REVERT: A 2340 MET cc_start: 0.3306 (mmm) cc_final: 0.2926 (mmm) REVERT: B 496 MET cc_start: 0.9586 (mmp) cc_final: 0.9175 (mmm) REVERT: B 840 MET cc_start: 0.7938 (mmt) cc_final: 0.7621 (mmm) REVERT: B 895 MET cc_start: 0.9556 (mmm) cc_final: 0.9290 (mtm) REVERT: B 1005 MET cc_start: 0.9144 (mpp) cc_final: 0.8767 (mpp) REVERT: B 1022 MET cc_start: 0.9718 (ppp) cc_final: 0.9222 (ppp) REVERT: B 1041 MET cc_start: 0.9658 (mmp) cc_final: 0.9132 (mmm) REVERT: B 1180 MET cc_start: 0.9388 (mmm) cc_final: 0.9097 (mmm) REVERT: B 1993 PHE cc_start: 0.9245 (m-10) cc_final: 0.9026 (m-80) REVERT: B 2064 MET cc_start: 0.9168 (mmm) cc_final: 0.8727 (mtp) outliers start: 11 outliers final: 6 residues processed: 261 average time/residue: 0.4413 time to fit residues: 200.4163 Evaluate side-chains 203 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 197 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 383 optimal weight: 0.9980 chunk 344 optimal weight: 8.9990 chunk 190 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 355 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 412 optimal weight: 0.9980 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN A 916 ASN ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2102 HIS ** A2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 310 HIS ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1039 ASN ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1439 HIS ** B1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2220 ASN B2352 GLN ** B2400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36988 Z= 0.180 Angle : 0.609 9.845 50147 Z= 0.312 Chirality : 0.039 0.196 5869 Planarity : 0.004 0.055 6299 Dihedral : 6.247 142.228 4844 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.80 % Favored : 97.17 % Rotamer: Outliers : 0.57 % Allowed : 6.07 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.12), residues: 4493 helix: 0.75 (0.09), residues: 3019 sheet: -0.86 (0.45), residues: 112 loop : -0.60 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1048 HIS 0.006 0.001 HIS B 310 PHE 0.017 0.001 PHE A1275 TYR 0.034 0.001 TYR B2706 ARG 0.005 0.000 ARG A1204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 231 time to evaluate : 3.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 MET cc_start: 0.8269 (tpp) cc_final: 0.7161 (tpp) REVERT: A 775 GLU cc_start: 0.8259 (tp30) cc_final: 0.7803 (tp30) REVERT: A 1022 MET cc_start: 0.8909 (tmm) cc_final: 0.8580 (tmm) REVERT: A 1149 MET cc_start: 0.8877 (mmm) cc_final: 0.8493 (mmm) REVERT: A 1180 MET cc_start: 0.9196 (mmm) cc_final: 0.8729 (tmm) REVERT: A 1342 MET cc_start: 0.8860 (tpp) cc_final: 0.8467 (tpp) REVERT: A 1397 ILE cc_start: 0.9381 (mm) cc_final: 0.9059 (tt) REVERT: A 1440 MET cc_start: 0.8717 (mmp) cc_final: 0.8140 (mmm) REVERT: A 1518 MET cc_start: 0.9120 (ppp) cc_final: 0.8774 (ppp) REVERT: A 1816 ASP cc_start: 0.8232 (p0) cc_final: 0.7993 (p0) REVERT: A 1926 GLU cc_start: 0.8212 (tp30) cc_final: 0.7913 (tp30) REVERT: A 1968 TYR cc_start: 0.8023 (t80) cc_final: 0.7482 (t80) REVERT: A 2012 ASP cc_start: 0.8504 (m-30) cc_final: 0.8231 (t70) REVERT: A 2196 MET cc_start: 0.3904 (mmm) cc_final: 0.3697 (mmm) REVERT: A 2295 PHE cc_start: 0.8839 (t80) cc_final: 0.8613 (t80) REVERT: A 2296 TRP cc_start: 0.7819 (m100) cc_final: 0.6739 (m100) REVERT: A 2310 TYR cc_start: 0.8748 (t80) cc_final: 0.8480 (t80) REVERT: A 2340 MET cc_start: 0.3444 (mmm) cc_final: 0.3059 (mmm) REVERT: B 119 HIS cc_start: 0.8331 (t-90) cc_final: 0.7897 (t70) REVERT: B 376 MET cc_start: 0.9568 (mpp) cc_final: 0.9264 (mpp) REVERT: B 496 MET cc_start: 0.9578 (mmp) cc_final: 0.9285 (mmm) REVERT: B 707 MET cc_start: 0.9067 (ttt) cc_final: 0.8761 (mmm) REVERT: B 739 MET cc_start: 0.9482 (tpp) cc_final: 0.9245 (mmm) REVERT: B 895 MET cc_start: 0.9578 (mmm) cc_final: 0.9242 (mtm) REVERT: B 932 MET cc_start: 0.8411 (pmm) cc_final: 0.7915 (pmm) REVERT: B 968 MET cc_start: 0.9865 (mmt) cc_final: 0.9610 (mmm) REVERT: B 1005 MET cc_start: 0.9094 (mpp) cc_final: 0.8714 (mpp) REVERT: B 1022 MET cc_start: 0.9647 (ppp) cc_final: 0.9248 (ppp) REVERT: B 1023 MET cc_start: 0.8796 (mmm) cc_final: 0.8403 (mmm) REVERT: B 1035 MET cc_start: 0.8680 (pmm) cc_final: 0.8365 (pmm) REVERT: B 1041 MET cc_start: 0.9634 (mmp) cc_final: 0.9018 (mmm) REVERT: B 1180 MET cc_start: 0.9414 (mmm) cc_final: 0.9134 (mmm) REVERT: B 1518 MET cc_start: -0.4344 (pmm) cc_final: -0.4581 (pmm) REVERT: B 2064 MET cc_start: 0.9166 (mmm) cc_final: 0.8815 (mtp) outliers start: 23 outliers final: 11 residues processed: 243 average time/residue: 0.4345 time to fit residues: 183.5841 Evaluate side-chains 215 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 204 time to evaluate : 4.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1987 ASP Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 1440 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 229 optimal weight: 40.0000 chunk 127 optimal weight: 2.9990 chunk 343 optimal weight: 7.9990 chunk 280 optimal weight: 0.0370 chunk 113 optimal weight: 3.9990 chunk 413 optimal weight: 0.0170 chunk 446 optimal weight: 0.0050 chunk 367 optimal weight: 20.0000 chunk 409 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 331 optimal weight: 8.9990 overall best weight: 1.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 HIS ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 310 HIS B 315 GLN ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2220 ASN ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36988 Z= 0.187 Angle : 0.578 9.201 50147 Z= 0.294 Chirality : 0.039 0.275 5869 Planarity : 0.004 0.051 6299 Dihedral : 5.815 137.191 4842 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 1.01 % Allowed : 9.07 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.13), residues: 4493 helix: 1.13 (0.09), residues: 3034 sheet: -0.93 (0.45), residues: 106 loop : -0.57 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1314 HIS 0.005 0.001 HIS A2084 PHE 0.018 0.001 PHE B1905 TYR 0.028 0.001 TYR B2706 ARG 0.004 0.000 ARG A1204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 226 time to evaluate : 4.092 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 108 MET cc_start: 0.9198 (ppp) cc_final: 0.8894 (ppp) REVERT: A 236 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8231 (mp10) REVERT: A 349 MET cc_start: 0.8340 (tpp) cc_final: 0.7320 (tpp) REVERT: A 760 MET cc_start: 0.9183 (mmt) cc_final: 0.8402 (mmt) REVERT: A 775 GLU cc_start: 0.8320 (tp30) cc_final: 0.7858 (tp30) REVERT: A 1149 MET cc_start: 0.8919 (mmm) cc_final: 0.8627 (mmm) REVERT: A 1180 MET cc_start: 0.9179 (mmm) cc_final: 0.8736 (mmm) REVERT: A 1342 MET cc_start: 0.8945 (tpp) cc_final: 0.8563 (tpp) REVERT: A 1440 MET cc_start: 0.8729 (mmp) cc_final: 0.8153 (mmm) REVERT: A 1518 MET cc_start: 0.9032 (ppp) cc_final: 0.8663 (ppp) REVERT: A 1791 PHE cc_start: 0.7516 (m-80) cc_final: 0.7147 (m-80) REVERT: A 1816 ASP cc_start: 0.8235 (p0) cc_final: 0.7993 (p0) REVERT: A 1926 GLU cc_start: 0.8191 (tp30) cc_final: 0.7958 (tp30) REVERT: A 1968 TYR cc_start: 0.8199 (t80) cc_final: 0.7560 (t80) REVERT: A 2271 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7827 (mm-30) REVERT: A 2296 TRP cc_start: 0.7872 (m100) cc_final: 0.6827 (m100) REVERT: A 2310 TYR cc_start: 0.8747 (t80) cc_final: 0.8517 (t80) REVERT: A 2340 MET cc_start: 0.3513 (mmm) cc_final: 0.3064 (mmm) REVERT: B 119 HIS cc_start: 0.8253 (t-90) cc_final: 0.7849 (t70) REVERT: B 376 MET cc_start: 0.9558 (mpp) cc_final: 0.9225 (mpp) REVERT: B 496 MET cc_start: 0.9563 (mmp) cc_final: 0.9196 (mmm) REVERT: B 707 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8822 (mmm) REVERT: B 739 MET cc_start: 0.9479 (tpp) cc_final: 0.9200 (mmm) REVERT: B 760 MET cc_start: 0.6601 (mmt) cc_final: 0.6310 (mmt) REVERT: B 968 MET cc_start: 0.9866 (mmt) cc_final: 0.9533 (mmm) REVERT: B 1005 MET cc_start: 0.9033 (mpp) cc_final: 0.8621 (mpp) REVERT: B 1022 MET cc_start: 0.9693 (ppp) cc_final: 0.9220 (ppp) REVERT: B 1023 MET cc_start: 0.9042 (mmm) cc_final: 0.8590 (mmm) REVERT: B 1035 MET cc_start: 0.8601 (pmm) cc_final: 0.8241 (pmm) REVERT: B 1041 MET cc_start: 0.9655 (mmp) cc_final: 0.9079 (mmm) REVERT: B 1050 MET cc_start: 0.8824 (tpt) cc_final: 0.8564 (mmp) REVERT: B 1180 MET cc_start: 0.9409 (mmm) cc_final: 0.9155 (mmm) REVERT: B 1260 MET cc_start: -0.2537 (OUTLIER) cc_final: -0.4305 (mtm) REVERT: B 1927 TYR cc_start: 0.8787 (p90) cc_final: 0.8419 (p90) REVERT: B 2064 MET cc_start: 0.9208 (mmm) cc_final: 0.8884 (mtp) outliers start: 41 outliers final: 18 residues processed: 252 average time/residue: 0.4501 time to fit residues: 198.3445 Evaluate side-chains 228 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 4.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 277 CYS Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1780 LEU Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2033 MET Chi-restraints excluded: chain A residue 2057 ILE Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2271 GLU Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 1260 MET Chi-restraints excluded: chain B residue 1440 MET Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1957 LEU Chi-restraints excluded: chain B residue 1999 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 408 optimal weight: 3.9990 chunk 310 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 277 optimal weight: 0.0370 chunk 414 optimal weight: 4.9990 chunk 438 optimal weight: 0.9990 chunk 216 optimal weight: 7.9990 chunk 392 optimal weight: 2.9990 chunk 118 optimal weight: 0.0020 overall best weight: 1.6072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN A 589 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1251 HIS ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2352 GLN ** B2400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36988 Z= 0.215 Angle : 0.584 12.679 50147 Z= 0.296 Chirality : 0.039 0.192 5869 Planarity : 0.004 0.049 6299 Dihedral : 5.595 129.009 4842 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.34 % Favored : 96.64 % Rotamer: Outliers : 1.23 % Allowed : 10.99 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.13), residues: 4493 helix: 1.30 (0.10), residues: 3031 sheet: -0.89 (0.45), residues: 106 loop : -0.43 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1314 HIS 0.005 0.001 HIS A1922 PHE 0.019 0.001 PHE A1389 TYR 0.025 0.001 TYR B2706 ARG 0.004 0.000 ARG A1204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 212 time to evaluate : 4.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.9223 (ppp) cc_final: 0.8909 (ppp) REVERT: A 236 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: A 349 MET cc_start: 0.8362 (tpp) cc_final: 0.7358 (tpp) REVERT: A 775 GLU cc_start: 0.8340 (tp30) cc_final: 0.7869 (tp30) REVERT: A 968 MET cc_start: 0.8764 (mpp) cc_final: 0.8551 (mpp) REVERT: A 1050 MET cc_start: 0.8057 (mmm) cc_final: 0.7843 (tpt) REVERT: A 1101 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8683 (mm110) REVERT: A 1149 MET cc_start: 0.8923 (mmm) cc_final: 0.8551 (mmm) REVERT: A 1180 MET cc_start: 0.9155 (mmm) cc_final: 0.8568 (mmm) REVERT: A 1342 MET cc_start: 0.8959 (tpp) cc_final: 0.8559 (tpp) REVERT: A 1440 MET cc_start: 0.8692 (mmp) cc_final: 0.8291 (mmp) REVERT: A 1518 MET cc_start: 0.8980 (ppp) cc_final: 0.8682 (ppp) REVERT: A 1791 PHE cc_start: 0.7490 (m-80) cc_final: 0.7084 (m-80) REVERT: A 1816 ASP cc_start: 0.8082 (p0) cc_final: 0.7823 (p0) REVERT: A 1926 GLU cc_start: 0.8255 (tp30) cc_final: 0.8029 (tp30) REVERT: A 2064 MET cc_start: 0.7137 (mpp) cc_final: 0.6602 (mpp) REVERT: A 2296 TRP cc_start: 0.7386 (m100) cc_final: 0.6910 (m100) REVERT: A 2310 TYR cc_start: 0.8751 (t80) cc_final: 0.8526 (t80) REVERT: A 2340 MET cc_start: 0.3716 (mmm) cc_final: 0.3239 (mmm) REVERT: B 108 MET cc_start: 0.9600 (mmm) cc_final: 0.9341 (ppp) REVERT: B 119 HIS cc_start: 0.8264 (t-90) cc_final: 0.7826 (t70) REVERT: B 376 MET cc_start: 0.9545 (mpp) cc_final: 0.9196 (mpp) REVERT: B 496 MET cc_start: 0.9631 (mmp) cc_final: 0.9280 (mmm) REVERT: B 707 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8844 (mmm) REVERT: B 715 GLU cc_start: 0.9497 (OUTLIER) cc_final: 0.9291 (mp0) REVERT: B 739 MET cc_start: 0.9463 (tpp) cc_final: 0.9190 (mmm) REVERT: B 760 MET cc_start: 0.6710 (mmt) cc_final: 0.6158 (mmt) REVERT: B 968 MET cc_start: 0.9854 (mmt) cc_final: 0.9525 (mmm) REVERT: B 1005 MET cc_start: 0.9019 (mpp) cc_final: 0.8605 (mpp) REVERT: B 1022 MET cc_start: 0.9698 (ppp) cc_final: 0.9209 (ppp) REVERT: B 1023 MET cc_start: 0.9125 (mmm) cc_final: 0.8686 (mmm) REVERT: B 1041 MET cc_start: 0.9667 (mmp) cc_final: 0.9075 (mmm) REVERT: B 1102 LEU cc_start: 0.9213 (mt) cc_final: 0.8870 (tp) REVERT: B 1180 MET cc_start: 0.9410 (mmm) cc_final: 0.9161 (mmm) REVERT: B 1927 TYR cc_start: 0.8854 (p90) cc_final: 0.8570 (p90) REVERT: B 2064 MET cc_start: 0.9220 (mmm) cc_final: 0.8917 (mtp) outliers start: 50 outliers final: 33 residues processed: 245 average time/residue: 0.4410 time to fit residues: 186.0805 Evaluate side-chains 241 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1063 CYS Chi-restraints excluded: chain A residue 1101 GLN Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1928 MET Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 1987 ASP Chi-restraints excluded: chain A residue 2033 MET Chi-restraints excluded: chain A residue 2057 ILE Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2287 ASP Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1250 ARG Chi-restraints excluded: chain B residue 1440 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1999 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 365 optimal weight: 50.0000 chunk 249 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 326 optimal weight: 0.8980 chunk 181 optimal weight: 0.7980 chunk 374 optimal weight: 3.9990 chunk 303 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 224 optimal weight: 9.9990 chunk 393 optimal weight: 3.9990 chunk 110 optimal weight: 0.0040 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2352 GLN ** B2400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36988 Z= 0.243 Angle : 0.593 9.733 50147 Z= 0.301 Chirality : 0.039 0.292 5869 Planarity : 0.004 0.048 6299 Dihedral : 5.429 116.200 4841 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 1.84 % Allowed : 12.10 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.13), residues: 4493 helix: 1.35 (0.10), residues: 3030 sheet: -0.87 (0.44), residues: 110 loop : -0.38 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A1314 HIS 0.006 0.001 HIS A1922 PHE 0.034 0.001 PHE B 71 TYR 0.023 0.001 TYR B2706 ARG 0.005 0.000 ARG A1204 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 207 time to evaluate : 4.294 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 108 MET cc_start: 0.9250 (ppp) cc_final: 0.8973 (ppp) REVERT: A 236 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8292 (mp10) REVERT: A 349 MET cc_start: 0.8339 (tpp) cc_final: 0.7818 (tpt) REVERT: A 590 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7917 (mmm) REVERT: A 760 MET cc_start: 0.9275 (mmt) cc_final: 0.8839 (mmt) REVERT: A 775 GLU cc_start: 0.8358 (tp30) cc_final: 0.7888 (tp30) REVERT: A 964 THR cc_start: 0.9610 (OUTLIER) cc_final: 0.9221 (p) REVERT: A 968 MET cc_start: 0.8788 (mpp) cc_final: 0.8520 (mpp) REVERT: A 1149 MET cc_start: 0.8967 (mmm) cc_final: 0.8701 (mmm) REVERT: A 1342 MET cc_start: 0.8972 (tpp) cc_final: 0.8562 (tpp) REVERT: A 1440 MET cc_start: 0.8674 (mmp) cc_final: 0.8141 (mmm) REVERT: A 2104 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9077 (pp) REVERT: A 2192 MET cc_start: 0.8341 (ttt) cc_final: 0.7886 (ttt) REVERT: A 2196 MET cc_start: 0.4511 (mmm) cc_final: 0.3966 (mmm) REVERT: A 2296 TRP cc_start: 0.7412 (m100) cc_final: 0.7048 (m100) REVERT: A 2310 TYR cc_start: 0.8731 (t80) cc_final: 0.8508 (t80) REVERT: A 2340 MET cc_start: 0.3802 (mmm) cc_final: 0.3322 (mmm) REVERT: B 108 MET cc_start: 0.9616 (mmm) cc_final: 0.9373 (ppp) REVERT: B 119 HIS cc_start: 0.8324 (t-90) cc_final: 0.7956 (t-170) REVERT: B 143 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8949 (t80) REVERT: B 376 MET cc_start: 0.9541 (mpp) cc_final: 0.9174 (mpp) REVERT: B 496 MET cc_start: 0.9669 (mmp) cc_final: 0.9318 (mmm) REVERT: B 707 MET cc_start: 0.9086 (OUTLIER) cc_final: 0.8847 (mmm) REVERT: B 715 GLU cc_start: 0.9499 (OUTLIER) cc_final: 0.9295 (mp0) REVERT: B 739 MET cc_start: 0.9451 (tpp) cc_final: 0.9159 (mmm) REVERT: B 760 MET cc_start: 0.6591 (mmt) cc_final: 0.6292 (mmt) REVERT: B 932 MET cc_start: 0.9017 (ptt) cc_final: 0.8287 (pmm) REVERT: B 968 MET cc_start: 0.9850 (mmt) cc_final: 0.9523 (mmm) REVERT: B 1005 MET cc_start: 0.9012 (mpp) cc_final: 0.8601 (mpp) REVERT: B 1022 MET cc_start: 0.9703 (ppp) cc_final: 0.9182 (ppp) REVERT: B 1023 MET cc_start: 0.9208 (mmm) cc_final: 0.8775 (mmm) REVERT: B 1041 MET cc_start: 0.9665 (mmp) cc_final: 0.9058 (mmm) REVERT: B 1102 LEU cc_start: 0.9236 (mt) cc_final: 0.8891 (tp) REVERT: B 1180 MET cc_start: 0.9383 (mmm) cc_final: 0.9132 (mmm) REVERT: B 1927 TYR cc_start: 0.8892 (p90) cc_final: 0.8634 (p90) REVERT: B 1957 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9513 (mm) REVERT: B 2064 MET cc_start: 0.9225 (mmm) cc_final: 0.8958 (mtp) outliers start: 75 outliers final: 45 residues processed: 260 average time/residue: 0.4482 time to fit residues: 201.3021 Evaluate side-chains 252 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 199 time to evaluate : 4.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 590 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1194 ASP Chi-restraints excluded: chain A residue 1215 MET Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1871 LEU Chi-restraints excluded: chain A residue 1890 ILE Chi-restraints excluded: chain A residue 1928 MET Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 1987 ASP Chi-restraints excluded: chain A residue 2033 MET Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2057 ILE Chi-restraints excluded: chain A residue 2070 ASN Chi-restraints excluded: chain A residue 2104 LEU Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2201 THR Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain A residue 2287 ASP Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1250 ARG Chi-restraints excluded: chain B residue 1440 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1942 ASN Chi-restraints excluded: chain B residue 1957 LEU Chi-restraints excluded: chain B residue 1999 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 147 optimal weight: 0.8980 chunk 395 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 439 optimal weight: 0.0050 chunk 364 optimal weight: 0.7980 chunk 203 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 230 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 GLN ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 36988 Z= 0.149 Angle : 0.561 9.985 50147 Z= 0.281 Chirality : 0.038 0.287 5869 Planarity : 0.004 0.048 6299 Dihedral : 5.141 95.913 4840 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.27 % Favored : 96.71 % Rotamer: Outliers : 1.43 % Allowed : 13.28 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4493 helix: 1.50 (0.10), residues: 3028 sheet: -0.60 (0.46), residues: 108 loop : -0.40 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A1314 HIS 0.004 0.001 HIS A1793 PHE 0.014 0.001 PHE B1993 TYR 0.025 0.001 TYR A1927 ARG 0.003 0.000 ARG B1807 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 218 time to evaluate : 4.218 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: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7670 (ptt) cc_final: 0.7458 (ppp) REVERT: A 108 MET cc_start: 0.9246 (ppp) cc_final: 0.9013 (ppp) REVERT: A 236 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8254 (mp10) REVERT: A 349 MET cc_start: 0.8340 (tpp) cc_final: 0.7300 (tpp) REVERT: A 775 GLU cc_start: 0.8348 (tp30) cc_final: 0.7888 (tp30) REVERT: A 964 THR cc_start: 0.9514 (OUTLIER) cc_final: 0.9133 (p) REVERT: A 1149 MET cc_start: 0.8939 (mmm) cc_final: 0.8664 (mmm) REVERT: A 1180 MET cc_start: 0.9011 (tpp) cc_final: 0.8757 (mmm) REVERT: A 1260 MET cc_start: 0.8668 (mpp) cc_final: 0.8237 (mpp) REVERT: A 1342 MET cc_start: 0.8974 (tpp) cc_final: 0.8563 (tpp) REVERT: A 1440 MET cc_start: 0.8703 (mmp) cc_final: 0.8164 (mmm) REVERT: A 1518 MET cc_start: 0.8830 (ppp) cc_final: 0.8620 (ppp) REVERT: A 1791 PHE cc_start: 0.7270 (m-80) cc_final: 0.6917 (m-80) REVERT: A 1926 GLU cc_start: 0.8141 (tp30) cc_final: 0.7866 (tp30) REVERT: A 2064 MET cc_start: 0.7057 (mpp) cc_final: 0.6731 (mpp) REVERT: A 2192 MET cc_start: 0.8320 (ttt) cc_final: 0.7898 (ttt) REVERT: A 2196 MET cc_start: 0.4591 (mmm) cc_final: 0.4208 (mmm) REVERT: A 2296 TRP cc_start: 0.7428 (m100) cc_final: 0.7059 (m100) REVERT: A 2309 LEU cc_start: 0.8484 (mt) cc_final: 0.8100 (mt) REVERT: A 2310 TYR cc_start: 0.8626 (t80) cc_final: 0.8392 (t80) REVERT: A 2340 MET cc_start: 0.3843 (mmm) cc_final: 0.3425 (mmm) REVERT: B 108 MET cc_start: 0.9601 (mmm) cc_final: 0.9363 (ppp) REVERT: B 143 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8926 (t80) REVERT: B 376 MET cc_start: 0.9550 (mpp) cc_final: 0.9173 (mpp) REVERT: B 496 MET cc_start: 0.9669 (mmp) cc_final: 0.9297 (mmm) REVERT: B 707 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8700 (mmm) REVERT: B 715 GLU cc_start: 0.9501 (OUTLIER) cc_final: 0.9292 (mp0) REVERT: B 739 MET cc_start: 0.9459 (tpp) cc_final: 0.9166 (mmm) REVERT: B 932 MET cc_start: 0.8763 (ptt) cc_final: 0.8549 (pmm) REVERT: B 1005 MET cc_start: 0.8993 (mpp) cc_final: 0.8589 (mpp) REVERT: B 1022 MET cc_start: 0.9699 (ppp) cc_final: 0.9165 (ppp) REVERT: B 1023 MET cc_start: 0.9196 (mmm) cc_final: 0.8745 (mmm) REVERT: B 1041 MET cc_start: 0.9686 (mmp) cc_final: 0.9105 (mmm) REVERT: B 1102 LEU cc_start: 0.9218 (mt) cc_final: 0.8841 (tp) REVERT: B 1180 MET cc_start: 0.9376 (mmm) cc_final: 0.9154 (mmm) REVERT: B 1927 TYR cc_start: 0.8749 (p90) cc_final: 0.8533 (p90) REVERT: B 2064 MET cc_start: 0.9194 (mmm) cc_final: 0.8895 (mtp) REVERT: B 2650 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8935 (mm) outliers start: 58 outliers final: 31 residues processed: 258 average time/residue: 0.4609 time to fit residues: 207.3871 Evaluate side-chains 242 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 205 time to evaluate : 4.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1516 ASP Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1965 LYS Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2033 MET Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2104 LEU Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2317 LEU Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1250 ARG Chi-restraints excluded: chain B residue 1440 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1942 ASN Chi-restraints excluded: chain B residue 2650 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 423 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 250 optimal weight: 7.9990 chunk 320 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 369 optimal weight: 50.0000 chunk 245 optimal weight: 6.9990 chunk 437 optimal weight: 3.9990 chunk 273 optimal weight: 20.0000 chunk 266 optimal weight: 0.9980 chunk 202 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 510 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 948 GLN ** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1794 GLN ** A1963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN B 697 ASN ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 36988 Z= 0.332 Angle : 0.659 12.577 50147 Z= 0.334 Chirality : 0.041 0.310 5869 Planarity : 0.004 0.048 6299 Dihedral : 5.171 84.350 4840 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.67 % Favored : 96.31 % Rotamer: Outliers : 1.92 % Allowed : 13.65 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.13), residues: 4493 helix: 1.35 (0.10), residues: 3037 sheet: -0.66 (0.43), residues: 118 loop : -0.39 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1314 HIS 0.009 0.001 HIS A1922 PHE 0.018 0.002 PHE A 250 TYR 0.026 0.001 TYR B1968 ARG 0.007 0.000 ARG A1204 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 203 time to evaluate : 3.818 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 68 MET cc_start: 0.7762 (ptt) cc_final: 0.7512 (ppp) REVERT: A 108 MET cc_start: 0.9283 (ppp) cc_final: 0.9034 (ppp) REVERT: A 236 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8404 (mp10) REVERT: A 349 MET cc_start: 0.8316 (tpp) cc_final: 0.7391 (tpp) REVERT: A 775 GLU cc_start: 0.8425 (tp30) cc_final: 0.7949 (tp30) REVERT: A 1180 MET cc_start: 0.9006 (tpp) cc_final: 0.8760 (mmm) REVERT: A 1260 MET cc_start: 0.8632 (mpp) cc_final: 0.8339 (mpp) REVERT: A 1342 MET cc_start: 0.8992 (tpp) cc_final: 0.8583 (tpp) REVERT: A 1440 MET cc_start: 0.8693 (mmp) cc_final: 0.8290 (mmp) REVERT: A 1728 LYS cc_start: 0.7099 (mttt) cc_final: 0.6878 (mmtm) REVERT: A 1926 GLU cc_start: 0.8312 (tp30) cc_final: 0.8054 (tp30) REVERT: A 2064 MET cc_start: 0.7393 (mpp) cc_final: 0.6863 (mpp) REVERT: A 2192 MET cc_start: 0.8329 (ttt) cc_final: 0.7936 (ttt) REVERT: A 2196 MET cc_start: 0.4937 (mmm) cc_final: 0.4567 (mmm) REVERT: A 2296 TRP cc_start: 0.7407 (m100) cc_final: 0.7072 (m100) REVERT: A 2309 LEU cc_start: 0.8575 (mt) cc_final: 0.8282 (mt) REVERT: A 2310 TYR cc_start: 0.8759 (t80) cc_final: 0.8508 (t80) REVERT: A 2340 MET cc_start: 0.3869 (mmm) cc_final: 0.3528 (mmm) REVERT: B 108 MET cc_start: 0.9619 (mmm) cc_final: 0.9394 (ppp) REVERT: B 143 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8859 (t80) REVERT: B 376 MET cc_start: 0.9541 (mpp) cc_final: 0.9147 (mpp) REVERT: B 496 MET cc_start: 0.9654 (mmp) cc_final: 0.9315 (mmm) REVERT: B 707 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8832 (mmm) REVERT: B 715 GLU cc_start: 0.9497 (OUTLIER) cc_final: 0.9295 (mp0) REVERT: B 739 MET cc_start: 0.9455 (tpp) cc_final: 0.9147 (mmm) REVERT: B 760 MET cc_start: 0.6584 (mmt) cc_final: 0.5954 (mmt) REVERT: B 1005 MET cc_start: 0.8985 (mpp) cc_final: 0.8671 (mpp) REVERT: B 1022 MET cc_start: 0.9701 (ppp) cc_final: 0.9497 (ppp) REVERT: B 1041 MET cc_start: 0.9687 (mmp) cc_final: 0.9093 (mmm) REVERT: B 1102 LEU cc_start: 0.9245 (mt) cc_final: 0.8894 (tp) REVERT: B 1180 MET cc_start: 0.9389 (mmm) cc_final: 0.9139 (mmm) REVERT: B 1260 MET cc_start: -0.1907 (pmm) cc_final: -0.4031 (mtt) REVERT: B 2064 MET cc_start: 0.9222 (mmm) cc_final: 0.8979 (mtp) REVERT: B 2650 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9061 (mm) outliers start: 78 outliers final: 52 residues processed: 260 average time/residue: 0.4674 time to fit residues: 214.5948 Evaluate side-chains 255 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 198 time to evaluate : 4.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1194 ASP Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1516 ASP Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1636 ASP Chi-restraints excluded: chain A residue 1855 LEU Chi-restraints excluded: chain A residue 1871 LEU Chi-restraints excluded: chain A residue 1890 ILE Chi-restraints excluded: chain A residue 1965 LYS Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 1987 ASP Chi-restraints excluded: chain A residue 1989 VAL Chi-restraints excluded: chain A residue 2033 MET Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2070 ASN Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain A residue 2287 ASP Chi-restraints excluded: chain A residue 2317 LEU Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 67 ASN Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1250 ARG Chi-restraints excluded: chain B residue 1440 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1856 LEU Chi-restraints excluded: chain B residue 1919 GLU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1942 ASN Chi-restraints excluded: chain B residue 1959 THR Chi-restraints excluded: chain B residue 2650 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 270 optimal weight: 20.0000 chunk 174 optimal weight: 0.5980 chunk 261 optimal weight: 20.0000 chunk 131 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 84 optimal weight: 0.2980 chunk 278 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 216 optimal weight: 30.0000 chunk 40 optimal weight: 1.9990 chunk 343 optimal weight: 0.0370 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN A 589 GLN A 697 ASN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 36988 Z= 0.152 Angle : 0.590 15.699 50147 Z= 0.289 Chirality : 0.039 0.300 5869 Planarity : 0.003 0.049 6299 Dihedral : 4.921 72.787 4840 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.27 % Favored : 96.71 % Rotamer: Outliers : 1.28 % Allowed : 14.29 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.13), residues: 4493 helix: 1.56 (0.10), residues: 3039 sheet: -0.56 (0.44), residues: 118 loop : -0.33 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP A1314 HIS 0.004 0.001 HIS A2402 PHE 0.035 0.001 PHE B 71 TYR 0.031 0.001 TYR B1927 ARG 0.003 0.000 ARG B1807 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 218 time to evaluate : 4.059 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 68 MET cc_start: 0.7681 (ptt) cc_final: 0.7449 (ppp) REVERT: A 236 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: A 349 MET cc_start: 0.8311 (tpp) cc_final: 0.7320 (tpp) REVERT: A 707 MET cc_start: 0.8975 (ttt) cc_final: 0.8185 (tmm) REVERT: A 775 GLU cc_start: 0.8350 (tp30) cc_final: 0.7889 (tp30) REVERT: A 1149 MET cc_start: 0.8841 (mmm) cc_final: 0.8428 (mmm) REVERT: A 1180 MET cc_start: 0.9001 (tpp) cc_final: 0.8798 (mmm) REVERT: A 1260 MET cc_start: 0.8551 (mpp) cc_final: 0.8337 (mpp) REVERT: A 1342 MET cc_start: 0.8982 (tpp) cc_final: 0.8558 (tpp) REVERT: A 1440 MET cc_start: 0.8712 (mmp) cc_final: 0.8334 (mmp) REVERT: A 1728 LYS cc_start: 0.7058 (mttt) cc_final: 0.6812 (mmtm) REVERT: A 1926 GLU cc_start: 0.8119 (tp30) cc_final: 0.7867 (tp30) REVERT: A 1956 LYS cc_start: 0.9381 (mppt) cc_final: 0.8904 (mttm) REVERT: A 2192 MET cc_start: 0.8310 (ttt) cc_final: 0.7905 (ttt) REVERT: A 2196 MET cc_start: 0.4810 (mmm) cc_final: 0.4454 (mmm) REVERT: A 2296 TRP cc_start: 0.7429 (m100) cc_final: 0.7066 (m100) REVERT: A 2310 TYR cc_start: 0.8697 (t80) cc_final: 0.8445 (t80) REVERT: A 2340 MET cc_start: 0.3836 (mmm) cc_final: 0.3551 (mmm) REVERT: B 108 MET cc_start: 0.9604 (mmm) cc_final: 0.9380 (ppp) REVERT: B 143 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8890 (t80) REVERT: B 376 MET cc_start: 0.9543 (mpp) cc_final: 0.9146 (mpp) REVERT: B 496 MET cc_start: 0.9645 (mmp) cc_final: 0.9347 (mmm) REVERT: B 497 VAL cc_start: 0.9773 (t) cc_final: 0.9508 (p) REVERT: B 544 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9227 (mm-30) REVERT: B 707 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8670 (mmm) REVERT: B 715 GLU cc_start: 0.9500 (OUTLIER) cc_final: 0.9295 (mp0) REVERT: B 739 MET cc_start: 0.9461 (tpp) cc_final: 0.9149 (mmm) REVERT: B 895 MET cc_start: 0.8682 (mtm) cc_final: 0.8343 (ptm) REVERT: B 1005 MET cc_start: 0.8991 (mpp) cc_final: 0.8602 (mpp) REVERT: B 1022 MET cc_start: 0.9699 (ppp) cc_final: 0.9167 (ppp) REVERT: B 1023 MET cc_start: 0.9252 (mmm) cc_final: 0.8782 (mmm) REVERT: B 1041 MET cc_start: 0.9704 (mmp) cc_final: 0.9121 (mmm) REVERT: B 1102 LEU cc_start: 0.9215 (mt) cc_final: 0.8835 (tp) REVERT: B 1180 MET cc_start: 0.9360 (mmm) cc_final: 0.9144 (mmm) REVERT: B 1260 MET cc_start: -0.2002 (pmm) cc_final: -0.4089 (mtt) REVERT: B 2064 MET cc_start: 0.9193 (mmm) cc_final: 0.8921 (mtp) REVERT: B 2650 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8983 (mm) outliers start: 52 outliers final: 31 residues processed: 253 average time/residue: 0.4504 time to fit residues: 198.0844 Evaluate side-chains 243 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 207 time to evaluate : 3.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 314 ARG Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 898 LEU Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1965 LYS Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2033 MET Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2186 GLU Chi-restraints excluded: chain A residue 2264 TYR Chi-restraints excluded: chain A residue 2317 LEU Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1250 ARG Chi-restraints excluded: chain B residue 1440 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 1942 ASN Chi-restraints excluded: chain B residue 2650 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 398 optimal weight: 0.9980 chunk 419 optimal weight: 2.9990 chunk 382 optimal weight: 0.7980 chunk 407 optimal weight: 0.7980 chunk 245 optimal weight: 4.9990 chunk 177 optimal weight: 0.0370 chunk 320 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 368 optimal weight: 10.0000 chunk 385 optimal weight: 0.5980 chunk 406 optimal weight: 0.4980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36988 Z= 0.155 Angle : 0.607 19.514 50147 Z= 0.295 Chirality : 0.039 0.340 5869 Planarity : 0.004 0.049 6299 Dihedral : 4.758 58.875 4840 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 1.01 % Allowed : 14.85 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.13), residues: 4493 helix: 1.61 (0.10), residues: 3028 sheet: -0.46 (0.42), residues: 131 loop : -0.30 (0.18), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A1314 HIS 0.004 0.001 HIS A1900 PHE 0.011 0.001 PHE A 250 TYR 0.021 0.001 TYR B2706 ARG 0.024 0.000 ARG A1809 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 3.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7626 (ptt) cc_final: 0.7418 (ppp) REVERT: A 236 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8324 (mp10) REVERT: A 349 MET cc_start: 0.8334 (tpp) cc_final: 0.7292 (tpp) REVERT: A 707 MET cc_start: 0.8873 (ttt) cc_final: 0.8140 (tmm) REVERT: A 775 GLU cc_start: 0.8349 (tp30) cc_final: 0.7880 (tp30) REVERT: A 1149 MET cc_start: 0.8812 (mmm) cc_final: 0.8449 (mmm) REVERT: A 1260 MET cc_start: 0.8518 (mpp) cc_final: 0.8311 (mpp) REVERT: A 1342 MET cc_start: 0.9016 (tpp) cc_final: 0.8629 (tpp) REVERT: A 1421 MET cc_start: 0.9409 (mmm) cc_final: 0.8962 (mmm) REVERT: A 1440 MET cc_start: 0.8698 (mmp) cc_final: 0.8318 (mmp) REVERT: A 1728 LYS cc_start: 0.6962 (mttt) cc_final: 0.6746 (mmtm) REVERT: A 1791 PHE cc_start: 0.7278 (m-80) cc_final: 0.6903 (m-80) REVERT: A 1926 GLU cc_start: 0.8105 (tp30) cc_final: 0.7891 (tp30) REVERT: A 2192 MET cc_start: 0.8311 (ttt) cc_final: 0.7918 (ttt) REVERT: A 2196 MET cc_start: 0.4836 (mmm) cc_final: 0.4482 (mmm) REVERT: A 2258 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7418 (pp) REVERT: A 2296 TRP cc_start: 0.7450 (m100) cc_final: 0.7113 (m100) REVERT: A 2310 TYR cc_start: 0.8686 (t80) cc_final: 0.8428 (t80) REVERT: A 2340 MET cc_start: 0.3800 (mmm) cc_final: 0.3520 (mmm) REVERT: B 71 PHE cc_start: 0.8605 (p90) cc_final: 0.8291 (p90) REVERT: B 108 MET cc_start: 0.9605 (mmm) cc_final: 0.9393 (ppp) REVERT: B 119 HIS cc_start: 0.8256 (t-90) cc_final: 0.8018 (t-170) REVERT: B 143 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8905 (t80) REVERT: B 376 MET cc_start: 0.9523 (mpp) cc_final: 0.9094 (mpp) REVERT: B 496 MET cc_start: 0.9654 (mmp) cc_final: 0.9322 (mmm) REVERT: B 577 MET cc_start: 0.9682 (tpp) cc_final: 0.9462 (tpt) REVERT: B 707 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8671 (mmm) REVERT: B 715 GLU cc_start: 0.9499 (OUTLIER) cc_final: 0.9294 (mp0) REVERT: B 739 MET cc_start: 0.9458 (tpp) cc_final: 0.9147 (mmm) REVERT: B 760 MET cc_start: 0.6636 (mmt) cc_final: 0.6110 (mmt) REVERT: B 895 MET cc_start: 0.8679 (mtm) cc_final: 0.8330 (ptm) REVERT: B 1005 MET cc_start: 0.8937 (mpp) cc_final: 0.8538 (mpp) REVERT: B 1041 MET cc_start: 0.9708 (mmp) cc_final: 0.9136 (mmm) REVERT: B 1102 LEU cc_start: 0.9222 (mt) cc_final: 0.8842 (tp) REVERT: B 1180 MET cc_start: 0.9361 (mmm) cc_final: 0.9142 (mmm) REVERT: B 2064 MET cc_start: 0.9208 (mmm) cc_final: 0.8876 (mtp) REVERT: B 2650 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8950 (mm) outliers start: 41 outliers final: 26 residues processed: 245 average time/residue: 0.4392 time to fit residues: 189.4497 Evaluate side-chains 241 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 209 time to evaluate : 4.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1181 GLU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1516 ASP Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1965 LYS Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2033 MET Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2258 LEU Chi-restraints excluded: chain A residue 2384 ILE Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1440 MET Chi-restraints excluded: chain B residue 1833 LEU Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 2650 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 267 optimal weight: 3.9990 chunk 431 optimal weight: 0.0670 chunk 263 optimal weight: 6.9990 chunk 204 optimal weight: 20.0000 chunk 299 optimal weight: 0.9990 chunk 452 optimal weight: 0.1980 chunk 416 optimal weight: 4.9990 chunk 360 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 278 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2218 GLN B2220 ASN ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36988 Z= 0.154 Angle : 0.618 18.867 50147 Z= 0.298 Chirality : 0.039 0.355 5869 Planarity : 0.004 0.049 6299 Dihedral : 4.662 50.611 4840 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 0.93 % Allowed : 15.07 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.13), residues: 4493 helix: 1.64 (0.10), residues: 3027 sheet: -0.39 (0.42), residues: 131 loop : -0.30 (0.18), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A1314 HIS 0.003 0.000 HIS A1900 PHE 0.021 0.001 PHE A1179 TYR 0.027 0.001 TYR B1968 ARG 0.006 0.000 ARG A1809 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8986 Ramachandran restraints generated. 4493 Oldfield, 0 Emsley, 4493 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 217 time to evaluate : 4.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8309 (mp10) REVERT: A 349 MET cc_start: 0.8351 (tpp) cc_final: 0.7280 (tpp) REVERT: A 707 MET cc_start: 0.8926 (ttt) cc_final: 0.8205 (tmm) REVERT: A 775 GLU cc_start: 0.8299 (tp30) cc_final: 0.7838 (tp30) REVERT: A 1149 MET cc_start: 0.8858 (mmm) cc_final: 0.8506 (mmm) REVERT: A 1260 MET cc_start: 0.8503 (mpp) cc_final: 0.8294 (mpp) REVERT: A 1421 MET cc_start: 0.9425 (mmm) cc_final: 0.8949 (mmm) REVERT: A 1440 MET cc_start: 0.8708 (mmp) cc_final: 0.8273 (mmp) REVERT: A 1728 LYS cc_start: 0.6955 (mttt) cc_final: 0.6743 (mmtm) REVERT: A 1791 PHE cc_start: 0.7266 (m-80) cc_final: 0.6891 (m-80) REVERT: A 2192 MET cc_start: 0.8293 (ttt) cc_final: 0.7897 (ttt) REVERT: A 2196 MET cc_start: 0.4849 (mmm) cc_final: 0.4491 (mmm) REVERT: A 2258 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7420 (pp) REVERT: A 2296 TRP cc_start: 0.7463 (m100) cc_final: 0.7148 (m100) REVERT: A 2310 TYR cc_start: 0.8681 (t80) cc_final: 0.8397 (t80) REVERT: A 2340 MET cc_start: 0.3771 (mmm) cc_final: 0.3474 (mmm) REVERT: B 108 MET cc_start: 0.9585 (mmm) cc_final: 0.9374 (ppp) REVERT: B 119 HIS cc_start: 0.8256 (t-90) cc_final: 0.8008 (t-170) REVERT: B 143 PHE cc_start: 0.9181 (OUTLIER) cc_final: 0.8923 (t80) REVERT: B 301 ASP cc_start: 0.9275 (m-30) cc_final: 0.9069 (m-30) REVERT: B 376 MET cc_start: 0.9525 (mpp) cc_final: 0.9134 (mpp) REVERT: B 496 MET cc_start: 0.9648 (mmp) cc_final: 0.9296 (mmm) REVERT: B 577 MET cc_start: 0.9671 (tpp) cc_final: 0.9440 (tpt) REVERT: B 707 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8676 (mmm) REVERT: B 715 GLU cc_start: 0.9493 (OUTLIER) cc_final: 0.9283 (mp0) REVERT: B 739 MET cc_start: 0.9456 (tpp) cc_final: 0.9164 (mmm) REVERT: B 760 MET cc_start: 0.6585 (mmt) cc_final: 0.6022 (mmt) REVERT: B 895 MET cc_start: 0.8677 (mtm) cc_final: 0.8329 (ptm) REVERT: B 1005 MET cc_start: 0.8948 (mpp) cc_final: 0.8546 (mpp) REVERT: B 1023 MET cc_start: 0.9159 (mmm) cc_final: 0.8809 (mmm) REVERT: B 1041 MET cc_start: 0.9710 (mmp) cc_final: 0.9191 (mmm) REVERT: B 1102 LEU cc_start: 0.9234 (mt) cc_final: 0.8879 (tp) REVERT: B 1180 MET cc_start: 0.9330 (mmm) cc_final: 0.9094 (mmm) REVERT: B 1919 GLU cc_start: 0.8013 (mp0) cc_final: 0.7704 (mm-30) REVERT: B 2064 MET cc_start: 0.9212 (mmm) cc_final: 0.8854 (mtp) REVERT: B 2650 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8893 (mm) outliers start: 38 outliers final: 25 residues processed: 241 average time/residue: 0.3977 time to fit residues: 168.6921 Evaluate side-chains 241 residues out of total 4090 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 210 time to evaluate : 4.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 1073 MET Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1085 LEU Chi-restraints excluded: chain A residue 1305 LEU Chi-restraints excluded: chain A residue 1513 ARG Chi-restraints excluded: chain A residue 1516 ASP Chi-restraints excluded: chain A residue 1525 LEU Chi-restraints excluded: chain A residue 1597 ILE Chi-restraints excluded: chain A residue 1984 ASP Chi-restraints excluded: chain A residue 2033 MET Chi-restraints excluded: chain A residue 2053 MET Chi-restraints excluded: chain A residue 2258 LEU Chi-restraints excluded: chain A residue 2384 ILE Chi-restraints excluded: chain A residue 2701 THR Chi-restraints excluded: chain B residue 143 PHE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 538 MET Chi-restraints excluded: chain B residue 707 MET Chi-restraints excluded: chain B residue 715 GLU Chi-restraints excluded: chain B residue 1440 MET Chi-restraints excluded: chain B residue 1925 LEU Chi-restraints excluded: chain B residue 2053 MET Chi-restraints excluded: chain B residue 2650 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 454 random chunks: chunk 286 optimal weight: 0.8980 chunk 383 optimal weight: 0.9990 chunk 110 optimal weight: 0.6980 chunk 332 optimal weight: 30.0000 chunk 53 optimal weight: 0.2980 chunk 100 optimal weight: 0.0170 chunk 360 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 370 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 756 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1039 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** A2595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2688 ASN ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 614 ASN ** B1426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2218 GLN B2220 ASN ** B2319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.097758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073322 restraints weight = 243749.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.072937 restraints weight = 122774.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.073143 restraints weight = 104971.749| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 36988 Z= 0.155 Angle : 0.619 19.461 50147 Z= 0.298 Chirality : 0.039 0.345 5869 Planarity : 0.003 0.049 6299 Dihedral : 4.606 52.333 4840 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.82 % Rotamer: Outliers : 0.86 % Allowed : 15.24 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.13), residues: 4493 helix: 1.66 (0.10), residues: 3021 sheet: -0.36 (0.42), residues: 131 loop : -0.26 (0.18), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A1314 HIS 0.004 0.000 HIS A1900 PHE 0.011 0.001 PHE A 894 TYR 0.022 0.001 TYR B2706 ARG 0.005 0.000 ARG A1809 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6847.23 seconds wall clock time: 128 minutes 42.83 seconds (7722.83 seconds total)