Starting phenix.real_space_refine on Thu Mar 21 10:16:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps9_17847/03_2024/8ps9_17847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps9_17847/03_2024/8ps9_17847.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps9_17847/03_2024/8ps9_17847_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps9_17847/03_2024/8ps9_17847_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps9_17847/03_2024/8ps9_17847_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps9_17847/03_2024/8ps9_17847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps9_17847/03_2024/8ps9_17847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps9_17847/03_2024/8ps9_17847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ps9_17847/03_2024/8ps9_17847_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 4 5.49 5 S 108 5.16 5 C 18936 2.51 5 N 4974 2.21 5 O 5713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 384": "OE1" <-> "OE2" Residue "A ASP 487": "OD1" <-> "OD2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A TYR 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 912": "OE1" <-> "OE2" Residue "A GLU 981": "OE1" <-> "OE2" Residue "A PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1142": "OE1" <-> "OE2" Residue "A TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A PHE 1376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1378": "OE1" <-> "OE2" Residue "A ASP 1391": "OD1" <-> "OD2" Residue "A TYR 1438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1534": "OD1" <-> "OD2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A PHE 1646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1702": "OE1" <-> "OE2" Residue "A ASP 1708": "OD1" <-> "OD2" Residue "A ASP 1713": "OD1" <-> "OD2" Residue "A ASP 1784": "OD1" <-> "OD2" Residue "A PHE 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1850": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G ASP 186": "OD1" <-> "OD2" Residue "G GLU 290": "OE1" <-> "OE2" Residue "G GLU 312": "OE1" <-> "OE2" Residue "G ASP 539": "OD1" <-> "OD2" Residue "G PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "G PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 890": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 913": "OD1" <-> "OD2" Residue "G GLU 955": "OE1" <-> "OE2" Residue "G GLU 956": "OE1" <-> "OE2" Residue "G ASP 977": "OD1" <-> "OD2" Residue "G ASP 1110": "OD1" <-> "OD2" Residue "G GLU 1136": "OE1" <-> "OE2" Residue "G PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1162": "OD1" <-> "OD2" Residue "G TYR 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1289": "OD1" <-> "OD2" Residue "G ASP 1453": "OD1" <-> "OD2" Residue "G GLU 1497": "OE1" <-> "OE2" Residue "G GLU 1534": "OE1" <-> "OE2" Residue "G PHE 1584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1700": "OD1" <-> "OD2" Residue "G ASP 1708": "OD1" <-> "OD2" Residue "G TYR 1733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1846": "OE1" <-> "OE2" Residue "G TYR 1852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1894": "OE1" <-> "OE2" Residue "G ASP 1908": "OD1" <-> "OD2" Residue "G PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 2024": "OE1" <-> "OE2" Residue "G GLU 2036": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29735 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1589, 12409 Classifications: {'peptide': 1589} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1527} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1223 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain: "G" Number of atoms: 16018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2036, 16018 Classifications: {'peptide': 2036} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1926} Chain breaks: 1 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'FMN': 1, 'MLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.28, per 1000 atoms: 0.48 Number of scatterers: 29735 At special positions: 0 Unit cell: (184.625, 180.405, 176.185, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 4 15.00 O 5713 8.00 N 4974 7.00 C 18936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.93 Conformation dependent library (CDL) restraints added in 5.0 seconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 27 sheets defined 45.1% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.14 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 removed outlier: 4.756A pdb=" N ALA A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 66 through 72 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 330 through 349 Processing helix chain 'A' and resid 356 through 382 Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.045A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.745A pdb=" N SER A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU A 435 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 441 " --> pdb=" O ASN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 456 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 464 through 482 Processing helix chain 'A' and resid 522 through 531 Processing helix chain 'A' and resid 609 through 615 removed outlier: 3.595A pdb=" N SER A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 668 Processing helix chain 'A' and resid 688 through 698 Processing helix chain 'A' and resid 712 through 725 Processing helix chain 'A' and resid 742 through 753 Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 786 through 795 Processing helix chain 'A' and resid 797 through 812 Processing helix chain 'A' and resid 839 through 855 removed outlier: 4.096A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 891 removed outlier: 4.364A pdb=" N GLU A 886 " --> pdb=" O ASN A 882 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLY A 887 " --> pdb=" O ILE A 883 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.715A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 936 through 968 removed outlier: 3.547A pdb=" N LEU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.845A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1009 No H-bonds generated for 'chain 'A' and resid 1007 through 1009' Processing helix chain 'A' and resid 1033 through 1041 Processing helix chain 'A' and resid 1047 through 1057 Processing helix chain 'A' and resid 1086 through 1099 removed outlier: 4.276A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1110 No H-bonds generated for 'chain 'A' and resid 1108 through 1110' Processing helix chain 'A' and resid 1138 through 1151 removed outlier: 6.968A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LYS A1151 " --> pdb=" O GLN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1198 No H-bonds generated for 'chain 'A' and resid 1195 through 1198' Processing helix chain 'A' and resid 1202 through 1205 No H-bonds generated for 'chain 'A' and resid 1202 through 1205' Processing helix chain 'A' and resid 1210 through 1226 removed outlier: 3.538A pdb=" N PHE A1214 " --> pdb=" O PRO A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1236 Processing helix chain 'A' and resid 1254 through 1261 Processing helix chain 'A' and resid 1272 through 1278 removed outlier: 4.612A pdb=" N LEU A1275 " --> pdb=" O ASN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1290 Processing helix chain 'A' and resid 1304 through 1321 removed outlier: 4.751A pdb=" N SER A1308 " --> pdb=" O CYS A1305 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A1311 " --> pdb=" O SER A1308 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A1314 " --> pdb=" O SER A1311 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A1321 " --> pdb=" O THR A1318 " (cutoff:3.500A) Processing helix chain 'A' and resid 1337 through 1345 Processing helix chain 'A' and resid 1352 through 1357 Processing helix chain 'A' and resid 1362 through 1364 No H-bonds generated for 'chain 'A' and resid 1362 through 1364' Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1445 through 1475 Processing helix chain 'A' and resid 1482 through 1509 Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 3.659A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR A1529 " --> pdb=" O ALA A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1533 through 1535 No H-bonds generated for 'chain 'A' and resid 1533 through 1535' Processing helix chain 'A' and resid 1547 through 1563 removed outlier: 3.822A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 3.670A pdb=" N THR A1581 " --> pdb=" O LYS A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1585 through 1600 removed outlier: 4.541A pdb=" N GLY A1589 " --> pdb=" O GLY A1586 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 removed outlier: 3.529A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1664 removed outlier: 3.706A pdb=" N TYR A1662 " --> pdb=" O ASP A1659 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A1663 " --> pdb=" O TYR A1660 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1693 Processing helix chain 'A' and resid 1711 through 1716 Processing helix chain 'A' and resid 1741 through 1744 No H-bonds generated for 'chain 'A' and resid 1741 through 1744' Processing helix chain 'A' and resid 1747 through 1759 removed outlier: 3.700A pdb=" N MET A1759 " --> pdb=" O MET A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1778 No H-bonds generated for 'chain 'A' and resid 1776 through 1778' Processing helix chain 'A' and resid 1784 through 1790 Processing helix chain 'A' and resid 1793 through 1801 removed outlier: 3.639A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1823 Processing helix chain 'A' and resid 1834 through 1836 No H-bonds generated for 'chain 'A' and resid 1834 through 1836' Processing helix chain 'A' and resid 1854 through 1861 Processing helix chain 'B' and resid 147 through 158 removed outlier: 3.804A pdb=" N HIS B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 180 through 194 Processing helix chain 'B' and resid 206 through 214 removed outlier: 4.137A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 235 Processing helix chain 'B' and resid 243 through 253 Processing helix chain 'B' and resid 258 through 270 Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'G' and resid 24 through 40 removed outlier: 3.617A pdb=" N PHE G 27 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N PHE G 28 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE G 29 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER G 31 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 33 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN G 34 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU G 35 " --> pdb=" O GLN G 32 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS G 39 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 57 through 71 Processing helix chain 'G' and resid 80 through 95 Processing helix chain 'G' and resid 101 through 111 Processing helix chain 'G' and resid 116 through 132 Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 169 through 179 removed outlier: 3.564A pdb=" N LEU G 176 " --> pdb=" O LEU G 173 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN G 178 " --> pdb=" O ASP G 175 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR G 179 " --> pdb=" O LEU G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 201 removed outlier: 5.803A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 208 No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 228 through 231 No H-bonds generated for 'chain 'G' and resid 228 through 231' Processing helix chain 'G' and resid 234 through 255 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 260 through 266 removed outlier: 3.717A pdb=" N TYR G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 285 removed outlier: 3.600A pdb=" N ALA G 280 " --> pdb=" O LEU G 277 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 281 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE G 283 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU G 285 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 313 Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'G' and resid 346 through 359 removed outlier: 3.942A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 364 No H-bonds generated for 'chain 'G' and resid 362 through 364' Processing helix chain 'G' and resid 383 through 396 removed outlier: 3.569A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 411 No H-bonds generated for 'chain 'G' and resid 409 through 411' Processing helix chain 'G' and resid 430 through 445 removed outlier: 3.560A pdb=" N VAL G 433 " --> pdb=" O HIS G 430 " (cutoff:3.500A) Proline residue: G 434 - end of helix removed outlier: 3.960A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE G 439 " --> pdb=" O SER G 436 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN G 440 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL G 444 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 454 No H-bonds generated for 'chain 'G' and resid 452 through 454' Processing helix chain 'G' and resid 475 through 484 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 512 through 519 Processing helix chain 'G' and resid 544 through 548 removed outlier: 3.990A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 544 through 548' Processing helix chain 'G' and resid 552 through 554 No H-bonds generated for 'chain 'G' and resid 552 through 554' Processing helix chain 'G' and resid 561 through 564 No H-bonds generated for 'chain 'G' and resid 561 through 564' Processing helix chain 'G' and resid 582 through 587 removed outlier: 3.856A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 613 Processing helix chain 'G' and resid 621 through 623 No H-bonds generated for 'chain 'G' and resid 621 through 623' Processing helix chain 'G' and resid 627 through 640 Processing helix chain 'G' and resid 656 through 671 Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 688 through 697 Processing helix chain 'G' and resid 710 through 722 Processing helix chain 'G' and resid 748 through 758 removed outlier: 5.270A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 778 through 782 Processing helix chain 'G' and resid 784 through 789 removed outlier: 3.943A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 803 through 807 removed outlier: 4.364A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 823 Processing helix chain 'G' and resid 829 through 836 removed outlier: 4.939A pdb=" N GLU G 833 " --> pdb=" O ASP G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 877 through 898 removed outlier: 4.427A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 3.664A pdb=" N GLU G 885 " --> pdb=" O VAL G 881 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA G 886 " --> pdb=" O PRO G 882 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 914 through 916 No H-bonds generated for 'chain 'G' and resid 914 through 916' Processing helix chain 'G' and resid 919 through 930 Processing helix chain 'G' and resid 941 through 958 Processing helix chain 'G' and resid 970 through 974 Processing helix chain 'G' and resid 976 through 986 Processing helix chain 'G' and resid 988 through 991 Processing helix chain 'G' and resid 997 through 1006 Processing helix chain 'G' and resid 1023 through 1030 removed outlier: 4.500A pdb=" N GLU G1026 " --> pdb=" O ARG G1023 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE G1029 " --> pdb=" O GLU G1026 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS G1030 " --> pdb=" O ILE G1027 " (cutoff:3.500A) Processing helix chain 'G' and resid 1035 through 1038 Processing helix chain 'G' and resid 1040 through 1042 No H-bonds generated for 'chain 'G' and resid 1040 through 1042' Processing helix chain 'G' and resid 1048 through 1050 No H-bonds generated for 'chain 'G' and resid 1048 through 1050' Processing helix chain 'G' and resid 1059 through 1061 No H-bonds generated for 'chain 'G' and resid 1059 through 1061' Processing helix chain 'G' and resid 1070 through 1089 Processing helix chain 'G' and resid 1094 through 1096 No H-bonds generated for 'chain 'G' and resid 1094 through 1096' Processing helix chain 'G' and resid 1135 through 1143 Processing helix chain 'G' and resid 1149 through 1155 Processing helix chain 'G' and resid 1169 through 1174 Processing helix chain 'G' and resid 1190 through 1192 No H-bonds generated for 'chain 'G' and resid 1190 through 1192' Processing helix chain 'G' and resid 1258 through 1270 removed outlier: 3.535A pdb=" N LYS G1268 " --> pdb=" O GLU G1264 " (cutoff:3.500A) Processing helix chain 'G' and resid 1294 through 1304 Processing helix chain 'G' and resid 1309 through 1311 No H-bonds generated for 'chain 'G' and resid 1309 through 1311' Processing helix chain 'G' and resid 1323 through 1338 removed outlier: 3.905A pdb=" N GLY G1330 " --> pdb=" O ILE G1327 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TRP G1331 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1341 through 1343 No H-bonds generated for 'chain 'G' and resid 1341 through 1343' Processing helix chain 'G' and resid 1438 through 1446 Processing helix chain 'G' and resid 1515 through 1523 Processing helix chain 'G' and resid 1551 through 1557 removed outlier: 3.685A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) Processing helix chain 'G' and resid 1562 through 1564 No H-bonds generated for 'chain 'G' and resid 1562 through 1564' Processing helix chain 'G' and resid 1567 through 1572 Processing helix chain 'G' and resid 1582 through 1596 Processing helix chain 'G' and resid 1602 through 1604 No H-bonds generated for 'chain 'G' and resid 1602 through 1604' Processing helix chain 'G' and resid 1678 through 1683 removed outlier: 3.712A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1685 through 1702 Processing helix chain 'G' and resid 1706 through 1711 Processing helix chain 'G' and resid 1723 through 1734 Processing helix chain 'G' and resid 1770 through 1772 No H-bonds generated for 'chain 'G' and resid 1770 through 1772' Processing helix chain 'G' and resid 1774 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1810 through 1818 Processing helix chain 'G' and resid 1824 through 1839 Processing helix chain 'G' and resid 1859 through 1862 No H-bonds generated for 'chain 'G' and resid 1859 through 1862' Processing helix chain 'G' and resid 1868 through 1882 Processing helix chain 'G' and resid 1904 through 1920 Processing helix chain 'G' and resid 1924 through 1929 removed outlier: 3.601A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1935 through 1953 removed outlier: 3.765A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU G1946 " --> pdb=" O GLU G1942 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA G1947 " --> pdb=" O ILE G1943 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1979 through 1981 No H-bonds generated for 'chain 'G' and resid 1979 through 1981' Processing helix chain 'G' and resid 1984 through 1993 Processing helix chain 'G' and resid 1998 through 2000 No H-bonds generated for 'chain 'G' and resid 1998 through 2000' Processing helix chain 'G' and resid 2003 through 2006 No H-bonds generated for 'chain 'G' and resid 2003 through 2006' Processing helix chain 'G' and resid 2023 through 2032 Processing helix chain 'G' and resid 2036 through 2043 Processing helix chain 'G' and resid 2045 through 2049 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.483A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLU A 46 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU A 79 " --> pdb=" O GLU A 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.467A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE A 769 " --> pdb=" O THR A 681 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 497 through 503 Processing sheet with id= D, first strand: chain 'A' and resid 649 through 651 removed outlier: 4.336A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 820 through 822 Processing sheet with id= F, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.859A pdb=" N ILE A1326 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A1402 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A1654 " --> pdb=" O ALA A1405 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A1407 " --> pdb=" O GLN A1652 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN A1652 " --> pdb=" O ALA A1407 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR A1409 " --> pdb=" O GLY A1650 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLY A1650 " --> pdb=" O THR A1409 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N SER A1640 " --> pdb=" O GLY A1537 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A1539 " --> pdb=" O SER A1640 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR A1642 " --> pdb=" O ALA A1539 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE A1541 " --> pdb=" O THR A1642 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N PHE A1644 " --> pdb=" O PHE A1541 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE A1573 " --> pdb=" O ALA A1539 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE A1541 " --> pdb=" O ILE A1573 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL A1575 " --> pdb=" O PHE A1541 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1060 through 1067 removed outlier: 3.688A pdb=" N ARG A1070 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id= I, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id= J, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= K, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id= L, first strand: chain 'A' and resid 1838 through 1840 Processing sheet with id= M, first strand: chain 'G' and resid 7 through 13 removed outlier: 3.631A pdb=" N VAL G 22 " --> pdb=" O ARG G 7 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 526 through 529 removed outlier: 7.913A pdb=" N ALA G 158 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ALA G 270 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N PHE G 160 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY G 272 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N GLY G 272 " --> pdb=" O PRO G 458 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR G 460 " --> pdb=" O GLY G 272 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 417 through 420 removed outlier: 6.043A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 568 through 571 Processing sheet with id= Q, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.822A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE G 649 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU G 679 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE G 681 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY G 798 " --> pdb=" O PHE G 767 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= S, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 6.290A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE G1218 " --> pdb=" O LEU G1214 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= U, first strand: chain 'G' and resid 1289 through 1291 removed outlier: 6.868A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASN G1383 " --> pdb=" O GLY G1387 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY G1387 " --> pdb=" O ASN G1383 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ARG G1606 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N PHE G1612 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL G1650 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU G1641 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE G1626 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ARG G1643 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR G1624 " --> pdb=" O ARG G1643 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N HIS G1628 " --> pdb=" O PRO G1538 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 1423 through 1427 removed outlier: 3.834A pdb=" N SER G1482 " --> pdb=" O THR G1473 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY G1487 " --> pdb=" O VAL G1504 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 1431 through 1435 removed outlier: 3.679A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 6.834A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ALA G1805 " --> pdb=" O PHE G1666 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 1717 through 1720 Processing sheet with id= Z, first strand: chain 'G' and resid 1737 through 1741 removed outlier: 3.829A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 1966 through 1968 removed outlier: 6.406A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) 1214 hydrogen bonds defined for protein. 3315 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: 15.68 Time building geometry restraints manager: 10.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5095 1.31 - 1.44: 7659 1.44 - 1.57: 17404 1.57 - 1.70: 8 1.70 - 1.84: 190 Bond restraints: 30356 Sorted by residual: bond pdb=" C1' MLC G2102 " pdb=" C2' MLC G2102 " ideal model delta sigma weight residual 1.323 1.517 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C3' MLC G2102 " pdb=" C4' MLC G2102 " ideal model delta sigma weight residual 1.365 1.537 -0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" C1' MLC G2102 " pdb=" O4' MLC G2102 " ideal model delta sigma weight residual 1.603 1.433 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" C4 MLC G2102 " pdb=" C5 MLC G2102 " ideal model delta sigma weight residual 1.335 1.470 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" CP6 MLC G2102 " pdb=" NP2 MLC G2102 " ideal model delta sigma weight residual 1.472 1.345 0.127 2.00e-02 2.50e+03 4.05e+01 ... (remaining 30351 not shown) Histogram of bond angle deviations from ideal: 94.79 - 103.19: 282 103.19 - 111.60: 11731 111.60 - 120.01: 17683 120.01 - 128.41: 11262 128.41 - 136.82: 166 Bond angle restraints: 41124 Sorted by residual: angle pdb=" CA ASP A1612 " pdb=" CB ASP A1612 " pdb=" CG ASP A1612 " ideal model delta sigma weight residual 112.60 120.09 -7.49 1.00e+00 1.00e+00 5.60e+01 angle pdb=" C LYS B 179 " pdb=" N SER B 180 " pdb=" CA SER B 180 " ideal model delta sigma weight residual 120.38 129.18 -8.80 1.37e+00 5.33e-01 4.13e+01 angle pdb=" CA ASP G 540 " pdb=" CB ASP G 540 " pdb=" CG ASP G 540 " ideal model delta sigma weight residual 112.60 118.25 -5.65 1.00e+00 1.00e+00 3.19e+01 angle pdb=" C ASN A 388 " pdb=" N GLY A 389 " pdb=" CA GLY A 389 " ideal model delta sigma weight residual 120.22 127.22 -7.00 1.27e+00 6.20e-01 3.04e+01 angle pdb=" C THR G1160 " pdb=" CA THR G1160 " pdb=" CB THR G1160 " ideal model delta sigma weight residual 109.53 118.40 -8.87 1.65e+00 3.67e-01 2.89e+01 ... (remaining 41119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 17105 21.54 - 43.08: 993 43.08 - 64.63: 150 64.63 - 86.17: 58 86.17 - 107.71: 5 Dihedral angle restraints: 18311 sinusoidal: 7371 harmonic: 10940 Sorted by residual: dihedral pdb=" CA LEU B 277 " pdb=" C LEU B 277 " pdb=" N GLY B 278 " pdb=" CA GLY B 278 " ideal model delta harmonic sigma weight residual -180.00 -149.44 -30.56 0 5.00e+00 4.00e-02 3.74e+01 dihedral pdb=" C5' FMN G2101 " pdb=" O5' FMN G2101 " pdb=" P FMN G2101 " pdb=" O1P FMN G2101 " ideal model delta sinusoidal sigma weight residual 75.26 -177.03 -107.71 1 2.00e+01 2.50e-03 3.13e+01 dihedral pdb=" CA GLY B 178 " pdb=" C GLY B 178 " pdb=" N LYS B 179 " pdb=" CA LYS B 179 " ideal model delta harmonic sigma weight residual -180.00 -152.56 -27.44 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 18308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2244 0.064 - 0.129: 1718 0.129 - 0.193: 562 0.193 - 0.258: 88 0.258 - 0.322: 6 Chirality restraints: 4618 Sorted by residual: chirality pdb=" CA ILE G1751 " pdb=" N ILE G1751 " pdb=" C ILE G1751 " pdb=" CB ILE G1751 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA VAL A1027 " pdb=" N VAL A1027 " pdb=" C VAL A1027 " pdb=" CB VAL A1027 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA VAL A 893 " pdb=" N VAL A 893 " pdb=" C VAL A 893 " pdb=" CB VAL A 893 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 4615 not shown) Planarity restraints: 5304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " -0.011 2.00e-02 2.50e+03 2.79e-02 3.71e+01 pdb=" C10 FMN G2101 " 0.027 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.034 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.004 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.040 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.053 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.014 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.016 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.051 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.009 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.020 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " -0.000 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.026 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.013 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.021 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.030 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.044 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.010 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CP5 MLC G2102 " -0.065 2.00e-02 2.50e+03 5.40e-02 3.65e+01 pdb=" CP6 MLC G2102 " 0.030 2.00e-02 2.50e+03 pdb=" CP7 MLC G2102 " -0.052 2.00e-02 2.50e+03 pdb=" NP2 MLC G2102 " 0.082 2.00e-02 2.50e+03 pdb=" OP2 MLC G2102 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 722 " 0.050 2.00e-02 2.50e+03 2.72e-02 1.48e+01 pdb=" CG TYR A 722 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 722 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 722 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 722 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 722 " -0.017 2.00e-02 2.50e+03 pdb=" CZ TYR A 722 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 722 " 0.035 2.00e-02 2.50e+03 ... (remaining 5301 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 614 2.69 - 3.24: 29061 3.24 - 3.79: 46666 3.79 - 4.35: 66904 4.35 - 4.90: 106724 Nonbonded interactions: 249969 Sorted by model distance: nonbonded pdb=" O GLU G 693 " pdb=" OG1 THR G 697 " model vdw 2.131 2.440 nonbonded pdb=" OG SER A1201 " pdb=" OD1 ASP A1203 " model vdw 2.164 2.440 nonbonded pdb=" OG1 THR G1473 " pdb=" OG SER G1481 " model vdw 2.267 2.440 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.304 2.440 nonbonded pdb=" O LEU G1771 " pdb=" OG1 THR G1777 " model vdw 2.304 2.440 ... (remaining 249964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.920 Check model and map are aligned: 0.450 Set scattering table: 0.290 Process input model: 77.400 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.194 30356 Z= 0.874 Angle : 1.857 11.699 41124 Z= 1.359 Chirality : 0.089 0.322 4618 Planarity : 0.006 0.054 5304 Dihedral : 14.571 107.709 11267 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.93 % Favored : 94.83 % Rotamer: Outliers : 0.37 % Allowed : 4.40 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.12), residues: 3774 helix: -2.43 (0.09), residues: 1662 sheet: -1.58 (0.21), residues: 511 loop : -1.15 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.008 TRP G1449 HIS 0.022 0.004 HIS A1689 PHE 0.047 0.006 PHE G 796 TYR 0.050 0.007 TYR A 722 ARG 0.017 0.001 ARG A1609 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 391 time to evaluate : 3.462 Fit side-chains revert: symmetry clash REVERT: A 333 LYS cc_start: 0.8266 (mttt) cc_final: 0.8045 (mttm) REVERT: A 403 ASP cc_start: 0.8720 (p0) cc_final: 0.8518 (p0) REVERT: A 632 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7693 (ttp80) REVERT: A 675 ASP cc_start: 0.8515 (m-30) cc_final: 0.8196 (m-30) REVERT: A 901 MET cc_start: 0.9160 (tpt) cc_final: 0.8722 (tpt) REVERT: A 1129 GLU cc_start: 0.7969 (tp30) cc_final: 0.7727 (tp30) REVERT: A 1180 ARG cc_start: 0.7069 (mpt90) cc_final: 0.6754 (mmt-90) REVERT: A 1374 ASN cc_start: 0.8516 (t0) cc_final: 0.8295 (t0) REVERT: A 1377 MET cc_start: 0.9227 (tpp) cc_final: 0.8873 (tpp) REVERT: A 1472 LEU cc_start: 0.8747 (mm) cc_final: 0.8371 (mm) REVERT: A 1476 GLU cc_start: 0.7517 (mp0) cc_final: 0.7311 (mp0) REVERT: A 1794 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7591 (tm-30) REVERT: A 1857 LYS cc_start: 0.8538 (mttp) cc_final: 0.8290 (mptt) REVERT: B 143 GLU cc_start: 0.7379 (pt0) cc_final: 0.6718 (pm20) REVERT: B 179 LYS cc_start: 0.3323 (mmpt) cc_final: 0.2671 (mmmt) REVERT: B 193 GLU cc_start: 0.7401 (tp30) cc_final: 0.7198 (tp30) REVERT: B 242 THR cc_start: 0.8953 (p) cc_final: 0.8698 (p) REVERT: G 97 GLU cc_start: 0.7329 (mm-30) cc_final: 0.7101 (tp30) REVERT: G 120 LYS cc_start: 0.8780 (mmtm) cc_final: 0.8513 (mttp) REVERT: G 132 MET cc_start: 0.8531 (mmp) cc_final: 0.8287 (mpm) REVERT: G 171 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8022 (mm-30) REVERT: G 175 ASP cc_start: 0.8815 (m-30) cc_final: 0.8494 (m-30) REVERT: G 229 ASP cc_start: 0.8726 (t0) cc_final: 0.8474 (t0) REVERT: G 329 GLU cc_start: 0.8177 (pp20) cc_final: 0.7883 (pp20) REVERT: G 442 ASP cc_start: 0.8779 (m-30) cc_final: 0.8529 (m-30) REVERT: G 863 MET cc_start: 0.9074 (mmm) cc_final: 0.8744 (mmm) REVERT: G 877 LYS cc_start: 0.8132 (mmpt) cc_final: 0.7662 (mttt) REVERT: G 1001 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: G 1106 GLU cc_start: 0.8601 (tp30) cc_final: 0.8137 (tm-30) REVERT: G 1272 ASP cc_start: 0.8368 (t0) cc_final: 0.7897 (p0) REVERT: G 1417 THR cc_start: 0.8902 (m) cc_final: 0.8648 (p) REVERT: G 1455 GLU cc_start: 0.7999 (mp0) cc_final: 0.7704 (pm20) REVERT: G 1615 MET cc_start: 0.8834 (mtm) cc_final: 0.8629 (mtp) REVERT: G 1678 MET cc_start: 0.8981 (mmp) cc_final: 0.8572 (mmp) REVERT: G 1689 ASP cc_start: 0.8980 (t70) cc_final: 0.8706 (t0) REVERT: G 1836 MET cc_start: 0.9285 (mmt) cc_final: 0.9020 (mmm) REVERT: G 1872 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7804 (tp-100) REVERT: G 1908 ASP cc_start: 0.8337 (t0) cc_final: 0.8083 (t0) REVERT: G 1916 PHE cc_start: 0.7910 (t80) cc_final: 0.7674 (t80) REVERT: G 1959 LYS cc_start: 0.8607 (tptm) cc_final: 0.8265 (mmtt) outliers start: 12 outliers final: 4 residues processed: 398 average time/residue: 1.7170 time to fit residues: 781.9114 Evaluate side-chains 282 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 277 time to evaluate : 3.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain G residue 1001 ASP Chi-restraints excluded: chain G residue 1544 SER Chi-restraints excluded: chain G residue 1650 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 6.9990 chunk 285 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 295 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 342 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN A 475 GLN A 618 ASN A 882 ASN A 898 GLN A 989 GLN A1239 HIS A1276 GLN A1432 HIS A1465 ASN A1549 ASN A1610 ASN A1690 ASN A1790 ASN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN G 79 GLN G 102 HIS G 153 ASN G 163 GLN G 224 ASN G 245 GLN G 330 ASN G 440 ASN G 640 GLN G 715 GLN G 718 ASN G 747 HIS G 993 GLN G1046 GLN G1088 GLN G1241 ASN G1384 GLN G1523 ASN G1669 GLN G1674 GLN G1839 GLN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN G1928 GLN G2044 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30356 Z= 0.208 Angle : 0.551 7.704 41124 Z= 0.291 Chirality : 0.042 0.155 4618 Planarity : 0.004 0.036 5304 Dihedral : 6.044 100.350 4068 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.07 % Rotamer: Outliers : 1.60 % Allowed : 8.73 % Favored : 89.67 % 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: -0.09 (0.13), residues: 3774 helix: 0.47 (0.12), residues: 1674 sheet: -0.96 (0.21), residues: 524 loop : -0.11 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 PHE 0.020 0.002 PHE A 35 TYR 0.015 0.001 TYR A 417 ARG 0.006 0.001 ARG G1023 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 302 time to evaluate : 3.248 Fit side-chains REVERT: A 333 LYS cc_start: 0.8351 (mttt) cc_final: 0.8108 (mttp) REVERT: A 403 ASP cc_start: 0.8644 (p0) cc_final: 0.8428 (p0) REVERT: A 675 ASP cc_start: 0.8489 (m-30) cc_final: 0.8201 (m-30) REVERT: A 1374 ASN cc_start: 0.8599 (t0) cc_final: 0.8370 (t0) REVERT: A 1377 MET cc_start: 0.8965 (tpp) cc_final: 0.8726 (tpp) REVERT: A 1476 GLU cc_start: 0.7453 (mp0) cc_final: 0.7183 (mp0) REVERT: A 1498 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8634 (tp30) REVERT: B 143 GLU cc_start: 0.7337 (pt0) cc_final: 0.6632 (pm20) REVERT: B 179 LYS cc_start: 0.3109 (mmpt) cc_final: 0.2008 (mmmt) REVERT: B 202 GLU cc_start: 0.7613 (pm20) cc_final: 0.6875 (pm20) REVERT: B 207 GLU cc_start: 0.7140 (pp20) cc_final: 0.6866 (pm20) REVERT: B 280 GLU cc_start: 0.7010 (tp30) cc_final: 0.6794 (tp30) REVERT: B 297 ILE cc_start: 0.8397 (tp) cc_final: 0.8126 (mp) REVERT: G 7 ARG cc_start: 0.4837 (tpt170) cc_final: 0.4364 (ttt90) REVERT: G 21 LEU cc_start: 0.8467 (mm) cc_final: 0.7972 (mm) REVERT: G 120 LYS cc_start: 0.8794 (mmtm) cc_final: 0.8575 (mttp) REVERT: G 132 MET cc_start: 0.8512 (mmp) cc_final: 0.8180 (mpm) REVERT: G 171 GLU cc_start: 0.8236 (mm-30) cc_final: 0.8029 (mm-30) REVERT: G 175 ASP cc_start: 0.8902 (m-30) cc_final: 0.8506 (m-30) REVERT: G 445 LYS cc_start: 0.9123 (tptp) cc_final: 0.8769 (tmmt) REVERT: G 863 MET cc_start: 0.9112 (mmm) cc_final: 0.8778 (mmm) REVERT: G 1064 LYS cc_start: 0.8319 (mmpt) cc_final: 0.8081 (mmmt) REVERT: G 1106 GLU cc_start: 0.8608 (tp30) cc_final: 0.8055 (tm-30) REVERT: G 1180 MET cc_start: 0.8863 (mtp) cc_final: 0.8617 (mtm) REVERT: G 1286 LYS cc_start: 0.8970 (ttmm) cc_final: 0.8752 (mtpp) REVERT: G 1367 GLN cc_start: 0.8384 (mt0) cc_final: 0.8150 (mt0) REVERT: G 1455 GLU cc_start: 0.7844 (mp0) cc_final: 0.7538 (pm20) REVERT: G 1615 MET cc_start: 0.8831 (mtm) cc_final: 0.8610 (mtp) REVERT: G 1678 MET cc_start: 0.8927 (mmp) cc_final: 0.8618 (mmp) REVERT: G 1689 ASP cc_start: 0.8941 (t70) cc_final: 0.8735 (t0) REVERT: G 1836 MET cc_start: 0.9182 (mmt) cc_final: 0.8958 (mmm) REVERT: G 1872 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7745 (tp-100) REVERT: G 1916 PHE cc_start: 0.7911 (t80) cc_final: 0.7628 (t80) outliers start: 52 outliers final: 17 residues processed: 336 average time/residue: 1.7234 time to fit residues: 667.0967 Evaluate side-chains 279 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 261 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 334 ASP Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1265 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1654 GLU Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 9.9990 chunk 106 optimal weight: 0.3980 chunk 284 optimal weight: 20.0000 chunk 233 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 342 optimal weight: 2.9990 chunk 370 optimal weight: 0.8980 chunk 305 optimal weight: 8.9990 chunk 340 optimal weight: 9.9990 chunk 116 optimal weight: 10.0000 chunk 275 optimal weight: 2.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN G 38 ASN G 82 GLN G 142 ASN G 153 ASN G 517 HIS G 640 GLN G 723 HIS G1178 GLN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30356 Z= 0.213 Angle : 0.518 8.644 41124 Z= 0.269 Chirality : 0.042 0.147 4618 Planarity : 0.004 0.041 5304 Dihedral : 5.875 93.891 4064 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.23 % Favored : 97.75 % Rotamer: Outliers : 1.81 % Allowed : 10.06 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3774 helix: 1.17 (0.13), residues: 1670 sheet: -0.66 (0.21), residues: 535 loop : 0.22 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.014 0.001 TYR G 266 ARG 0.008 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 293 time to evaluate : 3.735 Fit side-chains REVERT: A 333 LYS cc_start: 0.8333 (mttt) cc_final: 0.8074 (mttp) REVERT: A 675 ASP cc_start: 0.8466 (m-30) cc_final: 0.8184 (m-30) REVERT: A 1123 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8776 (tt0) REVERT: A 1251 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8611 (mtm) REVERT: A 1374 ASN cc_start: 0.8555 (t0) cc_final: 0.8262 (t0) REVERT: A 1476 GLU cc_start: 0.7393 (mp0) cc_final: 0.7087 (mp0) REVERT: A 1498 GLU cc_start: 0.9022 (OUTLIER) cc_final: 0.8602 (tp30) REVERT: B 143 GLU cc_start: 0.7370 (pt0) cc_final: 0.6652 (pm20) REVERT: B 179 LYS cc_start: 0.3257 (mmpt) cc_final: 0.2480 (mmmt) REVERT: B 200 LYS cc_start: 0.7097 (tptm) cc_final: 0.6723 (ptpt) REVERT: B 208 GLU cc_start: 0.6929 (pm20) cc_final: 0.6474 (pm20) REVERT: B 280 GLU cc_start: 0.6974 (tp30) cc_final: 0.6768 (tp30) REVERT: B 297 ILE cc_start: 0.8356 (tp) cc_final: 0.8084 (mp) REVERT: G 7 ARG cc_start: 0.4745 (tpt170) cc_final: 0.4295 (ttt90) REVERT: G 21 LEU cc_start: 0.8457 (mm) cc_final: 0.7962 (mm) REVERT: G 94 CYS cc_start: 0.8318 (m) cc_final: 0.8016 (t) REVERT: G 132 MET cc_start: 0.8494 (mmp) cc_final: 0.8233 (mpm) REVERT: G 171 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7979 (mm-30) REVERT: G 175 ASP cc_start: 0.8946 (m-30) cc_final: 0.8576 (m-30) REVERT: G 445 LYS cc_start: 0.9144 (tptp) cc_final: 0.8882 (tmmt) REVERT: G 553 ASN cc_start: 0.8218 (m-40) cc_final: 0.7666 (t0) REVERT: G 863 MET cc_start: 0.9081 (mmm) cc_final: 0.8780 (mmm) REVERT: G 1064 LYS cc_start: 0.8323 (mmpt) cc_final: 0.8061 (mmmt) REVERT: G 1106 GLU cc_start: 0.8604 (tp30) cc_final: 0.8053 (tm-30) REVERT: G 1286 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8763 (mtpp) REVERT: G 1455 GLU cc_start: 0.7781 (mp0) cc_final: 0.7530 (pm20) REVERT: G 1678 MET cc_start: 0.8935 (mmp) cc_final: 0.8610 (mmp) REVERT: G 1872 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7700 (tp-100) REVERT: G 1939 HIS cc_start: 0.8319 (t-170) cc_final: 0.8112 (t-90) REVERT: G 1981 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8487 (pp) outliers start: 59 outliers final: 19 residues processed: 329 average time/residue: 1.7048 time to fit residues: 650.8205 Evaluate side-chains 284 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1034 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1555 ARG Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1654 GLU Chi-restraints excluded: chain G residue 1981 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 9.9990 chunk 257 optimal weight: 0.0270 chunk 177 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 163 optimal weight: 0.0670 chunk 230 optimal weight: 6.9990 chunk 344 optimal weight: 5.9990 chunk 364 optimal weight: 8.9990 chunk 179 optimal weight: 6.9990 chunk 326 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 overall best weight: 3.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 36 GLN G 38 ASN G 153 ASN G1367 GLN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30356 Z= 0.231 Angle : 0.514 9.083 41124 Z= 0.266 Chirality : 0.042 0.189 4618 Planarity : 0.004 0.043 5304 Dihedral : 5.639 92.655 4062 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.20 % Favored : 97.77 % Rotamer: Outliers : 1.78 % Allowed : 11.22 % Favored : 86.99 % 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: 0.83 (0.14), residues: 3774 helix: 1.29 (0.13), residues: 1668 sheet: -0.54 (0.21), residues: 539 loop : 0.33 (0.16), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.019 0.001 TYR G 67 ARG 0.009 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 285 time to evaluate : 3.371 Fit side-chains REVERT: A 59 ARG cc_start: 0.8210 (mtt-85) cc_final: 0.7867 (ttm-80) REVERT: A 333 LYS cc_start: 0.8288 (mttt) cc_final: 0.8038 (mttm) REVERT: A 632 ARG cc_start: 0.7830 (ttp80) cc_final: 0.7490 (ttp80) REVERT: A 1123 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8765 (tt0) REVERT: A 1162 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 1251 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8586 (mtm) REVERT: A 1327 CYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8722 (t) REVERT: A 1374 ASN cc_start: 0.8539 (t0) cc_final: 0.8231 (t0) REVERT: A 1476 GLU cc_start: 0.7323 (mp0) cc_final: 0.6970 (mp0) REVERT: A 1498 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8571 (tp30) REVERT: B 143 GLU cc_start: 0.7463 (pt0) cc_final: 0.6718 (pm20) REVERT: B 179 LYS cc_start: 0.3181 (mmpt) cc_final: 0.2303 (mmmt) REVERT: B 200 LYS cc_start: 0.6937 (tptm) cc_final: 0.6592 (ptpt) REVERT: B 208 GLU cc_start: 0.6943 (pm20) cc_final: 0.6434 (pm20) REVERT: B 297 ILE cc_start: 0.8347 (tp) cc_final: 0.8075 (mp) REVERT: G 7 ARG cc_start: 0.4767 (tpt170) cc_final: 0.4304 (ttt90) REVERT: G 9 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.6125 (tp) REVERT: G 21 LEU cc_start: 0.8458 (mm) cc_final: 0.7972 (mm) REVERT: G 71 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8899 (tm) REVERT: G 94 CYS cc_start: 0.8295 (m) cc_final: 0.8029 (t) REVERT: G 132 MET cc_start: 0.8454 (mmp) cc_final: 0.8206 (mpm) REVERT: G 171 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8016 (mm-30) REVERT: G 175 ASP cc_start: 0.8948 (m-30) cc_final: 0.8610 (m-30) REVERT: G 329 GLU cc_start: 0.8176 (pt0) cc_final: 0.7779 (pm20) REVERT: G 445 LYS cc_start: 0.9163 (tptp) cc_final: 0.8914 (tmmt) REVERT: G 1064 LYS cc_start: 0.8315 (mmpt) cc_final: 0.8037 (mmmt) REVERT: G 1106 GLU cc_start: 0.8627 (tp30) cc_final: 0.8082 (tm-30) REVERT: G 1272 ASP cc_start: 0.8576 (t0) cc_final: 0.8185 (p0) REVERT: G 1286 LYS cc_start: 0.9016 (ttmm) cc_final: 0.8772 (mtpp) REVERT: G 1455 GLU cc_start: 0.7792 (mp0) cc_final: 0.7523 (pm20) REVERT: G 1678 MET cc_start: 0.8947 (mmp) cc_final: 0.8531 (mmp) REVERT: G 1872 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7737 (tp-100) REVERT: G 1981 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8520 (pp) outliers start: 58 outliers final: 24 residues processed: 326 average time/residue: 1.6482 time to fit residues: 621.7295 Evaluate side-chains 294 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 263 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 843 ILE Chi-restraints excluded: chain G residue 1034 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1392 VAL Chi-restraints excluded: chain G residue 1555 ARG Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1654 GLU Chi-restraints excluded: chain G residue 1847 LEU Chi-restraints excluded: chain G residue 1981 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 310 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 GLN A1063 HIS A1482 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 153 ASN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30356 Z= 0.263 Angle : 0.527 10.608 41124 Z= 0.271 Chirality : 0.043 0.155 4618 Planarity : 0.004 0.044 5304 Dihedral : 5.668 93.868 4062 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.52 % Favored : 97.46 % Rotamer: Outliers : 1.94 % Allowed : 12.30 % Favored : 85.76 % 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: 0.85 (0.14), residues: 3774 helix: 1.27 (0.13), residues: 1672 sheet: -0.47 (0.21), residues: 539 loop : 0.36 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.017 0.001 TYR G 67 ARG 0.011 0.001 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 280 time to evaluate : 3.532 Fit side-chains REVERT: A 59 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7833 (ttm-80) REVERT: A 333 LYS cc_start: 0.8283 (mttt) cc_final: 0.8062 (mttm) REVERT: A 1123 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8770 (tt0) REVERT: A 1162 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 1251 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8577 (mtm) REVERT: A 1327 CYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8704 (t) REVERT: A 1374 ASN cc_start: 0.8549 (t0) cc_final: 0.8221 (t0) REVERT: A 1498 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8625 (tp30) REVERT: B 143 GLU cc_start: 0.7476 (pt0) cc_final: 0.6708 (pm20) REVERT: B 179 LYS cc_start: 0.3278 (mmpt) cc_final: 0.2077 (mmmt) REVERT: B 200 LYS cc_start: 0.6958 (tptm) cc_final: 0.6673 (ptpt) REVERT: B 208 GLU cc_start: 0.6837 (pm20) cc_final: 0.6219 (pm20) REVERT: B 297 ILE cc_start: 0.8329 (tp) cc_final: 0.8056 (mp) REVERT: G 7 ARG cc_start: 0.5059 (tpt170) cc_final: 0.4579 (tpt90) REVERT: G 9 LEU cc_start: 0.6333 (OUTLIER) cc_final: 0.6053 (tp) REVERT: G 21 LEU cc_start: 0.8446 (mm) cc_final: 0.7978 (mm) REVERT: G 94 CYS cc_start: 0.8290 (m) cc_final: 0.8040 (t) REVERT: G 132 MET cc_start: 0.8453 (mmp) cc_final: 0.8203 (mpm) REVERT: G 175 ASP cc_start: 0.8961 (m-30) cc_final: 0.8719 (m-30) REVERT: G 445 LYS cc_start: 0.9190 (tptp) cc_final: 0.8947 (tmmt) REVERT: G 1064 LYS cc_start: 0.8283 (mmpt) cc_final: 0.7995 (mmmt) REVERT: G 1106 GLU cc_start: 0.8630 (tp30) cc_final: 0.8102 (tm-30) REVERT: G 1272 ASP cc_start: 0.8583 (t0) cc_final: 0.8185 (p0) REVERT: G 1286 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8781 (mtpp) REVERT: G 1455 GLU cc_start: 0.7801 (mp0) cc_final: 0.7556 (pm20) REVERT: G 1678 MET cc_start: 0.8963 (mmp) cc_final: 0.8555 (mmp) REVERT: G 1872 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7745 (tp-100) REVERT: G 1981 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8514 (pp) outliers start: 63 outliers final: 32 residues processed: 321 average time/residue: 1.6701 time to fit residues: 621.2088 Evaluate side-chains 296 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 258 time to evaluate : 3.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1788 GLU Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 660 GLN Chi-restraints excluded: chain G residue 843 ILE Chi-restraints excluded: chain G residue 1034 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1392 VAL Chi-restraints excluded: chain G residue 1555 ARG Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1654 GLU Chi-restraints excluded: chain G residue 1842 VAL Chi-restraints excluded: chain G residue 1847 LEU Chi-restraints excluded: chain G residue 1981 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 4.9990 chunk 328 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 213 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 364 optimal weight: 9.9990 chunk 302 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 120 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN G 715 GLN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30356 Z= 0.173 Angle : 0.497 11.974 41124 Z= 0.255 Chirality : 0.041 0.173 4618 Planarity : 0.003 0.047 5304 Dihedral : 5.533 92.967 4062 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.69 % Allowed : 12.88 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.14), residues: 3774 helix: 1.38 (0.13), residues: 1672 sheet: -0.31 (0.21), residues: 532 loop : 0.40 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 661 HIS 0.005 0.001 HIS A1689 PHE 0.024 0.001 PHE A 35 TYR 0.014 0.001 TYR G 67 ARG 0.012 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 273 time to evaluate : 3.785 Fit side-chains REVERT: A 59 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7885 (ttm-80) REVERT: A 333 LYS cc_start: 0.8289 (mttt) cc_final: 0.8065 (mttm) REVERT: A 675 ASP cc_start: 0.8511 (m-30) cc_final: 0.8236 (m-30) REVERT: A 1123 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8778 (tt0) REVERT: A 1162 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 1251 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8560 (mtm) REVERT: A 1374 ASN cc_start: 0.8515 (t0) cc_final: 0.8190 (t0) REVERT: B 143 GLU cc_start: 0.7554 (pt0) cc_final: 0.6787 (pm20) REVERT: B 179 LYS cc_start: 0.3049 (mmpt) cc_final: 0.1908 (mmmt) REVERT: B 200 LYS cc_start: 0.6918 (tptm) cc_final: 0.6675 (ptpt) REVERT: B 208 GLU cc_start: 0.6796 (pm20) cc_final: 0.6347 (pm20) REVERT: B 297 ILE cc_start: 0.8294 (tp) cc_final: 0.8016 (mp) REVERT: G 7 ARG cc_start: 0.5001 (tpt170) cc_final: 0.4509 (tpt90) REVERT: G 21 LEU cc_start: 0.8452 (mm) cc_final: 0.7967 (mm) REVERT: G 94 CYS cc_start: 0.8280 (m) cc_final: 0.8074 (t) REVERT: G 132 MET cc_start: 0.8446 (mmp) cc_final: 0.8210 (mpm) REVERT: G 175 ASP cc_start: 0.8963 (m-30) cc_final: 0.8721 (m-30) REVERT: G 445 LYS cc_start: 0.9183 (tptp) cc_final: 0.8947 (tmmt) REVERT: G 1064 LYS cc_start: 0.8294 (mmpt) cc_final: 0.8001 (mmmt) REVERT: G 1106 GLU cc_start: 0.8599 (tp30) cc_final: 0.8060 (tm-30) REVERT: G 1272 ASP cc_start: 0.8571 (t0) cc_final: 0.8204 (p0) REVERT: G 1286 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8759 (mtpp) REVERT: G 1678 MET cc_start: 0.8964 (mmp) cc_final: 0.8524 (mmp) REVERT: G 1872 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7672 (tp-100) REVERT: G 1981 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8484 (pp) outliers start: 55 outliers final: 26 residues processed: 309 average time/residue: 1.7593 time to fit residues: 633.5674 Evaluate side-chains 291 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 261 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1347 LYS Chi-restraints excluded: chain A residue 1788 GLU Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 660 GLN Chi-restraints excluded: chain G residue 843 ILE Chi-restraints excluded: chain G residue 1034 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1555 ARG Chi-restraints excluded: chain G residue 1632 ILE Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1842 VAL Chi-restraints excluded: chain G residue 1847 LEU Chi-restraints excluded: chain G residue 1981 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 307 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 363 optimal weight: 8.9990 chunk 227 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 167 optimal weight: 0.0980 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN B 214 GLN B 224 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN ** G1890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30356 Z= 0.202 Angle : 0.506 11.509 41124 Z= 0.258 Chirality : 0.041 0.146 4618 Planarity : 0.004 0.052 5304 Dihedral : 5.519 92.154 4062 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.66 % Allowed : 13.41 % 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: 1.03 (0.14), residues: 3774 helix: 1.38 (0.13), residues: 1673 sheet: -0.23 (0.21), residues: 529 loop : 0.42 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.024 0.001 PHE A 35 TYR 0.013 0.001 TYR A 722 ARG 0.013 0.000 ARG G1413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 272 time to evaluate : 3.745 Fit side-chains REVERT: A 59 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7843 (ttm-80) REVERT: A 333 LYS cc_start: 0.8305 (mttt) cc_final: 0.8072 (mttp) REVERT: A 675 ASP cc_start: 0.8522 (m-30) cc_final: 0.8253 (m-30) REVERT: A 949 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8060 (pp20) REVERT: A 1123 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8787 (tt0) REVERT: A 1162 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 1251 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8560 (mtm) REVERT: A 1327 CYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8651 (t) REVERT: A 1374 ASN cc_start: 0.8533 (t0) cc_final: 0.8196 (t0) REVERT: B 143 GLU cc_start: 0.7561 (pt0) cc_final: 0.6823 (pm20) REVERT: B 179 LYS cc_start: 0.3585 (mmpt) cc_final: 0.2410 (mmmt) REVERT: B 200 LYS cc_start: 0.6926 (tptm) cc_final: 0.6660 (ptpt) REVERT: B 208 GLU cc_start: 0.6770 (pm20) cc_final: 0.6348 (pm20) REVERT: B 297 ILE cc_start: 0.8290 (tp) cc_final: 0.8010 (mp) REVERT: G 7 ARG cc_start: 0.4991 (tpt170) cc_final: 0.4506 (tpt90) REVERT: G 21 LEU cc_start: 0.8494 (mm) cc_final: 0.8010 (mm) REVERT: G 132 MET cc_start: 0.8427 (mmp) cc_final: 0.8203 (mpm) REVERT: G 175 ASP cc_start: 0.9011 (m-30) cc_final: 0.8658 (m-30) REVERT: G 445 LYS cc_start: 0.9191 (tptp) cc_final: 0.8964 (tmmt) REVERT: G 1064 LYS cc_start: 0.8259 (mmpt) cc_final: 0.7963 (mmmt) REVERT: G 1106 GLU cc_start: 0.8675 (tp30) cc_final: 0.8153 (tm-30) REVERT: G 1272 ASP cc_start: 0.8571 (t0) cc_final: 0.8193 (p0) REVERT: G 1286 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8517 (tmtt) REVERT: G 1678 MET cc_start: 0.8965 (mmp) cc_final: 0.8533 (mmp) REVERT: G 1872 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7679 (tp-100) REVERT: G 1981 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8462 (pp) outliers start: 54 outliers final: 29 residues processed: 308 average time/residue: 1.7354 time to fit residues: 625.1480 Evaluate side-chains 290 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 255 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1347 LYS Chi-restraints excluded: chain A residue 1788 GLU Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 660 GLN Chi-restraints excluded: chain G residue 843 ILE Chi-restraints excluded: chain G residue 1034 LEU Chi-restraints excluded: chain G residue 1323 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1555 ARG Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1842 VAL Chi-restraints excluded: chain G residue 1847 LEU Chi-restraints excluded: chain G residue 1953 VAL Chi-restraints excluded: chain G residue 1981 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 0.0870 chunk 231 optimal weight: 10.0000 chunk 247 optimal weight: 20.0000 chunk 179 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 285 optimal weight: 10.0000 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 153 ASN G1890 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 30356 Z= 0.314 Angle : 0.563 13.428 41124 Z= 0.288 Chirality : 0.043 0.169 4618 Planarity : 0.004 0.057 5304 Dihedral : 5.730 95.751 4062 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.09 % Allowed : 13.47 % Favored : 84.44 % 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: 0.89 (0.14), residues: 3774 helix: 1.22 (0.13), residues: 1673 sheet: -0.25 (0.21), residues: 531 loop : 0.38 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 661 HIS 0.007 0.001 HIS A1689 PHE 0.026 0.002 PHE A1376 TYR 0.015 0.002 TYR G 565 ARG 0.014 0.001 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 262 time to evaluate : 3.484 Fit side-chains REVERT: A 59 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7847 (ttm-80) REVERT: A 333 LYS cc_start: 0.8331 (mttt) cc_final: 0.8101 (mttp) REVERT: A 675 ASP cc_start: 0.8592 (m-30) cc_final: 0.8329 (m-30) REVERT: A 949 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8070 (pp20) REVERT: A 1251 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8571 (mtm) REVERT: A 1327 CYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8695 (t) REVERT: A 1374 ASN cc_start: 0.8549 (t0) cc_final: 0.8262 (t0) REVERT: A 1861 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7251 (pp20) REVERT: B 143 GLU cc_start: 0.7548 (pt0) cc_final: 0.6804 (pm20) REVERT: B 158 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8469 (tptm) REVERT: B 179 LYS cc_start: 0.2771 (mmpt) cc_final: 0.1353 (mmmt) REVERT: B 208 GLU cc_start: 0.6889 (pm20) cc_final: 0.6519 (pm20) REVERT: B 297 ILE cc_start: 0.8271 (tp) cc_final: 0.7995 (mp) REVERT: G 7 ARG cc_start: 0.5086 (tpt170) cc_final: 0.4599 (tpt90) REVERT: G 9 LEU cc_start: 0.6336 (OUTLIER) cc_final: 0.6088 (tp) REVERT: G 21 LEU cc_start: 0.8480 (mm) cc_final: 0.8046 (mm) REVERT: G 132 MET cc_start: 0.8395 (mmp) cc_final: 0.8165 (mpm) REVERT: G 175 ASP cc_start: 0.9025 (m-30) cc_final: 0.8783 (m-30) REVERT: G 445 LYS cc_start: 0.9205 (tptp) cc_final: 0.8981 (tmmt) REVERT: G 878 ASN cc_start: 0.7784 (p0) cc_final: 0.7510 (p0) REVERT: G 1064 LYS cc_start: 0.8282 (mmpt) cc_final: 0.7961 (mmmt) REVERT: G 1106 GLU cc_start: 0.8656 (tp30) cc_final: 0.8116 (tm-30) REVERT: G 1272 ASP cc_start: 0.8585 (t0) cc_final: 0.8182 (p0) REVERT: G 1286 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8802 (mtpp) REVERT: G 1678 MET cc_start: 0.8980 (mmp) cc_final: 0.8580 (mmp) REVERT: G 1872 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7731 (tp-100) outliers start: 68 outliers final: 38 residues processed: 307 average time/residue: 1.7112 time to fit residues: 607.2074 Evaluate side-chains 298 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 253 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 352 MET Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1202 ASP Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1347 LYS Chi-restraints excluded: chain A residue 1391 ASP Chi-restraints excluded: chain A residue 1788 GLU Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain G residue 9 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 660 GLN Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 843 ILE Chi-restraints excluded: chain G residue 1034 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1392 VAL Chi-restraints excluded: chain G residue 1555 ARG Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1842 VAL Chi-restraints excluded: chain G residue 1847 LEU Chi-restraints excluded: chain G residue 1940 LEU Chi-restraints excluded: chain G residue 1953 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 7.9990 chunk 348 optimal weight: 0.0570 chunk 317 optimal weight: 0.9990 chunk 338 optimal weight: 6.9990 chunk 203 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 265 optimal weight: 0.3980 chunk 103 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 337 optimal weight: 4.9990 overall best weight: 1.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN A1563 HIS B 184 ASN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G1088 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30356 Z= 0.159 Angle : 0.497 11.448 41124 Z= 0.253 Chirality : 0.041 0.144 4618 Planarity : 0.003 0.060 5304 Dihedral : 5.445 94.654 4062 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.23 % Allowed : 14.54 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3774 helix: 1.44 (0.13), residues: 1670 sheet: -0.16 (0.21), residues: 521 loop : 0.45 (0.16), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 661 HIS 0.004 0.001 HIS A1689 PHE 0.025 0.001 PHE A 35 TYR 0.026 0.001 TYR G1873 ARG 0.014 0.000 ARG A1789 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 3.349 Fit side-chains REVERT: A 59 ARG cc_start: 0.8274 (mtt-85) cc_final: 0.7865 (ttm-80) REVERT: A 333 LYS cc_start: 0.8284 (mttt) cc_final: 0.8059 (mttp) REVERT: A 344 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8297 (mm-40) REVERT: A 632 ARG cc_start: 0.7605 (ttp80) cc_final: 0.7374 (ttp80) REVERT: A 675 ASP cc_start: 0.8554 (m-30) cc_final: 0.8241 (m-30) REVERT: A 802 MET cc_start: 0.9162 (mtm) cc_final: 0.8903 (mtp) REVERT: A 949 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8078 (pp20) REVERT: A 1135 GLU cc_start: 0.8583 (tt0) cc_final: 0.7921 (tm-30) REVERT: A 1327 CYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8618 (t) REVERT: A 1374 ASN cc_start: 0.8478 (t0) cc_final: 0.8118 (t0) REVERT: A 1476 GLU cc_start: 0.7141 (mp0) cc_final: 0.6848 (mp0) REVERT: A 1861 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7279 (pp20) REVERT: B 143 GLU cc_start: 0.7587 (pt0) cc_final: 0.6841 (pm20) REVERT: B 179 LYS cc_start: 0.3489 (mmpt) cc_final: 0.2418 (mmmt) REVERT: B 202 GLU cc_start: 0.7553 (pm20) cc_final: 0.7238 (pm20) REVERT: B 297 ILE cc_start: 0.8249 (tp) cc_final: 0.8036 (mp) REVERT: G 7 ARG cc_start: 0.5244 (tpt170) cc_final: 0.4732 (tpt90) REVERT: G 21 LEU cc_start: 0.8490 (mm) cc_final: 0.8006 (mm) REVERT: G 132 MET cc_start: 0.8441 (mmp) cc_final: 0.8236 (mmt) REVERT: G 175 ASP cc_start: 0.9010 (m-30) cc_final: 0.8662 (m-30) REVERT: G 329 GLU cc_start: 0.8169 (pt0) cc_final: 0.7800 (pm20) REVERT: G 445 LYS cc_start: 0.9185 (tptp) cc_final: 0.8973 (tmmt) REVERT: G 461 ASP cc_start: 0.7771 (t70) cc_final: 0.7487 (t0) REVERT: G 1064 LYS cc_start: 0.8252 (mmpt) cc_final: 0.7944 (mmmt) REVERT: G 1106 GLU cc_start: 0.8586 (tp30) cc_final: 0.8057 (tm-30) REVERT: G 1272 ASP cc_start: 0.8580 (t0) cc_final: 0.8208 (p0) REVERT: G 1286 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8464 (tmtt) REVERT: G 1678 MET cc_start: 0.8966 (mmp) cc_final: 0.8489 (mmp) REVERT: G 1685 LYS cc_start: 0.8585 (tppt) cc_final: 0.8371 (ttpt) REVERT: G 1820 ASP cc_start: 0.8624 (m-30) cc_final: 0.8325 (t0) REVERT: G 1872 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7646 (tp-100) outliers start: 40 outliers final: 21 residues processed: 289 average time/residue: 1.6792 time to fit residues: 560.7954 Evaluate side-chains 275 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 251 time to evaluate : 3.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1788 GLU Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 843 ILE Chi-restraints excluded: chain G residue 1323 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1842 VAL Chi-restraints excluded: chain G residue 1847 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 0.8980 chunk 358 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 375 optimal weight: 5.9990 chunk 345 optimal weight: 1.9990 chunk 299 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 231 optimal weight: 9.9990 chunk 183 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 ASN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30356 Z= 0.183 Angle : 0.512 13.086 41124 Z= 0.260 Chirality : 0.041 0.144 4618 Planarity : 0.004 0.064 5304 Dihedral : 5.418 90.971 4062 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.95 % Allowed : 14.91 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3774 helix: 1.45 (0.13), residues: 1671 sheet: -0.13 (0.21), residues: 528 loop : 0.49 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 661 HIS 0.005 0.001 HIS A1689 PHE 0.024 0.001 PHE A 35 TYR 0.024 0.001 TYR G1873 ARG 0.015 0.000 ARG A1789 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 250 time to evaluate : 3.221 Fit side-chains REVERT: A 59 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.7845 (ttm-80) REVERT: A 333 LYS cc_start: 0.8288 (mttt) cc_final: 0.8064 (mttp) REVERT: A 344 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8299 (mm-40) REVERT: A 632 ARG cc_start: 0.7682 (ttp80) cc_final: 0.7419 (ttp80) REVERT: A 675 ASP cc_start: 0.8482 (m-30) cc_final: 0.8243 (m-30) REVERT: A 802 MET cc_start: 0.9157 (mtm) cc_final: 0.8891 (mtp) REVERT: A 949 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8075 (pp20) REVERT: A 1327 CYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8654 (t) REVERT: A 1374 ASN cc_start: 0.8496 (t0) cc_final: 0.8163 (t0) REVERT: A 1476 GLU cc_start: 0.7144 (mp0) cc_final: 0.6828 (mp0) REVERT: A 1861 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7280 (pp20) REVERT: B 143 GLU cc_start: 0.7603 (pt0) cc_final: 0.6856 (pm20) REVERT: B 179 LYS cc_start: 0.3377 (mmpt) cc_final: 0.2310 (mmmt) REVERT: B 200 LYS cc_start: 0.6805 (tptm) cc_final: 0.6558 (ptpt) REVERT: B 297 ILE cc_start: 0.8244 (tp) cc_final: 0.8032 (mp) REVERT: G 7 ARG cc_start: 0.5172 (tpt170) cc_final: 0.4680 (tpt90) REVERT: G 21 LEU cc_start: 0.8488 (mm) cc_final: 0.8006 (mm) REVERT: G 132 MET cc_start: 0.8438 (mmp) cc_final: 0.8237 (mmt) REVERT: G 175 ASP cc_start: 0.9003 (m-30) cc_final: 0.8682 (m-30) REVERT: G 329 GLU cc_start: 0.8186 (pt0) cc_final: 0.7807 (pm20) REVERT: G 445 LYS cc_start: 0.9178 (tptp) cc_final: 0.8971 (tmmt) REVERT: G 1064 LYS cc_start: 0.8308 (mmpt) cc_final: 0.7999 (mmmt) REVERT: G 1106 GLU cc_start: 0.8587 (tp30) cc_final: 0.8065 (tm-30) REVERT: G 1272 ASP cc_start: 0.8581 (t0) cc_final: 0.8225 (p0) REVERT: G 1286 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8487 (tmtt) REVERT: G 1678 MET cc_start: 0.8970 (mmp) cc_final: 0.8514 (mmp) REVERT: G 1685 LYS cc_start: 0.8598 (tppt) cc_final: 0.8352 (ttmm) REVERT: G 1820 ASP cc_start: 0.8647 (m-30) cc_final: 0.8336 (t0) REVERT: G 1872 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7657 (tp-100) outliers start: 31 outliers final: 23 residues processed: 275 average time/residue: 1.6538 time to fit residues: 527.3815 Evaluate side-chains 272 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 246 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1788 GLU Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 540 ASP Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 843 ILE Chi-restraints excluded: chain G residue 1323 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1751 ILE Chi-restraints excluded: chain G residue 1842 VAL Chi-restraints excluded: chain G residue 1847 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 275 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 299 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 307 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 ASN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.091887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.069914 restraints weight = 59061.981| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.76 r_work: 0.2759 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30356 Z= 0.234 Angle : 0.530 13.002 41124 Z= 0.269 Chirality : 0.042 0.153 4618 Planarity : 0.004 0.065 5304 Dihedral : 5.471 88.731 4062 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.14 % Allowed : 14.85 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.14), residues: 3774 helix: 1.41 (0.13), residues: 1670 sheet: -0.11 (0.21), residues: 531 loop : 0.47 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1813 HIS 0.006 0.001 HIS A1689 PHE 0.023 0.001 PHE A 35 TYR 0.023 0.001 TYR G1873 ARG 0.015 0.001 ARG G1023 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10624.13 seconds wall clock time: 189 minutes 30.99 seconds (11370.99 seconds total)