Starting phenix.real_space_refine on Thu Jul 25 18:42:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/07_2024/8psl_17855.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/07_2024/8psl_17855.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/8psl_17855/07_2024/8psl_17855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/07_2024/8psl_17855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/07_2024/8psl_17855.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psl_17855/07_2024/8psl_17855.cif" } 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= 0.008 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 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ASP 403": "OD1" <-> "OD2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A TYR 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A ASP 716": "OD1" <-> "OD2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A PHE 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 912": "OE1" <-> "OE2" Residue "A GLU 915": "OE1" <-> "OE2" Residue "A GLU 935": "OE1" <-> "OE2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A GLU 1016": "OE1" <-> "OE2" Residue "A GLU 1026": "OE1" <-> "OE2" Residue "A GLU 1038": "OE1" <-> "OE2" Residue "A GLU 1052": "OE1" <-> "OE2" Residue "A GLU 1117": "OE1" <-> "OE2" Residue "A GLU 1132": "OE1" <-> "OE2" Residue "A GLU 1135": "OE1" <-> "OE2" Residue "A GLU 1156": "OE1" <-> "OE2" Residue "A ASP 1313": "OD1" <-> "OD2" Residue "A GLU 1317": "OE1" <-> "OE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A PHE 1376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1391": "OD1" <-> "OD2" Residue "A TYR 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1498": "OE1" <-> "OE2" Residue "A GLU 1568": "OE1" <-> "OE2" Residue "A GLU 1681": "OE1" <-> "OE2" Residue "A PHE 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1817": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 138": "OD1" <-> "OD2" Residue "G PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 437": "OD1" <-> "OD2" Residue "G ASP 481": "OD1" <-> "OD2" Residue "G ASP 538": "OD1" <-> "OD2" Residue "G ASP 549": "OD1" <-> "OD2" Residue "G PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 580": "OE1" <-> "OE2" Residue "G PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 919": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 920": "OE1" <-> "OE2" Residue "G GLU 955": "OE1" <-> "OE2" Residue "G GLU 992": "OE1" <-> "OE2" Residue "G PHE 1003": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1106": "OE1" <-> "OE2" Residue "G PHE 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1183": "OE1" <-> "OE2" Residue "G PHE 1325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1471": "OE1" <-> "OE2" Residue "G PHE 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1497": "OE1" <-> "OE2" Residue "G TYR 1545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1646": "OD1" <-> "OD2" Residue "G GLU 1767": "OE1" <-> "OE2" Residue "G GLU 1790": "OE1" <-> "OE2" Residue "G TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 14.26, per 1000 atoms: 0.48 Number of scatterers: 29610 At special positions: 0 Unit cell: (181.46, 181.46, 174.075, 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=2.10 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.36 Conformation dependent library (CDL) restraints added in 5.3 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... Secondary structure from input PDB file: 171 helices and 31 sheets defined 50.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 4.669A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 removed outlier: 4.657A pdb=" N VAL A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 64 removed outlier: 4.389A pdb=" N ARG A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR A 60 " --> pdb=" O MET A 56 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.586A pdb=" N LYS A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 removed outlier: 4.281A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.563A pdb=" N TRP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 421 " --> pdb=" O TYR A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 4.451A pdb=" N VAL A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 438 " --> pdb=" O SER A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 456 Processing helix chain 'A' and resid 463 through 483 Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.536A pdb=" N ALA A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 669 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.921A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 725 Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 839 through 845 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.511A pdb=" N PHE A 850 " --> pdb=" O GLU A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 860 removed outlier: 4.441A pdb=" N ASN A 860 " --> pdb=" O SER A 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 935 through 956 removed outlier: 4.350A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 4.066A pdb=" N GLU A 964 " --> pdb=" O GLU A 960 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 968 " --> pdb=" O GLU A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.526A pdb=" N VAL A1001 " --> pdb=" O PRO A 997 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 4.014A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1042 removed outlier: 3.574A pdb=" N TRP A1037 " --> pdb=" O ALA A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 4.431A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1115 through 1118 Processing helix chain 'A' and resid 1137 through 1149 removed outlier: 3.719A pdb=" N GLN A1147 " --> pdb=" O GLN A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1206 Processing helix chain 'A' and resid 1209 through 1225 removed outlier: 3.940A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1232 through 1237 Processing helix chain 'A' and resid 1239 through 1243 removed outlier: 4.239A pdb=" N VAL A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1262 removed outlier: 3.755A pdb=" N LEU A1257 " --> pdb=" O GLY A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1279 removed outlier: 3.848A pdb=" N GLU A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1291 removed outlier: 4.483A pdb=" N SER A1284 " --> pdb=" O ILE A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1336 through 1347 Processing helix chain 'A' and resid 1351 through 1358 removed outlier: 3.540A pdb=" N GLU A1357 " --> pdb=" O LEU A1353 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1365 removed outlier: 3.579A pdb=" N MET A1365 " --> pdb=" O PRO A1362 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1424 through 1430 removed outlier: 3.622A pdb=" N ALA A1429 " --> pdb=" O LEU A1426 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A1430 " --> pdb=" O THR A1427 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1444 through 1475 removed outlier: 3.599A pdb=" N LYS A1471 " --> pdb=" O LEU A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1510 removed outlier: 4.048A pdb=" N ASN A1483 " --> pdb=" O SER A1479 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A1484 " --> pdb=" O GLU A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1528 Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.544A pdb=" N ASP A1550 " --> pdb=" O THR A1546 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A1564 " --> pdb=" O MET A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.748A pdb=" N THR A1581 " --> pdb=" O GLN A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1586 No H-bonds generated for 'chain 'A' and resid 1584 through 1586' Processing helix chain 'A' and resid 1587 through 1603 removed outlier: 3.519A pdb=" N TRP A1591 " --> pdb=" O ALA A1587 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A1601 " --> pdb=" O LEU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1621 Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 3.981A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A1663 " --> pdb=" O ASP A1659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1658 through 1663' Processing helix chain 'A' and resid 1666 through 1694 Processing helix chain 'A' and resid 1710 through 1717 removed outlier: 3.610A pdb=" N ASP A1717 " --> pdb=" O ASP A1713 " (cutoff:3.500A) Processing helix chain 'A' and resid 1734 through 1738 removed outlier: 3.574A pdb=" N ILE A1738 " --> pdb=" O SER A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 3.962A pdb=" N TYR A1744 " --> pdb=" O SER A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1758 Processing helix chain 'A' and resid 1777 through 1779 No H-bonds generated for 'chain 'A' and resid 1777 through 1779' Processing helix chain 'A' and resid 1783 through 1791 removed outlier: 3.644A pdb=" N ARG A1789 " --> pdb=" O THR A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1800 Processing helix chain 'A' and resid 1804 through 1824 Processing helix chain 'A' and resid 1833 through 1835 No H-bonds generated for 'chain 'A' and resid 1833 through 1835' Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 3.834A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A1862 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.889A pdb=" N LEU B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 176' Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.617A pdb=" N GLN B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.797A pdb=" N GLU B 203 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 4.028A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 236 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.592A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 Processing helix chain 'G' and resid 26 through 41 removed outlier: 3.596A pdb=" N ALA G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 72 removed outlier: 3.888A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 96 removed outlier: 4.436A pdb=" N VAL G 83 " --> pdb=" O GLN G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 Processing helix chain 'G' and resid 115 through 133 removed outlier: 3.639A pdb=" N THR G 119 " --> pdb=" O THR G 115 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU G 122 " --> pdb=" O LYS G 118 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS G 124 " --> pdb=" O LYS G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 168 through 180 removed outlier: 4.367A pdb=" N GLU G 172 " --> pdb=" O ASP G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 6.807A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 removed outlier: 4.253A pdb=" N VAL G 208 " --> pdb=" O ASP G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.669A pdb=" N SER G 233 " --> pdb=" O ASP G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 256 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 266 Processing helix chain 'G' and resid 276 through 286 removed outlier: 3.917A pdb=" N GLU G 285 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 314 removed outlier: 3.576A pdb=" N LYS G 298 " --> pdb=" O VAL G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 330 Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.923A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 Processing helix chain 'G' and resid 382 through 397 removed outlier: 3.689A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 429 through 433 removed outlier: 3.519A pdb=" N LEU G 432 " --> pdb=" O SER G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 446 removed outlier: 4.427A pdb=" N LEU G 438 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL G 444 " --> pdb=" O ASN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 485 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 507 through 510 Processing helix chain 'G' and resid 511 through 520 removed outlier: 3.719A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 549 removed outlier: 4.219A pdb=" N ILE G 547 " --> pdb=" O PHE G 543 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 555 Processing helix chain 'G' and resid 560 through 565 Processing helix chain 'G' and resid 581 through 588 removed outlier: 3.531A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 614 removed outlier: 3.622A pdb=" N ALA G 609 " --> pdb=" O ASP G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 622 through 624 No H-bonds generated for 'chain 'G' and resid 622 through 624' Processing helix chain 'G' and resid 626 through 639 removed outlier: 3.682A pdb=" N MET G 630 " --> pdb=" O SER G 626 " (cutoff:3.500A) Processing helix chain 'G' and resid 655 through 672 removed outlier: 3.538A pdb=" N LEU G 659 " --> pdb=" O ASN G 655 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 698 removed outlier: 3.582A pdb=" N GLU G 693 " --> pdb=" O GLU G 689 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 747 through 759 removed outlier: 5.458A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 777 through 783 Processing helix chain 'G' and resid 785 through 790 removed outlier: 3.642A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP G 790 " --> pdb=" O THR G 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 806 removed outlier: 3.650A pdb=" N MET G 806 " --> pdb=" O SER G 803 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 824 Processing helix chain 'G' and resid 831 through 835 removed outlier: 3.520A pdb=" N THR G 835 " --> pdb=" O TRP G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 859 through 872 removed outlier: 4.026A pdb=" N TRP G 865 " --> pdb=" O GLY G 861 " (cutoff:3.500A) Processing helix chain 'G' and resid 876 through 887 removed outlier: 4.191A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix Processing helix chain 'G' and resid 887 through 899 Processing helix chain 'G' and resid 913 through 917 Processing helix chain 'G' and resid 918 through 930 Processing helix chain 'G' and resid 940 through 959 Processing helix chain 'G' and resid 969 through 975 removed outlier: 3.757A pdb=" N LYS G 975 " --> pdb=" O LEU G 972 " (cutoff:3.500A) Processing helix chain 'G' and resid 976 through 987 removed outlier: 3.754A pdb=" N GLU G 981 " --> pdb=" O ASP G 977 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS G 982 " --> pdb=" O GLU G 978 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 992 Processing helix chain 'G' and resid 996 through 1007 Processing helix chain 'G' and resid 1024 through 1031 removed outlier: 3.583A pdb=" N LYS G1030 " --> pdb=" O GLU G1026 " (cutoff:3.500A) Processing helix chain 'G' and resid 1034 through 1039 Processing helix chain 'G' and resid 1047 through 1051 Processing helix chain 'G' and resid 1058 through 1063 removed outlier: 3.604A pdb=" N GLN G1061 " --> pdb=" O VAL G1058 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR G1063 " --> pdb=" O ALA G1060 " (cutoff:3.500A) Processing helix chain 'G' and resid 1069 through 1089 Processing helix chain 'G' and resid 1093 through 1097 Processing helix chain 'G' and resid 1134 through 1144 Processing helix chain 'G' and resid 1148 through 1156 removed outlier: 3.543A pdb=" N PHE G1154 " --> pdb=" O ARG G1150 " (cutoff:3.500A) Processing helix chain 'G' and resid 1168 through 1174 removed outlier: 3.622A pdb=" N LYS G1172 " --> pdb=" O ASN G1168 " (cutoff:3.500A) Processing helix chain 'G' and resid 1257 through 1271 removed outlier: 3.558A pdb=" N LYS G1268 " --> pdb=" O GLU G1264 " (cutoff:3.500A) Processing helix chain 'G' and resid 1293 through 1304 Processing helix chain 'G' and resid 1308 through 1312 Processing helix chain 'G' and resid 1325 through 1337 removed outlier: 3.577A pdb=" N VAL G1329 " --> pdb=" O PHE G1325 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS G1336 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1346 through 1348 No H-bonds generated for 'chain 'G' and resid 1346 through 1348' Processing helix chain 'G' and resid 1437 through 1447 removed outlier: 3.806A pdb=" N ILE G1441 " --> pdb=" O THR G1437 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1523 Processing helix chain 'G' and resid 1550 through 1558 removed outlier: 3.814A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) Processing helix chain 'G' and resid 1561 through 1565 Processing helix chain 'G' and resid 1566 through 1573 removed outlier: 3.660A pdb=" N ALA G1570 " --> pdb=" O SER G1566 " (cutoff:3.500A) Processing helix chain 'G' and resid 1581 through 1597 Processing helix chain 'G' and resid 1677 through 1684 removed outlier: 3.636A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1685 through 1702 removed outlier: 3.581A pdb=" N VAL G1690 " --> pdb=" O ALA G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1723 through 1736 removed outlier: 3.588A pdb=" N ARG G1728 " --> pdb=" O GLU G1724 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET G1736 " --> pdb=" O ASN G1732 " (cutoff:3.500A) Processing helix chain 'G' and resid 1769 through 1772 Processing helix chain 'G' and resid 1773 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1809 through 1819 removed outlier: 3.804A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1841 removed outlier: 3.695A pdb=" N GLU G1829 " --> pdb=" O GLU G1825 " (cutoff:3.500A) Processing helix chain 'G' and resid 1858 through 1863 removed outlier: 3.969A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA G1863 " --> pdb=" O PRO G1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1858 through 1863' Processing helix chain 'G' and resid 1867 through 1883 removed outlier: 3.523A pdb=" N TYR G1873 " --> pdb=" O GLU G1869 " (cutoff:3.500A) Processing helix chain 'G' and resid 1905 through 1921 removed outlier: 3.830A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) Processing helix chain 'G' and resid 1923 through 1930 removed outlier: 3.857A pdb=" N LEU G1927 " --> pdb=" O ASP G1923 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1934 through 1949 removed outlier: 4.114A pdb=" N GLY G1938 " --> pdb=" O GLU G1934 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) Processing helix chain 'G' and resid 1978 through 1983 removed outlier: 4.664A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1996 removed outlier: 4.083A pdb=" N PHE G1988 " --> pdb=" O GLY G1984 " (cutoff:3.500A) Processing helix chain 'G' and resid 1997 through 2001 removed outlier: 3.618A pdb=" N VAL G2001 " --> pdb=" O LYS G1998 " (cutoff:3.500A) Processing helix chain 'G' and resid 2022 through 2033 Processing helix chain 'G' and resid 2036 through 2044 Processing helix chain 'G' and resid 2045 through 2047 No H-bonds generated for 'chain 'G' and resid 2045 through 2047' Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.191A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN G1897 " --> pdb=" O ASN G1892 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.191A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN G1897 " --> pdb=" O ASN G1892 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 80 removed outlier: 6.022A pdb=" N VAL A 44 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG A 43 " --> pdb=" O THR G1663 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL G1665 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 45 " --> pdb=" O VAL G1665 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 402 removed outlier: 7.021A pdb=" N VAL A 703 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL A 735 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 705 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 679 " --> pdb=" O ILE A 769 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.906A pdb=" N VAL A 671 " --> pdb=" O TYR A 490 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 500 through 503 Processing sheet with id=AA7, first strand: chain 'A' and resid 649 through 651 Processing sheet with id=AA8, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA9, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AB1, first strand: chain 'A' and resid 1326 through 1333 removed outlier: 6.646A pdb=" N ALA A1382 " --> pdb=" O GLU A1026 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU A1026 " --> pdb=" O ALA A1382 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE A1384 " --> pdb=" O PHE A1024 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE A1024 " --> pdb=" O ILE A1384 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A1386 " --> pdb=" O THR A1022 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A1402 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A1539 " --> pdb=" O VAL A1575 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id=AB3, first strand: chain 'A' and resid 1119 through 1126 removed outlier: 3.982A pdb=" N MET A1121 " --> pdb=" O LYS A1177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB5, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB6, first strand: chain 'A' and resid 1723 through 1724 removed outlier: 3.540A pdb=" N THR A1732 " --> pdb=" O SER A1723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id=AB8, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id=AB9, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.586A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 269 through 272 removed outlier: 3.880A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 157 " --> pdb=" O HIS G 500 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 418 through 420 removed outlier: 6.400A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 592 through 594 removed outlier: 6.657A pdb=" N LEU G 592 " --> pdb=" O THR G 616 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N GLU G 618 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL G 594 " --> pdb=" O GLU G 618 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ALA G 620 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N THR G 733 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE G 766 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU G 730 " --> pdb=" O ILE G 766 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY G 768 " --> pdb=" O LEU G 730 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TRP G 732 " --> pdb=" O GLY G 768 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 800 " --> pdb=" O PHE G 767 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.897A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC6, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC7, first strand: chain 'G' and resid 1126 through 1128 removed outlier: 3.685A pdb=" N VAL G1209 " --> pdb=" O LEU G1197 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL G1201 " --> pdb=" O LEU G1205 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU G1205 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 1158 through 1161 removed outlier: 3.637A pdb=" N MET G1164 " --> pdb=" O GLN G1161 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 3.740A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP G1289 " --> pdb=" O VAL G1372 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL G1372 " --> pdb=" O ASP G1289 " (cutoff:3.500A) removed outlier: 13.203A pdb=" N VAL G1377 " --> pdb=" O VAL G1427 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N VAL G1427 " --> pdb=" O VAL G1377 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU G1379 " --> pdb=" O LYS G1425 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 3.740A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASP G1289 " --> pdb=" O VAL G1372 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL G1372 " --> pdb=" O ASP G1289 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER G1354 " --> pdb=" O SER G1409 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG G1635 " --> pdb=" O MET G1631 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET G1631 " --> pdb=" O ARG G1635 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU G1637 " --> pdb=" O VAL G1629 " (cutoff:3.500A) removed outlier: 14.558A pdb=" N LYS G1623 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 12.340A pdb=" N ILE G1539 " --> pdb=" O LYS G1623 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N SER G1625 " --> pdb=" O ILE G1537 " (cutoff:3.500A) removed outlier: 10.239A pdb=" N ILE G1537 " --> pdb=" O SER G1625 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N GLN G1627 " --> pdb=" O ASN G1535 " (cutoff:3.500A) removed outlier: 10.846A pdb=" N ASN G1535 " --> pdb=" O GLN G1627 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL G1629 " --> pdb=" O LEU G1533 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 1432 through 1435 removed outlier: 3.514A pdb=" N ILE G1435 " --> pdb=" O LYS G1462 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY G1487 " --> pdb=" O ILE G1503 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE G1503 " --> pdb=" O GLY G1487 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE G1489 " --> pdb=" O ILE G1501 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id=AD4, first strand: chain 'G' and resid 1737 through 1741 1373 hydrogen bonds defined for protein. 3861 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: 14.46 Time building geometry restraints manager: 11.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 6547 1.33 - 1.49: 8383 1.49 - 1.64: 15111 1.64 - 1.79: 70 1.79 - 1.95: 117 Bond restraints: 30228 Sorted by residual: bond pdb=" CG MET A1121 " pdb=" SD MET A1121 " ideal model delta sigma weight residual 1.803 1.948 -0.145 2.50e-02 1.60e+03 3.38e+01 bond pdb=" N THR G 56 " pdb=" CA THR G 56 " ideal model delta sigma weight residual 1.455 1.495 -0.040 7.00e-03 2.04e+04 3.32e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.458 1.496 -0.038 7.70e-03 1.69e+04 2.46e+01 bond pdb=" N VAL A 957 " pdb=" CA VAL A 957 " ideal model delta sigma weight residual 1.460 1.502 -0.042 8.60e-03 1.35e+04 2.34e+01 bond pdb=" C TYR A 725 " pdb=" O TYR A 725 " ideal model delta sigma weight residual 1.235 1.288 -0.053 1.10e-02 8.26e+03 2.32e+01 ... (remaining 30223 not shown) Histogram of bond angle deviations from ideal: 94.80 - 103.22: 237 103.22 - 111.64: 11452 111.64 - 120.07: 17978 120.07 - 128.49: 11115 128.49 - 136.91: 162 Bond angle restraints: 40944 Sorted by residual: angle pdb=" CB GLU A 381 " pdb=" CG GLU A 381 " pdb=" CD GLU A 381 " ideal model delta sigma weight residual 112.60 130.57 -17.97 1.70e+00 3.46e-01 1.12e+02 angle pdb=" CB GLU A1317 " pdb=" CG GLU A1317 " pdb=" CD GLU A1317 " ideal model delta sigma weight residual 112.60 124.21 -11.61 1.70e+00 3.46e-01 4.67e+01 angle pdb=" CB GLU A 780 " pdb=" CG GLU A 780 " pdb=" CD GLU A 780 " ideal model delta sigma weight residual 112.60 124.00 -11.40 1.70e+00 3.46e-01 4.50e+01 angle pdb=" CA GLY A1582 " pdb=" C GLY A1582 " pdb=" O GLY A1582 " ideal model delta sigma weight residual 122.52 117.24 5.28 7.90e-01 1.60e+00 4.46e+01 angle pdb=" C GLU B 272 " pdb=" N PRO B 273 " pdb=" CA PRO B 273 " ideal model delta sigma weight residual 119.87 113.04 6.83 1.04e+00 9.25e-01 4.32e+01 ... (remaining 40939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 16499 18.09 - 36.18: 1403 36.18 - 54.26: 240 54.26 - 72.35: 76 72.35 - 90.44: 32 Dihedral angle restraints: 18250 sinusoidal: 7338 harmonic: 10912 Sorted by residual: dihedral pdb=" CA ALA G 897 " pdb=" C ALA G 897 " pdb=" N ASP G 898 " pdb=" CA ASP G 898 " ideal model delta harmonic sigma weight residual -180.00 -153.23 -26.77 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ILE G1503 " pdb=" C ILE G1503 " pdb=" N VAL G1504 " pdb=" CA VAL G1504 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA GLY A1565 " pdb=" C GLY A1565 " pdb=" N ARG A1566 " pdb=" CA ARG A1566 " ideal model delta harmonic sigma weight residual 180.00 156.16 23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 18247 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2092 0.060 - 0.120: 1744 0.120 - 0.181: 648 0.181 - 0.241: 113 0.241 - 0.301: 6 Chirality restraints: 4603 Sorted by residual: 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 2.73 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA ILE G 652 " pdb=" N ILE G 652 " pdb=" C ILE G 652 " pdb=" CB ILE G 652 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.83e+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 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 4600 not shown) Planarity restraints: 5285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1401 " -0.059 2.00e-02 2.50e+03 2.98e-02 1.77e+01 pdb=" CG TYR A1401 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A1401 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A1401 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A1401 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A1401 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1401 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1401 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1376 " 0.035 2.00e-02 2.50e+03 2.41e-02 1.02e+01 pdb=" CG PHE A1376 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A1376 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A1376 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A1376 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A1376 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A1376 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 718 " -0.043 2.00e-02 2.50e+03 2.15e-02 9.28e+00 pdb=" CG TYR A 718 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 718 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 718 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 718 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 718 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 718 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 718 " -0.021 2.00e-02 2.50e+03 ... (remaining 5282 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 654 2.68 - 3.23: 28707 3.23 - 3.79: 46102 3.79 - 4.34: 64685 4.34 - 4.90: 104553 Nonbonded interactions: 244701 Sorted by model distance: nonbonded pdb=" O GLY B 222 " pdb=" OG SER B 226 " model vdw 2.124 2.440 nonbonded pdb=" O VAL G1443 " pdb=" OG SER G1446 " model vdw 2.202 2.440 nonbonded pdb=" O GLN G 456 " pdb=" NH1 ARG G 469 " model vdw 2.204 2.520 nonbonded pdb=" O PHE G1419 " pdb=" OG1 THR G1422 " model vdw 2.205 2.440 nonbonded pdb=" OE1 GLU A1107 " pdb=" OG1 THR A1191 " model vdw 2.207 2.440 ... (remaining 244696 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.060 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 76.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 0.145 30228 Z= 0.910 Angle : 1.890 17.974 40944 Z= 1.379 Chirality : 0.086 0.301 4603 Planarity : 0.006 0.030 5285 Dihedral : 14.721 90.442 11219 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.29 % Favored : 92.24 % Rotamer: Outliers : 0.22 % Allowed : 3.70 % Favored : 96.09 % 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: -3.55 (0.11), residues: 3761 helix: -2.57 (0.10), residues: 1628 sheet: -2.36 (0.21), residues: 460 loop : -1.93 (0.14), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.006 TRP A1286 HIS 0.015 0.003 HIS G1697 PHE 0.050 0.004 PHE A1376 TYR 0.059 0.005 TYR A1401 ARG 0.010 0.001 ARG A1430 *********************** 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 316 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 309 time to evaluate : 3.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8767 (ttm) cc_final: 0.8557 (tpp) REVERT: A 384 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8936 (pt0) REVERT: A 419 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8952 (mt-10) REVERT: A 440 MET cc_start: 0.9522 (mmm) cc_final: 0.9283 (mmm) REVERT: A 847 GLU cc_start: 0.9146 (mp0) cc_final: 0.8873 (mp0) REVERT: A 952 GLU cc_start: 0.9043 (pp20) cc_final: 0.8837 (pp20) REVERT: A 991 ASP cc_start: 0.9180 (t0) cc_final: 0.8961 (t0) REVERT: A 1268 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8830 (tt0) REVERT: A 1273 ASP cc_start: 0.9187 (p0) cc_final: 0.8895 (p0) REVERT: A 1338 GLU cc_start: 0.8694 (mp0) cc_final: 0.8070 (mt-10) REVERT: A 1430 ARG cc_start: 0.4923 (tmt-80) cc_final: 0.4315 (tpt170) REVERT: A 1646 PHE cc_start: 0.9128 (m-10) cc_final: 0.8925 (m-10) REVERT: A 1649 LYS cc_start: 0.4656 (mmtt) cc_final: 0.4039 (mmtt) REVERT: A 1690 ASN cc_start: 0.9580 (t0) cc_final: 0.9330 (t0) REVERT: A 1819 VAL cc_start: 0.8493 (t) cc_final: 0.8267 (m) REVERT: B 185 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8750 (mt-10) REVERT: B 211 GLU cc_start: 0.8926 (mp0) cc_final: 0.8685 (mp0) REVERT: B 292 GLN cc_start: 0.9198 (mp10) cc_final: 0.8834 (mp10) REVERT: B 301 ASP cc_start: 0.8556 (t0) cc_final: 0.8201 (t0) REVERT: G 764 MET cc_start: 0.9038 (ttm) cc_final: 0.8834 (ttm) REVERT: G 863 MET cc_start: 0.9164 (mmm) cc_final: 0.8832 (mmm) REVERT: G 870 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9088 (pt0) REVERT: G 1221 MET cc_start: 0.8830 (tmm) cc_final: 0.8557 (tmm) REVERT: G 1229 MET cc_start: 0.4974 (tpt) cc_final: 0.4685 (tpt) REVERT: G 1323 MET cc_start: 0.6898 (ptp) cc_final: 0.6463 (ptp) REVERT: G 1359 MET cc_start: 0.6497 (tpp) cc_final: 0.5625 (tpt) REVERT: G 1784 MET cc_start: 0.8140 (tmm) cc_final: 0.7308 (tmm) REVERT: G 1829 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8950 (mm-30) REVERT: G 1838 MET cc_start: 0.9001 (tmm) cc_final: 0.8736 (tmm) REVERT: G 1876 GLU cc_start: 0.7583 (tp30) cc_final: 0.7318 (tp30) REVERT: G 2005 ARG cc_start: 0.8291 (mtp85) cc_final: 0.7982 (mtp180) outliers start: 7 outliers final: 0 residues processed: 311 average time/residue: 0.4302 time to fit residues: 212.5750 Evaluate side-chains 218 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 6.9990 chunk 284 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 152 optimal weight: 6.9990 chunk 294 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 219 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 40 ASN A 341 GLN A 344 GLN A 374 GLN A 379 ASN ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN A 527 GLN A 777 GLN A 821 GLN A 983 GLN A 987 ASN A 989 GLN A1000 GLN A1207 GLN A1380 GLN A1542 HIS A1648 GLN A1652 GLN A1783 ASN ** A1845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1854 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN G 79 GLN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 GLN G 181 HIS G 275 GLN G 330 ASN G 354 ASN G 372 ASN G 390 ASN G 440 ASN G 747 HIS ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1061 GLN G1078 HIS G1217 ASN G1355 ASN G1514 ASN G1595 ASN G1619 ASN G1659 GLN G1697 HIS G1896 GLN G1912 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1570 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= 0.226 Angle : 0.578 10.814 40944 Z= 0.301 Chirality : 0.042 0.187 4603 Planarity : 0.004 0.037 5285 Dihedral : 4.934 82.776 4028 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.98 % Favored : 96.89 % Rotamer: Outliers : 0.83 % Allowed : 7.55 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 3761 helix: -0.04 (0.12), residues: 1675 sheet: -1.70 (0.22), residues: 515 loop : -0.86 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1813 HIS 0.011 0.001 HIS G 102 PHE 0.016 0.001 PHE G 209 TYR 0.018 0.002 TYR G1891 ARG 0.006 0.000 ARG G1956 *********************** 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 273 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 246 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8855 (pt0) REVERT: A 847 GLU cc_start: 0.9113 (mp0) cc_final: 0.8692 (tm-30) REVERT: A 923 MET cc_start: 0.8053 (ttp) cc_final: 0.7793 (ttp) REVERT: A 946 GLU cc_start: 0.9202 (mp0) cc_final: 0.8874 (pp20) REVERT: A 1128 GLU cc_start: 0.8640 (mt-10) cc_final: 0.7881 (mp0) REVERT: A 1273 ASP cc_start: 0.8953 (p0) cc_final: 0.8546 (p0) REVERT: A 1317 GLU cc_start: 0.7796 (tt0) cc_final: 0.7509 (tt0) REVERT: A 1338 GLU cc_start: 0.8660 (mp0) cc_final: 0.7954 (mt-10) REVERT: A 1430 ARG cc_start: 0.4821 (tmt-80) cc_final: 0.4517 (tpt170) REVERT: A 1498 GLU cc_start: 0.8890 (tt0) cc_final: 0.8554 (tp30) REVERT: A 1646 PHE cc_start: 0.8969 (m-10) cc_final: 0.8750 (m-10) REVERT: A 1649 LYS cc_start: 0.4379 (mmtt) cc_final: 0.3858 (mmtt) REVERT: A 1759 MET cc_start: 0.7594 (tmm) cc_final: 0.7044 (tmm) REVERT: B 185 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8452 (mt-10) REVERT: B 207 GLU cc_start: 0.9081 (pp20) cc_final: 0.8338 (tp30) REVERT: B 216 THR cc_start: 0.8187 (p) cc_final: 0.7930 (p) REVERT: B 237 MET cc_start: 0.8865 (mmm) cc_final: 0.8580 (tpp) REVERT: B 290 MET cc_start: 0.9147 (mmt) cc_final: 0.8890 (mmt) REVERT: B 301 ASP cc_start: 0.8570 (t0) cc_final: 0.8297 (t0) REVERT: G 132 MET cc_start: 0.8613 (mpp) cc_final: 0.8179 (mmt) REVERT: G 331 ASN cc_start: 0.9310 (m110) cc_final: 0.9083 (m-40) REVERT: G 447 ASN cc_start: 0.9037 (m-40) cc_final: 0.8510 (p0) REVERT: G 764 MET cc_start: 0.8748 (ttm) cc_final: 0.8500 (ttm) REVERT: G 794 MET cc_start: 0.9215 (tpp) cc_final: 0.8606 (mmt) REVERT: G 870 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8946 (pt0) REVERT: G 1221 MET cc_start: 0.8718 (tmm) cc_final: 0.8479 (tmm) REVERT: G 1359 MET cc_start: 0.5890 (tpp) cc_final: 0.5270 (tpt) REVERT: G 1631 MET cc_start: 0.8239 (mmm) cc_final: 0.7469 (mmm) REVERT: G 1784 MET cc_start: 0.8439 (tmm) cc_final: 0.7837 (tmm) REVERT: G 1822 MET cc_start: 0.8472 (ptp) cc_final: 0.8079 (ptp) REVERT: G 1829 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8941 (mm-30) REVERT: G 1838 MET cc_start: 0.9035 (tmm) cc_final: 0.8806 (tmm) REVERT: G 1876 GLU cc_start: 0.7386 (tp30) cc_final: 0.7131 (tp30) REVERT: G 2005 ARG cc_start: 0.8326 (mtp85) cc_final: 0.7877 (tpp-160) outliers start: 27 outliers final: 12 residues processed: 264 average time/residue: 0.4199 time to fit residues: 179.5349 Evaluate side-chains 226 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 214 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 284 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 342 optimal weight: 8.9990 chunk 369 optimal weight: 10.0000 chunk 304 optimal weight: 5.9990 chunk 339 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1433 HIS A1482 GLN A1794 GLN ** A1845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 30228 Z= 0.305 Angle : 0.582 11.487 40944 Z= 0.300 Chirality : 0.043 0.166 4603 Planarity : 0.004 0.045 5285 Dihedral : 4.807 74.447 4028 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.77 % Rotamer: Outliers : 1.26 % Allowed : 9.24 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3761 helix: 0.60 (0.13), residues: 1667 sheet: -1.56 (0.22), residues: 512 loop : -0.60 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1030 HIS 0.010 0.001 HIS G 102 PHE 0.024 0.002 PHE B 241 TYR 0.016 0.002 TYR G2048 ARG 0.005 0.000 ARG B 276 *********************** 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 279 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 238 time to evaluate : 3.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8626 (mm) cc_final: 0.8077 (tp) REVERT: A 384 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8827 (pt0) REVERT: A 435 GLU cc_start: 0.9130 (tt0) cc_final: 0.8842 (tt0) REVERT: A 826 MET cc_start: 0.9161 (mmm) cc_final: 0.8762 (mtp) REVERT: A 847 GLU cc_start: 0.9202 (mp0) cc_final: 0.8750 (tm-30) REVERT: A 946 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8931 (mp0) REVERT: A 1124 GLU cc_start: 0.9262 (tt0) cc_final: 0.8948 (tt0) REVERT: A 1128 GLU cc_start: 0.8680 (mt-10) cc_final: 0.7970 (mp0) REVERT: A 1273 ASP cc_start: 0.8932 (p0) cc_final: 0.8528 (p0) REVERT: A 1338 GLU cc_start: 0.8640 (mp0) cc_final: 0.7880 (mt-10) REVERT: A 1498 GLU cc_start: 0.8873 (tt0) cc_final: 0.8459 (tp30) REVERT: A 1649 LYS cc_start: 0.3915 (mmtt) cc_final: 0.3363 (mmtt) REVERT: A 1759 MET cc_start: 0.7689 (tmm) cc_final: 0.7386 (tmm) REVERT: A 1783 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.7219 (m110) REVERT: B 185 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8500 (mt-10) REVERT: B 237 MET cc_start: 0.8717 (mmm) cc_final: 0.8386 (tpp) REVERT: B 301 ASP cc_start: 0.8575 (t0) cc_final: 0.8323 (t0) REVERT: G 119 THR cc_start: 0.7992 (m) cc_final: 0.7721 (p) REVERT: G 132 MET cc_start: 0.8500 (mpp) cc_final: 0.8199 (mmt) REVERT: G 167 ASP cc_start: 0.8411 (p0) cc_final: 0.8160 (p0) REVERT: G 325 GLU cc_start: 0.9409 (OUTLIER) cc_final: 0.9207 (mt-10) REVERT: G 447 ASN cc_start: 0.9072 (m-40) cc_final: 0.8530 (p0) REVERT: G 794 MET cc_start: 0.9177 (tpp) cc_final: 0.8555 (mmt) REVERT: G 870 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8993 (pt0) REVERT: G 1164 MET cc_start: 0.8353 (mmm) cc_final: 0.8088 (tpp) REVERT: G 1221 MET cc_start: 0.8637 (tmm) cc_final: 0.8422 (tmm) REVERT: G 1359 MET cc_start: 0.5757 (tpp) cc_final: 0.5123 (tpt) REVERT: G 1413 ARG cc_start: 0.9166 (mtp85) cc_final: 0.8939 (mmm-85) REVERT: G 1631 MET cc_start: 0.8187 (mmm) cc_final: 0.7233 (mmm) REVERT: G 1639 LYS cc_start: 0.9354 (pttp) cc_final: 0.9097 (ptpp) REVERT: G 1784 MET cc_start: 0.8486 (tmm) cc_final: 0.7892 (tmm) REVERT: G 1822 MET cc_start: 0.8451 (ptp) cc_final: 0.8073 (ptp) REVERT: G 1829 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8969 (mm-30) REVERT: G 1838 MET cc_start: 0.9043 (tmm) cc_final: 0.8771 (tmm) REVERT: G 1876 GLU cc_start: 0.7418 (tp30) cc_final: 0.7109 (tp30) REVERT: G 2005 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7817 (tpp-160) outliers start: 41 outliers final: 23 residues processed: 268 average time/residue: 0.4239 time to fit residues: 183.4416 Evaluate side-chains 234 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 3.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1783 ASN Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 417 SER Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 30.0000 chunk 257 optimal weight: 0.0070 chunk 177 optimal weight: 0.0010 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 0.0770 chunk 229 optimal weight: 2.9990 chunk 343 optimal weight: 20.0000 chunk 363 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 325 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1845 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 GLN G 677 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30228 Z= 0.143 Angle : 0.501 11.083 40944 Z= 0.255 Chirality : 0.040 0.148 4603 Planarity : 0.003 0.042 5285 Dihedral : 4.427 64.956 4028 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.26 % Rotamer: Outliers : 1.05 % Allowed : 10.57 % Favored : 88.38 % 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: 1.05 (0.13), residues: 1664 sheet: -1.23 (0.22), residues: 520 loop : -0.35 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1508 HIS 0.007 0.001 HIS G 102 PHE 0.027 0.001 PHE A 35 TYR 0.018 0.001 TYR G2048 ARG 0.005 0.000 ARG A 709 *********************** 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 278 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 244 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8562 (mm) cc_final: 0.8031 (tp) REVERT: A 352 MET cc_start: 0.8802 (ttm) cc_final: 0.8091 (tmm) REVERT: A 384 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8825 (pt0) REVERT: A 826 MET cc_start: 0.9076 (mmm) cc_final: 0.8667 (mtp) REVERT: A 847 GLU cc_start: 0.9194 (mp0) cc_final: 0.8965 (mp0) REVERT: A 946 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8892 (pp20) REVERT: A 1124 GLU cc_start: 0.9213 (tt0) cc_final: 0.8935 (tt0) REVERT: A 1128 GLU cc_start: 0.8611 (mt-10) cc_final: 0.7833 (mp0) REVERT: A 1273 ASP cc_start: 0.9009 (p0) cc_final: 0.8590 (p0) REVERT: A 1333 ASP cc_start: 0.9086 (OUTLIER) cc_final: 0.8668 (m-30) REVERT: A 1338 GLU cc_start: 0.8601 (mp0) cc_final: 0.7925 (mt-10) REVERT: A 1498 GLU cc_start: 0.8900 (tt0) cc_final: 0.8405 (pt0) REVERT: A 1511 ASP cc_start: 0.9085 (m-30) cc_final: 0.8604 (p0) REVERT: A 1649 LYS cc_start: 0.3928 (mmtt) cc_final: 0.3497 (mmtt) REVERT: A 1748 ASN cc_start: 0.7403 (t0) cc_final: 0.7066 (t0) REVERT: B 185 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8447 (mt-10) REVERT: B 207 GLU cc_start: 0.8891 (pp20) cc_final: 0.8513 (tp30) REVERT: B 301 ASP cc_start: 0.8506 (t0) cc_final: 0.8217 (t0) REVERT: G 119 THR cc_start: 0.8051 (m) cc_final: 0.7758 (p) REVERT: G 167 ASP cc_start: 0.8435 (p0) cc_final: 0.8156 (p0) REVERT: G 245 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8609 (mt0) REVERT: G 447 ASN cc_start: 0.9036 (m-40) cc_final: 0.8521 (p0) REVERT: G 794 MET cc_start: 0.9100 (tpp) cc_final: 0.8586 (mmt) REVERT: G 870 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8933 (pt0) REVERT: G 956 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8827 (tt0) REVERT: G 1164 MET cc_start: 0.8327 (mmm) cc_final: 0.8054 (tpp) REVERT: G 1221 MET cc_start: 0.8736 (tmm) cc_final: 0.8484 (tmm) REVERT: G 1359 MET cc_start: 0.5816 (tpp) cc_final: 0.5169 (tpt) REVERT: G 1631 MET cc_start: 0.8127 (mmm) cc_final: 0.7113 (mmm) REVERT: G 1680 LEU cc_start: 0.9346 (mp) cc_final: 0.9075 (mt) REVERT: G 1784 MET cc_start: 0.8494 (tmm) cc_final: 0.7895 (tmm) REVERT: G 1822 MET cc_start: 0.8420 (ptp) cc_final: 0.8016 (ptp) REVERT: G 1829 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8892 (mm-30) REVERT: G 1838 MET cc_start: 0.9074 (tmm) cc_final: 0.8803 (tmm) REVERT: G 1876 GLU cc_start: 0.7509 (tp30) cc_final: 0.7197 (tp30) REVERT: G 2005 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7956 (tpp-160) outliers start: 34 outliers final: 16 residues processed: 269 average time/residue: 0.4151 time to fit residues: 183.2299 Evaluate side-chains 236 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 217 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 292 GLN Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 10.0000 chunk 206 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 chunk 310 optimal weight: 5.9990 chunk 251 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 185 optimal weight: 10.0000 chunk 326 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1549 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1161 GLN G1226 ASN G1619 ASN G2027 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30228 Z= 0.204 Angle : 0.515 9.787 40944 Z= 0.261 Chirality : 0.041 0.157 4603 Planarity : 0.003 0.042 5285 Dihedral : 4.373 61.255 4028 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.32 % Favored : 96.65 % Rotamer: Outliers : 1.36 % Allowed : 11.46 % Favored : 87.18 % 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: 0.30 (0.14), residues: 3761 helix: 1.18 (0.13), residues: 1657 sheet: -1.14 (0.22), residues: 519 loop : -0.25 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 865 HIS 0.014 0.001 HIS A1703 PHE 0.025 0.001 PHE A 35 TYR 0.018 0.001 TYR G2048 ARG 0.004 0.000 ARG G1413 *********************** 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 268 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 224 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ILE cc_start: 0.8573 (mm) cc_final: 0.8044 (tp) REVERT: A 352 MET cc_start: 0.8856 (ttm) cc_final: 0.8117 (tmm) REVERT: A 384 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8849 (pt0) REVERT: A 826 MET cc_start: 0.9032 (mmm) cc_final: 0.8691 (mtp) REVERT: A 847 GLU cc_start: 0.9215 (mp0) cc_final: 0.8960 (mp0) REVERT: A 946 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8843 (pp20) REVERT: A 1124 GLU cc_start: 0.9271 (tt0) cc_final: 0.8972 (tt0) REVERT: A 1128 GLU cc_start: 0.8611 (mt-10) cc_final: 0.7855 (mp0) REVERT: A 1273 ASP cc_start: 0.8973 (p0) cc_final: 0.8564 (p0) REVERT: A 1333 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8662 (m-30) REVERT: A 1335 PHE cc_start: 0.9216 (t80) cc_final: 0.8773 (t80) REVERT: A 1338 GLU cc_start: 0.8624 (mp0) cc_final: 0.7954 (mt-10) REVERT: A 1498 GLU cc_start: 0.8899 (tt0) cc_final: 0.8410 (pt0) REVERT: A 1511 ASP cc_start: 0.9149 (m-30) cc_final: 0.8593 (p0) REVERT: A 1649 LYS cc_start: 0.3891 (mmtt) cc_final: 0.3461 (mmtt) REVERT: A 1748 ASN cc_start: 0.7479 (t0) cc_final: 0.7141 (t0) REVERT: A 1759 MET cc_start: 0.7639 (tmm) cc_final: 0.7193 (tmm) REVERT: B 185 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8479 (mt-10) REVERT: B 207 GLU cc_start: 0.8874 (pp20) cc_final: 0.8469 (tp30) REVERT: B 301 ASP cc_start: 0.8499 (t0) cc_final: 0.8231 (t0) REVERT: G 119 THR cc_start: 0.8071 (m) cc_final: 0.7786 (p) REVERT: G 245 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8529 (mm-40) REVERT: G 447 ASN cc_start: 0.9046 (m-40) cc_final: 0.8667 (p0) REVERT: G 794 MET cc_start: 0.9106 (tpp) cc_final: 0.8560 (mmt) REVERT: G 930 MET cc_start: 0.9427 (mtt) cc_final: 0.9207 (mtt) REVERT: G 956 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8836 (tt0) REVERT: G 1164 MET cc_start: 0.8316 (mmm) cc_final: 0.7945 (mmm) REVERT: G 1221 MET cc_start: 0.8678 (tmm) cc_final: 0.8344 (tmm) REVERT: G 1359 MET cc_start: 0.5805 (tpp) cc_final: 0.5161 (tpt) REVERT: G 1631 MET cc_start: 0.8132 (mmm) cc_final: 0.7373 (mmt) REVERT: G 1680 LEU cc_start: 0.9327 (mp) cc_final: 0.9038 (mt) REVERT: G 1784 MET cc_start: 0.8522 (tmm) cc_final: 0.7934 (tmm) REVERT: G 1822 MET cc_start: 0.8442 (ptp) cc_final: 0.7993 (ptp) REVERT: G 1829 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8935 (mm-30) REVERT: G 1838 MET cc_start: 0.9097 (tmm) cc_final: 0.8813 (tmm) REVERT: G 1876 GLU cc_start: 0.7432 (tp30) cc_final: 0.7128 (tp30) REVERT: G 2005 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7934 (tpp-160) outliers start: 44 outliers final: 25 residues processed: 256 average time/residue: 0.3954 time to fit residues: 168.0306 Evaluate side-chains 239 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 3.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 0.0470 chunk 327 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 213 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 chunk 363 optimal weight: 30.0000 chunk 301 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 chunk 120 optimal weight: 8.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN ** A1385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN G 275 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30228 Z= 0.138 Angle : 0.485 9.349 40944 Z= 0.245 Chirality : 0.040 0.143 4603 Planarity : 0.003 0.042 5285 Dihedral : 4.188 58.766 4028 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.63 % Favored : 97.34 % Rotamer: Outliers : 0.99 % Allowed : 12.45 % Favored : 86.56 % 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: 0.53 (0.14), residues: 3761 helix: 1.33 (0.13), residues: 1664 sheet: -0.93 (0.23), residues: 516 loop : -0.13 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 661 HIS 0.006 0.001 HIS A1703 PHE 0.012 0.001 PHE G1450 TYR 0.018 0.001 TYR G 67 ARG 0.003 0.000 ARG A 709 *********************** 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 267 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 235 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8862 (ttm) cc_final: 0.8102 (tmm) REVERT: A 384 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8817 (pt0) REVERT: A 826 MET cc_start: 0.8950 (mmm) cc_final: 0.8611 (mtp) REVERT: A 847 GLU cc_start: 0.9262 (mp0) cc_final: 0.9003 (mp0) REVERT: A 946 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8894 (pp20) REVERT: A 1124 GLU cc_start: 0.9222 (tt0) cc_final: 0.8969 (tt0) REVERT: A 1128 GLU cc_start: 0.8587 (mt-10) cc_final: 0.7829 (mp0) REVERT: A 1273 ASP cc_start: 0.8884 (p0) cc_final: 0.8469 (p0) REVERT: A 1333 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8625 (m-30) REVERT: A 1335 PHE cc_start: 0.9181 (t80) cc_final: 0.8756 (t80) REVERT: A 1338 GLU cc_start: 0.8508 (mp0) cc_final: 0.7993 (mt-10) REVERT: A 1498 GLU cc_start: 0.8881 (tt0) cc_final: 0.8362 (pt0) REVERT: A 1507 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8867 (tp40) REVERT: A 1511 ASP cc_start: 0.9056 (m-30) cc_final: 0.8636 (p0) REVERT: A 1649 LYS cc_start: 0.3964 (mmtt) cc_final: 0.3448 (mmtt) REVERT: A 1748 ASN cc_start: 0.7254 (t0) cc_final: 0.6907 (t0) REVERT: B 185 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8456 (mt-10) REVERT: B 301 ASP cc_start: 0.8404 (t0) cc_final: 0.8097 (t0) REVERT: G 119 THR cc_start: 0.8191 (m) cc_final: 0.7907 (p) REVERT: G 245 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8558 (mm-40) REVERT: G 447 ASN cc_start: 0.9029 (m-40) cc_final: 0.8689 (p0) REVERT: G 794 MET cc_start: 0.9043 (tpp) cc_final: 0.8567 (mmt) REVERT: G 930 MET cc_start: 0.9373 (mtt) cc_final: 0.9137 (mtt) REVERT: G 992 GLU cc_start: 0.8966 (pm20) cc_final: 0.8743 (pm20) REVERT: G 1221 MET cc_start: 0.8695 (tmm) cc_final: 0.8385 (tmm) REVERT: G 1359 MET cc_start: 0.5825 (tpp) cc_final: 0.5170 (tpt) REVERT: G 1631 MET cc_start: 0.8097 (mmm) cc_final: 0.7363 (mmt) REVERT: G 1784 MET cc_start: 0.8561 (tmm) cc_final: 0.7962 (tmm) REVERT: G 1822 MET cc_start: 0.8408 (ptp) cc_final: 0.8053 (ptp) REVERT: G 1829 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8898 (mm-30) REVERT: G 1838 MET cc_start: 0.9090 (tmm) cc_final: 0.8817 (tmm) REVERT: G 1876 GLU cc_start: 0.7421 (tp30) cc_final: 0.7192 (tp30) REVERT: G 2005 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7888 (tpp-160) outliers start: 32 outliers final: 22 residues processed: 258 average time/residue: 0.3844 time to fit residues: 164.2246 Evaluate side-chains 234 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1873 HIS Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 391 LEU Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 207 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 205 optimal weight: 9.9990 chunk 306 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 362 optimal weight: 40.0000 chunk 226 optimal weight: 10.0000 chunk 220 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 30228 Z= 0.246 Angle : 0.538 12.074 40944 Z= 0.271 Chirality : 0.041 0.322 4603 Planarity : 0.003 0.043 5285 Dihedral : 4.291 58.735 4028 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 1.54 % Allowed : 12.88 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3761 helix: 1.30 (0.13), residues: 1657 sheet: -0.95 (0.23), residues: 513 loop : -0.12 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1030 HIS 0.008 0.001 HIS A1703 PHE 0.020 0.001 PHE G 64 TYR 0.019 0.001 TYR G1553 ARG 0.005 0.000 ARG G1728 *********************** 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 272 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 222 time to evaluate : 4.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8879 (ttm) cc_final: 0.8108 (tmm) REVERT: A 384 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8844 (pt0) REVERT: A 826 MET cc_start: 0.9024 (mmm) cc_final: 0.8722 (mtp) REVERT: A 847 GLU cc_start: 0.9286 (mp0) cc_final: 0.9013 (mp0) REVERT: A 946 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8834 (pp20) REVERT: A 1128 GLU cc_start: 0.8604 (mt-10) cc_final: 0.7866 (mp0) REVERT: A 1273 ASP cc_start: 0.8924 (p0) cc_final: 0.8541 (p0) REVERT: A 1333 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8677 (m-30) REVERT: A 1335 PHE cc_start: 0.9272 (t80) cc_final: 0.8776 (t80) REVERT: A 1338 GLU cc_start: 0.8628 (mp0) cc_final: 0.7950 (mt-10) REVERT: A 1498 GLU cc_start: 0.8893 (tt0) cc_final: 0.8367 (pt0) REVERT: A 1507 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8823 (tp40) REVERT: A 1511 ASP cc_start: 0.9185 (m-30) cc_final: 0.8610 (p0) REVERT: A 1649 LYS cc_start: 0.3930 (mmtt) cc_final: 0.3475 (mmtt) REVERT: A 1748 ASN cc_start: 0.7460 (t0) cc_final: 0.7105 (t0) REVERT: A 1759 MET cc_start: 0.7551 (tmm) cc_final: 0.7316 (tmm) REVERT: B 290 MET cc_start: 0.9348 (mmt) cc_final: 0.9076 (mmt) REVERT: B 301 ASP cc_start: 0.8455 (t0) cc_final: 0.8179 (t0) REVERT: G 119 THR cc_start: 0.8169 (m) cc_final: 0.7900 (p) REVERT: G 245 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8393 (mm-40) REVERT: G 447 ASN cc_start: 0.9051 (m-40) cc_final: 0.8706 (p0) REVERT: G 794 MET cc_start: 0.9102 (tpp) cc_final: 0.8553 (mmt) REVERT: G 930 MET cc_start: 0.9411 (mtt) cc_final: 0.9200 (mtt) REVERT: G 956 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8864 (tt0) REVERT: G 1164 MET cc_start: 0.7950 (mmm) cc_final: 0.7568 (tpp) REVERT: G 1221 MET cc_start: 0.8652 (tmm) cc_final: 0.8337 (tmm) REVERT: G 1323 MET cc_start: 0.7402 (ptp) cc_final: 0.6987 (ptp) REVERT: G 1359 MET cc_start: 0.5820 (tpp) cc_final: 0.5118 (tpt) REVERT: G 1631 MET cc_start: 0.8081 (mmm) cc_final: 0.7380 (mmt) REVERT: G 1784 MET cc_start: 0.8553 (tmm) cc_final: 0.7947 (tmm) REVERT: G 1829 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8925 (mm-30) REVERT: G 1838 MET cc_start: 0.9122 (tmm) cc_final: 0.8836 (tmm) REVERT: G 1876 GLU cc_start: 0.7354 (tp30) cc_final: 0.7026 (tp30) REVERT: G 1880 LYS cc_start: 0.8678 (tttt) cc_final: 0.8326 (ttmt) REVERT: G 2005 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7970 (tpp-160) outliers start: 50 outliers final: 35 residues processed: 261 average time/residue: 0.4201 time to fit residues: 179.8123 Evaluate side-chains 249 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 210 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1254 VAL Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Chi-restraints excluded: chain G residue 2003 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 216 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 70 optimal weight: 0.0370 chunk 230 optimal weight: 6.9990 chunk 246 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 33 optimal weight: 20.0000 chunk 284 optimal weight: 7.9990 overall best weight: 4.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1245 ASN A1483 ASN A1854 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 30228 Z= 0.276 Angle : 0.561 11.183 40944 Z= 0.283 Chirality : 0.042 0.316 4603 Planarity : 0.004 0.042 5285 Dihedral : 4.401 59.036 4028 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 1.54 % Allowed : 13.28 % Favored : 85.18 % 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: 0.46 (0.14), residues: 3761 helix: 1.23 (0.13), residues: 1657 sheet: -0.92 (0.23), residues: 512 loop : -0.12 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 28 HIS 0.008 0.001 HIS G 102 PHE 0.018 0.001 PHE A 35 TYR 0.020 0.001 TYR G 67 ARG 0.008 0.000 ARG A 709 *********************** 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 265 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 215 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.9241 (mt0) cc_final: 0.8913 (mt0) REVERT: A 352 MET cc_start: 0.8884 (ttm) cc_final: 0.8118 (tmm) REVERT: A 384 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8840 (pt0) REVERT: A 826 MET cc_start: 0.9053 (mmm) cc_final: 0.8762 (mtp) REVERT: A 847 GLU cc_start: 0.9301 (OUTLIER) cc_final: 0.9044 (mp0) REVERT: A 946 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8846 (pp20) REVERT: A 1128 GLU cc_start: 0.8602 (mt-10) cc_final: 0.7864 (mp0) REVERT: A 1273 ASP cc_start: 0.8976 (p0) cc_final: 0.8607 (p0) REVERT: A 1333 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8693 (m-30) REVERT: A 1335 PHE cc_start: 0.9302 (t80) cc_final: 0.8863 (t80) REVERT: A 1338 GLU cc_start: 0.8659 (mp0) cc_final: 0.7888 (mt-10) REVERT: A 1498 GLU cc_start: 0.8936 (tt0) cc_final: 0.8474 (pt0) REVERT: A 1507 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.9051 (tp40) REVERT: A 1540 SER cc_start: 0.9344 (t) cc_final: 0.8838 (p) REVERT: A 1649 LYS cc_start: 0.3955 (mmtt) cc_final: 0.3511 (mmtt) REVERT: A 1759 MET cc_start: 0.7573 (tmm) cc_final: 0.7299 (tmm) REVERT: B 290 MET cc_start: 0.9342 (mmt) cc_final: 0.9007 (mmt) REVERT: B 301 ASP cc_start: 0.8556 (t0) cc_final: 0.8313 (t0) REVERT: G 119 THR cc_start: 0.8221 (m) cc_final: 0.7963 (p) REVERT: G 245 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8561 (mm-40) REVERT: G 794 MET cc_start: 0.9109 (tpp) cc_final: 0.8559 (mmt) REVERT: G 930 MET cc_start: 0.9412 (mtt) cc_final: 0.9204 (mtt) REVERT: G 1164 MET cc_start: 0.7991 (mmm) cc_final: 0.7666 (tpp) REVERT: G 1221 MET cc_start: 0.8722 (tmm) cc_final: 0.8416 (tmm) REVERT: G 1359 MET cc_start: 0.5824 (tpp) cc_final: 0.4986 (tpt) REVERT: G 1631 MET cc_start: 0.8092 (mmm) cc_final: 0.7355 (mmt) REVERT: G 1784 MET cc_start: 0.8564 (tmm) cc_final: 0.7958 (tmm) REVERT: G 1829 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8941 (mm-30) REVERT: G 1838 MET cc_start: 0.9142 (tmm) cc_final: 0.8869 (tmm) REVERT: G 1876 GLU cc_start: 0.7379 (tp30) cc_final: 0.7053 (tp30) REVERT: G 1880 LYS cc_start: 0.8661 (tttt) cc_final: 0.8305 (ttmt) REVERT: G 2005 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7862 (tpp-160) outliers start: 50 outliers final: 37 residues processed: 253 average time/residue: 0.4205 time to fit residues: 174.6679 Evaluate side-chains 250 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 208 time to evaluate : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 946 GLU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1374 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Chi-restraints excluded: chain G residue 2003 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: 20.0000 chunk 316 optimal weight: 0.3980 chunk 337 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 147 optimal weight: 7.9990 chunk 265 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 chunk 319 optimal weight: 30.0000 chunk 336 optimal weight: 5.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1854 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30228 Z= 0.283 Angle : 0.567 11.788 40944 Z= 0.287 Chirality : 0.042 0.270 4603 Planarity : 0.004 0.042 5285 Dihedral : 4.418 57.481 4028 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 1.76 % Allowed : 13.31 % Favored : 84.93 % 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: 0.44 (0.14), residues: 3761 helix: 1.20 (0.13), residues: 1662 sheet: -0.95 (0.23), residues: 500 loop : -0.13 (0.16), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1030 HIS 0.008 0.001 HIS A1703 PHE 0.014 0.001 PHE A1376 TYR 0.019 0.002 TYR G 67 ARG 0.008 0.000 ARG A 709 *********************** 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 272 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 215 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.9228 (mt0) cc_final: 0.8898 (mt0) REVERT: A 352 MET cc_start: 0.8890 (ttm) cc_final: 0.8120 (tmm) REVERT: A 384 GLU cc_start: 0.9096 (mt-10) cc_final: 0.8835 (pt0) REVERT: A 826 MET cc_start: 0.9075 (mmm) cc_final: 0.8784 (mtp) REVERT: A 847 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.9057 (mp0) REVERT: A 1124 GLU cc_start: 0.9221 (tt0) cc_final: 0.9017 (tt0) REVERT: A 1128 GLU cc_start: 0.8601 (mt-10) cc_final: 0.7855 (mp0) REVERT: A 1273 ASP cc_start: 0.8965 (p0) cc_final: 0.8560 (p0) REVERT: A 1333 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8693 (m-30) REVERT: A 1335 PHE cc_start: 0.9285 (t80) cc_final: 0.8873 (t80) REVERT: A 1338 GLU cc_start: 0.8663 (mp0) cc_final: 0.7898 (mt-10) REVERT: A 1498 GLU cc_start: 0.8931 (tt0) cc_final: 0.8474 (pt0) REVERT: A 1507 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.9072 (tp40) REVERT: A 1540 SER cc_start: 0.9314 (t) cc_final: 0.8841 (p) REVERT: A 1649 LYS cc_start: 0.3807 (mmtt) cc_final: 0.3359 (mmtt) REVERT: A 1759 MET cc_start: 0.7539 (tmm) cc_final: 0.7253 (tmm) REVERT: B 290 MET cc_start: 0.9311 (mmt) cc_final: 0.8993 (mmt) REVERT: B 301 ASP cc_start: 0.8568 (t0) cc_final: 0.8338 (t0) REVERT: G 119 THR cc_start: 0.8225 (m) cc_final: 0.8007 (p) REVERT: G 245 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8560 (mm-40) REVERT: G 794 MET cc_start: 0.9110 (tpp) cc_final: 0.8555 (mmt) REVERT: G 1164 MET cc_start: 0.8059 (mmm) cc_final: 0.7718 (tpp) REVERT: G 1221 MET cc_start: 0.8754 (tmm) cc_final: 0.8443 (tmm) REVERT: G 1359 MET cc_start: 0.5823 (tpp) cc_final: 0.5152 (tpt) REVERT: G 1631 MET cc_start: 0.8076 (mmm) cc_final: 0.7288 (mmt) REVERT: G 1784 MET cc_start: 0.8537 (tmm) cc_final: 0.7894 (tmm) REVERT: G 1829 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8961 (mm-30) REVERT: G 1838 MET cc_start: 0.9151 (tmm) cc_final: 0.8884 (tmm) REVERT: G 1876 GLU cc_start: 0.7377 (tp30) cc_final: 0.7063 (tp30) REVERT: G 1880 LYS cc_start: 0.8647 (tttt) cc_final: 0.8284 (ttmt) REVERT: G 2005 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7856 (tpp-160) outliers start: 57 outliers final: 46 residues processed: 258 average time/residue: 0.4030 time to fit residues: 171.2408 Evaluate side-chains 257 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 207 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1374 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1690 VAL Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Chi-restraints excluded: chain G residue 2003 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 10.0000 chunk 357 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 374 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 230 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN A1854 ASN A1877 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 500 HIS ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30228 Z= 0.344 Angle : 0.609 12.675 40944 Z= 0.308 Chirality : 0.043 0.248 4603 Planarity : 0.004 0.042 5285 Dihedral : 4.575 55.386 4028 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.17 % Favored : 95.80 % Rotamer: Outliers : 1.66 % Allowed : 13.65 % Favored : 84.68 % 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: 1.09 (0.13), residues: 1671 sheet: -0.93 (0.23), residues: 505 loop : -0.20 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 28 HIS 0.009 0.001 HIS A1703 PHE 0.021 0.002 PHE A 35 TYR 0.021 0.002 TYR G 180 ARG 0.009 0.000 ARG A 709 ********************** 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 263 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 209 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.9215 (mt0) cc_final: 0.8902 (mt0) REVERT: A 384 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8841 (pt0) REVERT: A 826 MET cc_start: 0.9097 (mmm) cc_final: 0.8824 (mtp) REVERT: A 847 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.9041 (mp0) REVERT: A 1128 GLU cc_start: 0.8616 (mt-10) cc_final: 0.7870 (mp0) REVERT: A 1273 ASP cc_start: 0.8997 (p0) cc_final: 0.8589 (p0) REVERT: A 1333 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8655 (m-30) REVERT: A 1338 GLU cc_start: 0.8698 (mp0) cc_final: 0.7927 (mt-10) REVERT: A 1498 GLU cc_start: 0.8938 (tt0) cc_final: 0.8479 (pt0) REVERT: A 1507 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.9029 (tp40) REVERT: A 1540 SER cc_start: 0.9333 (t) cc_final: 0.8858 (p) REVERT: A 1649 LYS cc_start: 0.3699 (mmtt) cc_final: 0.3231 (mmtt) REVERT: A 1759 MET cc_start: 0.7562 (tmm) cc_final: 0.7277 (tmm) REVERT: B 290 MET cc_start: 0.9293 (mmt) cc_final: 0.8958 (mmt) REVERT: G 119 THR cc_start: 0.8239 (m) cc_final: 0.8028 (p) REVERT: G 245 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8432 (mm-40) REVERT: G 630 MET cc_start: 0.9082 (tpp) cc_final: 0.8835 (mpp) REVERT: G 794 MET cc_start: 0.9154 (tpp) cc_final: 0.8589 (mmt) REVERT: G 1164 MET cc_start: 0.8072 (mmm) cc_final: 0.7489 (tpp) REVERT: G 1221 MET cc_start: 0.8725 (tmm) cc_final: 0.8409 (tmm) REVERT: G 1359 MET cc_start: 0.5796 (tpp) cc_final: 0.5121 (tpt) REVERT: G 1631 MET cc_start: 0.8104 (mmm) cc_final: 0.7310 (mmt) REVERT: G 1784 MET cc_start: 0.8401 (tmm) cc_final: 0.7822 (tmm) REVERT: G 1829 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8961 (mm-30) REVERT: G 1838 MET cc_start: 0.9167 (tmm) cc_final: 0.8859 (tmm) REVERT: G 1876 GLU cc_start: 0.7339 (tp30) cc_final: 0.6981 (tp30) REVERT: G 1880 LYS cc_start: 0.8621 (tttt) cc_final: 0.8260 (ttmt) REVERT: G 2005 ARG cc_start: 0.8323 (mtp85) cc_final: 0.7936 (tpp-160) outliers start: 54 outliers final: 46 residues processed: 251 average time/residue: 0.4234 time to fit residues: 176.7571 Evaluate side-chains 249 residues out of total 3246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 199 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 1112 ASN Chi-restraints excluded: chain A residue 1130 ASP Chi-restraints excluded: chain A residue 1168 LEU Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1507 GLN Chi-restraints excluded: chain A residue 1730 SER Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1746 ASN Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 220 GLU Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 351 ASP Chi-restraints excluded: chain G residue 379 VAL Chi-restraints excluded: chain G residue 389 LEU Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 1223 MET Chi-restraints excluded: chain G residue 1245 ASP Chi-restraints excluded: chain G residue 1374 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1417 THR Chi-restraints excluded: chain G residue 1427 VAL Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1486 PHE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1646 ASP Chi-restraints excluded: chain G residue 1690 VAL Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1774 THR Chi-restraints excluded: chain G residue 1939 HIS Chi-restraints excluded: chain G residue 1983 ASN Chi-restraints excluded: chain G residue 2003 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 0.9980 chunk 317 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 275 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 298 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 306 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 GLN A1549 ASN A1854 ASN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.077106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060041 restraints weight = 125452.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060768 restraints weight = 60561.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.061283 restraints weight = 35169.131| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30228 Z= 0.159 Angle : 0.537 12.318 40944 Z= 0.269 Chirality : 0.041 0.231 4603 Planarity : 0.003 0.041 5285 Dihedral : 4.264 55.579 4028 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.13 % Rotamer: Outliers : 1.33 % Allowed : 14.14 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3761 helix: 1.34 (0.13), residues: 1659 sheet: -0.83 (0.23), residues: 508 loop : -0.07 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1030 HIS 0.006 0.001 HIS G 102 PHE 0.015 0.001 PHE A1820 TYR 0.022 0.001 TYR G 180 ARG 0.009 0.000 ARG A 709 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4964.21 seconds wall clock time: 91 minutes 18.16 seconds (5478.16 seconds total)