Starting phenix.real_space_refine on Thu Jul 25 16:32:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/07_2024/8psk_17854.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/07_2024/8psk_17854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/07_2024/8psk_17854.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/07_2024/8psk_17854.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/07_2024/8psk_17854.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psk_17854/07_2024/8psk_17854.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 106 5.16 5 C 18867 2.51 5 N 4954 2.21 5 O 5676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A ASP 744": "OD1" <-> "OD2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1082": "OE1" <-> "OE2" Residue "A ASP 1085": "OD1" <-> "OD2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A ASP 1150": "OD1" <-> "OD2" Residue "A GLU 1162": "OE1" <-> "OE2" Residue "A ASP 1202": "OD1" <-> "OD2" Residue "A GLU 1310": "OE1" <-> "OE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A ASP 1391": "OD1" <-> "OD2" Residue "A TYR 1438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1668": "OD1" <-> "OD2" Residue "A GLU 1672": "OE1" <-> "OE2" Residue "A GLU 1709": "OE1" <-> "OE2" Residue "A GLU 1711": "OE1" <-> "OE2" Residue "A GLU 1782": "OE1" <-> "OE2" Residue "A PHE 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ASP 288": "OD1" <-> "OD2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 100": "OD1" <-> "OD2" Residue "G ASP 138": "OD1" <-> "OD2" Residue "G PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G ASP 175": "OD1" <-> "OD2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "G TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 285": "OE1" <-> "OE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 329": "OE1" <-> "OE2" Residue "G TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 403": "OD1" <-> "OD2" Residue "G GLU 491": "OE1" <-> "OE2" Residue "G PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 618": "OE1" <-> "OE2" Residue "G PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1067": "OD1" <-> "OD2" Residue "G ASP 1075": "OD1" <-> "OD2" Residue "G GLU 1135": "OE1" <-> "OE2" Residue "G GLU 1222": "OE1" <-> "OE2" Residue "G TYR 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1273": "OE1" <-> "OE2" Residue "G ASP 1278": "OD1" <-> "OD2" Residue "G GLU 1309": "OE1" <-> "OE2" Residue "G ASP 1346": "OD1" <-> "OD2" Residue "G GLU 1654": "OE1" <-> "OE2" Residue "G ASP 1689": "OD1" <-> "OD2" Residue "G GLU 1757": "OE1" <-> "OE2" Residue "G PHE 1804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1829": "OE1" <-> "OE2" Residue "G TYR 1873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 2019": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29604 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1579, 12346 Classifications: {'peptide': 1579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1517} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1223 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain: "G" Number of atoms: 16004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16004 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.11, per 1000 atoms: 0.54 Number of scatterers: 29604 At special positions: 0 Unit cell: (183.57, 182.515, 176.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 1 15.00 O 5676 8.00 N 4954 7.00 C 18867 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1246 " - pdb=" SG CYS A1327 " distance=2.21 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: 12.47 Conformation dependent library (CDL) restraints added in 5.8 seconds 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 30 sheets defined 51.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.81 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.729A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'A' and resid 355 through 382 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 404 through 422 removed outlier: 4.086A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 463 through 483 Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 652 through 670 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.559A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 726 Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.748A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.571A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.583A pdb=" N VAL A 933 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 970 Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.839A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.782A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1043 Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1087 through 1100 removed outlier: 4.597A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1194 through 1198 Processing helix chain 'A' and resid 1201 through 1208 removed outlier: 3.570A pdb=" N GLN A1207 " --> pdb=" O ASP A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1226 removed outlier: 3.813A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A1214 " --> pdb=" O PRO A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1237 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1253 through 1262 Processing helix chain 'A' and resid 1275 through 1280 removed outlier: 6.303A pdb=" N ILE A1280 " --> pdb=" O GLU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1291 Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1336 through 1346 Processing helix chain 'A' and resid 1351 through 1358 Processing helix chain 'A' and resid 1361 through 1365 Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1444 through 1475 removed outlier: 3.672A pdb=" N GLU A1475 " --> pdb=" O LYS A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1509 removed outlier: 4.321A pdb=" N ASN A1483 " --> pdb=" O SER A1479 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU A1484 " --> pdb=" O GLU A1480 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1528 removed outlier: 3.538A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1536 Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.769A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 Processing helix chain 'A' and resid 1584 through 1586 No H-bonds generated for 'chain 'A' and resid 1584 through 1586' Processing helix chain 'A' and resid 1587 through 1601 Processing helix chain 'A' and resid 1615 through 1621 removed outlier: 3.665A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 4.014A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY A1663 " --> pdb=" O ASP A1659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1658 through 1663' Processing helix chain 'A' and resid 1666 through 1694 Processing helix chain 'A' and resid 1710 through 1717 Processing helix chain 'A' and resid 1734 through 1738 Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 4.152A pdb=" N TYR A1744 " --> pdb=" O SER A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1758 Processing helix chain 'A' and resid 1777 through 1779 No H-bonds generated for 'chain 'A' and resid 1777 through 1779' Processing helix chain 'A' and resid 1783 through 1791 removed outlier: 3.574A pdb=" N ILE A1787 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1801 removed outlier: 3.666A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1824 Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 3.847A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A1860 " --> pdb=" O LYS A1856 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A1862 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 160 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.536A pdb=" N GLN B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.712A pdb=" N LEU B 209 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 237 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 279 through 299 Processing helix chain 'G' and resid 26 through 41 Processing helix chain 'G' and resid 56 through 72 removed outlier: 3.753A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 96 Processing helix chain 'G' and resid 100 through 111 removed outlier: 3.611A pdb=" N GLN G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 133 Processing helix chain 'G' and resid 143 through 151 Processing helix chain 'G' and resid 168 through 180 removed outlier: 3.935A pdb=" N GLU G 172 " --> pdb=" O ASP G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 5.797A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 233 through 255 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 266 Processing helix chain 'G' and resid 275 through 284 removed outlier: 4.112A pdb=" N THR G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 314 removed outlier: 3.993A pdb=" N SER G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG G 297 " --> pdb=" O PHE G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 330 Processing helix chain 'G' and resid 345 through 360 removed outlier: 4.072A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU G 360 " --> pdb=" O THR G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 Processing helix chain 'G' and resid 382 through 397 removed outlier: 3.539A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 429 through 434 Proline residue: G 434 - end of helix Processing helix chain 'G' and resid 435 through 445 removed outlier: 3.838A pdb=" N LYS G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 471 Processing helix chain 'G' and resid 474 through 485 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 507 through 510 Processing helix chain 'G' and resid 511 through 521 removed outlier: 3.714A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 removed outlier: 3.899A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 555 Processing helix chain 'G' and resid 560 through 565 Processing helix chain 'G' and resid 581 through 588 removed outlier: 3.777A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 612 Processing helix chain 'G' and resid 622 through 624 No H-bonds generated for 'chain 'G' and resid 622 through 624' Processing helix chain 'G' and resid 626 through 641 Processing helix chain 'G' and resid 655 through 672 Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 698 Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 747 through 759 removed outlier: 5.388A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 773 through 783 removed outlier: 3.816A pdb=" N THR G 777 " --> pdb=" O SER G 773 " (cutoff:3.500A) Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 788 removed outlier: 3.838A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 808 removed outlier: 4.342A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 823 Processing helix chain 'G' and resid 831 through 837 Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 876 through 899 removed outlier: 4.600A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 5.206A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 918 through 930 Processing helix chain 'G' and resid 940 through 959 Processing helix chain 'G' and resid 969 through 974 Processing helix chain 'G' and resid 975 through 987 removed outlier: 3.605A pdb=" N ALA G 979 " --> pdb=" O LYS G 975 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 992 Processing helix chain 'G' and resid 996 through 1007 Processing helix chain 'G' and resid 1024 through 1031 Processing helix chain 'G' and resid 1035 through 1043 removed outlier: 4.653A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU G1041 " --> pdb=" O GLU G1038 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1051 Processing helix chain 'G' and resid 1058 through 1062 Processing helix chain 'G' and resid 1069 through 1090 Processing helix chain 'G' and resid 1093 through 1097 removed outlier: 3.551A pdb=" N ILE G1097 " --> pdb=" O GLU G1094 " (cutoff:3.500A) Processing helix chain 'G' and resid 1134 through 1144 Processing helix chain 'G' and resid 1148 through 1156 Processing helix chain 'G' and resid 1168 through 1174 Processing helix chain 'G' and resid 1189 through 1192 Processing helix chain 'G' and resid 1257 through 1271 Processing helix chain 'G' and resid 1293 through 1305 Processing helix chain 'G' and resid 1324 through 1337 removed outlier: 4.058A pdb=" N VAL G1328 " --> pdb=" O ASP G1324 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA G1337 " --> pdb=" O ALA G1333 " (cutoff:3.500A) Processing helix chain 'G' and resid 1346 through 1348 No H-bonds generated for 'chain 'G' and resid 1346 through 1348' Processing helix chain 'G' and resid 1418 through 1422 Processing helix chain 'G' and resid 1437 through 1447 removed outlier: 3.886A pdb=" N ILE G1441 " --> pdb=" O THR G1437 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G1447 " --> pdb=" O VAL G1443 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1524 Processing helix chain 'G' and resid 1550 through 1558 Processing helix chain 'G' and resid 1561 through 1565 Processing helix chain 'G' and resid 1566 through 1573 Processing helix chain 'G' and resid 1581 through 1597 Processing helix chain 'G' and resid 1601 through 1603 No H-bonds generated for 'chain 'G' and resid 1601 through 1603' Processing helix chain 'G' and resid 1677 through 1682 Processing helix chain 'G' and resid 1684 through 1703 Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1722 through 1735 Processing helix chain 'G' and resid 1769 through 1772 Processing helix chain 'G' and resid 1773 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1809 through 1818 removed outlier: 3.939A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1841 Processing helix chain 'G' and resid 1858 through 1863 removed outlier: 4.036A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA G1863 " --> pdb=" O PRO G1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1858 through 1863' Processing helix chain 'G' and resid 1867 through 1882 Processing helix chain 'G' and resid 1904 through 1921 removed outlier: 3.593A pdb=" N ASP G1908 " --> pdb=" O LEU G1904 " (cutoff:3.500A) Processing helix chain 'G' and resid 1924 through 1930 removed outlier: 3.510A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1935 through 1952 removed outlier: 3.987A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G1947 " --> pdb=" O ILE G1943 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1979 through 1983 removed outlier: 4.002A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1994 removed outlier: 3.624A pdb=" N PHE G1988 " --> pdb=" O GLY G1984 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER G1990 " --> pdb=" O LYS G1986 " (cutoff:3.500A) Processing helix chain 'G' and resid 1997 through 2001 Processing helix chain 'G' and resid 2022 through 2033 Processing helix chain 'G' and resid 2035 through 2044 Processing helix chain 'G' and resid 2044 through 2050 removed outlier: 3.782A pdb=" N GLN G2050 " --> pdb=" O GLU G2046 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.692A pdb=" N VAL G1899 " --> pdb=" O VAL G1889 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR G1891 " --> pdb=" O GLN G1897 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLN G1897 " --> pdb=" O TYR G1891 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 6.654A pdb=" N ARG A 43 " --> pdb=" O THR G1663 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL G1665 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 45 " --> pdb=" O VAL G1665 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.606A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA6, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA7, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 3.520A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A1649 " --> pdb=" O GLY A1645 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1060 through 1067 removed outlier: 3.803A pdb=" N ARG A1070 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AB1, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id=AB2, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB3, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB4, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB5, first strand: chain 'A' and resid 1768 through 1775 removed outlier: 3.619A pdb=" N ASP A1866 " --> pdb=" O THR A1885 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id=AB7, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.843A pdb=" N VAL G 22 " --> pdb=" O ARG G 7 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 459 through 460 removed outlier: 7.554A pdb=" N ALA G 270 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N THR G 271 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA G 158 " --> pdb=" O THR G 271 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL G 527 " --> pdb=" O GLY G 542 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 417 through 420 removed outlier: 6.081A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC2, first strand: chain 'G' and resid 592 through 594 removed outlier: 3.906A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR G 733 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY G 798 " --> pdb=" O LEU G 765 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.666A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC5, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC6, first strand: chain 'G' and resid 1126 through 1128 removed outlier: 6.406A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE G1218 " --> pdb=" O LEU G1214 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE G1158 " --> pdb=" O ILE G1251 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N GLU G1253 " --> pdb=" O PHE G1158 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR G1160 " --> pdb=" O GLU G1253 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 1285 through 1286 Processing sheet with id=AC8, first strand: chain 'G' and resid 1285 through 1286 removed outlier: 5.200A pdb=" N THR G1374 " --> pdb=" O SER G1397 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER G1397 " --> pdb=" O THR G1374 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALA G1376 " --> pdb=" O THR G1395 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR G1395 " --> pdb=" O ALA G1376 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE G1378 " --> pdb=" O VAL G1393 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL G1393 " --> pdb=" O ILE G1378 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL G1403 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N MET G1359 " --> pdb=" O VAL G1403 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU G1405 " --> pdb=" O TYR G1357 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR G1357 " --> pdb=" O GLU G1405 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR G1407 " --> pdb=" O ASN G1355 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASN G1355 " --> pdb=" O THR G1407 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER G1409 " --> pdb=" O LEU G1353 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG G1606 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N PHE G1612 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL G1650 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG G1635 " --> pdb=" O MET G1631 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET G1631 " --> pdb=" O ARG G1635 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU G1637 " --> pdb=" O VAL G1629 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA G1540 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N HIS G1628 " --> pdb=" O PRO G1538 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N GLY G1630 " --> pdb=" O PRO G1536 " (cutoff:3.500A) removed outlier: 14.288A pdb=" N ILE G1632 " --> pdb=" O GLU G1534 " (cutoff:3.500A) removed outlier: 14.547A pdb=" N GLU G1534 " --> pdb=" O ILE G1632 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 1424 through 1427 removed outlier: 6.598A pdb=" N CYS G1485 " --> pdb=" O ASP G1505 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP G1505 " --> pdb=" O CYS G1485 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY G1487 " --> pdb=" O ILE G1503 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE G1503 " --> pdb=" O GLY G1487 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE G1489 " --> pdb=" O ILE G1501 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1424 through 1427 removed outlier: 5.076A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id=AD3, first strand: chain 'G' and resid 1740 through 1741 removed outlier: 3.848A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) 1511 hydrogen bonds defined for protein. 4209 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: 16.19 Time building geometry restraints manager: 12.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5070 1.31 - 1.44: 7640 1.44 - 1.58: 17324 1.58 - 1.72: 1 1.72 - 1.86: 187 Bond restraints: 30222 Sorted by residual: bond pdb=" C PRO A1627 " pdb=" O PRO A1627 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.14e-02 7.69e+03 2.96e+01 bond pdb=" C PRO A1362 " pdb=" O PRO A1362 " ideal model delta sigma weight residual 1.237 1.171 0.067 1.26e-02 6.30e+03 2.80e+01 bond pdb=" C PRO A 736 " pdb=" O PRO A 736 " ideal model delta sigma weight residual 1.234 1.173 0.060 1.14e-02 7.69e+03 2.79e+01 bond pdb=" C PRO A1190 " pdb=" O PRO A1190 " ideal model delta sigma weight residual 1.233 1.173 0.060 1.16e-02 7.43e+03 2.63e+01 bond pdb=" C GLY A1248 " pdb=" O GLY A1248 " ideal model delta sigma weight residual 1.233 1.185 0.048 9.80e-03 1.04e+04 2.44e+01 ... (remaining 30217 not shown) Histogram of bond angle deviations from ideal: 91.11 - 100.04: 32 100.04 - 108.97: 3210 108.97 - 117.90: 20689 117.90 - 126.83: 16734 126.83 - 135.76: 271 Bond angle restraints: 40936 Sorted by residual: angle pdb=" C SER A1417 " pdb=" N VAL A1418 " pdb=" CA VAL A1418 " ideal model delta sigma weight residual 120.24 124.76 -4.52 6.30e-01 2.52e+00 5.15e+01 angle pdb=" N GLY B 240 " pdb=" CA GLY B 240 " pdb=" C GLY B 240 " ideal model delta sigma weight residual 114.69 106.29 8.40 1.19e+00 7.06e-01 4.99e+01 angle pdb=" C ILE A1189 " pdb=" CA ILE A1189 " pdb=" CB ILE A1189 " ideal model delta sigma weight residual 110.88 117.14 -6.26 9.80e-01 1.04e+00 4.08e+01 angle pdb=" C TRP G 661 " pdb=" N GLY G 662 " pdb=" CA GLY G 662 " ideal model delta sigma weight residual 119.94 126.78 -6.84 1.09e+00 8.42e-01 3.94e+01 angle pdb=" CB GLU G1309 " pdb=" CG GLU G1309 " pdb=" CD GLU G1309 " ideal model delta sigma weight residual 112.60 123.20 -10.60 1.70e+00 3.46e-01 3.89e+01 ... (remaining 40931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.58: 16897 20.58 - 41.17: 1118 41.17 - 61.75: 160 61.75 - 82.34: 55 82.34 - 102.92: 16 Dihedral angle restraints: 18246 sinusoidal: 7337 harmonic: 10909 Sorted by residual: dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual 93.00 17.54 75.46 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" C5' FMN G2101 " pdb=" O5' FMN G2101 " pdb=" P FMN G2101 " pdb=" O1P FMN G2101 " ideal model delta sinusoidal sigma weight residual 75.26 178.18 -102.92 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" CA ASP G 974 " pdb=" C ASP G 974 " pdb=" N LYS G 975 " pdb=" CA LYS G 975 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 18243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2171 0.061 - 0.122: 1695 0.122 - 0.183: 611 0.183 - 0.244: 109 0.244 - 0.306: 16 Chirality restraints: 4602 Sorted by residual: chirality pdb=" CA SER B 235 " pdb=" N SER B 235 " pdb=" C SER B 235 " pdb=" CB SER B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ILE G1751 " pdb=" N ILE G1751 " pdb=" C ILE G1751 " pdb=" CB ILE G1751 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA ILE A1403 " pdb=" N ILE A1403 " pdb=" C ILE A1403 " pdb=" CB ILE A1403 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4599 not shown) Planarity restraints: 5284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.013 2.00e-02 2.50e+03 3.61e-02 6.19e+01 pdb=" C10 FMN G2101 " 0.027 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.048 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.005 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.045 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.063 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.029 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.011 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.065 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.033 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.031 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " -0.006 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.041 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.015 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.037 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.031 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.049 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.031 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 722 " 0.074 2.00e-02 2.50e+03 3.82e-02 2.92e+01 pdb=" CG TYR A 722 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 722 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 722 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 722 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 722 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 722 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 722 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1529 " 0.068 2.00e-02 2.50e+03 3.52e-02 2.48e+01 pdb=" CG TYR A1529 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A1529 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A1529 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A1529 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A1529 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A1529 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A1529 " 0.035 2.00e-02 2.50e+03 ... (remaining 5281 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 711 2.69 - 3.25: 28877 3.25 - 3.80: 46398 3.80 - 4.35: 65492 4.35 - 4.90: 106406 Nonbonded interactions: 247884 Sorted by model distance: nonbonded pdb=" OD1 ASP G 287 " pdb=" OG SER G 291 " model vdw 2.142 2.440 nonbonded pdb=" O LEU B 221 " pdb=" OG SER B 225 " model vdw 2.213 2.440 nonbonded pdb=" OE1 GLU G1811 " pdb=" OH TYR G2010 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR G 615 " pdb=" OD1 ASP G1075 " model vdw 2.240 2.440 nonbonded pdb=" O LYS G 355 " pdb=" OG SER G 358 " model vdw 2.248 2.440 ... (remaining 247879 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 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: 0.020 Extract box with map and model: 1.650 Check model and map are aligned: 0.210 Set scattering table: 0.290 Process input model: 85.550 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.120 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:12.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 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 : 0.013 0.086 30222 Z= 0.871 Angle : 1.820 10.760 40936 Z= 1.339 Chirality : 0.088 0.306 4602 Planarity : 0.007 0.038 5284 Dihedral : 14.456 102.920 11217 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.52 % Favored : 95.21 % Rotamer: Outliers : 0.25 % Allowed : 3.21 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: -2.78 (0.12), residues: 3760 helix: -2.33 (0.10), residues: 1664 sheet: -1.39 (0.20), residues: 500 loop : -1.19 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.009 TRP G1449 HIS 0.015 0.004 HIS G1564 PHE 0.054 0.007 PHE G1300 TYR 0.074 0.008 TYR A 722 ARG 0.017 0.002 ARG A 396 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 387 time to evaluate : 3.367 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8926 (tp30) cc_final: 0.8396 (tp30) REVERT: A 340 ARG cc_start: 0.6764 (mmt180) cc_final: 0.6233 (mpt180) REVERT: A 364 GLU cc_start: 0.5576 (tt0) cc_final: 0.5361 (tt0) REVERT: A 529 MET cc_start: 0.8806 (mmp) cc_final: 0.8236 (mmp) REVERT: A 537 LYS cc_start: 0.7557 (tptt) cc_final: 0.7336 (mttm) REVERT: A 612 GLU cc_start: 0.8289 (tp30) cc_final: 0.7978 (tp30) REVERT: A 944 ARG cc_start: 0.8605 (ttm110) cc_final: 0.8396 (ttp80) REVERT: A 1162 GLU cc_start: 0.7960 (mp0) cc_final: 0.7345 (mp0) REVERT: A 1180 ARG cc_start: 0.7269 (mpt180) cc_final: 0.6799 (mpt90) REVERT: A 1260 MET cc_start: 0.9154 (ptp) cc_final: 0.8913 (ptm) REVERT: A 1496 GLU cc_start: 0.6696 (tt0) cc_final: 0.6462 (tt0) REVERT: B 168 MET cc_start: 0.6459 (mmm) cc_final: 0.5996 (tpp) REVERT: B 179 LYS cc_start: 0.8313 (mppt) cc_final: 0.7740 (mptt) REVERT: B 183 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7908 (tp40) REVERT: B 192 LYS cc_start: 0.8280 (pptt) cc_final: 0.8077 (ptmt) REVERT: B 237 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7454 (tpp) REVERT: B 261 GLN cc_start: 0.7962 (mt0) cc_final: 0.7541 (mt0) REVERT: B 271 ASN cc_start: 0.8370 (m110) cc_final: 0.8042 (m-40) REVERT: G 64 PHE cc_start: 0.8347 (t80) cc_final: 0.7985 (t80) REVERT: G 81 ASP cc_start: 0.7600 (m-30) cc_final: 0.7241 (m-30) REVERT: G 132 MET cc_start: 0.8609 (mmp) cc_final: 0.8216 (mpm) REVERT: G 217 GLU cc_start: 0.8342 (tp30) cc_final: 0.7861 (tp30) REVERT: G 221 ASN cc_start: 0.8470 (m110) cc_final: 0.7949 (m110) REVERT: G 325 GLU cc_start: 0.8530 (tp30) cc_final: 0.8076 (tp30) REVERT: G 329 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7861 (mt-10) REVERT: G 387 TYR cc_start: 0.8318 (t80) cc_final: 0.7928 (t80) REVERT: G 447 ASN cc_start: 0.8350 (t0) cc_final: 0.7577 (p0) REVERT: G 553 ASN cc_start: 0.8168 (m110) cc_final: 0.7948 (m-40) REVERT: G 881 VAL cc_start: 0.8911 (t) cc_final: 0.8704 (t) REVERT: G 1309 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6780 (mm-30) REVERT: G 1401 LYS cc_start: 0.8144 (pptt) cc_final: 0.7816 (pmtt) REVERT: G 1500 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7965 (tm-30) REVERT: G 1673 GLU cc_start: 0.8094 (pm20) cc_final: 0.7864 (pm20) REVERT: G 1784 MET cc_start: 0.8730 (tmm) cc_final: 0.8292 (tmt) REVERT: G 1962 ARG cc_start: 0.6707 (tmt-80) cc_final: 0.6437 (tmt-80) REVERT: G 2015 THR cc_start: 0.8505 (m) cc_final: 0.8261 (p) outliers start: 8 outliers final: 4 residues processed: 393 average time/residue: 1.7383 time to fit residues: 781.2037 Evaluate side-chains 272 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 267 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain G residue 1381 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 179 optimal weight: 0.0470 chunk 219 optimal weight: 0.0010 chunk 341 optimal weight: 6.9990 overall best weight: 2.2090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 524 GLN A 904 ASN A 989 GLN A1272 ASN A1380 GLN A1494 HIS A1495 ASN A1549 ASN A1563 HIS A1780 ASN A1877 GLN G 93 ASN G 102 HIS G 221 ASN G 346 GLN G 354 ASN G 440 ASN G 715 GLN G 718 ASN G 747 HIS G 908 ASN G 993 GLN G1088 GLN G1178 GLN G1217 ASN G1241 ASN G1341 ASN G1355 ASN G1399 ASN G1595 ASN G1851 ASN G1890 ASN G1897 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30222 Z= 0.204 Angle : 0.560 12.059 40936 Z= 0.299 Chirality : 0.043 0.182 4602 Planarity : 0.004 0.031 5284 Dihedral : 5.218 102.825 4034 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.78 % Favored : 98.14 % Rotamer: Outliers : 1.45 % Allowed : 8.79 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: -0.11 (0.13), residues: 3760 helix: 0.53 (0.12), residues: 1684 sheet: -0.83 (0.20), residues: 524 loop : -0.31 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 661 HIS 0.009 0.001 HIS A1689 PHE 0.025 0.002 PHE A 35 TYR 0.016 0.002 TYR A1529 ARG 0.005 0.000 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 282 time to evaluate : 3.442 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8925 (tp30) cc_final: 0.8523 (tp30) REVERT: A 340 ARG cc_start: 0.6897 (mmt180) cc_final: 0.6443 (mmt180) REVERT: A 1044 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8248 (pm20) REVERT: A 1162 GLU cc_start: 0.7877 (mp0) cc_final: 0.7580 (mp0) REVERT: A 1180 ARG cc_start: 0.7144 (mpt180) cc_final: 0.6399 (mpt90) REVERT: A 1260 MET cc_start: 0.9123 (ptp) cc_final: 0.8856 (ptm) REVERT: A 1491 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8200 (tmt170) REVERT: A 1496 GLU cc_start: 0.6363 (tt0) cc_final: 0.6070 (tt0) REVERT: A 1498 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8272 (tm-30) REVERT: B 168 MET cc_start: 0.6451 (mmm) cc_final: 0.5828 (tpp) REVERT: B 193 GLU cc_start: 0.7936 (tp30) cc_final: 0.7489 (tm-30) REVERT: B 202 GLU cc_start: 0.7492 (pm20) cc_final: 0.6792 (pm20) REVERT: B 224 GLN cc_start: 0.8103 (tp40) cc_final: 0.7865 (mm-40) REVERT: B 261 GLN cc_start: 0.7920 (mt0) cc_final: 0.7541 (mt0) REVERT: B 271 ASN cc_start: 0.7945 (m110) cc_final: 0.7536 (m110) REVERT: G 81 ASP cc_start: 0.7577 (m-30) cc_final: 0.7246 (m-30) REVERT: G 97 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: G 111 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7821 (mt-10) REVERT: G 132 MET cc_start: 0.8473 (mmp) cc_final: 0.8105 (mpm) REVERT: G 167 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8043 (p0) REVERT: G 221 ASN cc_start: 0.8290 (m-40) cc_final: 0.8048 (m110) REVERT: G 325 GLU cc_start: 0.8481 (tp30) cc_final: 0.7943 (tp30) REVERT: G 329 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7707 (mt-10) REVERT: G 387 TYR cc_start: 0.8217 (t80) cc_final: 0.7914 (t80) REVERT: G 447 ASN cc_start: 0.8417 (t0) cc_final: 0.7731 (p0) REVERT: G 764 MET cc_start: 0.9000 (mtm) cc_final: 0.8682 (mtm) REVERT: G 1309 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6554 (mm-30) REVERT: G 1401 LYS cc_start: 0.8038 (pptt) cc_final: 0.7769 (pptt) REVERT: G 1673 GLU cc_start: 0.8059 (pm20) cc_final: 0.7818 (pm20) REVERT: G 1811 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8342 (tt0) REVERT: G 1956 ARG cc_start: 0.6349 (mmp80) cc_final: 0.5978 (mmp80) outliers start: 47 outliers final: 14 residues processed: 312 average time/residue: 1.6200 time to fit residues: 584.4388 Evaluate side-chains 268 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 249 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1491 ARG Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1904 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 284 optimal weight: 20.0000 chunk 232 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 342 optimal weight: 0.1980 chunk 369 optimal weight: 3.9990 chunk 304 optimal weight: 7.9990 chunk 339 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 274 optimal weight: 8.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 475 GLN ** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 ASN A1063 HIS A1207 GLN A1494 HIS A1806 GLN G 650 ASN G1399 ASN G1421 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30222 Z= 0.175 Angle : 0.509 10.915 40936 Z= 0.267 Chirality : 0.042 0.163 4602 Planarity : 0.003 0.038 5284 Dihedral : 4.722 99.374 4029 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 1.82 % Allowed : 9.90 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.78 (0.14), residues: 3760 helix: 1.48 (0.13), residues: 1689 sheet: -0.52 (0.21), residues: 519 loop : -0.06 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 661 HIS 0.008 0.001 HIS A1689 PHE 0.024 0.001 PHE A 35 TYR 0.015 0.001 TYR A 722 ARG 0.006 0.000 ARG G1849 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 271 time to evaluate : 3.450 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7466 (tpt) cc_final: 0.6782 (tpt) REVERT: A 16 GLU cc_start: 0.8912 (tp30) cc_final: 0.8506 (tp30) REVERT: A 340 ARG cc_start: 0.6882 (mmt180) cc_final: 0.6451 (mmt180) REVERT: A 517 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7200 (mm-30) REVERT: A 529 MET cc_start: 0.8884 (mmp) cc_final: 0.8533 (mmp) REVERT: A 944 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8424 (ttp80) REVERT: A 1044 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8275 (pm20) REVERT: A 1159 GLU cc_start: 0.8099 (mp0) cc_final: 0.7761 (pm20) REVERT: A 1162 GLU cc_start: 0.7798 (mp0) cc_final: 0.7477 (mp0) REVERT: A 1180 ARG cc_start: 0.7149 (mpt180) cc_final: 0.6396 (mpt90) REVERT: A 1260 MET cc_start: 0.9080 (ptp) cc_final: 0.8770 (ptm) REVERT: A 1496 GLU cc_start: 0.6445 (tt0) cc_final: 0.5984 (tt0) REVERT: A 1498 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8208 (tm-30) REVERT: A 1806 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7098 (tt0) REVERT: B 168 MET cc_start: 0.6455 (mmm) cc_final: 0.5956 (tpp) REVERT: B 193 GLU cc_start: 0.7836 (tp30) cc_final: 0.7506 (tm-30) REVERT: B 202 GLU cc_start: 0.7335 (pm20) cc_final: 0.6562 (pm20) REVERT: B 261 GLN cc_start: 0.8004 (mt0) cc_final: 0.7654 (mt0) REVERT: G 81 ASP cc_start: 0.7666 (m-30) cc_final: 0.7336 (m-30) REVERT: G 97 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7431 (pt0) REVERT: G 111 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7784 (mt-10) REVERT: G 121 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8249 (mt-10) REVERT: G 132 MET cc_start: 0.8379 (mmp) cc_final: 0.7988 (mpm) REVERT: G 167 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7842 (p0) REVERT: G 325 GLU cc_start: 0.8534 (tp30) cc_final: 0.7926 (tp30) REVERT: G 329 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7571 (mt-10) REVERT: G 387 TYR cc_start: 0.8220 (t80) cc_final: 0.7812 (t80) REVERT: G 1309 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6556 (mm-30) REVERT: G 1319 MET cc_start: 0.8738 (ttt) cc_final: 0.8407 (ttt) REVERT: G 1500 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7825 (tm-30) REVERT: G 1784 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8680 (tmt) REVERT: G 1811 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8404 (tt0) REVERT: G 1838 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8377 (mmp) outliers start: 59 outliers final: 19 residues processed: 307 average time/residue: 1.5964 time to fit residues: 570.2729 Evaluate side-chains 271 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 243 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1806 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1689 ASP Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1838 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 6.9990 chunk 257 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 343 optimal weight: 2.9990 chunk 363 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 325 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 ASN A1494 HIS A1495 ASN ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 221 ASN G 346 GLN G1367 GLN G1399 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 30222 Z= 0.343 Angle : 0.570 10.805 40936 Z= 0.299 Chirality : 0.045 0.175 4602 Planarity : 0.004 0.041 5284 Dihedral : 4.921 100.514 4028 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.53 % Rotamer: Outliers : 2.31 % Allowed : 10.94 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.78 (0.14), residues: 3760 helix: 1.43 (0.13), residues: 1690 sheet: -0.51 (0.21), residues: 517 loop : -0.01 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 865 HIS 0.009 0.001 HIS A1689 PHE 0.023 0.002 PHE G 28 TYR 0.020 0.002 TYR A 722 ARG 0.007 0.001 ARG A1489 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 249 time to evaluate : 3.850 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7759 (tpt) cc_final: 0.7011 (tpt) REVERT: A 16 GLU cc_start: 0.8880 (tp30) cc_final: 0.8465 (tp30) REVERT: A 340 ARG cc_start: 0.6726 (mmt180) cc_final: 0.5867 (mpt180) REVERT: A 517 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: A 529 MET cc_start: 0.8878 (mmp) cc_final: 0.8578 (mmp) REVERT: A 750 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: A 881 ASN cc_start: 0.8386 (OUTLIER) cc_final: 0.8160 (p0) REVERT: A 944 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8422 (ttp80) REVERT: A 1044 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8283 (pm20) REVERT: A 1159 GLU cc_start: 0.8115 (mp0) cc_final: 0.7730 (pm20) REVERT: A 1162 GLU cc_start: 0.7867 (mp0) cc_final: 0.7522 (mp0) REVERT: A 1180 ARG cc_start: 0.7161 (mpt180) cc_final: 0.6423 (mpt90) REVERT: A 1498 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: B 168 MET cc_start: 0.6513 (mmm) cc_final: 0.5993 (tpp) REVERT: B 193 GLU cc_start: 0.7870 (tp30) cc_final: 0.7599 (tm-30) REVERT: B 194 PHE cc_start: 0.8121 (m-10) cc_final: 0.7790 (m-10) REVERT: B 202 GLU cc_start: 0.7380 (pm20) cc_final: 0.6591 (pm20) REVERT: B 224 GLN cc_start: 0.8371 (tp40) cc_final: 0.8046 (mm-40) REVERT: B 261 GLN cc_start: 0.7944 (mt0) cc_final: 0.7589 (mt0) REVERT: G 81 ASP cc_start: 0.7665 (m-30) cc_final: 0.7342 (m-30) REVERT: G 97 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7476 (pt0) REVERT: G 132 MET cc_start: 0.8391 (mmp) cc_final: 0.8074 (mpm) REVERT: G 167 ASP cc_start: 0.8292 (p0) cc_final: 0.7912 (p0) REVERT: G 325 GLU cc_start: 0.8587 (tp30) cc_final: 0.7961 (tp30) REVERT: G 329 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7576 (mt-10) REVERT: G 387 TYR cc_start: 0.8348 (t80) cc_final: 0.7919 (t80) REVERT: G 696 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: G 831 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8374 (mtmm) REVERT: G 1319 MET cc_start: 0.8774 (ttt) cc_final: 0.8525 (ttt) REVERT: G 1500 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7877 (tm-30) REVERT: G 1784 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8801 (tmt) outliers start: 75 outliers final: 33 residues processed: 300 average time/residue: 1.5884 time to fit residues: 557.9176 Evaluate side-chains 282 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 239 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1904 LEU Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 270 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 310 optimal weight: 9.9990 chunk 251 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 326 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1494 HIS A1783 ASN A1806 GLN G 346 GLN G 418 ASN G1399 ASN ** G1564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30222 Z= 0.294 Angle : 0.545 10.462 40936 Z= 0.285 Chirality : 0.044 0.168 4602 Planarity : 0.004 0.038 5284 Dihedral : 4.873 101.602 4028 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.56 % Allowed : 11.62 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.86 (0.14), residues: 3760 helix: 1.49 (0.13), residues: 1691 sheet: -0.37 (0.22), residues: 506 loop : -0.00 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 865 HIS 0.008 0.001 HIS A1689 PHE 0.026 0.002 PHE G 28 TYR 0.017 0.002 TYR A 722 ARG 0.007 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 258 time to evaluate : 3.569 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8852 (tp30) cc_final: 0.8439 (tp30) REVERT: A 340 ARG cc_start: 0.6719 (mmt180) cc_final: 0.6118 (mpt180) REVERT: A 517 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7146 (mm-30) REVERT: A 529 MET cc_start: 0.8867 (mmp) cc_final: 0.8617 (mmp) REVERT: A 537 LYS cc_start: 0.7363 (tptt) cc_final: 0.7147 (mttm) REVERT: A 944 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8445 (ttp80) REVERT: A 1044 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: A 1162 GLU cc_start: 0.7915 (mp0) cc_final: 0.7547 (mp0) REVERT: A 1180 ARG cc_start: 0.7267 (mpt180) cc_final: 0.6549 (mpt90) REVERT: A 1298 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8552 (tp) REVERT: A 1498 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8182 (tm-30) REVERT: A 1806 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.7159 (tt0) REVERT: B 168 MET cc_start: 0.6543 (mmm) cc_final: 0.5965 (tpp) REVERT: B 193 GLU cc_start: 0.7924 (tp30) cc_final: 0.7661 (tm-30) REVERT: B 194 PHE cc_start: 0.8131 (m-10) cc_final: 0.7790 (m-10) REVERT: G 81 ASP cc_start: 0.7668 (m-30) cc_final: 0.7383 (m-30) REVERT: G 97 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: G 132 MET cc_start: 0.8336 (mmp) cc_final: 0.7941 (mpm) REVERT: G 167 ASP cc_start: 0.8265 (p0) cc_final: 0.7868 (p0) REVERT: G 325 GLU cc_start: 0.8614 (tp30) cc_final: 0.7993 (tp30) REVERT: G 329 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7497 (mt-10) REVERT: G 387 TYR cc_start: 0.8366 (t80) cc_final: 0.7939 (t80) REVERT: G 696 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: G 1319 MET cc_start: 0.8753 (ttt) cc_final: 0.8530 (ttt) REVERT: G 1500 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7917 (tm-30) REVERT: G 1650 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8817 (m) REVERT: G 1784 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8786 (tmt) REVERT: G 1801 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7577 (p0) outliers start: 83 outliers final: 35 residues processed: 314 average time/residue: 1.6644 time to fit residues: 613.7040 Evaluate side-chains 295 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 249 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1806 GLN Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 418 ASN Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 553 ASN Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1904 LEU Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 2.9990 chunk 327 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 363 optimal weight: 7.9990 chunk 301 optimal weight: 0.0170 chunk 168 optimal weight: 0.5980 chunk 30 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 chunk 190 optimal weight: 9.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 ASN A1148 HIS A1494 HIS A1601 ASN B 261 GLN G 346 GLN G 418 ASN G 715 GLN G 752 GLN G1399 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 30222 Z= 0.139 Angle : 0.486 9.861 40936 Z= 0.253 Chirality : 0.041 0.155 4602 Planarity : 0.003 0.037 5284 Dihedral : 4.576 98.212 4028 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.61 % Rotamer: Outliers : 1.60 % Allowed : 13.16 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 1.07 (0.14), residues: 3760 helix: 1.63 (0.13), residues: 1715 sheet: -0.19 (0.22), residues: 509 loop : 0.10 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 661 HIS 0.005 0.001 HIS A1689 PHE 0.025 0.001 PHE A 35 TYR 0.014 0.001 TYR B 294 ARG 0.007 0.000 ARG A 709 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 266 time to evaluate : 3.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8897 (tp30) cc_final: 0.8492 (tp30) REVERT: A 340 ARG cc_start: 0.6683 (mmt180) cc_final: 0.6073 (mpt180) REVERT: A 529 MET cc_start: 0.8874 (mmp) cc_final: 0.8643 (mmp) REVERT: A 1142 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8449 (mt-10) REVERT: A 1159 GLU cc_start: 0.8062 (mp0) cc_final: 0.7704 (pm20) REVERT: A 1162 GLU cc_start: 0.7824 (mp0) cc_final: 0.7465 (mp0) REVERT: A 1180 ARG cc_start: 0.7258 (mpt180) cc_final: 0.6518 (mpt90) REVERT: A 1209 ASP cc_start: 0.8456 (t70) cc_final: 0.8235 (t70) REVERT: A 1498 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: B 168 MET cc_start: 0.6462 (mmm) cc_final: 0.5898 (tpp) REVERT: B 193 GLU cc_start: 0.7793 (tp30) cc_final: 0.7568 (tm-30) REVERT: B 194 PHE cc_start: 0.8106 (m-10) cc_final: 0.7779 (m-10) REVERT: B 237 MET cc_start: 0.7957 (mmp) cc_final: 0.7396 (mmp) REVERT: G 67 TYR cc_start: 0.8071 (t80) cc_final: 0.7660 (t80) REVERT: G 81 ASP cc_start: 0.7618 (m-30) cc_final: 0.7339 (m-30) REVERT: G 97 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7326 (pt0) REVERT: G 111 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7889 (mt-10) REVERT: G 132 MET cc_start: 0.8366 (mmp) cc_final: 0.7989 (mpm) REVERT: G 167 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7793 (p0) REVERT: G 325 GLU cc_start: 0.8607 (tp30) cc_final: 0.7965 (tp30) REVERT: G 329 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7480 (mt-10) REVERT: G 387 TYR cc_start: 0.8333 (t80) cc_final: 0.7991 (t80) REVERT: G 831 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8398 (mtmm) REVERT: G 1319 MET cc_start: 0.8716 (ttt) cc_final: 0.8493 (ttt) REVERT: G 1784 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8718 (tmt) outliers start: 52 outliers final: 26 residues processed: 305 average time/residue: 1.6061 time to fit residues: 570.8610 Evaluate side-chains 284 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 253 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 553 ASN Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 306 optimal weight: 9.9990 chunk 203 optimal weight: 2.9990 chunk 362 optimal weight: 5.9990 chunk 226 optimal weight: 8.9990 chunk 220 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1494 HIS A1806 GLN G 346 GLN ** G 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1399 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 30222 Z= 0.301 Angle : 0.545 10.189 40936 Z= 0.284 Chirality : 0.044 0.181 4602 Planarity : 0.004 0.038 5284 Dihedral : 4.763 98.661 4028 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.02 % Rotamer: Outliers : 1.85 % Allowed : 13.66 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 1.00 (0.14), residues: 3760 helix: 1.57 (0.13), residues: 1698 sheet: -0.28 (0.22), residues: 496 loop : 0.09 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 865 HIS 0.008 0.001 HIS A1689 PHE 0.027 0.002 PHE G 28 TYR 0.018 0.002 TYR A 722 ARG 0.007 0.001 ARG A 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 254 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8875 (tp30) cc_final: 0.8437 (tp30) REVERT: A 340 ARG cc_start: 0.6738 (mmt180) cc_final: 0.6150 (mpt180) REVERT: A 517 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7212 (mm-30) REVERT: A 537 LYS cc_start: 0.7344 (tptt) cc_final: 0.7115 (mttm) REVERT: A 944 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8430 (ttp80) REVERT: A 958 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7945 (m) REVERT: A 1162 GLU cc_start: 0.7766 (mp0) cc_final: 0.7391 (mp0) REVERT: A 1180 ARG cc_start: 0.7273 (mpt180) cc_final: 0.6528 (mpt90) REVERT: A 1209 ASP cc_start: 0.8510 (t70) cc_final: 0.8263 (t70) REVERT: A 1498 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8179 (tm-30) REVERT: B 168 MET cc_start: 0.6493 (mmm) cc_final: 0.5966 (tpp) REVERT: B 193 GLU cc_start: 0.7817 (tp30) cc_final: 0.7596 (tm-30) REVERT: B 194 PHE cc_start: 0.8099 (m-10) cc_final: 0.7773 (m-10) REVERT: G 60 LEU cc_start: 0.7217 (tp) cc_final: 0.7004 (mt) REVERT: G 67 TYR cc_start: 0.8190 (t80) cc_final: 0.7779 (t80) REVERT: G 97 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7370 (pt0) REVERT: G 111 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7930 (mt-10) REVERT: G 132 MET cc_start: 0.8351 (mmp) cc_final: 0.7968 (mpm) REVERT: G 167 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7901 (p0) REVERT: G 325 GLU cc_start: 0.8637 (tp30) cc_final: 0.8000 (tp30) REVERT: G 329 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7454 (mt-10) REVERT: G 387 TYR cc_start: 0.8382 (t80) cc_final: 0.8019 (t80) REVERT: G 659 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8357 (mp) REVERT: G 831 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8389 (mtmm) REVERT: G 1319 MET cc_start: 0.8725 (ttt) cc_final: 0.8517 (ttt) REVERT: G 1650 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8811 (m) REVERT: G 1784 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8786 (tmt) REVERT: G 2045 TRP cc_start: 0.7920 (t-100) cc_final: 0.7058 (t-100) outliers start: 60 outliers final: 31 residues processed: 301 average time/residue: 1.5640 time to fit residues: 552.2124 Evaluate side-chains 290 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 249 time to evaluate : 3.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 553 ASN Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1904 LEU Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 216 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 246 optimal weight: 20.0000 chunk 179 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1494 HIS ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** G 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1399 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30222 Z= 0.227 Angle : 0.515 9.835 40936 Z= 0.268 Chirality : 0.043 0.167 4602 Planarity : 0.004 0.036 5284 Dihedral : 4.679 97.816 4028 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.50 % Favored : 97.47 % Rotamer: Outliers : 1.88 % Allowed : 13.75 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 1.03 (0.14), residues: 3760 helix: 1.57 (0.13), residues: 1713 sheet: -0.19 (0.22), residues: 485 loop : 0.10 (0.16), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 PHE 0.027 0.001 PHE G 28 TYR 0.016 0.001 TYR B 294 ARG 0.008 0.000 ARG A1489 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 260 time to evaluate : 3.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8860 (tp30) cc_final: 0.8446 (tp30) REVERT: A 340 ARG cc_start: 0.6730 (mmt180) cc_final: 0.6154 (mpt180) REVERT: A 517 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: A 529 MET cc_start: 0.8867 (mmp) cc_final: 0.8527 (mmp) REVERT: A 537 LYS cc_start: 0.7309 (tptt) cc_final: 0.7071 (mttm) REVERT: A 958 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7926 (m) REVERT: A 1142 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8436 (mt-10) REVERT: A 1159 GLU cc_start: 0.8027 (mp0) cc_final: 0.7707 (pm20) REVERT: A 1162 GLU cc_start: 0.7739 (mp0) cc_final: 0.7344 (mp0) REVERT: A 1180 ARG cc_start: 0.7249 (mpt180) cc_final: 0.6502 (mpt90) REVERT: A 1209 ASP cc_start: 0.8485 (t70) cc_final: 0.8237 (t70) REVERT: A 1298 ILE cc_start: 0.8884 (OUTLIER) cc_final: 0.8498 (tp) REVERT: A 1498 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8161 (tm-30) REVERT: A 1757 GLU cc_start: 0.4986 (tt0) cc_final: 0.4743 (pt0) REVERT: B 168 MET cc_start: 0.6488 (mmm) cc_final: 0.5919 (tpp) REVERT: B 194 PHE cc_start: 0.8075 (m-10) cc_final: 0.7771 (m-10) REVERT: B 202 GLU cc_start: 0.8261 (pt0) cc_final: 0.7350 (pm20) REVERT: B 271 ASN cc_start: 0.8192 (m110) cc_final: 0.7811 (m110) REVERT: G 67 TYR cc_start: 0.8179 (t80) cc_final: 0.7618 (t80) REVERT: G 97 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7376 (pt0) REVERT: G 111 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7882 (mt-10) REVERT: G 132 MET cc_start: 0.8326 (mmp) cc_final: 0.7922 (mpm) REVERT: G 167 ASP cc_start: 0.8261 (p0) cc_final: 0.7892 (p0) REVERT: G 387 TYR cc_start: 0.8410 (t80) cc_final: 0.8023 (t80) REVERT: G 659 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8348 (mp) REVERT: G 831 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8377 (mtmm) REVERT: G 1650 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8792 (m) REVERT: G 1784 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8780 (tmt) REVERT: G 1836 MET cc_start: 0.8793 (mmm) cc_final: 0.8569 (mmp) REVERT: G 2045 TRP cc_start: 0.7918 (t-100) cc_final: 0.7034 (t-100) outliers start: 61 outliers final: 35 residues processed: 305 average time/residue: 1.5589 time to fit residues: 559.1204 Evaluate side-chains 297 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 253 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 553 ASN Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 1.9990 chunk 347 optimal weight: 9.9990 chunk 316 optimal weight: 0.6980 chunk 337 optimal weight: 0.0020 chunk 203 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 265 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 305 optimal weight: 8.9990 chunk 319 optimal weight: 9.9990 chunk 336 optimal weight: 8.9990 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1494 HIS ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1352 HIS G1399 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30222 Z= 0.193 Angle : 0.507 9.721 40936 Z= 0.263 Chirality : 0.042 0.179 4602 Planarity : 0.004 0.037 5284 Dihedral : 4.586 95.388 4028 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 1.76 % Allowed : 14.18 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 1.12 (0.14), residues: 3760 helix: 1.63 (0.13), residues: 1714 sheet: -0.13 (0.23), residues: 481 loop : 0.15 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.027 0.001 PHE G 28 TYR 0.018 0.001 TYR B 294 ARG 0.008 0.000 ARG A1489 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 263 time to evaluate : 3.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8848 (tp30) cc_final: 0.8421 (tp30) REVERT: A 340 ARG cc_start: 0.6717 (mmt180) cc_final: 0.6141 (mpt180) REVERT: A 517 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: A 529 MET cc_start: 0.8886 (mmp) cc_final: 0.8363 (mmp) REVERT: A 958 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7949 (m) REVERT: A 1142 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8445 (mt-10) REVERT: A 1159 GLU cc_start: 0.7993 (mp0) cc_final: 0.7680 (pm20) REVERT: A 1162 GLU cc_start: 0.7745 (mp0) cc_final: 0.7342 (mp0) REVERT: A 1180 ARG cc_start: 0.7295 (mpt180) cc_final: 0.6558 (mpt90) REVERT: A 1209 ASP cc_start: 0.8470 (t70) cc_final: 0.8267 (t70) REVERT: A 1498 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: A 1757 GLU cc_start: 0.5006 (tt0) cc_final: 0.4751 (pt0) REVERT: B 143 GLU cc_start: 0.7691 (tt0) cc_final: 0.7466 (tm-30) REVERT: B 168 MET cc_start: 0.6457 (mmm) cc_final: 0.5835 (tpp) REVERT: B 202 GLU cc_start: 0.8208 (pt0) cc_final: 0.7386 (pm20) REVERT: B 237 MET cc_start: 0.7897 (mmp) cc_final: 0.7301 (mmp) REVERT: B 271 ASN cc_start: 0.8121 (m110) cc_final: 0.7767 (m110) REVERT: B 272 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: G 67 TYR cc_start: 0.8160 (t80) cc_final: 0.7609 (t80) REVERT: G 97 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7342 (pt0) REVERT: G 111 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7864 (mt-10) REVERT: G 132 MET cc_start: 0.8330 (mmp) cc_final: 0.7928 (mpm) REVERT: G 167 ASP cc_start: 0.8262 (p0) cc_final: 0.7854 (p0) REVERT: G 387 TYR cc_start: 0.8400 (t80) cc_final: 0.8022 (t80) REVERT: G 659 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8336 (mp) REVERT: G 694 TYR cc_start: 0.8516 (m-10) cc_final: 0.8250 (m-10) REVERT: G 1650 VAL cc_start: 0.9155 (OUTLIER) cc_final: 0.8778 (m) REVERT: G 1784 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8731 (tmt) REVERT: G 1836 MET cc_start: 0.8778 (mmm) cc_final: 0.8520 (mmp) REVERT: G 1986 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6782 (ttpt) REVERT: G 2045 TRP cc_start: 0.7929 (t-100) cc_final: 0.7028 (t-100) outliers start: 57 outliers final: 35 residues processed: 306 average time/residue: 1.5358 time to fit residues: 550.3425 Evaluate side-chains 296 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 253 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 553 ASN Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 9.9990 chunk 357 optimal weight: 20.0000 chunk 217 optimal weight: 20.0000 chunk 169 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 374 optimal weight: 10.0000 chunk 344 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 230 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1494 HIS ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1877 GLN G 181 HIS G 418 ASN G 430 HIS G1399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 30222 Z= 0.462 Angle : 0.629 10.940 40936 Z= 0.327 Chirality : 0.047 0.215 4602 Planarity : 0.005 0.048 5284 Dihedral : 5.036 100.380 4028 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.79 % Allowed : 14.21 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 0.72 (0.14), residues: 3760 helix: 1.30 (0.12), residues: 1701 sheet: -0.30 (0.22), residues: 483 loop : -0.05 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 865 HIS 0.008 0.002 HIS A1689 PHE 0.027 0.002 PHE A1376 TYR 0.021 0.002 TYR A 722 ARG 0.012 0.001 ARG A 520 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 255 time to evaluate : 3.407 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8837 (tp30) cc_final: 0.8383 (tp30) REVERT: A 340 ARG cc_start: 0.6756 (mmt180) cc_final: 0.6241 (mpt180) REVERT: A 517 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7164 (mm-30) REVERT: A 529 MET cc_start: 0.8855 (mmp) cc_final: 0.8295 (mmp) REVERT: A 537 LYS cc_start: 0.7354 (tptt) cc_final: 0.7133 (mttm) REVERT: A 944 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8427 (ttp80) REVERT: A 958 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7914 (m) REVERT: A 1159 GLU cc_start: 0.7964 (mp0) cc_final: 0.7621 (pm20) REVERT: A 1162 GLU cc_start: 0.7906 (mp0) cc_final: 0.7453 (mp0) REVERT: A 1180 ARG cc_start: 0.7267 (mpt180) cc_final: 0.6520 (mpt90) REVERT: A 1209 ASP cc_start: 0.8573 (t70) cc_final: 0.8341 (t70) REVERT: A 1491 ARG cc_start: 0.8447 (tpt90) cc_final: 0.7881 (tpp80) REVERT: A 1498 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: A 1757 GLU cc_start: 0.5010 (tt0) cc_final: 0.4752 (pt0) REVERT: B 143 GLU cc_start: 0.7733 (tt0) cc_final: 0.7431 (tm-30) REVERT: B 168 MET cc_start: 0.6473 (mmm) cc_final: 0.5835 (tpp) REVERT: B 271 ASN cc_start: 0.8018 (m110) cc_final: 0.7669 (m110) REVERT: G 67 TYR cc_start: 0.8255 (t80) cc_final: 0.7712 (t80) REVERT: G 97 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7439 (pt0) REVERT: G 132 MET cc_start: 0.8106 (mmp) cc_final: 0.7854 (mpm) REVERT: G 167 ASP cc_start: 0.8300 (p0) cc_final: 0.7996 (p0) REVERT: G 338 MET cc_start: 0.8790 (mmm) cc_final: 0.8416 (mtm) REVERT: G 387 TYR cc_start: 0.8424 (t80) cc_final: 0.7996 (t80) REVERT: G 659 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8361 (mp) REVERT: G 696 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: G 1650 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8834 (m) REVERT: G 1685 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8389 (tttm) REVERT: G 1784 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8848 (tmt) REVERT: G 2045 TRP cc_start: 0.7892 (t-100) cc_final: 0.7029 (t-100) outliers start: 58 outliers final: 38 residues processed: 300 average time/residue: 1.5494 time to fit residues: 542.5711 Evaluate side-chains 295 residues out of total 3245 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 248 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 944 ARG Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1806 GLN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 418 ASN Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 553 ASN Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1638 ILE Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 0.8980 chunk 317 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 275 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 298 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 306 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1494 HIS ** A1806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.110490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.081747 restraints weight = 52552.793| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.99 r_work: 0.2901 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30222 Z= 0.155 Angle : 0.513 9.916 40936 Z= 0.266 Chirality : 0.042 0.208 4602 Planarity : 0.004 0.035 5284 Dihedral : 4.625 98.127 4028 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % Rotamer: Outliers : 1.33 % Allowed : 14.89 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: 1.07 (0.14), residues: 3760 helix: 1.58 (0.13), residues: 1715 sheet: -0.11 (0.23), residues: 480 loop : 0.13 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 661 HIS 0.006 0.001 HIS B 152 PHE 0.024 0.001 PHE A 35 TYR 0.020 0.001 TYR B 294 ARG 0.008 0.000 ARG A 709 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10693.75 seconds wall clock time: 189 minutes 11.86 seconds (11351.86 seconds total)