Starting phenix.real_space_refine on Thu Mar 21 09:29:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/03_2024/8psa_17848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/03_2024/8psa_17848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/03_2024/8psa_17848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/03_2024/8psa_17848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/03_2024/8psa_17848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/03_2024/8psa_17848_updated.pdb" } resolution = 3.6 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= -0.000 sd= 0.007 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 107 5.16 5 C 18912 2.51 5 N 4967 2.21 5 O 5694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A ASP 652": "OD1" <-> "OD2" Residue "A ASP 675": "OD1" <-> "OD2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A GLU 1048": "OE1" <-> "OE2" Residue "A TYR 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A GLU 1132": "OE1" <-> "OE2" Residue "A PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A TYR 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1267": "OD1" <-> "OD2" Residue "A GLU 1268": "OE1" <-> "OE2" Residue "A GLU 1317": "OE1" <-> "OE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1333": "OD1" <-> "OD2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A GLU 1357": "OE1" <-> "OE2" Residue "A TYR 1438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1475": "OE1" <-> "OE2" Residue "A PHE 1512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1612": "OD1" <-> "OD2" Residue "A PHE 1687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1712": "OE1" <-> "OE2" Residue "A ASP 1713": "OD1" <-> "OD2" Residue "A ASP 1742": "OD1" <-> "OD2" Residue "A ASP 1784": "OD1" <-> "OD2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 262": "OE1" <-> "OE2" Residue "G ASP 287": "OD1" <-> "OD2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G ASP 351": "OD1" <-> "OD2" Residue "G ASP 437": "OD1" <-> "OD2" Residue "G ASP 534": "OD1" <-> "OD2" Residue "G ASP 538": "OD1" <-> "OD2" Residue "G PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 689": "OE1" <-> "OE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "G TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 790": "OD1" <-> "OD2" Residue "G PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 870": "OE1" <-> "OE2" Residue "G GLU 885": "OE1" <-> "OE2" Residue "G GLU 981": "OE1" <-> "OE2" Residue "G GLU 992": "OE1" <-> "OE2" Residue "G GLU 1038": "OE1" <-> "OE2" Residue "G PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1299": "OD1" <-> "OD2" Residue "G PHE 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1310": "OD1" <-> "OD2" Residue "G PHE 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1420": "OE1" <-> "OE2" Residue "G GLU 1448": "OE1" <-> "OE2" Residue "G PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1467": "OE1" <-> "OE2" Residue "G GLU 1469": "OE1" <-> "OE2" Residue "G PHE 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1656": "OE1" <-> "OE2" Residue "G GLU 1658": "OE1" <-> "OE2" Residue "G PHE 1704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1749": "OE1" <-> "OE2" Residue "G PHE 1752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1757": "OE1" <-> "OE2" Residue "G ASP 1820": "OD1" <-> "OD2" Residue "G TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1846": "OE1" <-> "OE2" Residue "G PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29681 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1589, 12409 Classifications: {'peptide': 1589} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1527} Chain breaks: 3 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: 16018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2036, 16018 Classifications: {'peptide': 2036} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1926} 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: 14.55, per 1000 atoms: 0.49 Number of scatterers: 29681 At special positions: 0 Unit cell: (183.57, 181.46, 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 107 16.00 P 1 15.00 O 5694 8.00 N 4967 7.00 C 18912 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=2.15 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: 10.61 Conformation dependent library (CDL) restraints added in 5.4 seconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 163 helices and 31 sheets defined 43.6% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.95 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 Processing helix chain 'A' and resid 28 through 33 removed outlier: 3.580A pdb=" N ASP A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 330 through 350 Processing helix chain 'A' and resid 356 through 382 removed outlier: 3.723A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.008A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.904A pdb=" N ARG A 442 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 464 through 483 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 609 through 615 Processing helix chain 'A' and resid 626 through 629 Processing helix chain 'A' and resid 653 through 668 Processing helix chain 'A' and resid 688 through 698 Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'A' and resid 742 through 753 removed outlier: 3.559A pdb=" N ALA A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 812 Processing helix chain 'A' and resid 839 through 855 removed outlier: 4.024A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 882 through 891 removed outlier: 4.011A pdb=" N GLU A 886 " --> pdb=" O ILE A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.535A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 919 Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 936 through 968 removed outlier: 3.560A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 975 No H-bonds generated for 'chain 'A' and resid 972 through 975' Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.662A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1033 through 1041 Processing helix chain 'A' and resid 1047 through 1056 Processing helix chain 'A' and resid 1087 through 1099 removed outlier: 4.583A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1111 Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 7.655A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LYS A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1197 No H-bonds generated for 'chain 'A' and resid 1195 through 1197' Processing helix chain 'A' and resid 1202 through 1207 Processing helix chain 'A' and resid 1210 through 1226 Processing helix chain 'A' and resid 1231 through 1236 Processing helix chain 'A' and resid 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1254 through 1262 Processing helix chain 'A' and resid 1276 through 1278 No H-bonds generated for 'chain 'A' and resid 1276 through 1278' Processing helix chain 'A' and resid 1280 through 1290 removed outlier: 4.006A pdb=" N MET A1283 " --> pdb=" O ILE A1280 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A1284 " --> pdb=" O ASN A1281 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A1287 " --> pdb=" O SER A1284 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A1290 " --> pdb=" O VAL A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1307 through 1320 Processing helix chain 'A' and resid 1337 through 1346 Processing helix chain 'A' and resid 1352 through 1357 Processing helix chain 'A' and resid 1362 through 1365 Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1425 through 1428 Processing helix chain 'A' and resid 1445 through 1476 removed outlier: 3.542A pdb=" N GLN A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1508 Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 3.523A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR A1529 " --> pdb=" O ALA A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1535 No H-bonds generated for 'chain 'A' and resid 1533 through 1535' Processing helix chain 'A' and resid 1547 through 1564 removed outlier: 4.153A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 4.066A pdb=" N THR A1581 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1602 removed outlier: 4.563A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N MET A1592 " --> pdb=" O GLY A1589 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A1593 " --> pdb=" O ALA A1590 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A1596 " --> pdb=" O MET A1593 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN A1598 " --> pdb=" O GLY A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 removed outlier: 3.607A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1664 Processing helix chain 'A' and resid 1667 through 1693 Processing helix chain 'A' and resid 1711 through 1716 Processing helix chain 'A' and resid 1735 through 1737 No H-bonds generated for 'chain 'A' and resid 1735 through 1737' Processing helix chain 'A' and resid 1741 through 1744 No H-bonds generated for 'chain 'A' and resid 1741 through 1744' Processing helix chain 'A' and resid 1747 through 1757 Processing helix chain 'A' and resid 1784 through 1790 Processing helix chain 'A' and resid 1793 through 1799 Processing helix chain 'A' and resid 1805 through 1823 Processing helix chain 'A' and resid 1854 through 1861 Processing helix chain 'B' and resid 147 through 158 removed outlier: 4.354A pdb=" N HIS B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 180 through 194 Processing helix chain 'B' and resid 206 through 214 removed outlier: 3.747A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 235 Processing helix chain 'B' and resid 243 through 253 Processing helix chain 'B' and resid 258 through 270 removed outlier: 4.126A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 removed outlier: 3.718A pdb=" N TYR B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 40 removed outlier: 3.740A pdb=" N PHE G 27 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N PHE G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA G 30 " --> pdb=" O PHE G 27 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN G 34 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU G 35 " --> pdb=" O GLN G 32 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN G 36 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE G 37 " --> pdb=" O GLN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 57 through 71 Processing helix chain 'G' and resid 81 through 95 Processing helix chain 'G' and resid 101 through 111 Processing helix chain 'G' and resid 116 through 132 Processing helix chain 'G' and resid 144 through 150 Processing helix chain 'G' and resid 170 through 179 Processing helix chain 'G' and resid 181 through 201 removed outlier: 6.313A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS G 189 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 228 through 231 No H-bonds generated for 'chain 'G' and resid 228 through 231' Processing helix chain 'G' and resid 234 through 256 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 260 through 266 Processing helix chain 'G' and resid 274 through 285 removed outlier: 3.875A pdb=" N VAL G 278 " --> pdb=" O GLN G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 313 Processing helix chain 'G' and resid 321 through 330 removed outlier: 3.672A pdb=" N ASN G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 359 removed outlier: 3.857A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 383 through 396 removed outlier: 3.892A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 411 No H-bonds generated for 'chain 'G' and resid 409 through 411' Processing helix chain 'G' and resid 430 through 432 No H-bonds generated for 'chain 'G' and resid 430 through 432' Processing helix chain 'G' and resid 434 through 445 removed outlier: 3.755A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL G 444 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 512 through 520 Processing helix chain 'G' and resid 544 through 548 Processing helix chain 'G' and resid 561 through 564 No H-bonds generated for 'chain 'G' and resid 561 through 564' Processing helix chain 'G' and resid 582 through 587 removed outlier: 3.591A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 612 Processing helix chain 'G' and resid 627 through 640 removed outlier: 3.877A pdb=" N GLN G 640 " --> pdb=" O SER G 636 " (cutoff:3.500A) Processing helix chain 'G' and resid 656 through 672 removed outlier: 3.789A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 688 through 698 Processing helix chain 'G' and resid 710 through 723 Processing helix chain 'G' and resid 748 through 751 No H-bonds generated for 'chain 'G' and resid 748 through 751' Processing helix chain 'G' and resid 754 through 758 Processing helix chain 'G' and resid 775 through 782 Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 789 removed outlier: 4.045A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 804 through 807 removed outlier: 3.821A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 804 through 807' Processing helix chain 'G' and resid 815 through 822 Processing helix chain 'G' and resid 832 through 834 No H-bonds generated for 'chain 'G' and resid 832 through 834' Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 877 through 898 removed outlier: 4.706A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 3.524A pdb=" N ALA G 886 " --> pdb=" O PRO G 882 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 930 Processing helix chain 'G' and resid 941 through 958 Processing helix chain 'G' and resid 970 through 974 Processing helix chain 'G' and resid 976 through 986 Processing helix chain 'G' and resid 988 through 991 Processing helix chain 'G' and resid 997 through 1008 removed outlier: 3.776A pdb=" N GLN G1008 " --> pdb=" O LEU G1004 " (cutoff:3.500A) Processing helix chain 'G' and resid 1025 through 1030 Processing helix chain 'G' and resid 1037 through 1042 removed outlier: 3.930A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU G1041 " --> pdb=" O GLU G1038 " (cutoff:3.500A) Processing helix chain 'G' and resid 1048 through 1050 No H-bonds generated for 'chain 'G' and resid 1048 through 1050' Processing helix chain 'G' and resid 1058 through 1061 Processing helix chain 'G' and resid 1070 through 1089 removed outlier: 3.764A pdb=" N LYS G1084 " --> pdb=" O GLY G1080 " (cutoff:3.500A) Processing helix chain 'G' and resid 1094 through 1096 No H-bonds generated for 'chain 'G' and resid 1094 through 1096' Processing helix chain 'G' and resid 1135 through 1143 Processing helix chain 'G' and resid 1149 through 1155 Processing helix chain 'G' and resid 1169 through 1173 Processing helix chain 'G' and resid 1190 through 1192 No H-bonds generated for 'chain 'G' and resid 1190 through 1192' Processing helix chain 'G' and resid 1258 through 1269 Processing helix chain 'G' and resid 1294 through 1303 removed outlier: 4.145A pdb=" N HIS G1302 " --> pdb=" O TYR G1298 " (cutoff:3.500A) Processing helix chain 'G' and resid 1309 through 1311 No H-bonds generated for 'chain 'G' and resid 1309 through 1311' Processing helix chain 'G' and resid 1323 through 1335 removed outlier: 4.033A pdb=" N ILE G1327 " --> pdb=" O ASP G1324 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TRP G1331 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1438 through 1446 removed outlier: 3.591A pdb=" N VAL G1443 " --> pdb=" O LYS G1439 " (cutoff:3.500A) Processing helix chain 'G' and resid 1515 through 1522 removed outlier: 3.652A pdb=" N ARG G1522 " --> pdb=" O ASP G1518 " (cutoff:3.500A) Processing helix chain 'G' and resid 1551 through 1557 removed outlier: 3.543A pdb=" N ARG G1555 " --> pdb=" O GLU G1551 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) Processing helix chain 'G' and resid 1562 through 1564 No H-bonds generated for 'chain 'G' and resid 1562 through 1564' Processing helix chain 'G' and resid 1567 through 1572 Processing helix chain 'G' and resid 1582 through 1596 removed outlier: 3.647A pdb=" N LEU G1592 " --> pdb=" O SER G1588 " (cutoff:3.500A) Processing helix chain 'G' and resid 1685 through 1702 removed outlier: 3.656A pdb=" N VAL G1690 " --> pdb=" O ALA G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1706 through 1712 Processing helix chain 'G' and resid 1724 through 1735 removed outlier: 3.549A pdb=" N ASN G1732 " --> pdb=" O ARG G1728 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA G1735 " --> pdb=" O GLU G1731 " (cutoff:3.500A) Processing helix chain 'G' and resid 1770 through 1772 No H-bonds generated for 'chain 'G' and resid 1770 through 1772' Processing helix chain 'G' and resid 1774 through 1794 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1810 through 1819 Processing helix chain 'G' and resid 1824 through 1839 Processing helix chain 'G' and resid 1859 through 1862 No H-bonds generated for 'chain 'G' and resid 1859 through 1862' Processing helix chain 'G' and resid 1869 through 1881 removed outlier: 3.555A pdb=" N ARG G1881 " --> pdb=" O ARG G1877 " (cutoff:3.500A) Processing helix chain 'G' and resid 1905 through 1920 removed outlier: 4.069A pdb=" N VAL G1910 " --> pdb=" O ALA G1906 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) Processing helix chain 'G' and resid 1935 through 1950 removed outlier: 4.549A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS G1949 " --> pdb=" O ASP G1945 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1983 through 1995 removed outlier: 4.067A pdb=" N LYS G1986 " --> pdb=" O ASN G1983 " (cutoff:3.500A) Proline residue: G1987 - end of helix removed outlier: 3.620A pdb=" N PHE G1991 " --> pdb=" O PHE G1988 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS G1993 " --> pdb=" O SER G1990 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN G1995 " --> pdb=" O LEU G1992 " (cutoff:3.500A) Processing helix chain 'G' and resid 2023 through 2032 removed outlier: 3.631A pdb=" N LEU G2032 " --> pdb=" O ASP G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2036 through 2043 Processing helix chain 'G' and resid 2045 through 2049 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 removed outlier: 5.810A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU A 46 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU A 79 " --> pdb=" O GLU A 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.257A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE A 769 " --> pdb=" O THR A 681 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 497 through 503 Processing sheet with id= D, first strand: chain 'A' and resid 649 through 651 removed outlier: 4.498A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 820 through 822 Processing sheet with id= F, first strand: chain 'A' and resid 1573 through 1575 removed outlier: 3.587A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A1642 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1024 through 1027 Processing sheet with id= H, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id= I, first strand: chain 'A' and resid 1102 through 1105 removed outlier: 3.955A pdb=" N GLY A1102 " --> pdb=" O GLN A1188 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1119 through 1126 removed outlier: 3.577A pdb=" N MET A1121 " --> pdb=" O LYS A1177 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= L, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id= M, first strand: chain 'A' and resid 1838 through 1840 Processing sheet with id= N, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.688A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 269 through 272 removed outlier: 3.718A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS G 500 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE G 159 " --> pdb=" O HIS G 500 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU G 502 " --> pdb=" O ILE G 159 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG G 526 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASP G 503 " --> pdb=" O ARG G 526 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE G 528 " --> pdb=" O ASP G 503 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 417 through 420 removed outlier: 6.122A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 568 through 571 Processing sheet with id= R, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.563A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N GLY G 798 " --> pdb=" O PHE G 767 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= T, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 5.859A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL G1201 " --> pdb=" O LEU G1205 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU G1205 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET G1221 " --> pdb=" O LEU G1238 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU G1238 " --> pdb=" O MET G1221 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= V, first strand: chain 'G' and resid 1285 through 1287 removed outlier: 4.002A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 1354 through 1358 Processing sheet with id= X, first strand: chain 'G' and resid 1424 through 1426 removed outlier: 3.768A pdb=" N PHE G1486 " --> pdb=" O GLU G1469 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA G1508 " --> pdb=" O VAL G1483 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 1431 through 1434 removed outlier: 4.085A pdb=" N TYR G1431 " --> pdb=" O PHE G1466 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G1464 " --> pdb=" O MET G1433 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 1540 through 1546 removed outlier: 4.105A pdb=" N THR G1620 " --> pdb=" O THR G1546 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU G1651 " --> pdb=" O THR G1642 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 1635 through 1637 Processing sheet with id= AB, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 7.139A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA G1805 " --> pdb=" O PHE G1666 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id= AD, first strand: chain 'G' and resid 1737 through 1741 removed outlier: 3.747A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 1966 through 1968 removed outlier: 3.776A pdb=" N GLY G1853 " --> pdb=" O GLY G1902 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY G1902 " --> pdb=" O GLY G1853 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) 1179 hydrogen bonds defined for protein. 3255 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: 13.19 Time building geometry restraints manager: 11.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5215 1.32 - 1.47: 7890 1.47 - 1.62: 17006 1.62 - 1.76: 0 1.76 - 1.91: 189 Bond restraints: 30300 Sorted by residual: bond pdb=" C PRO A1399 " pdb=" O PRO A1399 " ideal model delta sigma weight residual 1.233 1.173 0.060 1.10e-02 8.26e+03 2.97e+01 bond pdb=" N GLU G1199 " pdb=" CA GLU G1199 " ideal model delta sigma weight residual 1.453 1.496 -0.043 8.30e-03 1.45e+04 2.66e+01 bond pdb=" C7 FMN G2101 " pdb=" C8 FMN G2101 " ideal model delta sigma weight residual 1.390 1.488 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.60e-03 1.35e+04 1.97e+01 bond pdb=" C TYR A1174 " pdb=" O TYR A1174 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.14e-02 7.69e+03 1.92e+01 ... (remaining 30295 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.67: 590 104.67 - 112.29: 13173 112.29 - 119.91: 15658 119.91 - 127.53: 11419 127.53 - 135.15: 201 Bond angle restraints: 41041 Sorted by residual: angle pdb=" CB GLU A 841 " pdb=" CG GLU A 841 " pdb=" CD GLU A 841 " ideal model delta sigma weight residual 112.60 125.67 -13.07 1.70e+00 3.46e-01 5.91e+01 angle pdb=" CB GLU A 780 " pdb=" CG GLU A 780 " pdb=" CD GLU A 780 " ideal model delta sigma weight residual 112.60 125.00 -12.40 1.70e+00 3.46e-01 5.32e+01 angle pdb=" CB GLU A 364 " pdb=" CG GLU A 364 " pdb=" CD GLU A 364 " ideal model delta sigma weight residual 112.60 124.41 -11.81 1.70e+00 3.46e-01 4.82e+01 angle pdb=" C SER A1417 " pdb=" N VAL A1418 " pdb=" CA VAL A1418 " ideal model delta sigma weight residual 120.33 125.87 -5.54 8.00e-01 1.56e+00 4.80e+01 angle pdb=" C SER G 233 " pdb=" N ILE G 234 " pdb=" CA ILE G 234 " ideal model delta sigma weight residual 120.24 124.54 -4.30 6.30e-01 2.52e+00 4.67e+01 ... (remaining 41036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 16356 17.84 - 35.67: 1522 35.67 - 53.51: 300 53.51 - 71.34: 79 71.34 - 89.18: 36 Dihedral angle restraints: 18293 sinusoidal: 7353 harmonic: 10940 Sorted by residual: dihedral pdb=" CA ALA G 897 " pdb=" C ALA G 897 " pdb=" N ASP G 898 " pdb=" CA ASP G 898 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PHE G1411 " pdb=" C PHE G1411 " pdb=" N TYR G1412 " pdb=" CA TYR G1412 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual -86.00 -43.85 -42.15 1 1.00e+01 1.00e-02 2.48e+01 ... (remaining 18290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1933 0.055 - 0.110: 1649 0.110 - 0.165: 800 0.165 - 0.219: 206 0.219 - 0.274: 25 Chirality restraints: 4613 Sorted by residual: chirality pdb=" CA ILE G 652 " pdb=" N ILE G 652 " pdb=" C ILE G 652 " pdb=" CB ILE G 652 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE A1384 " pdb=" N ILE A1384 " pdb=" C ILE A1384 " pdb=" CB ILE A1384 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE A1326 " pdb=" N ILE A1326 " pdb=" C ILE A1326 " pdb=" CB ILE A1326 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 4610 not shown) Planarity restraints: 5299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1660 " -0.045 2.00e-02 2.50e+03 2.59e-02 1.34e+01 pdb=" CG TYR A1660 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A1660 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1660 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A1660 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A1660 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A1660 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1660 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 624 " -0.042 2.00e-02 2.50e+03 2.21e-02 9.74e+00 pdb=" CG TYR G 624 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR G 624 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR G 624 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR G 624 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR G 624 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR G 624 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 624 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " -0.005 2.00e-02 2.50e+03 1.43e-02 9.74e+00 pdb=" C10 FMN G2101 " -0.017 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " 0.015 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.001 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " -0.031 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " -0.001 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.006 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " 0.008 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " 0.015 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " 0.001 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " 0.003 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.006 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.005 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " 0.003 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " -0.016 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " 0.017 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " -0.034 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " 0.015 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " 0.008 2.00e-02 2.50e+03 ... (remaining 5296 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1065 2.72 - 3.26: 30529 3.26 - 3.81: 47113 3.81 - 4.35: 64838 4.35 - 4.90: 104309 Nonbonded interactions: 247854 Sorted by model distance: nonbonded pdb=" OH TYR A 89 " pdb=" OD2 ASP G1791 " model vdw 2.170 2.440 nonbonded pdb=" OG1 THR G1470 " pdb=" ND2 ASN G1514 " model vdw 2.215 2.520 nonbonded pdb=" OH TYR G1266 " pdb=" OD1 ASN G1561 " model vdw 2.235 2.440 nonbonded pdb=" O GLY A 389 " pdb=" ND2 ASN A 738 " model vdw 2.245 2.520 nonbonded pdb=" O VAL G1381 " pdb=" OG1 THR G1422 " model vdw 2.268 2.440 ... (remaining 247849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.760 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 76.670 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.014 0.109 30300 Z= 0.908 Angle : 1.911 13.073 41041 Z= 1.394 Chirality : 0.088 0.274 4613 Planarity : 0.006 0.028 5299 Dihedral : 15.238 89.176 11246 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.87 % Favored : 91.55 % Rotamer: Outliers : 0.74 % Allowed : 5.14 % Favored : 94.13 % 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: -3.68 (0.11), residues: 3774 helix: -2.80 (0.09), residues: 1658 sheet: -2.25 (0.22), residues: 415 loop : -1.92 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.006 TRP G 865 HIS 0.014 0.003 HIS A1689 PHE 0.042 0.005 PHE G 939 TYR 0.053 0.005 TYR A1660 ARG 0.010 0.001 ARG A1036 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 337 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.9108 (mtm-85) cc_final: 0.8278 (mmt180) REVERT: A 431 GLU cc_start: 0.9151 (tp30) cc_final: 0.8852 (tp30) REVERT: A 708 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8462 (m) REVERT: A 713 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8617 (tm-30) REVERT: A 754 ASP cc_start: 0.9451 (t0) cc_final: 0.9182 (t0) REVERT: A 925 ASP cc_start: 0.9264 (t0) cc_final: 0.8946 (t70) REVERT: A 1124 GLU cc_start: 0.8766 (pp20) cc_final: 0.8353 (pp20) REVERT: A 1267 ASP cc_start: 0.8864 (t0) cc_final: 0.8649 (t70) REVERT: A 1268 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8669 (mm-30) REVERT: A 1332 TYR cc_start: 0.8924 (p90) cc_final: 0.8705 (p90) REVERT: B 185 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8333 (mt-10) REVERT: B 277 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7452 (mm) REVERT: G 229 ASP cc_start: 0.9056 (m-30) cc_final: 0.8586 (t0) REVERT: G 268 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8550 (mmmm) REVERT: G 425 SER cc_start: 0.9385 (t) cc_final: 0.9100 (p) REVERT: G 564 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8392 (tp30) REVERT: G 630 MET cc_start: 0.8812 (tpp) cc_final: 0.8307 (tpp) REVERT: G 750 MET cc_start: 0.8975 (mmt) cc_final: 0.8590 (mmt) REVERT: G 1011 MET cc_start: 0.9308 (mtt) cc_final: 0.8633 (tmm) REVERT: G 1067 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8530 (t70) REVERT: G 1136 GLU cc_start: 0.9107 (tp30) cc_final: 0.8860 (pp20) REVERT: G 1299 ASP cc_start: 0.9216 (t0) cc_final: 0.9008 (t0) REVERT: G 1405 GLU cc_start: 0.7370 (pt0) cc_final: 0.6925 (tm-30) REVERT: G 1631 MET cc_start: 0.5418 (tpt) cc_final: 0.4720 (tpp) REVERT: G 1676 MET cc_start: 0.7813 (ptm) cc_final: 0.7076 (ptm) REVERT: G 1784 MET cc_start: 0.8100 (tmm) cc_final: 0.7669 (tmm) outliers start: 24 outliers final: 10 residues processed: 354 average time/residue: 0.3931 time to fit residues: 228.2843 Evaluate side-chains 265 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 252 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1308 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1511 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 0.9980 chunk 285 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 114 optimal weight: 0.0670 chunk 179 optimal weight: 0.1980 chunk 219 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 overall best weight: 3.0522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 524 GLN A 758 ASN ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN A 881 ASN A 882 ASN A 987 ASN A 989 GLN A1063 HIS A1239 HIS A1271 GLN A1432 HIS A1482 GLN A1549 ASN A1563 HIS A1570 ASN A1610 ASN A1689 HIS A1703 HIS A1766 ASN A1783 ASN A1845 ASN B 271 ASN G 36 GLN G 85 ASN G 181 HIS G 245 GLN G 248 HIS G 350 GLN G 440 ASN G 640 GLN G 715 GLN G 747 HIS G 993 GLN G1241 ASN G1302 HIS G1355 ASN G1383 ASN G1424 GLN G1451 GLN G1476 ASN G1514 ASN ** G1628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1890 ASN G1995 ASN ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2044 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30300 Z= 0.227 Angle : 0.572 7.414 41041 Z= 0.303 Chirality : 0.042 0.240 4613 Planarity : 0.004 0.045 5299 Dihedral : 5.606 72.230 4061 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.05 % Favored : 96.87 % Rotamer: Outliers : 1.41 % Allowed : 9.01 % Favored : 89.58 % 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: -1.15 (0.13), residues: 3774 helix: -0.27 (0.12), residues: 1663 sheet: -1.61 (0.21), residues: 510 loop : -0.83 (0.15), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G1449 HIS 0.007 0.001 HIS G1352 PHE 0.021 0.002 PHE A 450 TYR 0.019 0.002 TYR A1513 ARG 0.005 0.000 ARG G1522 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 282 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.8976 (mtm-85) cc_final: 0.8160 (mmt180) REVERT: A 358 GLU cc_start: 0.8794 (tp30) cc_final: 0.8482 (tp30) REVERT: A 431 GLU cc_start: 0.8978 (tp30) cc_final: 0.8734 (tp30) REVERT: A 1124 GLU cc_start: 0.8837 (pp20) cc_final: 0.8489 (pp20) REVERT: A 1268 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8492 (mm-30) REVERT: A 1496 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8932 (mp0) REVERT: B 185 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8152 (mt-10) REVERT: B 272 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8384 (mp0) REVERT: B 277 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7190 (mm) REVERT: G 229 ASP cc_start: 0.8958 (m-30) cc_final: 0.8626 (t0) REVERT: G 630 MET cc_start: 0.8601 (tpp) cc_final: 0.8119 (tpp) REVERT: G 750 MET cc_start: 0.8900 (mmt) cc_final: 0.8318 (mmt) REVERT: G 850 MET cc_start: 0.8158 (mtm) cc_final: 0.7202 (tpt) REVERT: G 1011 MET cc_start: 0.9248 (mtt) cc_final: 0.8716 (tmm) REVERT: G 1067 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8715 (t70) REVERT: G 1412 TYR cc_start: 0.7174 (m-10) cc_final: 0.6398 (m-10) REVERT: G 1645 GLU cc_start: 0.3896 (OUTLIER) cc_final: 0.3681 (pm20) REVERT: G 1676 MET cc_start: 0.7762 (ptm) cc_final: 0.7145 (ptm) REVERT: G 1754 GLU cc_start: 0.8902 (mp0) cc_final: 0.8631 (pm20) REVERT: G 1784 MET cc_start: 0.8129 (tmm) cc_final: 0.7823 (tmm) REVERT: G 1822 MET cc_start: 0.6214 (mpp) cc_final: 0.5586 (mpp) outliers start: 46 outliers final: 23 residues processed: 312 average time/residue: 0.3700 time to fit residues: 191.2698 Evaluate side-chains 269 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 242 time to evaluate : 3.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1409 SER Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1645 GLU Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 284 optimal weight: 20.0000 chunk 233 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 7.9990 chunk 370 optimal weight: 20.0000 chunk 305 optimal weight: 8.9990 chunk 340 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 275 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 388 ASN A 438 ASN ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN B 271 ASN G 163 GLN G 910 GLN ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 30300 Z= 0.201 Angle : 0.527 9.610 41041 Z= 0.272 Chirality : 0.042 0.254 4613 Planarity : 0.004 0.053 5299 Dihedral : 5.102 70.625 4055 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 1.81 % Allowed : 10.61 % Favored : 87.58 % 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: -0.21 (0.14), residues: 3774 helix: 0.68 (0.13), residues: 1651 sheet: -1.24 (0.21), residues: 517 loop : -0.48 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G1449 HIS 0.005 0.001 HIS A 454 PHE 0.016 0.001 PHE A 450 TYR 0.022 0.001 TYR G1608 ARG 0.004 0.000 ARG G1881 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 269 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 841 GLU cc_start: 0.6088 (tp30) cc_final: 0.5268 (tp30) REVERT: A 847 GLU cc_start: 0.8990 (tt0) cc_final: 0.8550 (tm-30) REVERT: A 1124 GLU cc_start: 0.8831 (pp20) cc_final: 0.8493 (pp20) REVERT: A 1320 LEU cc_start: 0.9508 (mp) cc_final: 0.9288 (mt) REVERT: A 1496 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8840 (mp0) REVERT: B 185 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8145 (mt-10) REVERT: G 229 ASP cc_start: 0.8886 (m-30) cc_final: 0.8644 (t0) REVERT: G 528 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8451 (mm) REVERT: G 630 MET cc_start: 0.8570 (tpp) cc_final: 0.8088 (tpp) REVERT: G 750 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8154 (mmt) REVERT: G 917 MET cc_start: 0.8940 (mtp) cc_final: 0.8725 (mtp) REVERT: G 1011 MET cc_start: 0.9255 (mtt) cc_final: 0.8733 (tmm) REVERT: G 1067 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8694 (t70) REVERT: G 1106 GLU cc_start: 0.8296 (mp0) cc_final: 0.7817 (mp0) REVERT: G 1323 MET cc_start: 0.4984 (tpt) cc_final: 0.4505 (tpt) REVERT: G 1355 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.7868 (p0) REVERT: G 1404 MET cc_start: 0.6791 (ppp) cc_final: 0.4827 (ptp) REVERT: G 1405 GLU cc_start: 0.6954 (pp20) cc_final: 0.5937 (tm-30) REVERT: G 1604 ARG cc_start: 0.6691 (ptp90) cc_final: 0.6186 (mtm110) REVERT: G 1676 MET cc_start: 0.7841 (ptm) cc_final: 0.7358 (ptm) REVERT: G 1754 GLU cc_start: 0.8944 (mp0) cc_final: 0.8703 (pm20) REVERT: G 1784 MET cc_start: 0.8065 (tmm) cc_final: 0.7680 (tmm) outliers start: 59 outliers final: 31 residues processed: 308 average time/residue: 0.3816 time to fit residues: 197.9733 Evaluate side-chains 279 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 243 time to evaluate : 3.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1409 SER Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 7.9990 chunk 257 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 230 optimal weight: 10.0000 chunk 344 optimal weight: 9.9990 chunk 364 optimal weight: 9.9990 chunk 179 optimal weight: 0.9980 chunk 326 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 422 HIS A1758 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN B 292 GLN G 163 GLN G 500 HIS ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30300 Z= 0.280 Angle : 0.546 6.896 41041 Z= 0.282 Chirality : 0.042 0.286 4613 Planarity : 0.004 0.057 5299 Dihedral : 5.051 69.814 4049 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.66 % Favored : 96.29 % Rotamer: Outliers : 1.94 % Allowed : 12.18 % Favored : 85.89 % 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: -0.05 (0.14), residues: 3774 helix: 0.81 (0.13), residues: 1655 sheet: -1.20 (0.22), residues: 517 loop : -0.38 (0.16), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G1449 HIS 0.008 0.001 HIS G1568 PHE 0.023 0.002 PHE A 450 TYR 0.019 0.002 TYR A 81 ARG 0.003 0.000 ARG G1522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 258 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 GLU cc_start: 0.6102 (tp30) cc_final: 0.5208 (tp30) REVERT: A 847 GLU cc_start: 0.8974 (tt0) cc_final: 0.8542 (tm-30) REVERT: A 1124 GLU cc_start: 0.8790 (pp20) cc_final: 0.8457 (pp20) REVERT: A 1496 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8770 (mp0) REVERT: B 168 MET cc_start: 0.6632 (tpp) cc_final: 0.6322 (tpp) REVERT: B 185 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8235 (mt-10) REVERT: B 241 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: G 630 MET cc_start: 0.8631 (tpp) cc_final: 0.8137 (tpp) REVERT: G 750 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8267 (mmt) REVERT: G 1011 MET cc_start: 0.9257 (mtt) cc_final: 0.8727 (tmm) REVERT: G 1067 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8813 (t70) REVERT: G 1323 MET cc_start: 0.5407 (tpt) cc_final: 0.4958 (tpt) REVERT: G 1404 MET cc_start: 0.6762 (ppp) cc_final: 0.4739 (ptp) REVERT: G 1433 MET cc_start: 0.6047 (ptm) cc_final: 0.5844 (ptp) REVERT: G 1520 LEU cc_start: 0.6246 (mp) cc_final: 0.5578 (mt) REVERT: G 1604 ARG cc_start: 0.6810 (ptp90) cc_final: 0.6404 (mtm110) REVERT: G 1645 GLU cc_start: 0.3944 (OUTLIER) cc_final: 0.3512 (pm20) REVERT: G 1673 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: G 1676 MET cc_start: 0.7929 (ptm) cc_final: 0.7542 (ptm) REVERT: G 1763 THR cc_start: 0.9289 (m) cc_final: 0.8714 (p) REVERT: G 1784 MET cc_start: 0.8066 (tmm) cc_final: 0.7685 (tmm) outliers start: 63 outliers final: 43 residues processed: 300 average time/residue: 0.3908 time to fit residues: 197.8052 Evaluate side-chains 289 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 240 time to evaluate : 3.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1293 THR Chi-restraints excluded: chain G residue 1409 SER Chi-restraints excluded: chain G residue 1421 ASN Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1645 GLU Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1673 GLU Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1966 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 271 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 310 optimal weight: 10.0000 chunk 251 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 186 optimal weight: 20.0000 chunk 327 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 475 GLN A 527 GLN A1146 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN B 292 GLN G 224 ASN G1088 GLN ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1512 HIS G1523 ASN G1529 GLN ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 30300 Z= 0.345 Angle : 0.587 9.252 41041 Z= 0.304 Chirality : 0.044 0.299 4613 Planarity : 0.004 0.060 5299 Dihedral : 5.262 69.408 4049 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.71 % Rotamer: Outliers : 2.71 % Allowed : 13.31 % Favored : 83.98 % 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: -0.19 (0.14), residues: 3774 helix: 0.70 (0.13), residues: 1652 sheet: -1.19 (0.22), residues: 504 loop : -0.50 (0.16), residues: 1618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G2045 HIS 0.008 0.001 HIS G1568 PHE 0.022 0.002 PHE A 450 TYR 0.031 0.002 TYR G1608 ARG 0.005 0.001 ARG G1522 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 248 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.5132 (mmm) cc_final: 0.4894 (mmt) REVERT: A 691 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8722 (mm-30) REVERT: A 847 GLU cc_start: 0.8979 (tt0) cc_final: 0.8534 (tm-30) REVERT: A 1124 GLU cc_start: 0.8621 (pp20) cc_final: 0.8275 (pp20) REVERT: A 1496 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8755 (mp0) REVERT: B 179 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6425 (mmtt) REVERT: B 185 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8144 (mt-10) REVERT: B 241 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: G 630 MET cc_start: 0.8658 (tpp) cc_final: 0.8144 (tpp) REVERT: G 750 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8356 (mmt) REVERT: G 1011 MET cc_start: 0.9258 (mtt) cc_final: 0.8668 (tmm) REVERT: G 1323 MET cc_start: 0.5504 (tpt) cc_final: 0.4799 (mmm) REVERT: G 1359 MET cc_start: 0.2683 (mmm) cc_final: 0.2061 (mtt) REVERT: G 1404 MET cc_start: 0.6808 (ppp) cc_final: 0.4656 (ptp) REVERT: G 1433 MET cc_start: 0.6049 (ptm) cc_final: 0.5804 (ptp) REVERT: G 1520 LEU cc_start: 0.6470 (mp) cc_final: 0.5792 (mt) REVERT: G 1604 ARG cc_start: 0.6804 (ptp90) cc_final: 0.6505 (mtm110) REVERT: G 1645 GLU cc_start: 0.3865 (OUTLIER) cc_final: 0.3499 (pm20) REVERT: G 1673 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7894 (pm20) REVERT: G 1676 MET cc_start: 0.7847 (ptm) cc_final: 0.7462 (ptm) REVERT: G 1763 THR cc_start: 0.9301 (m) cc_final: 0.8890 (p) REVERT: G 1784 MET cc_start: 0.8052 (tmm) cc_final: 0.7262 (tmm) outliers start: 88 outliers final: 60 residues processed: 311 average time/residue: 0.3793 time to fit residues: 197.1032 Evaluate side-chains 300 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 234 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1875 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 248 LYS Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 246 LEU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 581 THR Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1285 ILE Chi-restraints excluded: chain G residue 1293 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1409 SER Chi-restraints excluded: chain G residue 1421 ASN Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1645 GLU Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1673 GLU Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 0.9990 chunk 328 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 213 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 364 optimal weight: 9.9990 chunk 302 optimal weight: 0.9980 chunk 168 optimal weight: 6.9990 chunk 30 optimal weight: 0.0000 chunk 120 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN A1552 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30300 Z= 0.143 Angle : 0.500 9.883 41041 Z= 0.255 Chirality : 0.041 0.318 4613 Planarity : 0.004 0.056 5299 Dihedral : 4.677 69.766 4047 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Rotamer: Outliers : 1.57 % Allowed : 14.24 % Favored : 84.19 % 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: 0.24 (0.14), residues: 3774 helix: 1.02 (0.13), residues: 1665 sheet: -1.05 (0.22), residues: 519 loop : -0.20 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1813 HIS 0.009 0.001 HIS G1568 PHE 0.014 0.001 PHE G 146 TYR 0.028 0.001 TYR G1762 ARG 0.003 0.000 ARG G 200 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 288 time to evaluate : 3.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 GLU cc_start: 0.5967 (tp30) cc_final: 0.4755 (tp30) REVERT: A 847 GLU cc_start: 0.8973 (tt0) cc_final: 0.8518 (tm-30) REVERT: A 1124 GLU cc_start: 0.8712 (pp20) cc_final: 0.8209 (tm-30) REVERT: A 1496 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8720 (mp0) REVERT: B 168 MET cc_start: 0.6844 (tpp) cc_final: 0.6559 (tpp) REVERT: B 179 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6348 (mmtm) REVERT: B 185 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8170 (mt-10) REVERT: B 241 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.6730 (m-80) REVERT: B 247 ARG cc_start: 0.8301 (mmm160) cc_final: 0.8085 (mmt180) REVERT: G 213 LEU cc_start: 0.8700 (mt) cc_final: 0.8335 (mt) REVERT: G 630 MET cc_start: 0.8574 (tpp) cc_final: 0.8117 (tpp) REVERT: G 750 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8146 (mmt) REVERT: G 1011 MET cc_start: 0.9244 (mtt) cc_final: 0.8688 (tmm) REVERT: G 1038 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8119 (mp0) REVERT: G 1106 GLU cc_start: 0.8138 (mp0) cc_final: 0.7610 (mp0) REVERT: G 1323 MET cc_start: 0.5438 (tpt) cc_final: 0.4786 (mmm) REVERT: G 1359 MET cc_start: 0.2858 (mmm) cc_final: 0.2080 (mtt) REVERT: G 1404 MET cc_start: 0.6844 (ppp) cc_final: 0.4934 (ptp) REVERT: G 1412 TYR cc_start: 0.7101 (m-10) cc_final: 0.6458 (m-10) REVERT: G 1604 ARG cc_start: 0.6791 (ptp90) cc_final: 0.6504 (mtm110) REVERT: G 1611 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: G 1652 THR cc_start: 0.7363 (p) cc_final: 0.6958 (m) REVERT: G 1676 MET cc_start: 0.7938 (ptm) cc_final: 0.7520 (ptm) REVERT: G 1763 THR cc_start: 0.9230 (m) cc_final: 0.8885 (p) REVERT: G 1784 MET cc_start: 0.8068 (tmm) cc_final: 0.7272 (tmm) outliers start: 51 outliers final: 29 residues processed: 324 average time/residue: 0.4030 time to fit residues: 215.5532 Evaluate side-chains 287 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 253 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1611 GLN Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 206 optimal weight: 7.9990 chunk 307 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 363 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 221 optimal weight: 0.0170 chunk 167 optimal weight: 5.9990 overall best weight: 5.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 ASN B 157 HIS ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1920 GLN ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30300 Z= 0.308 Angle : 0.564 10.389 41041 Z= 0.290 Chirality : 0.043 0.242 4613 Planarity : 0.004 0.057 5299 Dihedral : 4.908 68.744 4046 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.87 % Favored : 96.08 % Rotamer: Outliers : 2.24 % Allowed : 14.70 % Favored : 83.06 % 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: 0.11 (0.14), residues: 3774 helix: 0.92 (0.13), residues: 1660 sheet: -1.18 (0.22), residues: 524 loop : -0.24 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1813 HIS 0.008 0.001 HIS G1568 PHE 0.024 0.002 PHE A 450 TYR 0.020 0.002 TYR A 81 ARG 0.003 0.000 ARG G1881 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 248 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.5370 (mmm) cc_final: 0.5139 (mmm) REVERT: A 841 GLU cc_start: 0.6109 (tp30) cc_final: 0.5227 (tp30) REVERT: A 847 GLU cc_start: 0.8979 (tt0) cc_final: 0.8515 (tm-30) REVERT: A 1124 GLU cc_start: 0.8667 (pp20) cc_final: 0.8357 (pp20) REVERT: B 179 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6353 (mmtt) REVERT: B 185 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8111 (mt-10) REVERT: B 241 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.6551 (m-80) REVERT: B 247 ARG cc_start: 0.8421 (mmm160) cc_final: 0.7819 (mtp85) REVERT: G 213 LEU cc_start: 0.8717 (mt) cc_final: 0.8347 (mt) REVERT: G 630 MET cc_start: 0.8684 (tpp) cc_final: 0.8195 (tpp) REVERT: G 750 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8200 (mmt) REVERT: G 1011 MET cc_start: 0.9249 (mtt) cc_final: 0.8715 (tmm) REVERT: G 1038 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8080 (mp0) REVERT: G 1323 MET cc_start: 0.5458 (tpt) cc_final: 0.4790 (mmm) REVERT: G 1359 MET cc_start: 0.3251 (mmm) cc_final: 0.1664 (mtt) REVERT: G 1404 MET cc_start: 0.6888 (ppp) cc_final: 0.6682 (tmm) REVERT: G 1543 ASP cc_start: 0.5181 (OUTLIER) cc_final: 0.4909 (t0) REVERT: G 1604 ARG cc_start: 0.6752 (ptp90) cc_final: 0.6449 (mtm110) REVERT: G 1676 MET cc_start: 0.7918 (ptm) cc_final: 0.7462 (ptm) REVERT: G 1784 MET cc_start: 0.8055 (tmm) cc_final: 0.7232 (tmm) outliers start: 73 outliers final: 54 residues processed: 302 average time/residue: 0.4044 time to fit residues: 203.2843 Evaluate side-chains 297 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 239 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1442 ASN Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1875 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 216 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 305 PHE Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1293 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1434 HIS Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1483 VAL Chi-restraints excluded: chain G residue 1491 VAL Chi-restraints excluded: chain G residue 1531 VAL Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 285 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1442 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30300 Z= 0.209 Angle : 0.533 11.903 41041 Z= 0.271 Chirality : 0.042 0.290 4613 Planarity : 0.004 0.054 5299 Dihedral : 4.619 69.278 4043 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.85 % Allowed : 15.62 % Favored : 82.53 % 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: 0.22 (0.14), residues: 3774 helix: 0.98 (0.13), residues: 1662 sheet: -1.06 (0.22), residues: 530 loop : -0.17 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1813 HIS 0.010 0.001 HIS G1568 PHE 0.016 0.001 PHE B 286 TYR 0.023 0.001 TYR G1608 ARG 0.003 0.000 ARG G1522 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 254 time to evaluate : 3.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.5305 (mmm) cc_final: 0.4965 (mmm) REVERT: A 841 GLU cc_start: 0.6046 (tp30) cc_final: 0.4781 (tp30) REVERT: A 847 GLU cc_start: 0.8977 (tt0) cc_final: 0.8508 (tm-30) REVERT: A 1124 GLU cc_start: 0.8676 (pp20) cc_final: 0.8372 (pp20) REVERT: A 1406 MET cc_start: 0.9214 (ttp) cc_final: 0.8787 (ppp) REVERT: A 1496 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8769 (mp0) REVERT: B 179 LYS cc_start: 0.7291 (OUTLIER) cc_final: 0.6295 (mmtm) REVERT: B 185 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8095 (mt-10) REVERT: B 241 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.6471 (m-80) REVERT: G 213 LEU cc_start: 0.8753 (mt) cc_final: 0.8410 (mt) REVERT: G 630 MET cc_start: 0.8649 (tpp) cc_final: 0.8158 (tpp) REVERT: G 750 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8140 (mmt) REVERT: G 1011 MET cc_start: 0.9250 (mtt) cc_final: 0.8736 (tmm) REVERT: G 1038 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8034 (mp0) REVERT: G 1106 GLU cc_start: 0.8135 (mp0) cc_final: 0.7601 (mp0) REVERT: G 1268 LYS cc_start: 0.7910 (mmpt) cc_final: 0.7705 (tttt) REVERT: G 1323 MET cc_start: 0.5540 (tpt) cc_final: 0.4788 (mmm) REVERT: G 1359 MET cc_start: 0.3042 (mmm) cc_final: 0.2195 (mtt) REVERT: G 1404 MET cc_start: 0.6840 (ppp) cc_final: 0.4835 (ptp) REVERT: G 1543 ASP cc_start: 0.4985 (OUTLIER) cc_final: 0.4710 (t0) REVERT: G 1604 ARG cc_start: 0.6774 (ptp90) cc_final: 0.6478 (mtm110) REVERT: G 1611 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: G 1652 THR cc_start: 0.7308 (p) cc_final: 0.6864 (m) REVERT: G 1673 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8103 (pm20) REVERT: G 1676 MET cc_start: 0.7949 (ptm) cc_final: 0.7603 (ptm) REVERT: G 1763 THR cc_start: 0.9157 (m) cc_final: 0.8816 (p) REVERT: G 1784 MET cc_start: 0.8065 (tmm) cc_final: 0.7199 (tmm) outliers start: 60 outliers final: 47 residues processed: 299 average time/residue: 0.3933 time to fit residues: 194.6243 Evaluate side-chains 297 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 244 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1875 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 305 PHE Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1293 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1434 HIS Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1491 VAL Chi-restraints excluded: chain G residue 1531 VAL Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1611 GLN Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 20.0000 chunk 348 optimal weight: 5.9990 chunk 317 optimal weight: 9.9990 chunk 338 optimal weight: 9.9990 chunk 203 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 0.0980 chunk 103 optimal weight: 5.9990 chunk 305 optimal weight: 7.9990 chunk 320 optimal weight: 2.9990 chunk 337 optimal weight: 0.5980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1355 ASN ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30300 Z= 0.187 Angle : 0.528 12.346 41041 Z= 0.266 Chirality : 0.042 0.286 4613 Planarity : 0.004 0.054 5299 Dihedral : 4.471 68.520 4043 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.34 % Rotamer: Outliers : 1.88 % Allowed : 15.99 % Favored : 82.13 % 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: 0.34 (0.14), residues: 3774 helix: 1.06 (0.13), residues: 1671 sheet: -0.95 (0.22), residues: 534 loop : -0.10 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1813 HIS 0.010 0.001 HIS G1568 PHE 0.022 0.001 PHE G1466 TYR 0.025 0.001 TYR G1506 ARG 0.004 0.000 ARG G 200 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 259 time to evaluate : 3.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4166 (ttt) cc_final: 0.2887 (tpt) REVERT: A 599 MET cc_start: 0.5282 (mmm) cc_final: 0.4908 (mmm) REVERT: A 841 GLU cc_start: 0.5928 (tp30) cc_final: 0.4744 (tp30) REVERT: A 847 GLU cc_start: 0.8966 (tt0) cc_final: 0.8502 (tm-30) REVERT: A 1124 GLU cc_start: 0.8763 (pp20) cc_final: 0.8238 (tm-30) REVERT: A 1406 MET cc_start: 0.9260 (ttp) cc_final: 0.8804 (ppp) REVERT: A 1496 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: B 179 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6359 (mmtm) REVERT: B 185 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8202 (mt-10) REVERT: B 241 PHE cc_start: 0.7620 (OUTLIER) cc_final: 0.6469 (m-80) REVERT: B 247 ARG cc_start: 0.8460 (mmm160) cc_final: 0.7861 (mmt180) REVERT: G 213 LEU cc_start: 0.8733 (mt) cc_final: 0.8389 (mt) REVERT: G 533 LEU cc_start: 0.8632 (tt) cc_final: 0.8266 (tp) REVERT: G 630 MET cc_start: 0.8653 (tpp) cc_final: 0.8195 (tpp) REVERT: G 750 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8126 (mmt) REVERT: G 1011 MET cc_start: 0.9255 (mtt) cc_final: 0.8771 (tmm) REVERT: G 1038 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8039 (mp0) REVERT: G 1180 MET cc_start: 0.6175 (ptp) cc_final: 0.5634 (ptp) REVERT: G 1323 MET cc_start: 0.5492 (tpt) cc_final: 0.4731 (mmm) REVERT: G 1357 TYR cc_start: 0.8191 (m-80) cc_final: 0.7860 (m-80) REVERT: G 1359 MET cc_start: 0.3001 (mmm) cc_final: 0.2324 (mtt) REVERT: G 1404 MET cc_start: 0.6947 (ppp) cc_final: 0.4984 (ptp) REVERT: G 1543 ASP cc_start: 0.4855 (OUTLIER) cc_final: 0.4613 (t0) REVERT: G 1604 ARG cc_start: 0.6751 (ptp90) cc_final: 0.6091 (ptm160) REVERT: G 1611 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8106 (mt0) REVERT: G 1652 THR cc_start: 0.7297 (p) cc_final: 0.6919 (m) REVERT: G 1673 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8103 (pm20) REVERT: G 1676 MET cc_start: 0.7971 (ptm) cc_final: 0.7570 (ptm) REVERT: G 1763 THR cc_start: 0.9170 (m) cc_final: 0.8833 (p) REVERT: G 1784 MET cc_start: 0.8035 (tmm) cc_final: 0.7163 (tmm) REVERT: G 2006 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7384 (mm) outliers start: 61 outliers final: 49 residues processed: 306 average time/residue: 0.4097 time to fit residues: 206.9206 Evaluate side-chains 302 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 246 time to evaluate : 3.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1875 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 638 VAL Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1293 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1434 HIS Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1491 VAL Chi-restraints excluded: chain G residue 1531 VAL Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1611 GLN Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2006 LEU Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 7.9990 chunk 358 optimal weight: 30.0000 chunk 218 optimal weight: 20.0000 chunk 169 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 375 optimal weight: 10.0000 chunk 345 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 987 ASN A1444 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 718 ASN G1046 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1851 ASN ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 30300 Z= 0.432 Angle : 0.663 13.063 41041 Z= 0.341 Chirality : 0.046 0.316 4613 Planarity : 0.005 0.056 5299 Dihedral : 5.074 66.964 4042 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 2.03 % Allowed : 15.87 % Favored : 82.10 % 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: -0.23 (0.14), residues: 3774 helix: 0.62 (0.13), residues: 1655 sheet: -1.22 (0.22), residues: 528 loop : -0.43 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1813 HIS 0.009 0.001 HIS G1568 PHE 0.026 0.002 PHE A 450 TYR 0.027 0.002 TYR G1506 ARG 0.005 0.001 ARG G1643 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 238 time to evaluate : 3.407 Fit side-chains revert: symmetry clash REVERT: A 847 GLU cc_start: 0.9039 (tt0) cc_final: 0.8579 (tm-30) REVERT: A 1406 MET cc_start: 0.9269 (ttp) cc_final: 0.8832 (ppp) REVERT: A 1496 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8793 (mp0) REVERT: B 179 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6432 (mmtm) REVERT: B 185 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8159 (mt-10) REVERT: B 241 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.6456 (m-80) REVERT: B 247 ARG cc_start: 0.8404 (mmm160) cc_final: 0.7801 (mtp85) REVERT: G 213 LEU cc_start: 0.8903 (mt) cc_final: 0.8691 (mt) REVERT: G 630 MET cc_start: 0.8695 (tpp) cc_final: 0.8155 (tpp) REVERT: G 1011 MET cc_start: 0.9257 (mtt) cc_final: 0.8739 (tmm) REVERT: G 1038 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8026 (mp0) REVERT: G 1319 MET cc_start: 0.5794 (ptm) cc_final: 0.4815 (ttp) REVERT: G 1323 MET cc_start: 0.5498 (tpt) cc_final: 0.4757 (mmm) REVERT: G 1359 MET cc_start: 0.3424 (mmm) cc_final: 0.2499 (mtt) REVERT: G 1404 MET cc_start: 0.6764 (ppp) cc_final: 0.4656 (ptp) REVERT: G 1520 LEU cc_start: 0.6992 (mp) cc_final: 0.6431 (mt) REVERT: G 1543 ASP cc_start: 0.5095 (OUTLIER) cc_final: 0.4788 (t0) REVERT: G 1673 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8165 (pm20) REVERT: G 1676 MET cc_start: 0.7922 (ptm) cc_final: 0.7542 (ptm) REVERT: G 1763 THR cc_start: 0.9166 (m) cc_final: 0.8813 (p) REVERT: G 1784 MET cc_start: 0.8020 (tmm) cc_final: 0.7366 (tmm) REVERT: G 2006 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7492 (mm) outliers start: 66 outliers final: 53 residues processed: 291 average time/residue: 0.3943 time to fit residues: 189.2415 Evaluate side-chains 283 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 225 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1875 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 638 VAL Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1293 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1434 HIS Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1491 VAL Chi-restraints excluded: chain G residue 1531 VAL Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2006 LEU Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 275 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 307 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN A 987 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.086695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.066356 restraints weight = 109746.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.067946 restraints weight = 49489.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.068442 restraints weight = 25811.761| |-----------------------------------------------------------------------------| r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30300 Z= 0.194 Angle : 0.555 12.866 41041 Z= 0.280 Chirality : 0.042 0.293 4613 Planarity : 0.004 0.095 5299 Dihedral : 4.651 69.496 4042 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.61 % Rotamer: Outliers : 1.75 % Allowed : 16.36 % Favored : 81.89 % 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: 0.14 (0.14), residues: 3774 helix: 0.90 (0.13), residues: 1662 sheet: -1.09 (0.22), residues: 529 loop : -0.21 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1813 HIS 0.010 0.001 HIS G1568 PHE 0.032 0.001 PHE G1423 TYR 0.032 0.001 TYR G1506 ARG 0.024 0.000 ARG G1635 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5431.42 seconds wall clock time: 100 minutes 13.24 seconds (6013.24 seconds total)