Starting phenix.real_space_refine on Sat Apr 13 21:31:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psg_17852/04_2024/8psg_17852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psg_17852/04_2024/8psg_17852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psg_17852/04_2024/8psg_17852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psg_17852/04_2024/8psg_17852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psg_17852/04_2024/8psg_17852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psg_17852/04_2024/8psg_17852_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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 106 5.16 5 C 18870 2.51 5 N 4955 2.21 5 O 5678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 608": "OD1" <-> "OD2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A ASP 675": "OD1" <-> "OD2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A GLU 756": "OE1" <-> "OE2" Residue "A PHE 833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 847": "OE1" <-> "OE2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A GLU 994": "OE1" <-> "OE2" Residue "A ASP 1014": "OD1" <-> "OD2" Residue "A GLU 1128": "OE1" <-> "OE2" Residue "A PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1142": "OE1" <-> "OE2" Residue "A TYR 1163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1221": "OE1" <-> "OE2" Residue "A GLU 1233": "OE1" <-> "OE2" Residue "A PHE 1261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A GLU 1355": "OE1" <-> "OE2" Residue "A GLU 1364": "OE1" <-> "OE2" Residue "A PHE 1376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1391": "OD1" <-> "OD2" Residue "A GLU 1498": "OE1" <-> "OE2" Residue "A PHE 1541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1553": "OE1" <-> "OE2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1817": "OE1" <-> "OE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B ASP 174": "OD1" <-> "OD2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 90": "OE1" <-> "OE2" Residue "G PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "G ASP 186": "OD1" <-> "OD2" Residue "G GLU 285": "OE1" <-> "OE2" Residue "G GLU 367": "OE1" <-> "OE2" Residue "G TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 546": "OE1" <-> "OE2" Residue "G GLU 618": "OE1" <-> "OE2" Residue "G PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 849": "OE1" <-> "OE2" Residue "G PHE 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 978": "OE1" <-> "OE2" Residue "G GLU 981": "OE1" <-> "OE2" Residue "G GLU 992": "OE1" <-> "OE2" Residue "G PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1135": "OE1" <-> "OE2" Residue "G PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1391": "OD1" <-> "OD2" Residue "G GLU 1405": "OE1" <-> "OE2" Residue "G TYR 1416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1505": "OD1" <-> "OD2" Residue "G GLU 1507": "OE1" <-> "OE2" Residue "G GLU 1551": "OE1" <-> "OE2" Residue "G GLU 1673": "OE1" <-> "OE2" Residue "G ASP 1689": "OD1" <-> "OD2" Residue "G GLU 1767": "OE1" <-> "OE2" Residue "G TYR 1852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1876": "OE1" <-> "OE2" Residue "G TYR 1891": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1945": "OD1" <-> "OD2" Residue "G GLU 2036": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29610 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1579, 12346 Classifications: {'peptide': 1579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1517} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1223 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain: "G" Number of atoms: 16010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2035, 16010 Classifications: {'peptide': 2035} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1925} 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: 15.44, per 1000 atoms: 0.52 Number of scatterers: 29610 At special positions: 0 Unit cell: (179.35, 181.46, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 1 15.00 O 5678 8.00 N 4955 7.00 C 18870 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=2.12 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: 10.83 Conformation dependent library (CDL) restraints added in 6.0 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7028 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 167 helices and 33 sheets defined 43.2% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.33 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 Processing helix chain 'A' and resid 28 through 35 removed outlier: 3.594A pdb=" N ASP A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 64 Processing helix chain 'A' and resid 68 through 71 No H-bonds generated for 'chain 'A' and resid 68 through 71' Processing helix chain 'A' and resid 85 through 88 No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 331 through 350 removed outlier: 4.239A pdb=" N ARG A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.853A pdb=" N GLY A 357 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 382 removed outlier: 3.756A pdb=" N LYS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 369 " --> pdb=" O LYS A 365 " (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: 4.172A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 Processing helix chain 'A' and resid 445 through 455 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 464 through 485 removed outlier: 3.860A pdb=" N GLU A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASP A 485 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 531 Processing helix chain 'A' and resid 534 through 536 No H-bonds generated for 'chain 'A' and resid 534 through 536' Processing helix chain 'A' and resid 609 through 615 removed outlier: 3.767A pdb=" N ALA A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 668 Processing helix chain 'A' and resid 688 through 699 Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'A' and resid 742 through 753 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: 3.967A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.220A 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 885 through 891 removed outlier: 4.292A pdb=" N MET A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.782A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 919 removed outlier: 3.695A pdb=" N LYS A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 969 removed outlier: 3.625A pdb=" N LEU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.702A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.779A 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 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1033 through 1041 Processing helix chain 'A' and resid 1047 through 1056 Processing helix chain 'A' and resid 1086 through 1099 removed outlier: 4.274A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.560A 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 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 7.001A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LYS A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1198 No H-bonds generated for 'chain 'A' and resid 1195 through 1198' 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 1265 removed outlier: 3.942A pdb=" N GLY A1259 " --> pdb=" O SER A1255 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP A1263 " --> pdb=" O GLY A1259 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG A1264 " --> pdb=" O MET A1260 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A1265 " --> pdb=" O PHE A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1278 Processing helix chain 'A' and resid 1282 through 1290 Processing helix chain 'A' and resid 1306 through 1320 removed outlier: 4.131A pdb=" N SER A1311 " --> pdb=" O SER A1308 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A1314 " --> pdb=" O SER A1311 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A1316 " --> pdb=" O ASP A1313 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A1320 " --> pdb=" O GLU A1317 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1345 removed outlier: 3.835A pdb=" N GLU A1342 " --> pdb=" O GLU A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1357 Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1425 through 1429 Processing helix chain 'A' and resid 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1445 through 1474 Processing helix chain 'A' and resid 1482 through 1509 removed outlier: 3.545A pdb=" N GLU A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 4.309A 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 1563 removed outlier: 3.559A pdb=" N SER A1554 " --> pdb=" O ASP A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1581 No H-bonds generated for 'chain 'A' and resid 1578 through 1581' Processing helix chain 'A' and resid 1585 through 1600 removed outlier: 4.320A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A1590 " --> pdb=" O ALA A1587 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY A1595 " --> pdb=" O MET A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 Processing helix chain 'A' and resid 1658 through 1662 Processing helix chain 'A' and resid 1667 through 1694 removed outlier: 3.902A pdb=" N LYS A1682 " --> pdb=" O SER A1678 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A1683 " --> pdb=" O ALA A1679 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1693 " --> pdb=" O HIS A1689 " (cutoff:3.500A) Processing helix chain 'A' and resid 1711 through 1715 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 1776 through 1778 No H-bonds generated for 'chain 'A' and resid 1776 through 1778' Processing helix chain 'A' and resid 1784 through 1790 Processing helix chain 'A' and resid 1795 through 1801 removed outlier: 3.511A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1823 removed outlier: 3.629A pdb=" N GLU A1817 " --> pdb=" O TRP A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1854 through 1862 Processing helix chain 'B' and resid 147 through 159 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 181 through 194 Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.738A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 235 removed outlier: 3.588A pdb=" N ARG B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 253 Processing helix chain 'B' and resid 258 through 270 removed outlier: 3.776A pdb=" N ASP B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'G' and resid 27 through 40 removed outlier: 3.591A pdb=" N LEU G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 71 Processing helix chain 'G' and resid 81 through 94 removed outlier: 3.536A pdb=" N THR G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) 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 151 Processing helix chain 'G' and resid 169 through 179 removed outlier: 3.838A pdb=" N ARG G 174 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP G 175 " --> pdb=" O GLU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 201 removed outlier: 5.867A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 228 through 232 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: 3.858A pdb=" N ILE G 283 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU G 285 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 313 removed outlier: 3.770A pdb=" N VAL G 294 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL G 296 " --> pdb=" O PHE G 293 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS G 298 " --> pdb=" O SER G 295 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE G 300 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE G 306 " --> pdb=" O LEU G 303 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY G 307 " --> pdb=" O PHE G 304 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL G 308 " --> pdb=" O PHE G 305 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N CYS G 310 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 330 Processing helix chain 'G' and resid 346 through 359 removed outlier: 3.590A 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 394 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 445 Proline residue: G 434 - end of helix removed outlier: 4.301A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN G 440 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS G 441 " --> pdb=" O LEU G 438 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL G 444 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 454 No H-bonds generated for 'chain 'G' and resid 452 through 454' Processing helix chain 'G' and resid 475 through 484 Processing helix chain 'G' and resid 492 through 494 No H-bonds generated for 'chain 'G' and resid 492 through 494' Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 512 through 519 Processing helix chain 'G' and resid 544 through 548 removed outlier: 3.589A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) No H-bonds generated for '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: 3.763A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 612 removed outlier: 3.675A pdb=" N ALA G 609 " --> pdb=" O ASP G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 638 Processing helix chain 'G' and resid 656 through 671 Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 688 through 698 removed outlier: 3.646A pdb=" N LEU G 698 " --> pdb=" O TYR G 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 710 through 722 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 757 No H-bonds generated for 'chain 'G' and resid 754 through 757' Processing helix chain 'G' and resid 774 through 782 Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 789 removed outlier: 3.704A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 803 through 805 No H-bonds generated for 'chain 'G' and resid 803 through 805' Processing helix chain 'G' and resid 815 through 823 Processing helix chain 'G' and resid 831 through 834 Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 877 through 897 removed outlier: 4.389A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 5.783A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 919 through 930 removed outlier: 3.549A pdb=" N ARG G 925 " --> pdb=" O GLU G 921 " (cutoff:3.500A) 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: 3.679A pdb=" N ASP G1001 " --> pdb=" O ALA G 997 " (cutoff:3.500A) removed outlier: 3.678A 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 1048 through 1050 No H-bonds generated for 'chain 'G' and resid 1048 through 1050' Processing helix chain 'G' and resid 1059 through 1062 Processing helix chain 'G' and resid 1070 through 1089 removed outlier: 3.515A pdb=" N HIS G1087 " --> pdb=" O LYS G1083 " (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 1259 through 1270 removed outlier: 3.844A pdb=" N LEU G1269 " --> pdb=" O MET G1265 " (cutoff:3.500A) Processing helix chain 'G' and resid 1295 through 1304 removed outlier: 4.096A pdb=" N PHE G1300 " --> pdb=" O GLU G1296 " (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 1326 through 1338 removed outlier: 5.681A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS G1336 " --> pdb=" O ARG G1332 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA G1337 " --> pdb=" O ALA G1333 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ILE G1338 " --> pdb=" O ILE G1334 " (cutoff:3.500A) Processing helix chain 'G' and resid 1440 through 1446 Processing helix chain 'G' and resid 1515 through 1523 removed outlier: 3.864A pdb=" N ARG G1522 " --> pdb=" O ASP G1518 " (cutoff:3.500A) Processing helix chain 'G' and resid 1551 through 1557 removed outlier: 3.636A 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 1593 removed outlier: 4.600A pdb=" N LEU G1592 " --> pdb=" O SER G1588 " (cutoff:3.500A) Processing helix chain 'G' and resid 1678 through 1683 Processing helix chain 'G' and resid 1685 through 1701 Processing helix chain 'G' and resid 1706 through 1712 Processing helix chain 'G' and resid 1724 through 1733 removed outlier: 3.814A pdb=" N ARG G1728 " --> pdb=" O GLU G1724 " (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 1818 Processing helix chain 'G' and resid 1824 through 1840 removed outlier: 3.822A pdb=" N GLU G1829 " --> pdb=" O GLU G1825 " (cutoff:3.500A) Processing helix chain 'G' and resid 1859 through 1861 No H-bonds generated for 'chain 'G' and resid 1859 through 1861' Processing helix chain 'G' and resid 1868 through 1881 removed outlier: 3.733A pdb=" N GLN G1872 " --> pdb=" O GLN G1868 " (cutoff:3.500A) Processing helix chain 'G' and resid 1910 through 1920 removed outlier: 3.652A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G1919 " --> pdb=" O ASN G1915 " (cutoff:3.500A) Processing helix chain 'G' and resid 1927 through 1930 No H-bonds generated for 'chain 'G' and resid 1927 through 1930' Processing helix chain 'G' and resid 1935 through 1949 removed outlier: 3.625A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) Processing helix chain 'G' and resid 1986 through 1995 removed outlier: 3.784A pdb=" N SER G1990 " --> pdb=" O LYS G1986 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS G1994 " --> pdb=" O SER G1990 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN G1995 " --> pdb=" O PHE G1991 " (cutoff:3.500A) Processing helix chain 'G' and resid 2003 through 2006 No H-bonds generated for 'chain 'G' and resid 2003 through 2006' Processing helix chain 'G' and resid 2023 through 2032 Processing helix chain 'G' and resid 2036 through 2043 removed outlier: 3.699A pdb=" N ILE G2041 " --> pdb=" O PRO G2037 " (cutoff:3.500A) Processing helix chain 'G' and resid 2045 through 2049 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.855A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 497 through 503 Processing sheet with id= C, first strand: chain 'A' and resid 641 through 643 Processing sheet with id= D, first strand: chain 'A' and resid 678 through 681 removed outlier: 7.046A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE A 769 " --> pdb=" O THR A 681 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 702 through 707 removed outlier: 6.150A pdb=" N THR A 731 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N VAL A 705 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE A 733 " --> pdb=" O VAL A 705 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N THR A 707 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 735 " --> pdb=" O THR A 707 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 820 through 822 Processing sheet with id= G, first strand: chain 'A' and resid 867 through 869 removed outlier: 7.316A pdb=" N ALA A 924 " --> pdb=" O ILE A 868 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 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 1103 through 1105 removed outlier: 3.855A pdb=" N ARG A1104 " --> pdb=" O ALA A1186 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1119 through 1126 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 1243 through 1245 removed outlier: 6.311A pdb=" N ILE A1326 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1573 through 1575 removed outlier: 3.708A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A1642 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1722 through 1724 Processing sheet with id= O, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id= P, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id= Q, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.937A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 269 through 272 removed outlier: 4.072A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS G 500 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE G 159 " --> pdb=" O HIS G 500 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LEU G 502 " --> pdb=" O ILE G 159 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG G 526 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N ASP G 503 " --> pdb=" O ARG G 526 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE G 528 " --> pdb=" O ASP G 503 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 338 through 342 removed outlier: 5.977A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 568 through 571 removed outlier: 3.816A pdb=" N LYS G 568 " --> pdb=" O GLU G 580 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 570 " --> pdb=" O PHE G 578 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.751A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY G 798 " --> pdb=" O PHE G 767 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= W, first strand: chain 'G' and resid 1126 through 1128 removed outlier: 3.701A pdb=" N VAL G1209 " --> pdb=" O LEU G1197 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL G1201 " --> pdb=" O LEU G1205 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU G1205 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= Y, first strand: chain 'G' and resid 1285 through 1287 removed outlier: 4.095A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 1380 through 1382 Processing sheet with id= AA, first strand: chain 'G' and resid 1431 through 1434 removed outlier: 4.693A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY G1502 " --> pdb=" O ILE G1489 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 1469 through 1473 removed outlier: 3.693A pdb=" N SER G1482 " --> pdb=" O THR G1473 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 1609 through 1612 removed outlier: 3.686A pdb=" N THR G1652 " --> pdb=" O GLN G1611 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY G1630 " --> pdb=" O LEU G1637 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLU G1641 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE G1626 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ARG G1643 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THR G1624 " --> pdb=" O ARG G1643 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA G1540 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N HIS G1628 " --> pdb=" O PRO G1538 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 7.402A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA G1805 " --> pdb=" O PHE G1666 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id= AF, first strand: chain 'G' and resid 1737 through 1741 removed outlier: 3.697A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS G1747 " --> pdb=" O THR G1740 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 1852 through 1855 removed outlier: 3.635A pdb=" N GLY G1902 " --> pdb=" O GLY G1853 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) 1072 hydrogen bonds defined for protein. 2949 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: 14.77 Time building geometry restraints manager: 11.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 8217 1.34 - 1.49: 6518 1.49 - 1.63: 15306 1.63 - 1.78: 0 1.78 - 1.93: 187 Bond restraints: 30228 Sorted by residual: bond pdb=" CD GLU A1026 " pdb=" OE1 GLU A1026 " ideal model delta sigma weight residual 1.249 1.378 -0.129 1.90e-02 2.77e+03 4.62e+01 bond pdb=" C TYR A1174 " pdb=" O TYR A1174 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.14e-02 7.69e+03 2.53e+01 bond pdb=" CG MET A1121 " pdb=" SD MET A1121 " ideal model delta sigma weight residual 1.803 1.926 -0.123 2.50e-02 1.60e+03 2.41e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.60e-03 1.73e+04 2.25e+01 bond pdb=" N ILE G2011 " pdb=" CA ILE G2011 " ideal model delta sigma weight residual 1.458 1.494 -0.036 7.70e-03 1.69e+04 2.24e+01 ... (remaining 30223 not shown) Histogram of bond angle deviations from ideal: 95.19 - 103.11: 226 103.11 - 111.03: 8983 111.03 - 118.95: 18584 118.95 - 126.87: 12869 126.87 - 134.79: 282 Bond angle restraints: 40944 Sorted by residual: angle pdb=" CB GLU A 364 " pdb=" CG GLU A 364 " pdb=" CD GLU A 364 " ideal model delta sigma weight residual 112.60 127.80 -15.20 1.70e+00 3.46e-01 8.00e+01 angle pdb=" CB GLU A1317 " pdb=" CG GLU A1317 " pdb=" CD GLU A1317 " ideal model delta sigma weight residual 112.60 124.76 -12.16 1.70e+00 3.46e-01 5.12e+01 angle pdb=" CB GLU A1338 " pdb=" CG GLU A1338 " pdb=" CD GLU A1338 " ideal model delta sigma weight residual 112.60 124.40 -11.80 1.70e+00 3.46e-01 4.81e+01 angle pdb=" CA THR A1282 " pdb=" CB THR A1282 " pdb=" OG1 THR A1282 " ideal model delta sigma weight residual 109.60 99.51 10.09 1.50e+00 4.44e-01 4.53e+01 angle pdb=" CA ASP G1820 " pdb=" CB ASP G1820 " pdb=" CG ASP G1820 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 ... (remaining 40939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.41: 17232 24.41 - 48.83: 868 48.83 - 73.24: 116 73.24 - 97.66: 33 97.66 - 122.07: 1 Dihedral angle restraints: 18250 sinusoidal: 7338 harmonic: 10912 Sorted by residual: dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual -86.00 -18.51 -67.49 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" C5' FMN G2101 " pdb=" O5' FMN G2101 " pdb=" P FMN G2101 " pdb=" O1P FMN G2101 " ideal model delta sinusoidal sigma weight residual 75.26 -162.67 -122.07 1 2.00e+01 2.50e-03 3.67e+01 dihedral pdb=" CA CYS A1327 " pdb=" C CYS A1327 " pdb=" N ILE A1328 " pdb=" CA ILE A1328 " ideal model delta harmonic sigma weight residual 180.00 151.77 28.23 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 18247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1850 0.053 - 0.106: 1650 0.106 - 0.160: 868 0.160 - 0.213: 209 0.213 - 0.266: 26 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CA VAL A1302 " pdb=" N VAL A1302 " pdb=" C VAL A1302 " pdb=" CB VAL A1302 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.77e+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 2.69 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A1403 " pdb=" N ILE A1403 " pdb=" C ILE A1403 " pdb=" CB ILE A1403 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 4600 not shown) Planarity restraints: 5285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " -0.029 2.00e-02 2.50e+03 1.95e-02 1.80e+01 pdb=" C10 FMN G2101 " 0.014 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.017 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.006 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.018 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.023 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " -0.005 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.014 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.033 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.002 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.012 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.017 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.028 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.005 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.031 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.022 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.029 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.011 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 753 " 0.049 2.00e-02 2.50e+03 2.71e-02 1.47e+01 pdb=" CG TYR A 753 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 753 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 753 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 753 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 753 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 753 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 753 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1286 " 0.049 2.00e-02 2.50e+03 2.32e-02 1.34e+01 pdb=" CG TRP A1286 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A1286 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A1286 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A1286 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1286 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP A1286 " -0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1286 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1286 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1286 " 0.012 2.00e-02 2.50e+03 ... (remaining 5282 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1111 2.71 - 3.26: 30396 3.26 - 3.81: 47054 3.81 - 4.35: 64807 4.35 - 4.90: 104020 Nonbonded interactions: 247388 Sorted by model distance: nonbonded pdb=" OH TYR G 754 " pdb=" O PRO G 795 " model vdw 2.169 2.440 nonbonded pdb=" NH2 ARG G 888 " pdb=" OD1 ASP G 913 " model vdw 2.196 2.520 nonbonded pdb=" OD2 ASP A1534 " pdb=" OG SER A1567 " model vdw 2.223 2.440 nonbonded pdb=" NE2 HIS B 152 " pdb=" O LEU B 163 " model vdw 2.230 2.520 nonbonded pdb=" O GLY G 768 " pdb=" OG SER G 769 " model vdw 2.263 2.440 ... (remaining 247383 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.970 Check model and map are aligned: 0.430 Set scattering table: 0.230 Process input model: 82.170 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 0.129 30228 Z= 0.912 Angle : 1.885 15.203 40944 Z= 1.375 Chirality : 0.087 0.266 4603 Planarity : 0.006 0.028 5285 Dihedral : 14.858 122.075 11219 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.31 % Favored : 92.37 % Rotamer: Outliers : 0.65 % Allowed : 4.62 % Favored : 94.73 % 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: -3.71 (0.11), residues: 3761 helix: -2.77 (0.09), residues: 1599 sheet: -2.57 (0.22), residues: 448 loop : -1.93 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.006 TRP A1286 HIS 0.018 0.003 HIS A1689 PHE 0.048 0.005 PHE A1376 TYR 0.054 0.006 TYR A 753 ARG 0.010 0.001 ARG G1834 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 267 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8436 (ttp) cc_final: 0.8196 (ttt) REVERT: A 529 MET cc_start: 0.9514 (mmp) cc_final: 0.9281 (mmm) REVERT: A 746 GLU cc_start: 0.9560 (mt-10) cc_final: 0.9324 (mt-10) REVERT: A 1121 MET cc_start: 0.3628 (tpt) cc_final: 0.1496 (tpt) REVERT: A 1268 GLU cc_start: 0.8188 (mp0) cc_final: 0.7968 (mp0) REVERT: A 1317 GLU cc_start: 0.7258 (tt0) cc_final: 0.6516 (tt0) REVERT: A 1561 MET cc_start: 0.9365 (mmm) cc_final: 0.8925 (mmm) REVERT: A 1711 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6778 (tp30) REVERT: A 1742 ASP cc_start: 0.9104 (m-30) cc_final: 0.8848 (m-30) REVERT: A 1817 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7421 (mt-10) REVERT: B 174 ASP cc_start: 0.7865 (t0) cc_final: 0.6811 (t70) REVERT: B 208 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8463 (pp20) REVERT: B 243 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7344 (mm) REVERT: B 251 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8271 (mm-40) REVERT: B 292 GLN cc_start: 0.8558 (pp30) cc_final: 0.7590 (mm-40) REVERT: G 752 GLN cc_start: 0.9474 (mt0) cc_final: 0.8989 (tm-30) REVERT: G 764 MET cc_start: 0.9241 (mtm) cc_final: 0.8931 (mtm) REVERT: G 784 GLU cc_start: 0.9485 (pt0) cc_final: 0.9118 (tm-30) REVERT: G 917 MET cc_start: 0.9455 (mtt) cc_final: 0.9218 (mtt) REVERT: G 1136 GLU cc_start: 0.9306 (mp0) cc_final: 0.9021 (mp0) REVERT: G 1180 MET cc_start: 0.6939 (mtp) cc_final: 0.6550 (mtp) REVERT: G 1221 MET cc_start: 0.9004 (tmm) cc_final: 0.8656 (tmm) REVERT: G 1323 MET cc_start: 0.2488 (mmt) cc_final: 0.1518 (mmt) REVERT: G 1467 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8770 (mp0) REVERT: G 1676 MET cc_start: 0.7362 (mtt) cc_final: 0.6219 (mtt) REVERT: G 1678 MET cc_start: 0.8416 (mmp) cc_final: 0.8103 (mmm) REVERT: G 2036 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8423 (tm-30) outliers start: 21 outliers final: 9 residues processed: 279 average time/residue: 0.4417 time to fit residues: 201.7342 Evaluate side-chains 206 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 195 time to evaluate : 3.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 410 SER Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 2.9990 chunk 284 optimal weight: 10.0000 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 294 optimal weight: 40.0000 chunk 114 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 341 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 40 ASN A 457 ASN A 467 GLN A 506 ASN A 527 GLN A 698 GLN A1123 GLN A1207 GLN A1385 GLN A1433 HIS A1482 GLN A1577 GLN A1780 ASN A1783 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN G 79 GLN G 102 HIS G 163 GLN G 245 GLN G 248 HIS G 275 GLN G 718 ASN G 747 HIS G 900 GLN G 908 ASN G1008 GLN G1055 HIS G1061 GLN G1078 HIS G1226 ASN G1307 ASN G1434 HIS G1451 GLN G1659 GLN G1674 GLN G1697 HIS ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1896 GLN G1912 ASN G1915 ASN G2020 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30228 Z= 0.230 Angle : 0.556 9.018 40944 Z= 0.293 Chirality : 0.041 0.279 4603 Planarity : 0.004 0.034 5285 Dihedral : 5.831 108.848 4048 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.82 % Favored : 97.08 % Rotamer: Outliers : 0.80 % Allowed : 8.01 % Favored : 91.19 % 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: -1.33 (0.13), residues: 3761 helix: -0.38 (0.12), residues: 1648 sheet: -1.89 (0.22), residues: 462 loop : -0.92 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 661 HIS 0.005 0.001 HIS G1568 PHE 0.018 0.001 PHE G 64 TYR 0.021 0.002 TYR G2030 ARG 0.005 0.000 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 222 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8583 (ttp) cc_final: 0.8325 (ttt) REVERT: A 529 MET cc_start: 0.9409 (mmp) cc_final: 0.9097 (mmm) REVERT: A 746 GLU cc_start: 0.9508 (mt-10) cc_final: 0.9284 (mt-10) REVERT: A 1128 GLU cc_start: 0.8126 (pp20) cc_final: 0.7755 (pp20) REVERT: A 1268 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: A 1561 MET cc_start: 0.9389 (mmm) cc_final: 0.8880 (mmm) REVERT: A 1742 ASP cc_start: 0.9016 (m-30) cc_final: 0.8768 (m-30) REVERT: B 174 ASP cc_start: 0.7509 (t0) cc_final: 0.6914 (t70) REVERT: B 229 LEU cc_start: 0.8596 (mt) cc_final: 0.8234 (pp) REVERT: B 237 MET cc_start: 0.8498 (mmt) cc_final: 0.8252 (mmp) REVERT: B 292 GLN cc_start: 0.8529 (pp30) cc_final: 0.7684 (mm-40) REVERT: G 331 ASN cc_start: 0.9055 (t0) cc_final: 0.8836 (t0) REVERT: G 714 SER cc_start: 0.9099 (OUTLIER) cc_final: 0.8778 (p) REVERT: G 752 GLN cc_start: 0.9363 (mt0) cc_final: 0.9080 (tm-30) REVERT: G 784 GLU cc_start: 0.9474 (pt0) cc_final: 0.9118 (tm-30) REVERT: G 1180 MET cc_start: 0.6495 (mtp) cc_final: 0.6025 (mtp) REVERT: G 1221 MET cc_start: 0.8820 (tmm) cc_final: 0.8479 (tmm) REVERT: G 1265 MET cc_start: 0.9039 (tmm) cc_final: 0.8078 (ptp) REVERT: G 1323 MET cc_start: 0.2266 (mmt) cc_final: 0.1754 (mmt) REVERT: G 1467 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8744 (mp0) REVERT: G 1676 MET cc_start: 0.7406 (mtt) cc_final: 0.6319 (mtt) REVERT: G 1678 MET cc_start: 0.8339 (mmp) cc_final: 0.8021 (mmm) outliers start: 26 outliers final: 15 residues processed: 238 average time/residue: 0.4185 time to fit residues: 164.7498 Evaluate side-chains 212 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 674 TYR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 1257 ASP Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 284 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 342 optimal weight: 7.9990 chunk 369 optimal weight: 20.0000 chunk 304 optimal weight: 7.9990 chunk 339 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 274 optimal weight: 0.8980 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 GLN A1003 GLN A1780 ASN A1790 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G 354 ASN G 896 ASN G1188 ASN G1220 GLN G1529 GLN ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 30228 Z= 0.297 Angle : 0.550 8.340 40944 Z= 0.286 Chirality : 0.042 0.185 4603 Planarity : 0.004 0.033 5285 Dihedral : 5.232 107.796 4033 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.86 % Favored : 96.06 % Rotamer: Outliers : 1.26 % Allowed : 10.08 % Favored : 88.66 % 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: -0.56 (0.14), residues: 3761 helix: 0.43 (0.13), residues: 1640 sheet: -1.62 (0.22), residues: 473 loop : -0.67 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 661 HIS 0.005 0.001 HIS G1568 PHE 0.016 0.002 PHE A1111 TYR 0.019 0.002 TYR A 753 ARG 0.004 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 3.451 Fit side-chains revert: symmetry clash REVERT: A 352 MET cc_start: 0.8605 (ttp) cc_final: 0.8328 (ttt) REVERT: A 529 MET cc_start: 0.9334 (mmp) cc_final: 0.9036 (mmm) REVERT: A 746 GLU cc_start: 0.9486 (mt-10) cc_final: 0.9275 (mt-10) REVERT: A 923 MET cc_start: 0.9046 (tpp) cc_final: 0.8733 (ttp) REVERT: A 960 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8079 (tp30) REVERT: A 1120 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6848 (mt-10) REVERT: A 1121 MET cc_start: 0.2866 (tpt) cc_final: 0.2588 (tpt) REVERT: A 1268 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: A 1317 GLU cc_start: 0.7173 (tt0) cc_final: 0.6471 (tm-30) REVERT: A 1742 ASP cc_start: 0.8978 (m-30) cc_final: 0.8726 (m-30) REVERT: A 1817 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7138 (mt-10) REVERT: B 174 ASP cc_start: 0.7403 (t0) cc_final: 0.6676 (t70) REVERT: B 229 LEU cc_start: 0.8549 (mt) cc_final: 0.8187 (pp) REVERT: B 251 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8372 (mm-40) REVERT: B 292 GLN cc_start: 0.8625 (pp30) cc_final: 0.7709 (mm-40) REVERT: G 193 GLU cc_start: 0.9600 (OUTLIER) cc_final: 0.9359 (pt0) REVERT: G 331 ASN cc_start: 0.9038 (t0) cc_final: 0.8815 (t0) REVERT: G 714 SER cc_start: 0.9112 (OUTLIER) cc_final: 0.8734 (p) REVERT: G 752 GLN cc_start: 0.9389 (mt0) cc_final: 0.8965 (tm-30) REVERT: G 1180 MET cc_start: 0.6424 (mtp) cc_final: 0.5901 (mtp) REVERT: G 1221 MET cc_start: 0.8729 (tmm) cc_final: 0.8324 (tmm) REVERT: G 1355 ASN cc_start: 0.9287 (OUTLIER) cc_final: 0.8991 (p0) REVERT: G 1467 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8684 (mp0) REVERT: G 1676 MET cc_start: 0.7435 (mtt) cc_final: 0.6503 (mtt) REVERT: G 1678 MET cc_start: 0.8418 (mmp) cc_final: 0.8151 (mmm) REVERT: G 1887 GLU cc_start: 0.7484 (mt-10) cc_final: 0.6556 (pm20) outliers start: 41 outliers final: 28 residues processed: 236 average time/residue: 0.4149 time to fit residues: 163.0384 Evaluate side-chains 225 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 191 time to evaluate : 3.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 674 TYR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1257 ASP Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1830 VAL Chi-restraints excluded: chain G residue 1847 LEU Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 6.9990 chunk 257 optimal weight: 8.9990 chunk 177 optimal weight: 30.0000 chunk 37 optimal weight: 6.9990 chunk 163 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 343 optimal weight: 10.0000 chunk 363 optimal weight: 50.0000 chunk 179 optimal weight: 6.9990 chunk 325 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A1358 HIS A1780 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1890 ASN G1892 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30228 Z= 0.209 Angle : 0.504 7.924 40944 Z= 0.260 Chirality : 0.041 0.144 4603 Planarity : 0.003 0.043 5285 Dihedral : 4.985 106.677 4031 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.69 % Favored : 97.23 % Rotamer: Outliers : 1.29 % Allowed : 11.19 % Favored : 87.52 % 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: -0.13 (0.14), residues: 3761 helix: 0.82 (0.13), residues: 1640 sheet: -1.33 (0.23), residues: 470 loop : -0.51 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 661 HIS 0.004 0.001 HIS A1689 PHE 0.017 0.001 PHE G 64 TYR 0.018 0.001 TYR G2030 ARG 0.006 0.000 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 216 time to evaluate : 3.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8524 (ttp) cc_final: 0.8248 (ttt) REVERT: A 529 MET cc_start: 0.9281 (mmp) cc_final: 0.8732 (mmp) REVERT: A 746 GLU cc_start: 0.9482 (mt-10) cc_final: 0.9277 (mt-10) REVERT: A 923 MET cc_start: 0.8991 (tpp) cc_final: 0.8745 (ttp) REVERT: A 960 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8194 (tp30) REVERT: A 1120 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6857 (mt-10) REVERT: A 1268 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: A 1317 GLU cc_start: 0.7135 (tt0) cc_final: 0.6452 (tm-30) REVERT: A 1561 MET cc_start: 0.9446 (mmm) cc_final: 0.9080 (mmm) REVERT: B 174 ASP cc_start: 0.7539 (t0) cc_final: 0.6457 (t0) REVERT: B 229 LEU cc_start: 0.8573 (mt) cc_final: 0.8229 (pp) REVERT: B 237 MET cc_start: 0.8565 (mmt) cc_final: 0.8361 (mmt) REVERT: B 292 GLN cc_start: 0.8629 (pp30) cc_final: 0.7673 (mm-40) REVERT: G 351 ASP cc_start: 0.9343 (OUTLIER) cc_final: 0.9121 (m-30) REVERT: G 674 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: G 714 SER cc_start: 0.9125 (OUTLIER) cc_final: 0.8709 (p) REVERT: G 752 GLN cc_start: 0.9361 (mt0) cc_final: 0.9012 (tm-30) REVERT: G 784 GLU cc_start: 0.9497 (pt0) cc_final: 0.9160 (tm-30) REVERT: G 1180 MET cc_start: 0.6373 (mtp) cc_final: 0.5839 (mtp) REVERT: G 1255 MET cc_start: 0.8848 (tpp) cc_final: 0.8523 (pmm) REVERT: G 1355 ASN cc_start: 0.9282 (OUTLIER) cc_final: 0.9073 (p0) REVERT: G 1467 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8656 (mp0) REVERT: G 1676 MET cc_start: 0.7554 (mtt) cc_final: 0.6585 (mtt) REVERT: G 1678 MET cc_start: 0.8420 (mmp) cc_final: 0.8167 (mmm) REVERT: G 1887 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6578 (pm20) outliers start: 42 outliers final: 21 residues processed: 243 average time/residue: 0.4227 time to fit residues: 167.3365 Evaluate side-chains 230 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 3.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1226 SER Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 674 TYR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 753 MET Chi-restraints excluded: chain G residue 794 MET Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 270 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 chunk 310 optimal weight: 30.0000 chunk 251 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 185 optimal weight: 6.9990 chunk 326 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A1433 HIS A1780 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 HIS G1039 HIS G1306 ASN ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1939 HIS ** G2027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 30228 Z= 0.368 Angle : 0.590 8.438 40944 Z= 0.305 Chirality : 0.043 0.144 4603 Planarity : 0.004 0.040 5285 Dihedral : 5.219 108.920 4031 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 1.97 % Allowed : 12.05 % Favored : 85.98 % 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: -0.26 (0.14), residues: 3761 helix: 0.64 (0.13), residues: 1651 sheet: -1.14 (0.23), residues: 459 loop : -0.60 (0.15), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 661 HIS 0.004 0.001 HIS G1512 PHE 0.017 0.002 PHE A1376 TYR 0.024 0.002 TYR G1762 ARG 0.003 0.000 ARG G1834 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 197 time to evaluate : 3.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8478 (ttp) cc_final: 0.8148 (ttt) REVERT: A 529 MET cc_start: 0.9295 (mmp) cc_final: 0.9019 (mmm) REVERT: A 960 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8108 (tp30) REVERT: A 1120 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7251 (tp30) REVERT: A 1268 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: A 1338 GLU cc_start: 0.6834 (tt0) cc_final: 0.6574 (tt0) REVERT: B 203 GLU cc_start: 0.8400 (tp30) cc_final: 0.7695 (tp30) REVERT: B 229 LEU cc_start: 0.8517 (mt) cc_final: 0.8195 (pp) REVERT: B 237 MET cc_start: 0.8558 (mmt) cc_final: 0.8355 (mmt) REVERT: B 271 ASN cc_start: 0.8445 (t0) cc_final: 0.7447 (p0) REVERT: G 193 GLU cc_start: 0.9561 (OUTLIER) cc_final: 0.9332 (pt0) REVERT: G 674 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: G 752 GLN cc_start: 0.9397 (mt0) cc_final: 0.9049 (tm-30) REVERT: G 917 MET cc_start: 0.9374 (mtt) cc_final: 0.9144 (mtt) REVERT: G 1001 ASP cc_start: 0.9275 (m-30) cc_final: 0.8702 (t0) REVERT: G 1180 MET cc_start: 0.6672 (mtp) cc_final: 0.6401 (mtp) REVERT: G 1198 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8686 (p) REVERT: G 1221 MET cc_start: 0.8506 (tmm) cc_final: 0.7805 (tmm) REVERT: G 1355 ASN cc_start: 0.9235 (OUTLIER) cc_final: 0.9012 (p0) REVERT: G 1676 MET cc_start: 0.7585 (mtt) cc_final: 0.6609 (mtt) REVERT: G 1678 MET cc_start: 0.8600 (mmp) cc_final: 0.8351 (mmm) REVERT: G 1887 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7039 (tt0) REVERT: G 1923 ASP cc_start: 0.3917 (OUTLIER) cc_final: 0.2904 (p0) outliers start: 64 outliers final: 39 residues processed: 245 average time/residue: 0.4137 time to fit residues: 167.1200 Evaluate side-chains 233 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1310 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 193 GLU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 410 SER Chi-restraints excluded: chain G residue 454 ASP Chi-restraints excluded: chain G residue 674 TYR Chi-restraints excluded: chain G residue 753 MET Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1198 SER Chi-restraints excluded: chain G residue 1241 ASN Chi-restraints excluded: chain G residue 1257 ASP Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1389 ILE Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1465 THR Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1830 VAL Chi-restraints excluded: chain G residue 1847 LEU Chi-restraints excluded: chain G residue 1923 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 0.8980 chunk 327 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 213 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 363 optimal weight: 0.0060 chunk 301 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 GLN A1652 GLN A1780 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30228 Z= 0.137 Angle : 0.499 8.898 40944 Z= 0.254 Chirality : 0.041 0.165 4603 Planarity : 0.003 0.048 5285 Dihedral : 4.807 103.645 4031 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 1.26 % Allowed : 13.28 % Favored : 85.45 % 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: 3761 helix: 0.97 (0.13), residues: 1645 sheet: -1.03 (0.23), residues: 482 loop : -0.32 (0.16), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 661 HIS 0.004 0.001 HIS A 639 PHE 0.013 0.001 PHE G 946 TYR 0.013 0.001 TYR G2030 ARG 0.008 0.000 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 220 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8380 (ttp) cc_final: 0.7982 (ttt) REVERT: A 529 MET cc_start: 0.9212 (mmp) cc_final: 0.8649 (mmp) REVERT: A 1268 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: A 1317 GLU cc_start: 0.7572 (tt0) cc_final: 0.6765 (tm-30) REVERT: B 168 MET cc_start: 0.7695 (tpp) cc_final: 0.7290 (tpt) REVERT: B 174 ASP cc_start: 0.7354 (t70) cc_final: 0.6146 (t0) REVERT: B 203 GLU cc_start: 0.8362 (tp30) cc_final: 0.7571 (tp30) REVERT: B 229 LEU cc_start: 0.8560 (mt) cc_final: 0.8289 (pp) REVERT: B 251 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8367 (mm-40) REVERT: B 292 GLN cc_start: 0.8627 (pp30) cc_final: 0.7691 (mm110) REVERT: G 100 ASP cc_start: 0.8733 (t70) cc_final: 0.8416 (t0) REVERT: G 351 ASP cc_start: 0.9328 (OUTLIER) cc_final: 0.9110 (m-30) REVERT: G 454 ASP cc_start: 0.8612 (m-30) cc_final: 0.8030 (t0) REVERT: G 674 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: G 714 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8648 (p) REVERT: G 752 GLN cc_start: 0.9373 (mt0) cc_final: 0.8992 (tm-30) REVERT: G 764 MET cc_start: 0.8968 (mtm) cc_final: 0.8274 (mtm) REVERT: G 784 GLU cc_start: 0.9482 (pt0) cc_final: 0.9119 (tm-30) REVERT: G 831 LYS cc_start: 0.9366 (mttt) cc_final: 0.9159 (mppt) REVERT: G 917 MET cc_start: 0.9437 (mtt) cc_final: 0.9206 (mtt) REVERT: G 1001 ASP cc_start: 0.9226 (m-30) cc_final: 0.8570 (t0) REVERT: G 1136 GLU cc_start: 0.9235 (mp0) cc_final: 0.8873 (mp0) REVERT: G 1180 MET cc_start: 0.6603 (mtp) cc_final: 0.6316 (mtp) REVERT: G 1221 MET cc_start: 0.8379 (tmm) cc_final: 0.8004 (tmm) REVERT: G 1255 MET cc_start: 0.8854 (tpp) cc_final: 0.8544 (pmm) REVERT: G 1265 MET cc_start: 0.8991 (tmm) cc_final: 0.8756 (ppp) REVERT: G 1355 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.9059 (p0) REVERT: G 1467 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8512 (mp0) REVERT: G 1676 MET cc_start: 0.7555 (mtt) cc_final: 0.6685 (mtt) REVERT: G 1678 MET cc_start: 0.8541 (mmp) cc_final: 0.8307 (mmm) REVERT: G 1887 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7034 (tt0) outliers start: 41 outliers final: 24 residues processed: 251 average time/residue: 0.4251 time to fit residues: 176.2979 Evaluate side-chains 233 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 3.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 674 TYR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 753 MET Chi-restraints excluded: chain G residue 794 MET Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1465 THR Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 265 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 362 optimal weight: 30.0000 chunk 226 optimal weight: 0.0770 chunk 220 optimal weight: 8.9990 chunk 167 optimal weight: 10.0000 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 821 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 30228 Z= 0.291 Angle : 0.552 11.086 40944 Z= 0.282 Chirality : 0.042 0.171 4603 Planarity : 0.004 0.043 5285 Dihedral : 4.913 102.774 4031 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 1.60 % Allowed : 13.59 % Favored : 84.81 % 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: 0.13 (0.14), residues: 3761 helix: 0.94 (0.13), residues: 1638 sheet: -0.88 (0.24), residues: 464 loop : -0.36 (0.16), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 661 HIS 0.004 0.001 HIS G 13 PHE 0.015 0.001 PHE A1376 TYR 0.026 0.002 TYR G1762 ARG 0.004 0.000 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 200 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8387 (ttp) cc_final: 0.8094 (ttt) REVERT: A 529 MET cc_start: 0.9278 (mmp) cc_final: 0.9002 (mmm) REVERT: A 1123 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8547 (tp-100) REVERT: A 1268 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: A 1317 GLU cc_start: 0.7684 (tt0) cc_final: 0.6921 (tm-30) REVERT: B 160 LYS cc_start: 0.8837 (mmpt) cc_final: 0.8569 (ptmt) REVERT: B 229 LEU cc_start: 0.8567 (mt) cc_final: 0.8281 (pp) REVERT: B 237 MET cc_start: 0.8511 (mmt) cc_final: 0.7955 (mmm) REVERT: B 292 GLN cc_start: 0.8648 (pp30) cc_final: 0.7709 (mm110) REVERT: G 674 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: G 714 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8749 (p) REVERT: G 752 GLN cc_start: 0.9385 (mt0) cc_final: 0.9010 (tm-30) REVERT: G 764 MET cc_start: 0.8968 (mtm) cc_final: 0.8239 (mtm) REVERT: G 784 GLU cc_start: 0.9473 (pt0) cc_final: 0.9103 (tm-30) REVERT: G 1001 ASP cc_start: 0.9263 (m-30) cc_final: 0.8678 (t0) REVERT: G 1136 GLU cc_start: 0.9229 (mp0) cc_final: 0.8889 (mp0) REVERT: G 1180 MET cc_start: 0.6618 (mtp) cc_final: 0.6084 (mtp) REVERT: G 1221 MET cc_start: 0.8373 (tmm) cc_final: 0.7967 (tmm) REVERT: G 1255 MET cc_start: 0.8915 (tpp) cc_final: 0.8509 (pmm) REVERT: G 1355 ASN cc_start: 0.9243 (OUTLIER) cc_final: 0.9005 (p0) REVERT: G 1676 MET cc_start: 0.7545 (mtt) cc_final: 0.6663 (mtt) REVERT: G 1678 MET cc_start: 0.8635 (mmp) cc_final: 0.8385 (mmm) REVERT: G 1923 ASP cc_start: 0.3528 (OUTLIER) cc_final: 0.2469 (p0) outliers start: 52 outliers final: 36 residues processed: 234 average time/residue: 0.4320 time to fit residues: 166.5295 Evaluate side-chains 234 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 192 time to evaluate : 3.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1310 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1378 GLU Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 674 TYR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 753 MET Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1198 SER Chi-restraints excluded: chain G residue 1341 ASN Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1389 ILE Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1465 THR Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1847 LEU Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1923 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 216 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 70 optimal weight: 0.9990 chunk 230 optimal weight: 5.9990 chunk 246 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 284 optimal weight: 7.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30228 Z= 0.158 Angle : 0.509 10.713 40944 Z= 0.257 Chirality : 0.041 0.193 4603 Planarity : 0.003 0.046 5285 Dihedral : 4.688 98.527 4031 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.74 % Favored : 97.21 % Rotamer: Outliers : 1.23 % Allowed : 14.30 % Favored : 84.47 % 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: 0.27 (0.14), residues: 3761 helix: 1.00 (0.13), residues: 1654 sheet: -0.97 (0.23), residues: 494 loop : -0.17 (0.16), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 661 HIS 0.004 0.001 HIS A1689 PHE 0.013 0.001 PHE A 450 TYR 0.015 0.001 TYR A 417 ARG 0.007 0.000 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 212 time to evaluate : 3.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8329 (ttp) cc_final: 0.7875 (ttt) REVERT: A 529 MET cc_start: 0.9216 (mmp) cc_final: 0.8682 (mmp) REVERT: A 1121 MET cc_start: 0.3062 (tpt) cc_final: 0.1727 (tpt) REVERT: A 1123 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8569 (tp-100) REVERT: A 1262 LYS cc_start: 0.6063 (mptt) cc_final: 0.5833 (mptt) REVERT: A 1268 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: A 1317 GLU cc_start: 0.7605 (tt0) cc_final: 0.6827 (tm-30) REVERT: B 160 LYS cc_start: 0.8828 (mmpt) cc_final: 0.8559 (ptmt) REVERT: B 229 LEU cc_start: 0.8569 (mt) cc_final: 0.8302 (pp) REVERT: B 237 MET cc_start: 0.8435 (mmt) cc_final: 0.7867 (mmm) REVERT: B 292 GLN cc_start: 0.8666 (pp30) cc_final: 0.7821 (mm110) REVERT: G 100 ASP cc_start: 0.8728 (t70) cc_final: 0.8374 (t0) REVERT: G 351 ASP cc_start: 0.9326 (OUTLIER) cc_final: 0.9105 (m-30) REVERT: G 454 ASP cc_start: 0.8655 (m-30) cc_final: 0.8121 (t0) REVERT: G 674 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7872 (m-80) REVERT: G 714 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.8666 (p) REVERT: G 752 GLN cc_start: 0.9325 (mt0) cc_final: 0.8938 (tm-30) REVERT: G 764 MET cc_start: 0.8898 (mtm) cc_final: 0.8271 (mtm) REVERT: G 784 GLU cc_start: 0.9476 (pt0) cc_final: 0.9103 (tm-30) REVERT: G 831 LYS cc_start: 0.9359 (mttt) cc_final: 0.9158 (mppt) REVERT: G 1001 ASP cc_start: 0.9228 (m-30) cc_final: 0.8556 (t0) REVERT: G 1136 GLU cc_start: 0.9227 (mp0) cc_final: 0.8867 (mp0) REVERT: G 1180 MET cc_start: 0.6529 (mtp) cc_final: 0.6243 (mtp) REVERT: G 1255 MET cc_start: 0.8887 (tpp) cc_final: 0.8530 (pmm) REVERT: G 1355 ASN cc_start: 0.9278 (OUTLIER) cc_final: 0.9042 (p0) REVERT: G 1676 MET cc_start: 0.7524 (mtt) cc_final: 0.6642 (mtt) outliers start: 40 outliers final: 32 residues processed: 240 average time/residue: 0.4244 time to fit residues: 170.7114 Evaluate side-chains 241 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 203 time to evaluate : 3.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1310 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1378 GLU Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 674 TYR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 753 MET Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1465 THR Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 20.0000 chunk 347 optimal weight: 9.9990 chunk 316 optimal weight: 2.9990 chunk 337 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 305 optimal weight: 6.9990 chunk 319 optimal weight: 0.0970 chunk 336 optimal weight: 7.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30228 Z= 0.236 Angle : 0.534 11.088 40944 Z= 0.272 Chirality : 0.041 0.186 4603 Planarity : 0.004 0.052 5285 Dihedral : 4.709 95.972 4031 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.54 % Rotamer: Outliers : 1.60 % Allowed : 14.21 % 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: 0.32 (0.14), residues: 3761 helix: 1.02 (0.13), residues: 1646 sheet: -0.78 (0.24), residues: 475 loop : -0.19 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 661 HIS 0.003 0.001 HIS A 454 PHE 0.015 0.001 PHE A 450 TYR 0.027 0.001 TYR G1762 ARG 0.004 0.000 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 201 time to evaluate : 3.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8360 (ttp) cc_final: 0.7922 (ttt) REVERT: A 440 MET cc_start: 0.9039 (mmt) cc_final: 0.8796 (mmt) REVERT: A 529 MET cc_start: 0.9263 (mmp) cc_final: 0.8745 (mmp) REVERT: A 746 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8940 (mp0) REVERT: A 1120 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7039 (tp30) REVERT: A 1121 MET cc_start: 0.2861 (tpt) cc_final: 0.1432 (tpt) REVERT: A 1123 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8522 (tp-100) REVERT: A 1268 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: A 1317 GLU cc_start: 0.7635 (tt0) cc_final: 0.6846 (tm-30) REVERT: B 160 LYS cc_start: 0.8848 (mmpt) cc_final: 0.8574 (ptmt) REVERT: B 229 LEU cc_start: 0.8536 (mt) cc_final: 0.8260 (pp) REVERT: B 237 MET cc_start: 0.8453 (mmt) cc_final: 0.7886 (mmm) REVERT: B 292 GLN cc_start: 0.8689 (pp30) cc_final: 0.7820 (mm110) REVERT: G 100 ASP cc_start: 0.8733 (t70) cc_final: 0.8398 (t0) REVERT: G 351 ASP cc_start: 0.9339 (OUTLIER) cc_final: 0.9107 (m-30) REVERT: G 454 ASP cc_start: 0.8631 (m-30) cc_final: 0.8073 (t0) REVERT: G 674 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7858 (m-80) REVERT: G 714 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8619 (p) REVERT: G 752 GLN cc_start: 0.9349 (mt0) cc_final: 0.8961 (tm-30) REVERT: G 764 MET cc_start: 0.8938 (mtm) cc_final: 0.8232 (mtm) REVERT: G 784 GLU cc_start: 0.9472 (pt0) cc_final: 0.9094 (tm-30) REVERT: G 1001 ASP cc_start: 0.9249 (m-30) cc_final: 0.8611 (t0) REVERT: G 1136 GLU cc_start: 0.9226 (mp0) cc_final: 0.8863 (mp0) REVERT: G 1180 MET cc_start: 0.6576 (mtp) cc_final: 0.6288 (mtp) REVERT: G 1236 LEU cc_start: 0.8420 (tt) cc_final: 0.8197 (tp) REVERT: G 1255 MET cc_start: 0.8907 (tpp) cc_final: 0.8550 (pmm) REVERT: G 1355 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.9029 (p0) outliers start: 52 outliers final: 40 residues processed: 237 average time/residue: 0.4225 time to fit residues: 167.5951 Evaluate side-chains 247 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 200 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1226 SER Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1310 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1378 GLU Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 581 THR Chi-restraints excluded: chain G residue 674 TYR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 794 MET Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1198 SER Chi-restraints excluded: chain G residue 1341 ASN Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1372 VAL Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1465 THR Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 9.9990 chunk 357 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 169 optimal weight: 0.4980 chunk 248 optimal weight: 5.9990 chunk 374 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 230 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1652 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1217 ASN G1568 HIS ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30228 Z= 0.183 Angle : 0.519 11.603 40944 Z= 0.262 Chirality : 0.041 0.193 4603 Planarity : 0.003 0.045 5285 Dihedral : 4.597 91.263 4031 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.87 % Favored : 97.08 % Rotamer: Outliers : 1.57 % Allowed : 14.36 % Favored : 84.07 % 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: 0.36 (0.14), residues: 3761 helix: 1.03 (0.13), residues: 1654 sheet: -0.83 (0.24), residues: 481 loop : -0.10 (0.16), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 661 HIS 0.004 0.001 HIS A 454 PHE 0.017 0.001 PHE A 450 TYR 0.013 0.001 TYR A 417 ARG 0.007 0.000 ARG G1023 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 210 time to evaluate : 3.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8342 (ttp) cc_final: 0.7849 (ttt) REVERT: A 440 MET cc_start: 0.9046 (mmt) cc_final: 0.8846 (mmt) REVERT: A 529 MET cc_start: 0.9245 (mmp) cc_final: 0.8721 (mmp) REVERT: A 746 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8933 (mp0) REVERT: A 1121 MET cc_start: 0.2805 (tpt) cc_final: 0.1449 (tpt) REVERT: A 1123 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8519 (tp-100) REVERT: A 1268 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: A 1317 GLU cc_start: 0.7606 (tt0) cc_final: 0.6828 (tm-30) REVERT: A 1561 MET cc_start: 0.9506 (mmm) cc_final: 0.8946 (mmm) REVERT: B 160 LYS cc_start: 0.8842 (mmpt) cc_final: 0.8561 (ptmt) REVERT: B 229 LEU cc_start: 0.8535 (mt) cc_final: 0.8262 (pp) REVERT: B 237 MET cc_start: 0.8434 (mmt) cc_final: 0.7868 (mmm) REVERT: B 292 GLN cc_start: 0.8654 (pp30) cc_final: 0.7839 (mm110) REVERT: G 71 LEU cc_start: 0.9177 (mp) cc_final: 0.8837 (mt) REVERT: G 100 ASP cc_start: 0.8727 (t70) cc_final: 0.8400 (t0) REVERT: G 351 ASP cc_start: 0.9339 (OUTLIER) cc_final: 0.9111 (m-30) REVERT: G 454 ASP cc_start: 0.8720 (m-30) cc_final: 0.8143 (t0) REVERT: G 674 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7926 (m-80) REVERT: G 714 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8618 (p) REVERT: G 752 GLN cc_start: 0.9297 (mt0) cc_final: 0.8939 (tm-30) REVERT: G 784 GLU cc_start: 0.9467 (pt0) cc_final: 0.9087 (tm-30) REVERT: G 917 MET cc_start: 0.9319 (mtt) cc_final: 0.9084 (mtt) REVERT: G 1001 ASP cc_start: 0.9237 (m-30) cc_final: 0.8570 (t0) REVERT: G 1136 GLU cc_start: 0.9219 (mp0) cc_final: 0.8834 (mp0) REVERT: G 1180 MET cc_start: 0.6531 (mtp) cc_final: 0.6017 (mtp) REVERT: G 1255 MET cc_start: 0.8890 (tpp) cc_final: 0.8546 (pmm) REVERT: G 1355 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.9029 (p0) REVERT: G 1923 ASP cc_start: 0.3593 (OUTLIER) cc_final: 0.2477 (p0) outliers start: 51 outliers final: 42 residues processed: 245 average time/residue: 0.4294 time to fit residues: 175.5498 Evaluate side-chains 250 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 201 time to evaluate : 3.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1226 SER Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1310 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1378 GLU Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 281 VAL Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 581 THR Chi-restraints excluded: chain G residue 674 TYR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 794 MET Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1241 ASN Chi-restraints excluded: chain G residue 1341 ASN Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1372 VAL Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1465 THR Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1847 LEU Chi-restraints excluded: chain G residue 1923 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 2.9990 chunk 317 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 275 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.083035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.061430 restraints weight = 127994.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062941 restraints weight = 68777.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063181 restraints weight = 39460.844| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30228 Z= 0.195 Angle : 0.525 11.308 40944 Z= 0.265 Chirality : 0.041 0.194 4603 Planarity : 0.003 0.046 5285 Dihedral : 4.545 83.928 4031 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.03 % Favored : 96.94 % Rotamer: Outliers : 1.66 % Allowed : 14.33 % Favored : 84.01 % 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: 0.41 (0.14), residues: 3761 helix: 1.05 (0.13), residues: 1654 sheet: -0.64 (0.24), residues: 462 loop : -0.13 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 661 HIS 0.004 0.001 HIS A 454 PHE 0.015 0.001 PHE A 450 TYR 0.025 0.001 TYR G1762 ARG 0.004 0.000 ARG G1023 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5137.28 seconds wall clock time: 96 minutes 47.73 seconds (5807.73 seconds total)