Starting phenix.real_space_refine on Sat Feb 24 03:32:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wji_32544/02_2024/7wji_32544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wji_32544/02_2024/7wji_32544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wji_32544/02_2024/7wji_32544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wji_32544/02_2024/7wji_32544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wji_32544/02_2024/7wji_32544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wji_32544/02_2024/7wji_32544.pdb" } resolution = 4.5 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= -0.001 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 322 5.16 5 C 26630 2.51 5 N 6919 2.21 5 O 7302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1920": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1960": "OE1" <-> "OE2" Residue "A GLU 2080": "OE1" <-> "OE2" Residue "A ASP 2126": "OD1" <-> "OD2" Residue "A GLU 2255": "OE1" <-> "OE2" Residue "A TYR 2356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2488": "OE1" <-> "OE2" Residue "A GLU 2539": "OE1" <-> "OE2" Residue "A ASP 2551": "OD1" <-> "OD2" Residue "A PHE 2718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 683": "OE1" <-> "OE2" Residue "B TYR 868": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 873": "OE1" <-> "OE2" Residue "B GLU 876": "OE1" <-> "OE2" Residue "B GLU 962": "OE1" <-> "OE2" Residue "B PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1171": "OE1" <-> "OE2" Residue "B PHE 1341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2105": "OD1" <-> "OD2" Residue "B PHE 2177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2380": "OD1" <-> "OD2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 176": "OE1" <-> "OE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C ASP 668": "OD1" <-> "OD2" Residue "C PHE 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 958": "OD1" <-> "OD2" Residue "C PHE 1061": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "D TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 373": "OE1" <-> "OE2" Time to flip residues: 0.28s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41173 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 14143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1763, 14143 Classifications: {'peptide': 1763} Link IDs: {'PCIS': 3, 'PTRANS': 80, 'TRANS': 1679} Chain breaks: 11 Chain: "B" Number of atoms: 13146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1663, 13146 Classifications: {'peptide': 1663} Link IDs: {'PCIS': 2, 'PTRANS': 79, 'TRANS': 1581} Chain breaks: 11 Chain: "E" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 988 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 11413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1394, 11413 Classifications: {'peptide': 1394} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1340} Chain breaks: 5 Chain: "D" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1483 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 8, 'TRANS': 173} Chain breaks: 1 Time building chain proxies: 20.55, per 1000 atoms: 0.50 Number of scatterers: 41173 At special positions: 0 Unit cell: (141.31, 198.921, 332.622, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 322 16.00 O 7302 8.00 N 6919 7.00 C 26630 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: 15.36 Conformation dependent library (CDL) restraints added in 7.3 seconds 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9836 Finding SS restraints... Secondary structure from input PDB file: 261 helices and 7 sheets defined 66.1% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.79 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 removed outlier: 4.265A pdb=" N TRP A 27 " --> pdb=" O GLN A 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.662A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 94 removed outlier: 3.724A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 95 through 100 removed outlier: 3.570A pdb=" N GLY A 100 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 131 removed outlier: 4.509A pdb=" N ASN A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 131 " --> pdb=" O CYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 183 through 189 removed outlier: 3.758A pdb=" N LEU A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.558A pdb=" N ALA A 209 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER A 210 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.860A pdb=" N TRP A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.980A pdb=" N GLU A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.613A pdb=" N THR A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 removed outlier: 3.976A pdb=" N ARG A 325 " --> pdb=" O CYS A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 344 through 363 Processing helix chain 'A' and resid 654 through 663 removed outlier: 3.568A pdb=" N VAL A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 685 removed outlier: 3.566A pdb=" N VAL A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 800 Processing helix chain 'A' and resid 813 through 818 removed outlier: 4.036A pdb=" N LEU A 818 " --> pdb=" O SER A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 836 removed outlier: 3.710A pdb=" N LYS A 836 " --> pdb=" O THR A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 851 Processing helix chain 'A' and resid 854 through 866 removed outlier: 3.561A pdb=" N VAL A 858 " --> pdb=" O SER A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 915 removed outlier: 3.706A pdb=" N ILE A 899 " --> pdb=" O ASN A 895 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS A 906 " --> pdb=" O SER A 902 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N SER A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR A 910 " --> pdb=" O LYS A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 920 removed outlier: 3.744A pdb=" N LEU A 919 " --> pdb=" O THR A 915 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N HIS A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 915 through 920' Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 924 through 941 removed outlier: 4.639A pdb=" N GLN A 936 " --> pdb=" O ARG A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 952 through 958 Processing helix chain 'A' and resid 1178 through 1191 removed outlier: 4.197A pdb=" N GLN A1182 " --> pdb=" O GLY A1178 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1207 Processing helix chain 'A' and resid 1214 through 1232 removed outlier: 3.662A pdb=" N ARG A1218 " --> pdb=" O PRO A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1291 removed outlier: 4.191A pdb=" N LYS A1275 " --> pdb=" O TRP A1271 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR A1278 " --> pdb=" O ALA A1274 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A1287 " --> pdb=" O ALA A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1308 removed outlier: 3.644A pdb=" N TYR A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1321 Processing helix chain 'A' and resid 1338 through 1357 removed outlier: 3.832A pdb=" N LYS A1342 " --> pdb=" O PRO A1338 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A1357 " --> pdb=" O THR A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1460 through 1469 removed outlier: 4.059A pdb=" N ILE A1464 " --> pdb=" O LEU A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1500 Processing helix chain 'A' and resid 1556 through 1565 Processing helix chain 'A' and resid 1570 through 1579 Processing helix chain 'A' and resid 1584 through 1598 removed outlier: 3.714A pdb=" N TYR A1588 " --> pdb=" O THR A1584 " (cutoff:3.500A) Proline residue: A1593 - end of helix Processing helix chain 'A' and resid 1599 through 1601 No H-bonds generated for 'chain 'A' and resid 1599 through 1601' Processing helix chain 'A' and resid 1603 through 1621 Processing helix chain 'A' and resid 1622 through 1631 Processing helix chain 'A' and resid 1637 through 1653 removed outlier: 3.773A pdb=" N ARG A1641 " --> pdb=" O GLU A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1847 through 1860 removed outlier: 4.406A pdb=" N LEU A1852 " --> pdb=" O CYS A1848 " (cutoff:3.500A) Proline residue: A1853 - end of helix Processing helix chain 'A' and resid 1870 through 1883 Processing helix chain 'A' and resid 1893 through 1897 removed outlier: 3.803A pdb=" N LEU A1897 " --> pdb=" O LEU A1894 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1918 removed outlier: 4.199A pdb=" N GLU A1905 " --> pdb=" O ASN A1901 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A1914 " --> pdb=" O LEU A1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 1921 through 1942 removed outlier: 3.951A pdb=" N SER A1925 " --> pdb=" O PRO A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1947 through 1962 removed outlier: 4.578A pdb=" N PHE A1957 " --> pdb=" O ALA A1953 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU A1960 " --> pdb=" O THR A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 1963 through 1965 No H-bonds generated for 'chain 'A' and resid 1963 through 1965' Processing helix chain 'A' and resid 1970 through 1978 removed outlier: 3.924A pdb=" N LYS A1974 " --> pdb=" O PHE A1970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1982 through 1986 removed outlier: 3.744A pdb=" N LEU A1986 " --> pdb=" O GLU A1983 " (cutoff:3.500A) Processing helix chain 'A' and resid 2019 through 2031 removed outlier: 3.802A pdb=" N LEU A2023 " --> pdb=" O GLN A2019 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2038 Processing helix chain 'A' and resid 2078 through 2108 Processing helix chain 'A' and resid 2115 through 2130 Processing helix chain 'A' and resid 2134 through 2139 Processing helix chain 'A' and resid 2151 through 2174 removed outlier: 3.998A pdb=" N PHE A2155 " --> pdb=" O GLY A2151 " (cutoff:3.500A) Processing helix chain 'A' and resid 2184 through 2200 removed outlier: 4.120A pdb=" N LEU A2188 " --> pdb=" O ASP A2184 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL A2192 " --> pdb=" O LEU A2188 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE A2193 " --> pdb=" O PHE A2189 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A2197 " --> pdb=" O PHE A2193 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2221 removed outlier: 3.676A pdb=" N PHE A2221 " --> pdb=" O THR A2217 " (cutoff:3.500A) Processing helix chain 'A' and resid 2223 through 2228 removed outlier: 3.528A pdb=" N LEU A2227 " --> pdb=" O HIS A2223 " (cutoff:3.500A) Processing helix chain 'A' and resid 2233 through 2244 removed outlier: 3.521A pdb=" N TYR A2244 " --> pdb=" O VAL A2240 " (cutoff:3.500A) Processing helix chain 'A' and resid 2247 through 2265 Processing helix chain 'A' and resid 2266 through 2278 removed outlier: 3.664A pdb=" N VAL A2270 " --> pdb=" O ARG A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2279 through 2281 No H-bonds generated for 'chain 'A' and resid 2279 through 2281' Processing helix chain 'A' and resid 2296 through 2309 Processing helix chain 'A' and resid 2317 through 2321 Processing helix chain 'A' and resid 2343 through 2357 removed outlier: 3.554A pdb=" N ILE A2347 " --> pdb=" O ILE A2343 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A2357 " --> pdb=" O VAL A2353 " (cutoff:3.500A) Processing helix chain 'A' and resid 2360 through 2386 removed outlier: 3.955A pdb=" N LEU A2364 " --> pdb=" O SER A2360 " (cutoff:3.500A) Proline residue: A2375 - end of helix Processing helix chain 'A' and resid 2390 through 2413 Processing helix chain 'A' and resid 2414 through 2420 removed outlier: 5.620A pdb=" N VAL A2417 " --> pdb=" O SER A2414 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG A2420 " --> pdb=" O VAL A2417 " (cutoff:3.500A) Processing helix chain 'A' and resid 2479 through 2517 Proline residue: A2492 - end of helix Proline residue: A2509 - end of helix Processing helix chain 'A' and resid 2530 through 2546 Processing helix chain 'A' and resid 2551 through 2555 removed outlier: 3.945A pdb=" N THR A2554 " --> pdb=" O ASP A2551 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET A2555 " --> pdb=" O THR A2552 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2551 through 2555' Processing helix chain 'A' and resid 2557 through 2567 Processing helix chain 'A' and resid 2578 through 2599 removed outlier: 4.241A pdb=" N LEU A2582 " --> pdb=" O VAL A2578 " (cutoff:3.500A) Processing helix chain 'A' and resid 2599 through 2604 Processing helix chain 'A' and resid 2607 through 2625 removed outlier: 4.209A pdb=" N ALA A2611 " --> pdb=" O GLU A2607 " (cutoff:3.500A) Processing helix chain 'A' and resid 2626 through 2629 removed outlier: 3.842A pdb=" N SER A2629 " --> pdb=" O PRO A2626 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2626 through 2629' Processing helix chain 'A' and resid 2631 through 2647 removed outlier: 3.816A pdb=" N ARG A2635 " --> pdb=" O LEU A2631 " (cutoff:3.500A) Processing helix chain 'A' and resid 2670 through 2688 Processing helix chain 'A' and resid 2693 through 2698 removed outlier: 3.722A pdb=" N VAL A2697 " --> pdb=" O PRO A2693 " (cutoff:3.500A) Processing helix chain 'A' and resid 2703 through 2714 Processing helix chain 'A' and resid 2714 through 2723 removed outlier: 3.527A pdb=" N PHE A2718 " --> pdb=" O LEU A2714 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A2723 " --> pdb=" O VAL A2719 " (cutoff:3.500A) Processing helix chain 'A' and resid 2733 through 2749 removed outlier: 3.589A pdb=" N VAL A2737 " --> pdb=" O GLU A2733 " (cutoff:3.500A) Processing helix chain 'A' and resid 2788 through 2805 Processing helix chain 'A' and resid 2812 through 2827 removed outlier: 4.001A pdb=" N LEU A2816 " --> pdb=" O GLN A2812 " (cutoff:3.500A) Processing helix chain 'A' and resid 2830 through 2844 removed outlier: 3.728A pdb=" N TRP A2834 " --> pdb=" O GLY A2830 " (cutoff:3.500A) Processing helix chain 'A' and resid 2847 through 2850 Processing helix chain 'A' and resid 2851 through 2858 Processing helix chain 'A' and resid 2866 through 2882 removed outlier: 3.779A pdb=" N ARG A2882 " --> pdb=" O ASP A2878 " (cutoff:3.500A) Processing helix chain 'A' and resid 2891 through 2910 Processing helix chain 'B' and resid 2 through 21 removed outlier: 3.811A pdb=" N GLU B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 50 removed outlier: 3.638A pdb=" N TYR B 41 " --> pdb=" O ASN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 140 removed outlier: 3.648A pdb=" N VAL B 132 " --> pdb=" O GLN B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 163 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 173 through 180 removed outlier: 3.861A pdb=" N THR B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 208 removed outlier: 3.809A pdb=" N LYS B 191 " --> pdb=" O PRO B 187 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP B 192 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N SER B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N THR B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU B 202 " --> pdb=" O SER B 198 " (cutoff:3.500A) Proline residue: B 203 - end of helix Processing helix chain 'B' and resid 222 through 234 removed outlier: 3.507A pdb=" N THR B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 251 Processing helix chain 'B' and resid 253 through 265 removed outlier: 4.104A pdb=" N ASP B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 276 through 281 removed outlier: 4.201A pdb=" N TYR B 280 " --> pdb=" O MET B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.512A pdb=" N ASP B 334 " --> pdb=" O VAL B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 347 removed outlier: 4.259A pdb=" N GLU B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 343 through 347' Processing helix chain 'B' and resid 441 through 453 removed outlier: 4.177A pdb=" N ALA B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 456 No H-bonds generated for 'chain 'B' and resid 454 through 456' Processing helix chain 'B' and resid 499 through 509 removed outlier: 3.556A pdb=" N VAL B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 539 Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 568 through 576 Processing helix chain 'B' and resid 596 through 611 Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 617 through 635 removed outlier: 3.748A pdb=" N TRP B 621 " --> pdb=" O ASN B 617 " (cutoff:3.500A) Proline residue: B 626 - end of helix removed outlier: 3.944A pdb=" N GLU B 635 " --> pdb=" O ALA B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 653 removed outlier: 4.173A pdb=" N VAL B 647 " --> pdb=" O GLU B 643 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 649 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 675 removed outlier: 4.032A pdb=" N ARG B 673 " --> pdb=" O PHE B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 694 removed outlier: 4.439A pdb=" N GLN B 684 " --> pdb=" O SER B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 700 through 724 removed outlier: 3.704A pdb=" N LEU B 704 " --> pdb=" O PRO B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 815 removed outlier: 3.620A pdb=" N CYS B 800 " --> pdb=" O MET B 796 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 803 " --> pdb=" O ASN B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 825 through 840 Processing helix chain 'B' and resid 861 through 879 Processing helix chain 'B' and resid 950 through 964 removed outlier: 3.702A pdb=" N ARG B 954 " --> pdb=" O PRO B 950 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA B 964 " --> pdb=" O PHE B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 984 removed outlier: 3.602A pdb=" N LEU B 972 " --> pdb=" O GLU B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 996 Processing helix chain 'B' and resid 996 through 1007 removed outlier: 3.824A pdb=" N HIS B1006 " --> pdb=" O TYR B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 Processing helix chain 'B' and resid 1022 through 1035 Proline residue: B1029 - end of helix Processing helix chain 'B' and resid 1039 through 1053 removed outlier: 3.909A pdb=" N ILE B1043 " --> pdb=" O HIS B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1072 removed outlier: 3.762A pdb=" N ARG B1060 " --> pdb=" O ASP B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1099 removed outlier: 3.607A pdb=" N LYS B1086 " --> pdb=" O ASN B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1100 through 1102 No H-bonds generated for 'chain 'B' and resid 1100 through 1102' Processing helix chain 'B' and resid 1104 through 1116 removed outlier: 3.786A pdb=" N ASP B1116 " --> pdb=" O GLY B1112 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1137 Processing helix chain 'B' and resid 1140 through 1155 removed outlier: 3.640A pdb=" N ILE B1144 " --> pdb=" O ASP B1140 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B1145 " --> pdb=" O ARG B1141 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER B1146 " --> pdb=" O PRO B1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 1162 through 1178 Processing helix chain 'B' and resid 1226 through 1231 removed outlier: 4.390A pdb=" N ASP B1229 " --> pdb=" O SER B1226 " (cutoff:3.500A) Processing helix chain 'B' and resid 1271 through 1291 Processing helix chain 'B' and resid 1301 through 1315 Processing helix chain 'B' and resid 1336 through 1352 removed outlier: 4.138A pdb=" N ALA B1340 " --> pdb=" O THR B1336 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B1346 " --> pdb=" O ILE B1342 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLN B1347 " --> pdb=" O ALA B1343 " (cutoff:3.500A) Processing helix chain 'B' and resid 1353 through 1366 Proline residue: B1361 - end of helix removed outlier: 3.731A pdb=" N VAL B1366 " --> pdb=" O LEU B1362 " (cutoff:3.500A) Processing helix chain 'B' and resid 1392 through 1405 Processing helix chain 'B' and resid 1417 through 1427 removed outlier: 3.894A pdb=" N LEU B1421 " --> pdb=" O SER B1417 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS B1422 " --> pdb=" O LYS B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2037 removed outlier: 3.763A pdb=" N SER B2037 " --> pdb=" O PHE B2033 " (cutoff:3.500A) Processing helix chain 'B' and resid 2045 through 2055 removed outlier: 4.083A pdb=" N MET B2049 " --> pdb=" O LEU B2045 " (cutoff:3.500A) Processing helix chain 'B' and resid 2056 through 2058 No H-bonds generated for 'chain 'B' and resid 2056 through 2058' Processing helix chain 'B' and resid 2073 through 2090 removed outlier: 4.466A pdb=" N VAL B2077 " --> pdb=" O ASN B2073 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B2078 " --> pdb=" O ALA B2074 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS B2087 " --> pdb=" O ARG B2083 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLN B2088 " --> pdb=" O CYS B2084 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA B2090 " --> pdb=" O PHE B2086 " (cutoff:3.500A) Processing helix chain 'B' and resid 2091 through 2093 No H-bonds generated for 'chain 'B' and resid 2091 through 2093' Processing helix chain 'B' and resid 2130 through 2136 Processing helix chain 'B' and resid 2144 through 2159 removed outlier: 3.796A pdb=" N ILE B2148 " --> pdb=" O GLY B2144 " (cutoff:3.500A) Processing helix chain 'B' and resid 2173 through 2182 removed outlier: 4.124A pdb=" N PHE B2180 " --> pdb=" O GLN B2176 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B2182 " --> pdb=" O GLN B2178 " (cutoff:3.500A) Processing helix chain 'B' and resid 2194 through 2200 removed outlier: 4.026A pdb=" N ILE B2200 " --> pdb=" O SER B2196 " (cutoff:3.500A) Processing helix chain 'B' and resid 2201 through 2205 Processing helix chain 'B' and resid 2216 through 2223 Processing helix chain 'B' and resid 2225 through 2230 removed outlier: 3.579A pdb=" N ASN B2230 " --> pdb=" O PHE B2226 " (cutoff:3.500A) Processing helix chain 'B' and resid 2239 through 2248 removed outlier: 3.732A pdb=" N GLY B2243 " --> pdb=" O VAL B2239 " (cutoff:3.500A) Processing helix chain 'B' and resid 2251 through 2256 Processing helix chain 'B' and resid 2262 through 2270 removed outlier: 3.943A pdb=" N GLN B2268 " --> pdb=" O LEU B2264 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2290 removed outlier: 3.603A pdb=" N LEU B2282 " --> pdb=" O ASP B2278 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU B2283 " --> pdb=" O THR B2279 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU B2284 " --> pdb=" O ASN B2280 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL B2285 " --> pdb=" O LEU B2281 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE B2287 " --> pdb=" O LEU B2283 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE B2288 " --> pdb=" O LEU B2284 " (cutoff:3.500A) Processing helix chain 'B' and resid 2325 through 2334 removed outlier: 3.535A pdb=" N LEU B2329 " --> pdb=" O ILE B2325 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASP B2334 " --> pdb=" O ASP B2330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2336 through 2342 removed outlier: 3.513A pdb=" N LYS B2340 " --> pdb=" O HIS B2336 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B2342 " --> pdb=" O LEU B2338 " (cutoff:3.500A) Processing helix chain 'B' and resid 2356 through 2361 Processing helix chain 'B' and resid 2362 through 2367 Processing helix chain 'B' and resid 2368 through 2370 No H-bonds generated for 'chain 'B' and resid 2368 through 2370' Processing helix chain 'B' and resid 2371 through 2377 removed outlier: 3.626A pdb=" N ARG B2375 " --> pdb=" O MET B2371 " (cutoff:3.500A) Processing helix chain 'B' and resid 2383 through 2388 removed outlier: 4.351A pdb=" N TYR B2387 " --> pdb=" O ALA B2383 " (cutoff:3.500A) Processing helix chain 'B' and resid 2401 through 2426 removed outlier: 3.834A pdb=" N SER B2410 " --> pdb=" O ILE B2406 " (cutoff:3.500A) Processing helix chain 'B' and resid 2440 through 2442 No H-bonds generated for 'chain 'B' and resid 2440 through 2442' Processing helix chain 'B' and resid 2443 through 2448 removed outlier: 3.649A pdb=" N ALA B2448 " --> pdb=" O GLY B2444 " (cutoff:3.500A) Processing helix chain 'B' and resid 2448 through 2458 removed outlier: 3.864A pdb=" N ILE B2452 " --> pdb=" O ALA B2448 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL B2453 " --> pdb=" O ASP B2449 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE B2454 " --> pdb=" O HIS B2450 " (cutoff:3.500A) Processing helix chain 'B' and resid 2465 through 2470 Processing helix chain 'B' and resid 2470 through 2475 Processing helix chain 'B' and resid 2476 through 2491 removed outlier: 4.025A pdb=" N GLN B2480 " --> pdb=" O PHE B2476 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B2491 " --> pdb=" O GLU B2487 " (cutoff:3.500A) Processing helix chain 'B' and resid 2499 through 2527 Proline residue: B2518 - end of helix removed outlier: 3.819A pdb=" N ASN B2527 " --> pdb=" O LEU B2523 " (cutoff:3.500A) Processing helix chain 'B' and resid 2528 through 2549 removed outlier: 3.775A pdb=" N GLU B2532 " --> pdb=" O LYS B2528 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N HIS B2537 " --> pdb=" O MET B2533 " (cutoff:3.500A) Processing helix chain 'B' and resid 2550 through 2555 removed outlier: 3.542A pdb=" N VAL B2554 " --> pdb=" O SER B2550 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B2555 " --> pdb=" O THR B2551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2550 through 2555' Processing helix chain 'B' and resid 2560 through 2565 Processing helix chain 'B' and resid 2566 through 2571 removed outlier: 6.022A pdb=" N LYS B2569 " --> pdb=" O SER B2566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2572 through 2590 removed outlier: 3.592A pdb=" N GLN B2576 " --> pdb=" O SER B2572 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU B2577 " --> pdb=" O ALA B2573 " (cutoff:3.500A) Processing helix chain 'B' and resid 2598 through 2633 removed outlier: 4.281A pdb=" N ALA B2602 " --> pdb=" O GLY B2598 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 18 Processing helix chain 'E' and resid 31 through 41 removed outlier: 4.224A pdb=" N THR E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 87 through 93 removed outlier: 3.735A pdb=" N PHE E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 Processing helix chain 'E' and resid 118 through 130 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.662A pdb=" N HIS C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 43 " --> pdb=" O HIS C 39 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ILE C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE C 48 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 64 Processing helix chain 'C' and resid 64 through 84 removed outlier: 3.513A pdb=" N GLN C 68 " --> pdb=" O TYR C 64 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N PHE C 72 " --> pdb=" O GLN C 68 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR C 73 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 92 removed outlier: 3.931A pdb=" N HIS C 91 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 130 Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.669A pdb=" N GLY C 140 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C 144 " --> pdb=" O MET C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.749A pdb=" N ARG C 152 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 153 " --> pdb=" O ILE C 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 148 through 153' Processing helix chain 'C' and resid 163 through 200 removed outlier: 3.820A pdb=" N ILE C 167 " --> pdb=" O PRO C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 282 through 290 removed outlier: 3.831A pdb=" N MET C 286 " --> pdb=" O TRP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 309 Processing helix chain 'C' and resid 315 through 336 removed outlier: 3.978A pdb=" N TRP C 336 " --> pdb=" O PHE C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 380 Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.621A pdb=" N MET C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 440 Processing helix chain 'C' and resid 450 through 465 removed outlier: 3.664A pdb=" N VAL C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 480 removed outlier: 4.527A pdb=" N VAL C 479 " --> pdb=" O THR C 475 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU C 480 " --> pdb=" O TYR C 476 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 475 through 480' Processing helix chain 'C' and resid 481 through 488 removed outlier: 3.640A pdb=" N ILE C 486 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS C 487 " --> pdb=" O ARG C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 501 removed outlier: 3.750A pdb=" N GLU C 493 " --> pdb=" O SER C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 528 removed outlier: 3.771A pdb=" N VAL C 510 " --> pdb=" O LEU C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 552 removed outlier: 3.627A pdb=" N ALA C 543 " --> pdb=" O THR C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 568 removed outlier: 4.459A pdb=" N MET C 560 " --> pdb=" O TRP C 556 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ASN C 565 " --> pdb=" O ASP C 561 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA C 566 " --> pdb=" O GLN C 562 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 587 Processing helix chain 'C' and resid 589 through 603 Processing helix chain 'C' and resid 607 through 616 Processing helix chain 'C' and resid 627 through 634 Processing helix chain 'C' and resid 659 through 669 removed outlier: 3.864A pdb=" N ARG C 669 " --> pdb=" O GLN C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 736 removed outlier: 4.160A pdb=" N LYS C 722 " --> pdb=" O ASN C 718 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU C 723 " --> pdb=" O LEU C 719 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 826 removed outlier: 3.639A pdb=" N ILE C 808 " --> pdb=" O GLU C 804 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU C 826 " --> pdb=" O GLN C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 875 through 883 removed outlier: 4.367A pdb=" N TYR C 879 " --> pdb=" O TYR C 875 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY C 883 " --> pdb=" O TYR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 904 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 952 through 970 removed outlier: 4.284A pdb=" N VAL C 956 " --> pdb=" O ASP C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 989 Processing helix chain 'C' and resid 991 through 994 Processing helix chain 'C' and resid 995 through 1000 removed outlier: 3.534A pdb=" N LEU C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1011 Processing helix chain 'C' and resid 1015 through 1039 Processing helix chain 'C' and resid 1053 through 1057 Processing helix chain 'C' and resid 1100 through 1113 removed outlier: 3.711A pdb=" N SER C1113 " --> pdb=" O PHE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1127 removed outlier: 4.493A pdb=" N VAL C1120 " --> pdb=" O GLY C1116 " (cutoff:3.500A) Processing helix chain 'C' and resid 1132 through 1147 removed outlier: 3.922A pdb=" N ILE C1136 " --> pdb=" O HIS C1132 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N MET C1145 " --> pdb=" O PHE C1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 1147 through 1164 removed outlier: 3.681A pdb=" N ILE C1156 " --> pdb=" O VAL C1152 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY C1164 " --> pdb=" O ASN C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1169 through 1185 removed outlier: 4.047A pdb=" N ILE C1184 " --> pdb=" O SER C1180 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C1185 " --> pdb=" O ARG C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1197 through 1207 removed outlier: 3.602A pdb=" N ALA C1201 " --> pdb=" O ASP C1197 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C1206 " --> pdb=" O LYS C1202 " (cutoff:3.500A) Processing helix chain 'C' and resid 1209 through 1225 removed outlier: 3.512A pdb=" N ARG C1214 " --> pdb=" O PRO C1210 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU C1221 " --> pdb=" O ALA C1217 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C1224 " --> pdb=" O VAL C1220 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL C1225 " --> pdb=" O LEU C1221 " (cutoff:3.500A) Processing helix chain 'C' and resid 1226 through 1228 No H-bonds generated for 'chain 'C' and resid 1226 through 1228' Processing helix chain 'C' and resid 1238 through 1263 Processing helix chain 'C' and resid 1264 through 1271 Processing helix chain 'C' and resid 1271 through 1292 removed outlier: 3.762A pdb=" N ARG C1275 " --> pdb=" O SER C1271 " (cutoff:3.500A) Processing helix chain 'C' and resid 1296 through 1312 removed outlier: 3.917A pdb=" N TYR C1300 " --> pdb=" O ASN C1296 " (cutoff:3.500A) Processing helix chain 'C' and resid 1313 through 1317 removed outlier: 4.305A pdb=" N GLY C1316 " --> pdb=" O SER C1313 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS C1317 " --> pdb=" O ILE C1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1313 through 1317' Processing helix chain 'C' and resid 1319 through 1335 removed outlier: 3.545A pdb=" N LYS C1334 " --> pdb=" O VAL C1330 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER C1335 " --> pdb=" O SER C1331 " (cutoff:3.500A) Processing helix chain 'C' and resid 1337 through 1356 removed outlier: 3.544A pdb=" N GLY C1341 " --> pdb=" O PHE C1337 " (cutoff:3.500A) Processing helix chain 'C' and resid 1374 through 1386 Processing helix chain 'C' and resid 1390 through 1396 removed outlier: 3.567A pdb=" N ILE C1394 " --> pdb=" O ASP C1390 " (cutoff:3.500A) Processing helix chain 'C' and resid 1421 through 1435 removed outlier: 4.022A pdb=" N CYS C1428 " --> pdb=" O LEU C1424 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ILE C1433 " --> pdb=" O SER C1429 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE C1434 " --> pdb=" O PHE C1430 " (cutoff:3.500A) Processing helix chain 'C' and resid 1437 through 1449 Processing helix chain 'C' and resid 1463 through 1478 Processing helix chain 'C' and resid 1486 through 1490 removed outlier: 4.084A pdb=" N VAL C1490 " --> pdb=" O THR C1487 " (cutoff:3.500A) Processing helix chain 'C' and resid 1498 through 1502 removed outlier: 4.042A pdb=" N LEU C1501 " --> pdb=" O ARG C1498 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C1502 " --> pdb=" O GLY C1499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1498 through 1502' Processing helix chain 'C' and resid 1508 through 1519 Processing helix chain 'C' and resid 1532 through 1541 Processing helix chain 'C' and resid 1549 through 1584 Processing helix chain 'D' and resid 230 through 238 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 260 through 288 removed outlier: 3.548A pdb=" N ALA D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 313 Processing helix chain 'D' and resid 331 through 341 removed outlier: 4.126A pdb=" N LEU D 335 " --> pdb=" O LYS D 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1997 through 2000 Processing sheet with id=AA2, first strand: chain 'A' and resid 2041 through 2044 Processing sheet with id=AA3, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.785A pdb=" N LEU B 341 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N MET B 322 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU B 339 " --> pdb=" O MET B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 1045 through 1046 removed outlier: 4.419A pdb=" N LYS C1045 " --> pdb=" O ALA C1091 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA C1091 " --> pdb=" O LYS C1045 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 1060 through 1064 Processing sheet with id=AA7, first strand: chain 'D' and resid 328 through 329 removed outlier: 4.056A pdb=" N ILE D 328 " --> pdb=" O CYS D 376 " (cutoff:3.500A) 2127 hydrogen bonds defined for protein. 6282 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: 16.47 Time building geometry restraints manager: 16.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12580 1.34 - 1.47: 9979 1.47 - 1.59: 19056 1.59 - 1.72: 0 1.72 - 1.84: 496 Bond restraints: 42111 Sorted by residual: bond pdb=" C LEU A 20 " pdb=" N PRO A 21 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.20e-02 6.94e+03 1.91e+01 bond pdb=" N ILE B1416 " pdb=" CA ILE B1416 " ideal model delta sigma weight residual 1.458 1.493 -0.035 9.00e-03 1.23e+04 1.50e+01 bond pdb=" CB LYS C1322 " pdb=" CG LYS C1322 " ideal model delta sigma weight residual 1.520 1.409 0.111 3.00e-02 1.11e+03 1.37e+01 bond pdb=" N MET C 136 " pdb=" CA MET C 136 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.12e-02 7.97e+03 1.14e+01 bond pdb=" N LEU C 991 " pdb=" CA LEU C 991 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.18e-02 7.18e+03 1.03e+01 ... (remaining 42106 not shown) Histogram of bond angle deviations from ideal: 92.60 - 101.26: 139 101.26 - 109.92: 6493 109.92 - 118.58: 26908 118.58 - 127.24: 23013 127.24 - 135.89: 502 Bond angle restraints: 57055 Sorted by residual: angle pdb=" N LYS C1317 " pdb=" CA LYS C1317 " pdb=" C LYS C1317 " ideal model delta sigma weight residual 113.41 121.27 -7.86 1.22e+00 6.72e-01 4.15e+01 angle pdb=" N LEU C 991 " pdb=" CA LEU C 991 " pdb=" C LEU C 991 " ideal model delta sigma weight residual 112.72 105.52 7.20 1.14e+00 7.69e-01 3.99e+01 angle pdb=" C VAL C1355 " pdb=" N LEU C1356 " pdb=" CA LEU C1356 " ideal model delta sigma weight residual 122.46 111.12 11.34 1.80e+00 3.09e-01 3.97e+01 angle pdb=" N GLU A2096 " pdb=" CA GLU A2096 " pdb=" CB GLU A2096 " ideal model delta sigma weight residual 110.28 119.16 -8.88 1.55e+00 4.16e-01 3.28e+01 angle pdb=" N GLN A2734 " pdb=" CA GLN A2734 " pdb=" C GLN A2734 " ideal model delta sigma weight residual 109.81 122.18 -12.37 2.21e+00 2.05e-01 3.14e+01 ... (remaining 57050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.13: 22639 18.13 - 36.25: 2247 36.25 - 54.38: 354 54.38 - 72.51: 67 72.51 - 90.63: 38 Dihedral angle restraints: 25345 sinusoidal: 10269 harmonic: 15076 Sorted by residual: dihedral pdb=" CA TYR B1411 " pdb=" C TYR B1411 " pdb=" N ARG B1412 " pdb=" CA ARG B1412 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LEU C 551 " pdb=" C LEU C 551 " pdb=" N THR C 552 " pdb=" CA THR C 552 " ideal model delta harmonic sigma weight residual -180.00 -151.50 -28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ILE A2698 " pdb=" C ILE A2698 " pdb=" N SER A2699 " pdb=" CA SER A2699 " ideal model delta harmonic sigma weight residual -180.00 -151.52 -28.48 0 5.00e+00 4.00e-02 3.25e+01 ... (remaining 25342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 5801 0.106 - 0.212: 627 0.212 - 0.318: 76 0.318 - 0.424: 12 0.424 - 0.530: 4 Chirality restraints: 6520 Sorted by residual: chirality pdb=" CB ILE C 92 " pdb=" CA ILE C 92 " pdb=" CG1 ILE C 92 " pdb=" CG2 ILE C 92 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.02e+00 chirality pdb=" CB VAL C1355 " pdb=" CA VAL C1355 " pdb=" CG1 VAL C1355 " pdb=" CG2 VAL C1355 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CB ILE B1353 " pdb=" CA ILE B1353 " pdb=" CG1 ILE B1353 " pdb=" CG2 ILE B1353 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.57e+00 ... (remaining 6517 not shown) Planarity restraints: 7172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 688 " 0.032 2.00e-02 2.50e+03 3.67e-02 3.37e+01 pdb=" CG TRP B 688 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP B 688 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP B 688 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 688 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 688 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 688 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 688 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 688 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 688 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C1393 " 0.023 2.00e-02 2.50e+03 4.69e-02 2.20e+01 pdb=" C LYS C1393 " -0.081 2.00e-02 2.50e+03 pdb=" O LYS C1393 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE C1394 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 971 " 0.027 2.00e-02 2.50e+03 2.68e-02 1.79e+01 pdb=" CG TRP C 971 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP C 971 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP C 971 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP C 971 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 971 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 971 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 971 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 971 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 971 " 0.000 2.00e-02 2.50e+03 ... (remaining 7169 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8906 2.79 - 3.31: 38300 3.31 - 3.84: 68164 3.84 - 4.37: 76511 4.37 - 4.90: 125025 Nonbonded interactions: 316906 Sorted by model distance: nonbonded pdb=" O PHE B2458 " pdb=" OG SER B2462 " model vdw 2.258 2.440 nonbonded pdb=" OG1 THR B 634 " pdb=" OE1 GLU B 635 " model vdw 2.271 2.440 nonbonded pdb=" O LYS B1303 " pdb=" OG1 THR B1307 " model vdw 2.279 2.440 nonbonded pdb=" OE2 GLU C 323 " pdb=" OG SER C1451 " model vdw 2.281 2.440 nonbonded pdb=" O VAL A2849 " pdb=" OG SER B 225 " model vdw 2.290 2.440 ... (remaining 316901 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 8.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 29.840 Check model and map are aligned: 0.540 Set scattering table: 0.370 Process input model: 103.130 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.150 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 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 0.111 42111 Z= 0.364 Angle : 1.214 14.216 57055 Z= 0.665 Chirality : 0.070 0.530 6520 Planarity : 0.009 0.108 7172 Dihedral : 14.870 90.632 15509 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.11 % Favored : 93.87 % Rotamer: Outliers : 0.28 % Allowed : 1.09 % Favored : 98.62 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.65 % 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: -4.07 (0.09), residues: 5056 helix: -2.48 (0.07), residues: 3071 sheet: 0.22 (1.03), residues: 26 loop : -2.93 (0.12), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.003 TRP B 688 HIS 0.027 0.001 HIS D 287 PHE 0.073 0.003 PHE C1061 TYR 0.047 0.002 TYR A2795 ARG 0.025 0.001 ARG A2490 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 643 time to evaluate : 5.409 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: 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: symmetry clash revert: symmetry clash REVERT: A 1350 LEU cc_start: 0.9172 (mt) cc_final: 0.8667 (mt) REVERT: A 1662 MET cc_start: -0.1115 (mpp) cc_final: -0.2000 (mtt) REVERT: A 1903 GLN cc_start: 0.7454 (tt0) cc_final: 0.7109 (mm-40) REVERT: A 2017 ASP cc_start: 0.8677 (m-30) cc_final: 0.8046 (t0) REVERT: A 2120 VAL cc_start: 0.9348 (p) cc_final: 0.9091 (p) REVERT: A 2227 LEU cc_start: 0.8888 (mt) cc_final: 0.8515 (tt) REVERT: A 2336 ASN cc_start: 0.6833 (t0) cc_final: 0.6285 (p0) REVERT: A 2683 LEU cc_start: 0.8954 (mt) cc_final: 0.8687 (mt) REVERT: B 248 MET cc_start: 0.6254 (tpt) cc_final: 0.5963 (tmm) REVERT: B 541 MET cc_start: 0.0072 (tpt) cc_final: -0.0428 (tpp) REVERT: B 698 MET cc_start: 0.3194 (tpt) cc_final: 0.2935 (tpt) REVERT: B 804 MET cc_start: 0.8280 (ttp) cc_final: 0.7782 (ttp) REVERT: B 1059 MET cc_start: 0.8561 (tpp) cc_final: 0.8312 (tpp) REVERT: B 1089 LEU cc_start: 0.8878 (mt) cc_final: 0.8588 (pp) REVERT: B 1103 VAL cc_start: 0.8896 (m) cc_final: 0.8468 (t) REVERT: B 1157 ASP cc_start: 0.8641 (p0) cc_final: 0.8359 (p0) REVERT: B 1281 ILE cc_start: 0.9177 (mm) cc_final: 0.8868 (mm) REVERT: B 1296 GLU cc_start: 0.5786 (mt-10) cc_final: 0.5007 (mp0) REVERT: B 1397 MET cc_start: 0.8276 (mpp) cc_final: 0.6616 (ptt) REVERT: B 2069 MET cc_start: -0.2662 (tpp) cc_final: -0.3695 (tpp) REVERT: B 2251 LYS cc_start: 0.9070 (mmmm) cc_final: 0.8729 (ttpt) REVERT: B 2542 MET cc_start: 0.0301 (ptt) cc_final: -0.1209 (ttt) REVERT: C 50 VAL cc_start: 0.6892 (t) cc_final: 0.5249 (p) REVERT: C 86 MET cc_start: 0.0294 (mtt) cc_final: -0.0445 (mpp) REVERT: C 199 MET cc_start: -0.4145 (tpt) cc_final: -0.4353 (tpt) REVERT: C 335 MET cc_start: 0.1730 (ttp) cc_final: -0.0212 (mmm) REVERT: C 380 MET cc_start: 0.3507 (ttm) cc_final: 0.3298 (mmp) REVERT: C 495 PHE cc_start: 0.8644 (m-80) cc_final: 0.8339 (m-10) REVERT: C 547 MET cc_start: 0.6073 (mmm) cc_final: 0.5646 (mmm) REVERT: C 957 MET cc_start: 0.8022 (tpt) cc_final: 0.7109 (ptt) REVERT: C 1110 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8135 (pp20) REVERT: C 1119 GLU cc_start: 0.8993 (mp0) cc_final: 0.8525 (mp0) REVERT: C 1203 MET cc_start: 0.5143 (ptt) cc_final: 0.4664 (ptp) REVERT: C 1519 MET cc_start: 0.0352 (ppp) cc_final: -0.0634 (ptt) REVERT: D 246 CYS cc_start: 0.6831 (t) cc_final: 0.6202 (m) REVERT: D 345 LEU cc_start: 0.7785 (pp) cc_final: 0.7524 (tp) outliers start: 13 outliers final: 1 residues processed: 651 average time/residue: 0.5301 time to fit residues: 565.1422 Evaluate side-chains 399 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 398 time to evaluate : 4.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 511 random chunks: chunk 431 optimal weight: 6.9990 chunk 387 optimal weight: 0.5980 chunk 214 optimal weight: 0.0170 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 206 optimal weight: 4.9990 chunk 400 optimal weight: 0.0570 chunk 154 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 chunk 298 optimal weight: 0.9990 chunk 464 optimal weight: 20.0000 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 GLN A2078 HIS ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2191 ASN A2260 GLN ** A2613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 GLN A2713 ASN A2819 GLN B 684 GLN ** B 974 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2092 ASN B2136 ASN B2425 HIS ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 876 HIS C1126 HIS C1274 ASN C1318 HIS C1514 HIS D 242 ASN D 269 GLN D 273 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5644 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 42111 Z= 0.161 Angle : 0.636 11.725 57055 Z= 0.325 Chirality : 0.041 0.263 6520 Planarity : 0.005 0.072 7172 Dihedral : 5.287 26.278 5492 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: -2.32 (0.11), residues: 5056 helix: -0.98 (0.09), residues: 3154 sheet: -0.03 (0.95), residues: 26 loop : -2.40 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 688 HIS 0.009 0.001 HIS D 287 PHE 0.040 0.002 PHE C1141 TYR 0.019 0.001 TYR B 260 ARG 0.012 0.000 ARG B 877 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 471 time to evaluate : 4.474 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: 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: symmetry clash revert: symmetry clash REVERT: A 1662 MET cc_start: -0.1308 (mpp) cc_final: -0.1988 (mtm) REVERT: A 2017 ASP cc_start: 0.8557 (m-30) cc_final: 0.8054 (t0) REVERT: A 2123 LEU cc_start: 0.8912 (mt) cc_final: 0.8683 (mt) REVERT: A 2164 LEU cc_start: 0.9323 (mt) cc_final: 0.8822 (mt) REVERT: A 2187 MET cc_start: 0.8486 (ppp) cc_final: 0.8238 (ppp) REVERT: A 2227 LEU cc_start: 0.8946 (mt) cc_final: 0.8481 (tt) REVERT: A 2250 LEU cc_start: 0.8177 (tp) cc_final: 0.7924 (tp) REVERT: A 2264 LEU cc_start: 0.8642 (tp) cc_final: 0.8253 (tp) REVERT: A 2336 ASN cc_start: 0.6864 (t0) cc_final: 0.6205 (p0) REVERT: A 2368 MET cc_start: 0.8631 (mpp) cc_final: 0.8334 (mpp) REVERT: A 2719 VAL cc_start: 0.9355 (t) cc_final: 0.8945 (t) REVERT: B 541 MET cc_start: 0.0074 (tpt) cc_final: -0.0191 (tpp) REVERT: B 804 MET cc_start: 0.8308 (ttp) cc_final: 0.8013 (ttp) REVERT: B 1059 MET cc_start: 0.8596 (tpp) cc_final: 0.8359 (tpp) REVERT: B 1103 VAL cc_start: 0.8782 (m) cc_final: 0.8465 (t) REVERT: B 1285 MET cc_start: 0.8726 (mmp) cc_final: 0.8493 (mtp) REVERT: B 1296 GLU cc_start: 0.5889 (mt-10) cc_final: 0.5106 (mp0) REVERT: B 2069 MET cc_start: -0.2756 (tpp) cc_final: -0.3670 (tpp) REVERT: B 2117 MET cc_start: 0.6274 (mmm) cc_final: 0.5992 (mmm) REVERT: B 2542 MET cc_start: 0.0062 (ptt) cc_final: -0.0845 (ttt) REVERT: C 86 MET cc_start: 0.0361 (mtt) cc_final: -0.1470 (tpt) REVERT: C 286 MET cc_start: 0.5052 (tpt) cc_final: 0.4705 (tpt) REVERT: C 335 MET cc_start: 0.1150 (ttp) cc_final: -0.0802 (mmm) REVERT: C 380 MET cc_start: 0.3965 (ttm) cc_final: 0.3663 (mmp) REVERT: C 495 PHE cc_start: 0.8881 (m-80) cc_final: 0.8485 (m-10) REVERT: C 616 GLN cc_start: 0.8359 (mp-120) cc_final: 0.8136 (mm-40) REVERT: C 660 GLU cc_start: 0.7717 (tp30) cc_final: 0.6773 (tp30) REVERT: C 664 LYS cc_start: 0.8891 (ptpp) cc_final: 0.7546 (pttm) REVERT: C 936 LYS cc_start: 0.8148 (tptp) cc_final: 0.7747 (mmtt) REVERT: C 957 MET cc_start: 0.8247 (tpt) cc_final: 0.7173 (ptt) REVERT: C 1119 GLU cc_start: 0.9165 (mp0) cc_final: 0.8587 (mp0) REVERT: C 1203 MET cc_start: 0.4964 (ptt) cc_final: 0.2550 (mmm) REVERT: C 1364 GLU cc_start: 0.4233 (mp0) cc_final: 0.3528 (mp0) REVERT: C 1519 MET cc_start: 0.0857 (ppp) cc_final: -0.0222 (ptt) REVERT: D 246 CYS cc_start: 0.6428 (t) cc_final: 0.5801 (m) REVERT: D 345 LEU cc_start: 0.7954 (pp) cc_final: 0.7599 (tt) REVERT: D 348 ASN cc_start: 0.8068 (t0) cc_final: 0.7694 (p0) outliers start: 4 outliers final: 1 residues processed: 474 average time/residue: 0.5058 time to fit residues: 406.1342 Evaluate side-chains 367 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 366 time to evaluate : 5.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 511 random chunks: chunk 257 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 386 optimal weight: 7.9990 chunk 315 optimal weight: 50.0000 chunk 128 optimal weight: 0.7980 chunk 464 optimal weight: 5.9990 chunk 502 optimal weight: 0.7980 chunk 414 optimal weight: 0.8980 chunk 461 optimal weight: 8.9990 chunk 158 optimal weight: 2.9990 chunk 372 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1266 ASN A1461 HIS ** A1903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2040 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2613 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 GLN ** A2819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 974 ASN B 977 ASN B 998 GLN B2087 HIS B2425 HIS C 39 HIS C 829 ASN C1196 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 42111 Z= 0.161 Angle : 0.602 12.491 57055 Z= 0.305 Chirality : 0.040 0.241 6520 Planarity : 0.004 0.065 7172 Dihedral : 4.913 24.906 5492 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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 (0.11), residues: 5056 helix: -0.33 (0.09), residues: 3161 sheet: -0.79 (0.73), residues: 34 loop : -2.13 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 688 HIS 0.010 0.001 HIS C1137 PHE 0.032 0.001 PHE C 925 TYR 0.029 0.001 TYR B 196 ARG 0.008 0.000 ARG B1120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 450 time to evaluate : 5.243 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: 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 353 MET cc_start: 0.4810 (tpt) cc_final: 0.4456 (ttt) REVERT: A 840 MET cc_start: -0.3553 (ttp) cc_final: -0.5165 (mtp) REVERT: A 1662 MET cc_start: -0.0295 (mpp) cc_final: -0.1171 (mtm) REVERT: A 2017 ASP cc_start: 0.8627 (m-30) cc_final: 0.8159 (t0) REVERT: A 2187 MET cc_start: 0.8385 (ppp) cc_final: 0.8164 (ppp) REVERT: A 2227 LEU cc_start: 0.9031 (mt) cc_final: 0.8625 (tt) REVERT: A 2264 LEU cc_start: 0.8724 (tp) cc_final: 0.8280 (tp) REVERT: A 2269 PHE cc_start: 0.7142 (t80) cc_final: 0.6620 (t80) REVERT: A 2336 ASN cc_start: 0.7169 (t0) cc_final: 0.6397 (p0) REVERT: A 2370 LEU cc_start: 0.8863 (mt) cc_final: 0.8579 (mt) REVERT: A 2495 SER cc_start: 0.9445 (m) cc_final: 0.9194 (p) REVERT: A 2567 MET cc_start: 0.7082 (tpp) cc_final: 0.6788 (tpp) REVERT: B 231 MET cc_start: 0.8585 (mmp) cc_final: 0.8068 (mmt) REVERT: B 541 MET cc_start: 0.0839 (tpt) cc_final: 0.0629 (tpp) REVERT: B 804 MET cc_start: 0.8556 (ttp) cc_final: 0.8033 (ttp) REVERT: B 1103 VAL cc_start: 0.8687 (m) cc_final: 0.8384 (t) REVERT: B 1113 LEU cc_start: 0.9367 (mp) cc_final: 0.9158 (mt) REVERT: B 1157 ASP cc_start: 0.8173 (p0) cc_final: 0.7813 (p0) REVERT: B 1285 MET cc_start: 0.8805 (mmp) cc_final: 0.8526 (mtp) REVERT: B 1296 GLU cc_start: 0.5669 (mt-10) cc_final: 0.4974 (mp0) REVERT: B 2054 ARG cc_start: 0.3687 (ptm160) cc_final: 0.3442 (ptm160) REVERT: B 2069 MET cc_start: -0.2657 (tpp) cc_final: -0.3570 (tpp) REVERT: B 2125 ILE cc_start: 0.8349 (pt) cc_final: 0.8044 (pt) REVERT: B 2542 MET cc_start: -0.0172 (ptt) cc_final: -0.0902 (ttt) REVERT: C 55 MET cc_start: 0.0056 (tpt) cc_final: -0.0193 (tpt) REVERT: C 86 MET cc_start: 0.1601 (mtt) cc_final: -0.0607 (tpt) REVERT: C 286 MET cc_start: 0.5050 (tpt) cc_final: 0.4753 (tpt) REVERT: C 380 MET cc_start: 0.3992 (ttm) cc_final: 0.3672 (mmp) REVERT: C 492 LEU cc_start: 0.8960 (pp) cc_final: 0.8726 (pp) REVERT: C 495 PHE cc_start: 0.8920 (m-10) cc_final: 0.8565 (m-10) REVERT: C 585 PHE cc_start: 0.6862 (m-80) cc_final: 0.6631 (m-80) REVERT: C 936 LYS cc_start: 0.8113 (tptp) cc_final: 0.7773 (mmtt) REVERT: C 957 MET cc_start: 0.8238 (tpt) cc_final: 0.7127 (ptt) REVERT: C 997 PHE cc_start: 0.8629 (m-80) cc_final: 0.8079 (t80) REVERT: C 1105 MET cc_start: 0.8414 (ppp) cc_final: 0.7981 (ppp) REVERT: C 1119 GLU cc_start: 0.9181 (mp0) cc_final: 0.8754 (pm20) REVERT: C 1364 GLU cc_start: 0.4029 (mp0) cc_final: 0.3144 (mp0) REVERT: C 1425 MET cc_start: 0.8748 (mpp) cc_final: 0.8482 (mpp) REVERT: C 1432 VAL cc_start: 0.8427 (m) cc_final: 0.7751 (p) REVERT: C 1519 MET cc_start: 0.0638 (ppp) cc_final: -0.0204 (ptt) REVERT: D 246 CYS cc_start: 0.6550 (t) cc_final: 0.5911 (m) REVERT: D 336 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8265 (tm-30) REVERT: D 345 LEU cc_start: 0.7884 (pp) cc_final: 0.7224 (mp) outliers start: 2 outliers final: 0 residues processed: 451 average time/residue: 0.5044 time to fit residues: 386.7900 Evaluate side-chains 359 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 359 time to evaluate : 4.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 511 random chunks: chunk 459 optimal weight: 7.9990 chunk 349 optimal weight: 20.0000 chunk 241 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 221 optimal weight: 20.0000 chunk 312 optimal weight: 50.0000 chunk 466 optimal weight: 30.0000 chunk 493 optimal weight: 20.0000 chunk 243 optimal weight: 0.7980 chunk 442 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 HIS ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2040 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2200 HIS A2220 HIS A2613 ASN A2623 GLN ** A2686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 ASN B 998 GLN B1033 HIS B1049 ASN B1051 ASN ** B1275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 974 GLN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1469 HIS C1558 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5882 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 42111 Z= 0.224 Angle : 0.652 14.355 57055 Z= 0.333 Chirality : 0.041 0.217 6520 Planarity : 0.004 0.064 7172 Dihedral : 4.875 25.949 5492 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 0.02 % Allowed : 3.86 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: -1.19 (0.12), residues: 5056 helix: -0.09 (0.09), residues: 3143 sheet: -0.56 (0.76), residues: 34 loop : -1.93 (0.14), residues: 1879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 688 HIS 0.008 0.001 HIS B1152 PHE 0.030 0.002 PHE A1957 TYR 0.028 0.001 TYR D 271 ARG 0.007 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 428 time to evaluate : 4.769 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: 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 840 MET cc_start: -0.3509 (ttp) cc_final: -0.5096 (mtp) REVERT: A 1628 MET cc_start: 0.8981 (mpp) cc_final: 0.8664 (ptp) REVERT: A 1662 MET cc_start: -0.1068 (mpp) cc_final: -0.1815 (mtt) REVERT: A 2187 MET cc_start: 0.8606 (ppp) cc_final: 0.8356 (ppp) REVERT: A 2227 LEU cc_start: 0.9219 (mt) cc_final: 0.8821 (tt) REVERT: A 2269 PHE cc_start: 0.7776 (t80) cc_final: 0.7504 (t80) REVERT: A 2336 ASN cc_start: 0.7250 (t0) cc_final: 0.6387 (p0) REVERT: A 2370 LEU cc_start: 0.8942 (mt) cc_final: 0.8683 (mt) REVERT: A 2495 SER cc_start: 0.9567 (m) cc_final: 0.9298 (p) REVERT: B 248 MET cc_start: 0.6344 (ttt) cc_final: 0.5839 (ppp) REVERT: B 541 MET cc_start: 0.0769 (tpt) cc_final: 0.0559 (tpp) REVERT: B 804 MET cc_start: 0.8786 (ttp) cc_final: 0.7859 (ttp) REVERT: B 1103 VAL cc_start: 0.8743 (m) cc_final: 0.8341 (t) REVERT: B 2054 ARG cc_start: 0.3791 (ptm160) cc_final: 0.3568 (ptm160) REVERT: B 2069 MET cc_start: -0.2616 (tpp) cc_final: -0.3603 (tpp) REVERT: B 2117 MET cc_start: 0.7150 (mmm) cc_final: 0.6946 (mmm) REVERT: B 2251 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8520 (mttt) REVERT: B 2332 MET cc_start: -0.0970 (mmt) cc_final: -0.1188 (tpp) REVERT: B 2542 MET cc_start: 0.0036 (ptt) cc_final: -0.0554 (ttt) REVERT: E 37 MET cc_start: -0.4038 (ttm) cc_final: -0.4252 (ttm) REVERT: E 52 MET cc_start: 0.4611 (mtm) cc_final: 0.4373 (mtp) REVERT: C 55 MET cc_start: 0.0041 (tpt) cc_final: -0.0387 (tpt) REVERT: C 86 MET cc_start: 0.2106 (mtt) cc_final: -0.0055 (tpt) REVERT: C 199 MET cc_start: -0.3896 (tpt) cc_final: -0.4324 (tpt) REVERT: C 286 MET cc_start: 0.5074 (tpt) cc_final: 0.4773 (tpt) REVERT: C 495 PHE cc_start: 0.8944 (m-10) cc_final: 0.8590 (m-10) REVERT: C 517 LEU cc_start: 0.9100 (tp) cc_final: 0.8570 (pp) REVERT: C 936 LYS cc_start: 0.8153 (tptp) cc_final: 0.7806 (mmtt) REVERT: C 997 PHE cc_start: 0.8803 (m-80) cc_final: 0.8089 (m-80) REVERT: C 1105 MET cc_start: 0.8442 (ppp) cc_final: 0.8222 (ppp) REVERT: C 1108 LEU cc_start: 0.8847 (tp) cc_final: 0.8628 (tp) REVERT: C 1119 GLU cc_start: 0.9254 (mp0) cc_final: 0.8707 (mp0) REVERT: C 1425 MET cc_start: 0.8840 (mpp) cc_final: 0.8596 (mpp) REVERT: C 1519 MET cc_start: 0.0660 (ppp) cc_final: -0.0162 (ptt) REVERT: D 246 CYS cc_start: 0.6694 (t) cc_final: 0.6089 (m) outliers start: 1 outliers final: 1 residues processed: 429 average time/residue: 0.5004 time to fit residues: 365.2606 Evaluate side-chains 344 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 4.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 511 random chunks: chunk 411 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 367 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 421 optimal weight: 4.9990 chunk 341 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 252 optimal weight: 0.4980 chunk 443 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2040 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2605 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 GLN A2625 GLN ** A2819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2178 GLN B2353 HIS C 56 ASN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1189 HIS ** C1460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 42111 Z= 0.259 Angle : 0.689 14.855 57055 Z= 0.353 Chirality : 0.043 0.279 6520 Planarity : 0.005 0.066 7172 Dihedral : 4.964 23.129 5492 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.02 % Allowed : 3.56 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: -1.22 (0.12), residues: 5056 helix: -0.14 (0.09), residues: 3149 sheet: -0.66 (0.77), residues: 34 loop : -1.88 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 688 HIS 0.008 0.001 HIS B1152 PHE 0.041 0.002 PHE C1011 TYR 0.019 0.001 TYR C 406 ARG 0.012 0.001 ARG A2561 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 409 time to evaluate : 4.856 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: 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 840 MET cc_start: -0.3416 (ttp) cc_final: -0.5043 (mtp) REVERT: A 1350 LEU cc_start: 0.9363 (mt) cc_final: 0.9116 (mt) REVERT: A 1628 MET cc_start: 0.8997 (mpp) cc_final: 0.8717 (ptp) REVERT: A 1662 MET cc_start: -0.0927 (mpp) cc_final: -0.1574 (mtt) REVERT: A 1957 PHE cc_start: 0.8011 (t80) cc_final: 0.7779 (t80) REVERT: A 2227 LEU cc_start: 0.9236 (mt) cc_final: 0.8863 (tt) REVERT: A 2269 PHE cc_start: 0.8120 (t80) cc_final: 0.7866 (t80) REVERT: A 2370 LEU cc_start: 0.8929 (mt) cc_final: 0.8665 (mt) REVERT: A 2495 SER cc_start: 0.9591 (m) cc_final: 0.9347 (p) REVERT: A 2565 MET cc_start: 0.9227 (mpp) cc_final: 0.8597 (mpt) REVERT: B 178 MET cc_start: 0.7349 (tmm) cc_final: 0.6920 (ptp) REVERT: B 248 MET cc_start: 0.6255 (ttt) cc_final: 0.5815 (ppp) REVERT: B 541 MET cc_start: 0.0496 (tpt) cc_final: 0.0174 (tpp) REVERT: B 572 MET cc_start: 0.7911 (ptt) cc_final: 0.7552 (ptt) REVERT: B 804 MET cc_start: 0.8776 (ttp) cc_final: 0.7775 (ttp) REVERT: B 1103 VAL cc_start: 0.8783 (m) cc_final: 0.8373 (m) REVERT: B 1157 ASP cc_start: 0.8555 (p0) cc_final: 0.8142 (p0) REVERT: B 1281 ILE cc_start: 0.9396 (mm) cc_final: 0.8985 (mm) REVERT: B 1285 MET cc_start: 0.8802 (mtp) cc_final: 0.8411 (mmt) REVERT: B 2049 MET cc_start: 0.9322 (mmp) cc_final: 0.9035 (mmm) REVERT: B 2069 MET cc_start: -0.2570 (tpp) cc_final: -0.3616 (tpp) REVERT: B 2117 MET cc_start: 0.7423 (mmm) cc_final: 0.7142 (mmm) REVERT: B 2335 MET cc_start: -0.2722 (ttt) cc_final: -0.2964 (ttt) REVERT: B 2542 MET cc_start: 0.0158 (ptt) cc_final: -0.0498 (ttt) REVERT: E 37 MET cc_start: -0.4175 (ttm) cc_final: -0.4400 (ttm) REVERT: C 55 MET cc_start: 0.0697 (tpt) cc_final: 0.0279 (tpt) REVERT: C 86 MET cc_start: 0.2419 (mtt) cc_final: 0.0201 (tpt) REVERT: C 199 MET cc_start: -0.3850 (tpt) cc_final: -0.4327 (tpt) REVERT: C 286 MET cc_start: 0.5226 (tpt) cc_final: 0.4892 (tpt) REVERT: C 492 LEU cc_start: 0.9069 (pp) cc_final: 0.8663 (pp) REVERT: C 495 PHE cc_start: 0.8904 (m-80) cc_final: 0.8363 (m-80) REVERT: C 517 LEU cc_start: 0.9095 (tp) cc_final: 0.8555 (pp) REVERT: C 545 MET cc_start: -0.0296 (mmt) cc_final: -0.0873 (mpp) REVERT: C 661 SER cc_start: 0.9057 (p) cc_final: 0.8818 (t) REVERT: C 936 LYS cc_start: 0.8245 (tptp) cc_final: 0.7858 (mmtt) REVERT: C 997 PHE cc_start: 0.8970 (m-80) cc_final: 0.8085 (m-80) REVERT: C 1113 SER cc_start: 0.8791 (m) cc_final: 0.8511 (p) REVERT: C 1119 GLU cc_start: 0.9265 (mp0) cc_final: 0.8690 (mp0) REVERT: C 1425 MET cc_start: 0.8944 (mpp) cc_final: 0.8740 (mpp) REVERT: C 1519 MET cc_start: 0.1052 (ppp) cc_final: 0.0170 (ptt) REVERT: D 246 CYS cc_start: 0.6761 (t) cc_final: 0.6170 (m) outliers start: 1 outliers final: 0 residues processed: 409 average time/residue: 0.5265 time to fit residues: 368.6442 Evaluate side-chains 332 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 4.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 511 random chunks: chunk 166 optimal weight: 0.7980 chunk 444 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 494 optimal weight: 4.9990 chunk 410 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 ASN ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2040 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2265 HIS A2336 ASN A2605 GLN A2623 GLN ** A2819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2080 GLN B2353 HIS B2474 HIS C 569 HIS ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1291 HIS C1460 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 42111 Z= 0.206 Angle : 0.641 14.478 57055 Z= 0.324 Chirality : 0.041 0.234 6520 Planarity : 0.004 0.069 7172 Dihedral : 4.890 23.741 5492 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.07 % Allowed : 2.14 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: -0.99 (0.12), residues: 5056 helix: -0.00 (0.09), residues: 3174 sheet: -0.47 (0.77), residues: 34 loop : -1.72 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 688 HIS 0.005 0.001 HIS B2353 PHE 0.029 0.002 PHE B2177 TYR 0.018 0.001 TYR A1908 ARG 0.008 0.000 ARG A2852 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 406 time to evaluate : 4.764 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 MET cc_start: -0.3412 (ttp) cc_final: -0.5064 (mtp) REVERT: A 1350 LEU cc_start: 0.9327 (mt) cc_final: 0.9049 (mt) REVERT: A 1587 MET cc_start: -0.0861 (tpt) cc_final: -0.1192 (tpt) REVERT: A 1628 MET cc_start: 0.9023 (mpp) cc_final: 0.8686 (ptp) REVERT: A 1662 MET cc_start: -0.0889 (mpp) cc_final: -0.1386 (mtm) REVERT: A 1957 PHE cc_start: 0.7983 (t80) cc_final: 0.7707 (t80) REVERT: A 2227 LEU cc_start: 0.9195 (mt) cc_final: 0.8851 (tt) REVERT: A 2370 LEU cc_start: 0.8870 (mt) cc_final: 0.8607 (mt) REVERT: A 2495 SER cc_start: 0.9576 (m) cc_final: 0.9354 (p) REVERT: A 2565 MET cc_start: 0.8884 (mpp) cc_final: 0.8670 (mtt) REVERT: B 231 MET cc_start: 0.8645 (mmp) cc_final: 0.8130 (mmt) REVERT: B 248 MET cc_start: 0.6102 (ttt) cc_final: 0.5746 (ppp) REVERT: B 541 MET cc_start: 0.0552 (tpt) cc_final: 0.0211 (tpp) REVERT: B 572 MET cc_start: 0.8033 (ptt) cc_final: 0.7676 (ptt) REVERT: B 602 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8306 (pp20) REVERT: B 804 MET cc_start: 0.8686 (ttp) cc_final: 0.7628 (ttp) REVERT: B 1103 VAL cc_start: 0.8762 (m) cc_final: 0.8352 (m) REVERT: B 1157 ASP cc_start: 0.8540 (p0) cc_final: 0.8139 (p0) REVERT: B 1281 ILE cc_start: 0.9405 (mm) cc_final: 0.8964 (mm) REVERT: B 1285 MET cc_start: 0.8830 (mtp) cc_final: 0.8461 (mmt) REVERT: B 2049 MET cc_start: 0.9302 (mmp) cc_final: 0.9007 (mmm) REVERT: B 2054 ARG cc_start: 0.3571 (ptm160) cc_final: 0.3355 (ptm160) REVERT: B 2069 MET cc_start: -0.2352 (tpp) cc_final: -0.3400 (tpp) REVERT: B 2335 MET cc_start: -0.2280 (ttt) cc_final: -0.3081 (ttt) REVERT: B 2542 MET cc_start: 0.0259 (ptt) cc_final: -0.0326 (ttt) REVERT: C 55 MET cc_start: 0.0525 (tpt) cc_final: 0.0115 (tpt) REVERT: C 86 MET cc_start: 0.2313 (mtt) cc_final: 0.1210 (ptp) REVERT: C 199 MET cc_start: -0.3262 (tpt) cc_final: -0.3531 (tpt) REVERT: C 495 PHE cc_start: 0.8888 (m-80) cc_final: 0.8626 (m-10) REVERT: C 517 LEU cc_start: 0.9202 (tp) cc_final: 0.8664 (pp) REVERT: C 545 MET cc_start: 0.0053 (mmt) cc_final: -0.0472 (mpp) REVERT: C 570 MET cc_start: -0.0813 (mmm) cc_final: -0.1082 (tpt) REVERT: C 936 LYS cc_start: 0.8268 (tptp) cc_final: 0.7864 (mmtt) REVERT: C 997 PHE cc_start: 0.9047 (m-80) cc_final: 0.8175 (m-80) REVERT: C 1105 MET cc_start: 0.8341 (ppp) cc_final: 0.7969 (ppp) REVERT: C 1113 SER cc_start: 0.8739 (m) cc_final: 0.8468 (p) REVERT: C 1119 GLU cc_start: 0.9241 (mp0) cc_final: 0.8640 (mp0) REVERT: C 1258 MET cc_start: 0.1354 (tmm) cc_final: 0.1107 (tmm) REVERT: C 1432 VAL cc_start: 0.8313 (m) cc_final: 0.7700 (p) REVERT: C 1519 MET cc_start: 0.1023 (ppp) cc_final: 0.0105 (ptt) REVERT: D 246 CYS cc_start: 0.6806 (t) cc_final: 0.6218 (m) outliers start: 3 outliers final: 0 residues processed: 409 average time/residue: 0.5022 time to fit residues: 350.2947 Evaluate side-chains 331 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 5.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 511 random chunks: chunk 476 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 281 optimal weight: 0.8980 chunk 361 optimal weight: 30.0000 chunk 279 optimal weight: 4.9990 chunk 416 optimal weight: 10.0000 chunk 276 optimal weight: 0.2980 chunk 492 optimal weight: 10.0000 chunk 308 optimal weight: 0.6980 chunk 300 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 ASN ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1892 HIS ** A1903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 GLN A2625 GLN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2100 GLN ** C 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 42111 Z= 0.232 Angle : 0.658 14.230 57055 Z= 0.336 Chirality : 0.042 0.221 6520 Planarity : 0.004 0.072 7172 Dihedral : 4.913 24.106 5492 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.02 % Allowed : 1.90 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: -0.92 (0.12), residues: 5056 helix: 0.02 (0.09), residues: 3171 sheet: -0.11 (1.02), residues: 24 loop : -1.63 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 688 HIS 0.005 0.001 HIS A2265 PHE 0.027 0.002 PHE C1011 TYR 0.020 0.001 TYR C 64 ARG 0.011 0.001 ARG A2093 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 391 time to evaluate : 4.937 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1350 LEU cc_start: 0.9353 (mt) cc_final: 0.9073 (mt) REVERT: A 1587 MET cc_start: -0.0869 (tpt) cc_final: -0.1250 (tpt) REVERT: A 1628 MET cc_start: 0.9012 (mpp) cc_final: 0.8703 (ptp) REVERT: A 1662 MET cc_start: -0.0742 (mpp) cc_final: -0.1192 (mtm) REVERT: A 1909 MET cc_start: 0.8577 (mmp) cc_final: 0.8344 (mmm) REVERT: A 1948 MET cc_start: 0.6873 (ptt) cc_final: 0.6654 (ptt) REVERT: A 1957 PHE cc_start: 0.8021 (t80) cc_final: 0.7647 (t80) REVERT: A 2227 LEU cc_start: 0.9222 (mt) cc_final: 0.8853 (tt) REVERT: A 2269 PHE cc_start: 0.8125 (t80) cc_final: 0.7772 (t80) REVERT: A 2495 SER cc_start: 0.9590 (m) cc_final: 0.9374 (p) REVERT: A 2565 MET cc_start: 0.9055 (mpp) cc_final: 0.8729 (mtt) REVERT: A 2805 PHE cc_start: 0.8293 (m-80) cc_final: 0.8069 (m-80) REVERT: B 178 MET cc_start: 0.7568 (tmm) cc_final: 0.7040 (ptp) REVERT: B 541 MET cc_start: 0.0328 (tpt) cc_final: 0.0038 (tpp) REVERT: B 572 MET cc_start: 0.8167 (ptt) cc_final: 0.7845 (ptt) REVERT: B 804 MET cc_start: 0.8787 (ttp) cc_final: 0.7741 (ttp) REVERT: B 1103 VAL cc_start: 0.8761 (m) cc_final: 0.8411 (m) REVERT: B 1157 ASP cc_start: 0.8558 (p0) cc_final: 0.8150 (p0) REVERT: B 1281 ILE cc_start: 0.9448 (mm) cc_final: 0.9000 (mm) REVERT: B 1285 MET cc_start: 0.8828 (mtp) cc_final: 0.8458 (mmt) REVERT: B 2049 MET cc_start: 0.9323 (mmp) cc_final: 0.9041 (mmm) REVERT: B 2054 ARG cc_start: 0.3744 (ptm160) cc_final: 0.3529 (ptm160) REVERT: B 2069 MET cc_start: -0.2175 (tpp) cc_final: -0.3236 (tpp) REVERT: B 2335 MET cc_start: -0.1793 (ttt) cc_final: -0.2074 (ttt) REVERT: B 2542 MET cc_start: 0.0298 (ptt) cc_final: -0.0255 (ttt) REVERT: E 72 MET cc_start: 0.1448 (ptp) cc_final: 0.0323 (tpt) REVERT: C 55 MET cc_start: 0.0837 (tpt) cc_final: 0.0527 (tpt) REVERT: C 86 MET cc_start: 0.2485 (mtt) cc_final: 0.1447 (ptp) REVERT: C 199 MET cc_start: -0.3403 (tpt) cc_final: -0.3654 (tpt) REVERT: C 286 MET cc_start: 0.5342 (tpt) cc_final: 0.4900 (tpt) REVERT: C 495 PHE cc_start: 0.8967 (m-80) cc_final: 0.8688 (m-10) REVERT: C 517 LEU cc_start: 0.9249 (tp) cc_final: 0.8686 (pp) REVERT: C 545 MET cc_start: 0.0472 (mmt) cc_final: 0.0157 (mpp) REVERT: C 570 MET cc_start: -0.0570 (mmm) cc_final: -0.0880 (tpt) REVERT: C 936 LYS cc_start: 0.8257 (tptp) cc_final: 0.7852 (mmtt) REVERT: C 938 MET cc_start: -0.0263 (tpt) cc_final: -0.0840 (tpt) REVERT: C 997 PHE cc_start: 0.9088 (m-80) cc_final: 0.8324 (m-80) REVERT: C 1105 MET cc_start: 0.8455 (ppp) cc_final: 0.8179 (ppp) REVERT: C 1113 SER cc_start: 0.8855 (m) cc_final: 0.8620 (p) REVERT: C 1119 GLU cc_start: 0.9156 (mp0) cc_final: 0.8610 (mp0) REVERT: C 1151 PHE cc_start: 0.7833 (m-10) cc_final: 0.7269 (m-10) REVERT: C 1203 MET cc_start: 0.5024 (ptt) cc_final: 0.4478 (ptt) REVERT: C 1452 LEU cc_start: 0.8743 (pp) cc_final: 0.8343 (tt) REVERT: C 1519 MET cc_start: 0.1208 (ppp) cc_final: 0.0198 (ptt) REVERT: D 246 CYS cc_start: 0.6971 (t) cc_final: 0.6382 (m) outliers start: 1 outliers final: 0 residues processed: 392 average time/residue: 0.5273 time to fit residues: 355.3024 Evaluate side-chains 318 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 318 time to evaluate : 4.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 511 random chunks: chunk 304 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 chunk 294 optimal weight: 4.9990 chunk 148 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 95 optimal weight: 30.0000 chunk 313 optimal weight: 8.9990 chunk 335 optimal weight: 30.0000 chunk 243 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 387 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 895 ASN ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1892 HIS ** A2076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2336 ASN A2623 GLN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 HIS B1180 HIS B1396 GLN B2381 ASN B2588 HIS C 616 GLN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42111 Z= 0.205 Angle : 0.649 13.841 57055 Z= 0.330 Chirality : 0.041 0.218 6520 Planarity : 0.004 0.074 7172 Dihedral : 4.896 23.046 5492 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.04 % Allowed : 1.11 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: -0.83 (0.12), residues: 5056 helix: 0.09 (0.09), residues: 3174 sheet: -0.90 (0.77), residues: 34 loop : -1.58 (0.15), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP B 688 HIS 0.007 0.001 HIS B2588 PHE 0.044 0.002 PHE C1453 TYR 0.018 0.001 TYR A1908 ARG 0.012 0.000 ARG C 640 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 389 time to evaluate : 4.836 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: symmetry clash revert: symmetry clash REVERT: A 840 MET cc_start: -0.3556 (ttp) cc_final: -0.5213 (mtp) REVERT: A 1350 LEU cc_start: 0.9325 (mt) cc_final: 0.9034 (mt) REVERT: A 1587 MET cc_start: -0.0901 (tpt) cc_final: -0.1254 (tpt) REVERT: A 1628 MET cc_start: 0.9020 (mpp) cc_final: 0.8714 (ptp) REVERT: A 1662 MET cc_start: -0.0554 (mpp) cc_final: -0.1118 (mtt) REVERT: A 1957 PHE cc_start: 0.8036 (t80) cc_final: 0.7593 (t80) REVERT: A 2227 LEU cc_start: 0.9166 (mt) cc_final: 0.8800 (tt) REVERT: A 2269 PHE cc_start: 0.8071 (t80) cc_final: 0.7820 (t80) REVERT: A 2495 SER cc_start: 0.9588 (m) cc_final: 0.9354 (p) REVERT: A 2565 MET cc_start: 0.9065 (mpp) cc_final: 0.8546 (mtm) REVERT: B 178 MET cc_start: 0.7569 (tmm) cc_final: 0.7078 (ptp) REVERT: B 541 MET cc_start: 0.0093 (tpt) cc_final: -0.0435 (tpp) REVERT: B 572 MET cc_start: 0.8175 (ptt) cc_final: 0.7841 (ptt) REVERT: B 804 MET cc_start: 0.8787 (ttp) cc_final: 0.7762 (ttp) REVERT: B 1103 VAL cc_start: 0.8721 (m) cc_final: 0.8385 (m) REVERT: B 1157 ASP cc_start: 0.8557 (p0) cc_final: 0.8199 (p0) REVERT: B 1281 ILE cc_start: 0.9472 (mm) cc_final: 0.8897 (pt) REVERT: B 1285 MET cc_start: 0.8845 (mtp) cc_final: 0.8455 (mmt) REVERT: B 2049 MET cc_start: 0.9312 (mmp) cc_final: 0.8999 (mmm) REVERT: B 2054 ARG cc_start: 0.3723 (ptm160) cc_final: 0.3490 (ptm160) REVERT: B 2069 MET cc_start: -0.2077 (tpp) cc_final: -0.3211 (tpp) REVERT: B 2335 MET cc_start: -0.1450 (ttt) cc_final: -0.2149 (ttt) REVERT: B 2542 MET cc_start: 0.0458 (ptt) cc_final: -0.0172 (ttt) REVERT: E 72 MET cc_start: 0.1349 (ptp) cc_final: 0.0232 (tpt) REVERT: C 55 MET cc_start: 0.1078 (tpt) cc_final: 0.0782 (tpt) REVERT: C 86 MET cc_start: 0.2603 (mtt) cc_final: 0.1700 (ptp) REVERT: C 199 MET cc_start: -0.3635 (tpt) cc_final: -0.3858 (tpt) REVERT: C 286 MET cc_start: 0.4959 (tpt) cc_final: 0.4501 (tpt) REVERT: C 495 PHE cc_start: 0.8971 (m-80) cc_final: 0.8696 (m-10) REVERT: C 517 LEU cc_start: 0.9234 (tp) cc_final: 0.8688 (pp) REVERT: C 527 MET cc_start: 0.4562 (tpt) cc_final: 0.4183 (ptt) REVERT: C 570 MET cc_start: -0.0213 (mmm) cc_final: -0.0450 (tpt) REVERT: C 913 MET cc_start: 0.3896 (ttp) cc_final: 0.3547 (ttt) REVERT: C 936 LYS cc_start: 0.8279 (tptp) cc_final: 0.7854 (mmtt) REVERT: C 938 MET cc_start: -0.0255 (tpt) cc_final: -0.0736 (tpt) REVERT: C 997 PHE cc_start: 0.9103 (m-80) cc_final: 0.8434 (m-80) REVERT: C 1105 MET cc_start: 0.8473 (ppp) cc_final: 0.8232 (ppp) REVERT: C 1113 SER cc_start: 0.8803 (m) cc_final: 0.8582 (p) REVERT: C 1119 GLU cc_start: 0.9142 (mp0) cc_final: 0.8607 (mp0) REVERT: C 1151 PHE cc_start: 0.7852 (m-10) cc_final: 0.7266 (m-10) REVERT: C 1203 MET cc_start: 0.4962 (ptt) cc_final: 0.4423 (ptt) REVERT: C 1452 LEU cc_start: 0.8654 (pp) cc_final: 0.8256 (tt) REVERT: C 1468 ARG cc_start: 0.5597 (mtt180) cc_final: 0.5351 (tmt170) REVERT: C 1519 MET cc_start: 0.1172 (ppp) cc_final: 0.0194 (ptt) REVERT: D 246 CYS cc_start: 0.6835 (t) cc_final: 0.6273 (m) outliers start: 2 outliers final: 0 residues processed: 390 average time/residue: 0.5016 time to fit residues: 336.6446 Evaluate side-chains 310 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 4.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 511 random chunks: chunk 448 optimal weight: 7.9990 chunk 471 optimal weight: 5.9990 chunk 430 optimal weight: 10.0000 chunk 458 optimal weight: 0.9980 chunk 276 optimal weight: 6.9990 chunk 199 optimal weight: 4.9990 chunk 360 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 414 optimal weight: 0.7980 chunk 434 optimal weight: 2.9990 chunk 457 optimal weight: 0.0050 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2336 ASN A2623 GLN A2819 GLN B 312 HIS B 313 ASN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2178 GLN C 125 GLN C 198 GLN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1196 ASN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42111 Z= 0.160 Angle : 0.623 13.087 57055 Z= 0.311 Chirality : 0.041 0.215 6520 Planarity : 0.004 0.073 7172 Dihedral : 4.735 24.467 5492 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.02 % Allowed : 0.59 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: -0.62 (0.12), residues: 5056 helix: 0.24 (0.09), residues: 3187 sheet: -0.70 (0.76), residues: 34 loop : -1.48 (0.15), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B 688 HIS 0.004 0.001 HIS C 583 PHE 0.033 0.001 PHE D 368 TYR 0.031 0.001 TYR C 582 ARG 0.006 0.000 ARG A2135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 4.750 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: symmetry clash REVERT: A 1350 LEU cc_start: 0.9299 (mt) cc_final: 0.8997 (mt) REVERT: A 1457 MET cc_start: 0.5059 (mmp) cc_final: 0.3976 (tpp) REVERT: A 1587 MET cc_start: -0.0825 (tpt) cc_final: -0.1257 (tpt) REVERT: A 1628 MET cc_start: 0.9017 (mpp) cc_final: 0.8728 (ptp) REVERT: A 1909 MET cc_start: 0.8541 (mmp) cc_final: 0.8340 (mmm) REVERT: A 1957 PHE cc_start: 0.8025 (t80) cc_final: 0.7603 (t80) REVERT: A 2227 LEU cc_start: 0.9136 (mt) cc_final: 0.8702 (tt) REVERT: A 2269 PHE cc_start: 0.7873 (t80) cc_final: 0.7657 (t80) REVERT: A 2368 MET cc_start: 0.8497 (mpp) cc_final: 0.8053 (mpp) REVERT: A 2495 SER cc_start: 0.9569 (m) cc_final: 0.9287 (p) REVERT: A 2680 LEU cc_start: 0.9169 (mt) cc_final: 0.8748 (pp) REVERT: A 2801 ILE cc_start: 0.9151 (tt) cc_final: 0.8852 (tt) REVERT: B 178 MET cc_start: 0.7549 (tmm) cc_final: 0.7063 (ptp) REVERT: B 541 MET cc_start: 0.0071 (tpt) cc_final: -0.0486 (tpp) REVERT: B 572 MET cc_start: 0.8194 (ptt) cc_final: 0.7850 (ptt) REVERT: B 804 MET cc_start: 0.8724 (ttp) cc_final: 0.7706 (ttp) REVERT: B 809 LEU cc_start: 0.9450 (tt) cc_final: 0.9234 (tt) REVERT: B 1103 VAL cc_start: 0.8673 (m) cc_final: 0.8350 (m) REVERT: B 1157 ASP cc_start: 0.8489 (p0) cc_final: 0.8118 (p0) REVERT: B 1281 ILE cc_start: 0.9422 (mm) cc_final: 0.8848 (pt) REVERT: B 1285 MET cc_start: 0.8846 (mtp) cc_final: 0.8495 (mmt) REVERT: B 1397 MET cc_start: 0.8479 (mpp) cc_final: 0.7946 (mpp) REVERT: B 2049 MET cc_start: 0.9244 (mmp) cc_final: 0.8938 (mmm) REVERT: B 2069 MET cc_start: -0.2173 (tpp) cc_final: -0.3121 (tpp) REVERT: B 2335 MET cc_start: -0.1533 (ttt) cc_final: -0.2258 (ttt) REVERT: B 2542 MET cc_start: 0.0490 (ptt) cc_final: -0.0109 (ttt) REVERT: E 72 MET cc_start: 0.1765 (ptp) cc_final: 0.0728 (tpt) REVERT: C 55 MET cc_start: 0.0695 (tpt) cc_final: 0.0436 (tpt) REVERT: C 86 MET cc_start: 0.2655 (mtt) cc_final: 0.1563 (mpp) REVERT: C 286 MET cc_start: 0.5514 (tpt) cc_final: 0.5027 (tpt) REVERT: C 495 PHE cc_start: 0.8995 (m-80) cc_final: 0.8721 (m-10) REVERT: C 517 LEU cc_start: 0.9254 (tp) cc_final: 0.8697 (pp) REVERT: C 527 MET cc_start: 0.4584 (tpt) cc_final: 0.4247 (ptt) REVERT: C 570 MET cc_start: -0.0504 (mmm) cc_final: -0.0744 (tpt) REVERT: C 579 PHE cc_start: 0.7910 (m-10) cc_final: 0.6692 (t80) REVERT: C 936 LYS cc_start: 0.8258 (tptp) cc_final: 0.7873 (mmtm) REVERT: C 938 MET cc_start: -0.0321 (tpt) cc_final: -0.0731 (tpt) REVERT: C 997 PHE cc_start: 0.9138 (m-80) cc_final: 0.8442 (m-80) REVERT: C 1105 MET cc_start: 0.8557 (ppp) cc_final: 0.8314 (ppp) REVERT: C 1119 GLU cc_start: 0.9117 (mp0) cc_final: 0.8599 (mp0) REVERT: C 1151 PHE cc_start: 0.7915 (m-10) cc_final: 0.7393 (m-10) REVERT: C 1203 MET cc_start: 0.5341 (ptt) cc_final: 0.4978 (ptt) REVERT: C 1432 VAL cc_start: 0.8404 (m) cc_final: 0.7530 (p) REVERT: C 1452 LEU cc_start: 0.8994 (pp) cc_final: 0.8676 (tt) REVERT: C 1468 ARG cc_start: 0.5725 (mtt180) cc_final: 0.5451 (tmt170) REVERT: C 1519 MET cc_start: 0.0975 (ppp) cc_final: 0.0074 (ptt) REVERT: D 246 CYS cc_start: 0.6801 (t) cc_final: 0.6254 (m) outliers start: 1 outliers final: 1 residues processed: 394 average time/residue: 0.5079 time to fit residues: 344.8732 Evaluate side-chains 320 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 4.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 511 random chunks: chunk 301 optimal weight: 8.9990 chunk 485 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 230 optimal weight: 9.9990 chunk 337 optimal weight: 9.9990 chunk 509 optimal weight: 0.0670 chunk 468 optimal weight: 0.8980 chunk 405 optimal weight: 0.5980 chunk 42 optimal weight: 6.9990 chunk 313 optimal weight: 0.0000 chunk 248 optimal weight: 8.9990 overall best weight: 0.9124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2623 GLN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1396 GLN C 974 GLN ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 42111 Z= 0.156 Angle : 0.620 12.527 57055 Z= 0.308 Chirality : 0.041 0.220 6520 Planarity : 0.004 0.073 7172 Dihedral : 4.642 25.610 5492 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: -0.49 (0.12), residues: 5056 helix: 0.34 (0.09), residues: 3197 sheet: -0.55 (0.77), residues: 34 loop : -1.43 (0.15), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B 688 HIS 0.005 0.001 HIS A2115 PHE 0.030 0.001 PHE D 368 TYR 0.014 0.001 TYR A1908 ARG 0.007 0.000 ARG C1556 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10112 Ramachandran restraints generated. 5056 Oldfield, 0 Emsley, 5056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 5.271 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: symmetry clash REVERT: A 840 MET cc_start: -0.3545 (ttp) cc_final: -0.5228 (mtp) REVERT: A 1350 LEU cc_start: 0.9274 (mt) cc_final: 0.8961 (mt) REVERT: A 1457 MET cc_start: 0.5049 (mmp) cc_final: 0.3471 (tpp) REVERT: A 1587 MET cc_start: -0.0936 (tpt) cc_final: -0.1415 (tpt) REVERT: A 1628 MET cc_start: 0.9015 (mpp) cc_final: 0.8736 (ptp) REVERT: A 1909 MET cc_start: 0.8494 (mmp) cc_final: 0.8137 (mmm) REVERT: A 1957 PHE cc_start: 0.8048 (t80) cc_final: 0.7599 (t80) REVERT: A 2123 LEU cc_start: 0.8846 (mt) cc_final: 0.8631 (mt) REVERT: A 2227 LEU cc_start: 0.9112 (mt) cc_final: 0.8622 (tt) REVERT: A 2237 MET cc_start: 0.9014 (tpp) cc_final: 0.8695 (tpt) REVERT: A 2269 PHE cc_start: 0.7898 (t80) cc_final: 0.7668 (t80) REVERT: A 2368 MET cc_start: 0.8461 (mpp) cc_final: 0.8101 (mpp) REVERT: A 2495 SER cc_start: 0.9559 (m) cc_final: 0.9257 (p) REVERT: A 2565 MET cc_start: 0.8800 (mtm) cc_final: 0.7959 (mpp) REVERT: A 2680 LEU cc_start: 0.9163 (mt) cc_final: 0.8751 (pp) REVERT: B 178 MET cc_start: 0.7515 (tmm) cc_final: 0.7021 (ptp) REVERT: B 541 MET cc_start: 0.0179 (tpt) cc_final: -0.0340 (tpp) REVERT: B 572 MET cc_start: 0.8225 (ptt) cc_final: 0.7845 (ptt) REVERT: B 804 MET cc_start: 0.8737 (ttp) cc_final: 0.7718 (ttp) REVERT: B 1103 VAL cc_start: 0.8659 (m) cc_final: 0.8229 (m) REVERT: B 1157 ASP cc_start: 0.8482 (p0) cc_final: 0.8123 (p0) REVERT: B 1281 ILE cc_start: 0.9421 (mm) cc_final: 0.8965 (mm) REVERT: B 1285 MET cc_start: 0.8841 (mtp) cc_final: 0.8442 (mmt) REVERT: B 1397 MET cc_start: 0.8544 (mpp) cc_final: 0.7978 (mpp) REVERT: B 2049 MET cc_start: 0.9012 (mmp) cc_final: 0.8726 (mmm) REVERT: B 2069 MET cc_start: -0.2158 (tpp) cc_final: -0.3073 (tpp) REVERT: B 2335 MET cc_start: -0.1994 (ttt) cc_final: -0.2665 (ttt) REVERT: B 2542 MET cc_start: 0.0584 (ptt) cc_final: -0.0011 (ttt) REVERT: E 72 MET cc_start: 0.1475 (ptp) cc_final: 0.0478 (tpt) REVERT: C 55 MET cc_start: 0.0826 (tpt) cc_final: 0.0580 (tpt) REVERT: C 86 MET cc_start: 0.2606 (mtt) cc_final: 0.1600 (mpp) REVERT: C 286 MET cc_start: 0.5488 (tpt) cc_final: 0.4990 (tpt) REVERT: C 380 MET cc_start: 0.2268 (mpp) cc_final: 0.1871 (mmp) REVERT: C 495 PHE cc_start: 0.9033 (m-80) cc_final: 0.8664 (m-10) REVERT: C 517 LEU cc_start: 0.9275 (tp) cc_final: 0.8752 (pp) REVERT: C 527 MET cc_start: 0.4666 (tpt) cc_final: 0.4339 (ptt) REVERT: C 570 MET cc_start: -0.0414 (mmm) cc_final: -0.0616 (tpt) REVERT: C 929 MET cc_start: 0.6553 (mpp) cc_final: 0.6154 (mpp) REVERT: C 936 LYS cc_start: 0.8252 (tptp) cc_final: 0.7884 (mmtm) REVERT: C 997 PHE cc_start: 0.9127 (m-80) cc_final: 0.8445 (m-80) REVERT: C 1105 MET cc_start: 0.8558 (ppp) cc_final: 0.8332 (ppp) REVERT: C 1119 GLU cc_start: 0.9124 (mp0) cc_final: 0.8597 (mp0) REVERT: C 1151 PHE cc_start: 0.8044 (m-10) cc_final: 0.7478 (m-10) REVERT: C 1203 MET cc_start: 0.5296 (ptt) cc_final: 0.4902 (ptt) REVERT: C 1399 MET cc_start: 0.1086 (tpt) cc_final: 0.0773 (tpt) REVERT: C 1432 VAL cc_start: 0.8429 (m) cc_final: 0.7508 (p) REVERT: C 1468 ARG cc_start: 0.5707 (mtt180) cc_final: 0.5435 (tmt170) REVERT: C 1519 MET cc_start: 0.0792 (ppp) cc_final: 0.0057 (ptt) REVERT: D 246 CYS cc_start: 0.6980 (t) cc_final: 0.6422 (m) outliers start: 0 outliers final: 0 residues processed: 391 average time/residue: 0.5128 time to fit residues: 342.0257 Evaluate side-chains 319 residues out of total 4587 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 511 random chunks: chunk 322 optimal weight: 5.9990 chunk 431 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 373 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 112 optimal weight: 0.0670 chunk 406 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 416 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 overall best weight: 1.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 942 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2076 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2336 ASN A2623 GLN ** B 837 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1396 GLN C 451 HIS ** C1092 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.099530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.078710 restraints weight = 303488.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.076692 restraints weight = 236780.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.077270 restraints weight = 196714.197| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42111 Z= 0.192 Angle : 0.634 12.372 57055 Z= 0.319 Chirality : 0.041 0.216 6520 Planarity : 0.004 0.071 7172 Dihedral : 4.663 23.179 5492 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.02 % Allowed : 0.31 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % 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: -0.51 (0.12), residues: 5056 helix: 0.30 (0.09), residues: 3191 sheet: -0.34 (0.80), residues: 32 loop : -1.39 (0.16), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 688 HIS 0.005 0.001 HIS A2265 PHE 0.031 0.002 PHE D 368 TYR 0.013 0.001 TYR A1908 ARG 0.006 0.000 ARG C1556 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8524.10 seconds wall clock time: 157 minutes 14.02 seconds (9434.02 seconds total)