Starting phenix.real_space_refine on Sat Apr 13 22:27:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psp_17859/04_2024/8psp_17859_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psp_17859/04_2024/8psp_17859.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psp_17859/04_2024/8psp_17859_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/8psp_17859/04_2024/8psp_17859_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psp_17859/04_2024/8psp_17859_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psp_17859/04_2024/8psp_17859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psp_17859/04_2024/8psp_17859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psp_17859/04_2024/8psp_17859_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psp_17859/04_2024/8psp_17859_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= -0.002 sd= 0.013 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 2 5.49 5 S 108 5.16 5 C 18920 2.51 5 N 4969 2.21 5 O 5696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 33": "OD1" <-> "OD2" Residue "A ASP 38": "OD1" <-> "OD2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 487": "OD1" <-> "OD2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A TYR 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 939": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A ASP 1085": "OD1" <-> "OD2" Residue "A GLU 1124": "OE1" <-> "OE2" Residue "A GLU 1128": "OE1" <-> "OE2" Residue "A ASP 1203": "OD1" <-> "OD2" Residue "A GLU 1310": "OE1" <-> "OE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1619": "OE1" <-> "OE2" Residue "A TYR 1685": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1709": "OE1" <-> "OE2" Residue "A ASP 1742": "OD1" <-> "OD2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 203": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G ASP 227": "OD1" <-> "OD2" Residue "G ASP 229": "OD1" <-> "OD2" Residue "G ASP 287": "OD1" <-> "OD2" Residue "G PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 411": "OE1" <-> "OE2" Residue "G ASP 437": "OD1" <-> "OD2" Residue "G PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 454": "OD1" <-> "OD2" Residue "G GLU 491": "OE1" <-> "OE2" Residue "G PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 776": "OD1" <-> "OD2" Residue "G GLU 833": "OE1" <-> "OE2" Residue "G PHE 946": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1067": "OD1" <-> "OD2" Residue "G ASP 1092": "OD1" <-> "OD2" Residue "G GLU 1136": "OE1" <-> "OE2" Residue "G TYR 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1291": "OE1" <-> "OE2" Residue "G GLU 1309": "OE1" <-> "OE2" Residue "G GLU 1641": "OE1" <-> "OE2" Residue "G ASP 1689": "OD1" <-> "OD2" Residue "G GLU 1757": "OE1" <-> "OE2" Residue "G GLU 1767": "OE1" <-> "OE2" Residue "G TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1876": "OE1" <-> "OE2" Residue "G GLU 1887": "OE1" <-> "OE2" Residue "G ASP 1908": "OD1" <-> "OD2" Residue "G GLU 1926": "OE1" <-> "OE2" Residue "G PHE 1941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1946": "OE1" <-> "OE2" Residue "G GLU 1961": "OE1" <-> "OE2" Residue "G PHE 1976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 2019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 2046": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29695 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1589, 12402 Classifications: {'peptide': 1589} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1527} Chain breaks: 2 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: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.45, per 1000 atoms: 0.52 Number of scatterers: 29695 At special positions: 0 Unit cell: (180.405, 184.625, 174.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 2 15.00 O 5696 8.00 N 4969 7.00 C 18920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1246 " - pdb=" SG CYS A1327 " distance=2.19 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.31 Conformation dependent library (CDL) restraints added in 5.6 seconds 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 28 sheets defined 44.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.11 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 removed outlier: 4.353A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.573A pdb=" N ASN A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) 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 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.089A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 removed outlier: 3.582A pdb=" N SER A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 435 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN A 438 " --> pdb=" O GLU A 435 " (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 530 Processing helix chain 'A' and resid 609 through 614 Processing helix chain 'A' and resid 653 through 669 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: 3.615A pdb=" N LEU A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N THR A 848 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N PHE A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 885 through 891 removed outlier: 4.374A pdb=" N MET A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.757A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 909 " --> pdb=" O LEU A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 919 Processing helix chain 'A' and resid 930 through 932 No H-bonds generated for 'chain 'A' and resid 930 through 932' Processing helix chain 'A' and resid 936 through 969 removed outlier: 3.981A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 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: 4.347A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.528A 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: 7.137A pdb=" N ASP A1150 " --> pdb=" O HIS A1146 " (cutoff:3.500A) removed outlier: 7.404A 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 1225 removed outlier: 3.561A 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 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1254 through 1261 Processing helix chain 'A' and resid 1272 through 1278 removed outlier: 4.634A 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 1319 removed outlier: 5.389A pdb=" N SER A1308 " --> pdb=" O CYS A1305 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A1311 " --> pdb=" O SER A1308 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A1312 " --> pdb=" O VAL A1309 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A1316 " --> pdb=" O ASP A1313 " (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 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing helix chain 'A' and resid 1390 through 1396 Processing helix chain 'A' and resid 1425 through 1429 Processing helix chain 'A' and resid 1441 through 1443 No H-bonds generated for 'chain 'A' and resid 1441 through 1443' Processing helix chain 'A' and resid 1445 through 1475 removed outlier: 3.508A pdb=" N GLN A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A1469 " --> pdb=" O ASN A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1508 Processing helix chain 'A' and resid 1521 through 1529 removed outlier: 3.767A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.457A 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: 3.766A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1581 removed outlier: 3.736A 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) removed outlier: 3.570A pdb=" N MET A1593 " --> pdb=" O ALA A1590 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN A1598 " --> pdb=" O GLY A1595 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A1600 " --> pdb=" O LEU A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1620 removed outlier: 3.597A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1664 removed outlier: 4.544A 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 1708 through 1716 removed outlier: 4.763A pdb=" N GLU A1712 " --> pdb=" O ASP A1708 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A1713 " --> pdb=" O GLU A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1737 No H-bonds generated for 'chain 'A' and resid 1735 through 1737' Processing helix chain 'A' and resid 1741 through 1744 No H-bonds generated for 'chain 'A' and resid 1741 through 1744' Processing helix chain 'A' and resid 1747 through 1757 removed outlier: 3.600A pdb=" N ILE A1756 " --> pdb=" O THR A1752 " (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 1800 Processing helix chain 'A' and resid 1805 through 1822 Processing helix chain 'A' and resid 1854 through 1861 removed outlier: 3.551A pdb=" N GLU A1860 " --> pdb=" O LYS A1856 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 158 Processing helix chain 'B' and resid 172 through 176 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.519A pdb=" N GLU B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 206 through 213 removed outlier: 3.849A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 235 Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 258 through 270 removed outlier: 3.775A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 298 Processing helix chain 'G' and resid 24 through 26 No H-bonds generated for 'chain 'G' and resid 24 through 26' Processing helix chain 'G' and resid 28 through 40 removed outlier: 3.742A pdb=" N GLN G 32 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU G 35 " --> pdb=" O SER G 31 " (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 removed outlier: 3.546A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 95 removed outlier: 3.690A pdb=" N LEU G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 111 removed outlier: 3.553A pdb=" N GLU G 111 " --> pdb=" O LYS G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 132 Processing helix chain 'G' and resid 144 through 151 Processing helix chain 'G' and resid 170 through 179 Processing helix chain 'G' and resid 184 through 201 removed outlier: 3.904A pdb=" N ILE G 188 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS G 189 " --> pdb=" O ASP G 186 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA G 192 " --> pdb=" O LYS G 189 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER G 196 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE G 199 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR G 201 " --> pdb=" O LEU G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 220 Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 234 through 255 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 260 through 265 Processing helix chain 'G' and resid 274 through 283 removed outlier: 3.569A pdb=" N ALA G 280 " --> pdb=" O LEU G 277 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE G 283 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 313 removed outlier: 3.850A pdb=" N ARG G 297 " --> pdb=" O PHE G 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG G 309 " --> pdb=" O PHE G 305 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU G 312 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 329 Processing helix chain 'G' and resid 346 through 359 removed outlier: 4.053A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 396 removed outlier: 3.598A pdb=" N LYS G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.018A 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 443 removed outlier: 3.784A pdb=" N VAL G 433 " --> pdb=" O HIS G 430 " (cutoff:3.500A) Proline residue: G 434 - end of helix removed outlier: 3.997A pdb=" N ASP G 437 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN G 440 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU G 443 " --> pdb=" O ASN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 484 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 512 through 520 Processing helix chain 'G' and resid 544 through 548 Processing helix chain 'G' and resid 561 through 564 No H-bonds generated for 'chain 'G' and resid 561 through 564' Processing helix chain 'G' and resid 582 through 587 removed outlier: 3.734A 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 638 Processing helix chain 'G' and resid 656 through 671 Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 688 through 697 Processing helix chain 'G' and resid 710 through 722 Processing helix chain 'G' and resid 748 through 758 removed outlier: 5.199A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 774 through 782 Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 789 removed outlier: 3.783A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 803 through 805 No H-bonds generated for 'chain 'G' and resid 803 through 805' Processing helix chain 'G' and resid 815 through 823 Processing helix chain 'G' and resid 829 through 836 removed outlier: 3.896A pdb=" N TRP G 832 " --> pdb=" O ASP G 829 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU G 833 " --> pdb=" O ASP G 830 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR G 836 " --> pdb=" O GLU G 833 " (cutoff:3.500A) Processing helix chain 'G' and resid 860 through 871 Processing helix chain 'G' and resid 877 through 898 removed outlier: 4.440A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 5.405A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.204A 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 removed outlier: 3.537A pdb=" N ALA G 986 " --> pdb=" O LYS G 982 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 991 Processing helix chain 'G' and resid 997 through 1006 Processing helix chain 'G' and resid 1025 through 1030 Processing helix chain 'G' and resid 1036 through 1038 No H-bonds generated for 'chain 'G' and resid 1036 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 1044 through 1046 No H-bonds generated for 'chain 'G' and resid 1044 through 1046' 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: 3.606A 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 1324 through 1338 removed outlier: 3.509A pdb=" N GLY G1330 " --> pdb=" O ILE G1327 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TRP G1331 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG G1332 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE G1335 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1347 through 1349 No H-bonds generated for 'chain 'G' and resid 1347 through 1349' Processing helix chain 'G' and resid 1439 through 1446 Processing helix chain 'G' and resid 1515 through 1523 Processing helix chain 'G' and resid 1551 through 1557 Processing helix chain 'G' and resid 1562 through 1564 No H-bonds generated for 'chain 'G' and resid 1562 through 1564' Processing helix chain 'G' and resid 1567 through 1572 Processing helix chain 'G' and resid 1582 through 1596 removed outlier: 3.701A pdb=" N LEU G1592 " --> pdb=" O SER G1588 " (cutoff:3.500A) 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: 3.609A 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 1712 Processing helix chain 'G' and resid 1723 through 1734 removed outlier: 3.640A pdb=" N LYS G1727 " --> pdb=" O GLY G1723 " (cutoff:3.500A) Processing helix chain 'G' and resid 1774 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1808 through 1818 removed outlier: 3.713A pdb=" N ALA G1813 " --> pdb=" O GLY G1810 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA G1814 " --> pdb=" O GLU G1811 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA G1816 " --> pdb=" O ALA G1813 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU G1818 " --> pdb=" O LEU G1815 " (cutoff:3.500A) Processing helix chain 'G' and resid 1824 through 1840 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 1906 through 1920 removed outlier: 3.863A pdb=" N LEU G1919 " --> pdb=" O ASN G1915 " (cutoff:3.500A) Processing helix chain 'G' and resid 1927 through 1930 No H-bonds generated for 'chain 'G' and resid 1927 through 1930' Processing helix chain 'G' and resid 1936 through 1951 removed outlier: 4.070A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1979 through 1995 removed outlier: 4.115A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL G1985 " --> pdb=" O MET G1982 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS G1986 " --> pdb=" O ASN G1983 " (cutoff:3.500A) Proline residue: G1987 - end of helix removed outlier: 3.507A pdb=" N LYS G1993 " --> pdb=" O SER G1990 " (cutoff:3.500A) Processing helix chain 'G' and resid 2023 through 2032 removed outlier: 3.692A pdb=" N LEU G2032 " --> pdb=" O ASP G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2036 through 2043 removed outlier: 4.084A pdb=" N ILE G2041 " --> pdb=" O PRO G2037 " (cutoff:3.500A) Processing helix chain 'G' and resid 2045 through 2049 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.745A pdb=" N GLU A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU A 46 " --> pdb=" O GLU A 77 " (cutoff:3.500A) removed outlier: 6.818A 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: 6.706A pdb=" N ALA A 767 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N THR A 681 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 6.470A 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: 4.345A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA A 820 " --> pdb=" O THR A 863 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N CYS A 865 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL A 822 " --> pdb=" O CYS A 865 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ALA A 867 " --> pdb=" O VAL A 822 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU A 824 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 869 " --> pdb=" O LEU A 824 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET A 826 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id= F, first strand: chain 'A' and resid 1102 through 1105 removed outlier: 3.961A pdb=" N GLY A1102 " --> pdb=" O GLN A1188 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id= H, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= I, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.516A pdb=" N ILE A1326 " --> pdb=" O GLY A1244 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1573 through 1575 removed outlier: 7.615A pdb=" N ALA A1638 " --> pdb=" O GLY A1537 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA A1539 " --> pdb=" O ALA A1638 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER A1640 " --> pdb=" O ALA A1539 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE A1541 " --> pdb=" O SER A1640 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N THR A1642 " --> pdb=" O PHE A1541 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) 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 1837 through 1840 Processing sheet with id= M, first strand: chain 'G' and resid 6 through 13 Processing sheet with id= N, first strand: chain 'G' and resid 458 through 460 removed outlier: 4.570A pdb=" N GLY G 272 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N HIS G 500 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE G 159 " --> pdb=" O HIS G 500 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU G 502 " --> pdb=" O ILE G 159 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG G 526 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASP G 503 " --> pdb=" O ARG G 526 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ILE G 528 " --> pdb=" O ASP G 503 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 417 through 420 removed outlier: 6.249A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.442A 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: 6.772A pdb=" N GLY G 648 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE G 649 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU G 679 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU G 651 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE G 681 " --> pdb=" O LEU G 651 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR G 702 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ILE G 681 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY G 704 " --> pdb=" O ILE G 681 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LEU G 705 " --> pdb=" O PRO G 727 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ALA G 729 " --> pdb=" O LEU G 705 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 731 through 733 removed outlier: 6.349A pdb=" N ILE G 766 " --> pdb=" O TRP G 732 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY G 798 " --> pdb=" O PHE G 767 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'G' and resid 843 through 847 Processing sheet with id= T, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 6.561A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL G1201 " --> pdb=" O LEU G1205 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU G1205 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id= V, first strand: chain 'G' and resid 1377 through 1383 removed outlier: 6.739A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ASN G1383 " --> pdb=" O GLY G1387 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY G1387 " --> pdb=" O ASN G1383 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG G1606 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY G1630 " --> pdb=" O LEU G1637 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 1372 through 1374 removed outlier: 6.198A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 1431 through 1435 removed outlier: 3.736A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 1663 through 1666 removed outlier: 6.920A pdb=" N THR G1803 " --> pdb=" O PHE G1664 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N PHE G1666 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA G1805 " --> pdb=" O PHE G1666 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'G' and resid 1717 through 1720 Processing sheet with id= AA, first strand: chain 'G' and resid 1852 through 1857 removed outlier: 6.349A pdb=" N ALA G1901 " --> pdb=" O ILE G1888 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE G1888 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASP G1903 " --> pdb=" O VAL G1886 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL G1886 " --> pdb=" O ASP G1903 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 1537 through 1545 removed outlier: 7.158A pdb=" N ILE G1626 " --> pdb=" O ILE G1539 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL G1541 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N THR G1624 " --> pdb=" O VAL G1541 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP G1543 " --> pdb=" O LEU G1622 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU G1622 " --> pdb=" O ASP G1543 " (cutoff:3.500A) 1152 hydrogen bonds defined for protein. 3123 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.33 Time building geometry restraints manager: 12.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5087 1.31 - 1.45: 7675 1.45 - 1.59: 17359 1.59 - 1.73: 3 1.73 - 1.87: 190 Bond restraints: 30314 Sorted by residual: bond pdb=" C34 PNS B1901 " pdb=" N36 PNS B1901 " ideal model delta sigma weight residual 1.452 1.316 0.136 2.00e-02 2.50e+03 4.59e+01 bond pdb=" C39 PNS B1901 " pdb=" N41 PNS B1901 " ideal model delta sigma weight residual 1.452 1.333 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C PRO A1658 " pdb=" O PRO A1658 " ideal model delta sigma weight residual 1.238 1.168 0.070 1.37e-02 5.33e+03 2.58e+01 bond pdb=" C PRO G 795 " pdb=" O PRO G 795 " ideal model delta sigma weight residual 1.234 1.177 0.056 1.14e-02 7.69e+03 2.43e+01 bond pdb=" C4 FMN G2101 " pdb=" C4A FMN G2101 " ideal model delta sigma weight residual 1.390 1.489 -0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 30309 not shown) Histogram of bond angle deviations from ideal: 96.52 - 104.23: 520 104.23 - 111.93: 12632 111.93 - 119.63: 15724 119.63 - 127.33: 11977 127.33 - 135.04: 207 Bond angle restraints: 41060 Sorted by residual: angle pdb=" CB GLU A 841 " pdb=" CG GLU A 841 " pdb=" CD GLU A 841 " ideal model delta sigma weight residual 112.60 132.43 -19.83 1.70e+00 3.46e-01 1.36e+02 angle pdb=" CB GLU A 780 " pdb=" CG GLU A 780 " pdb=" CD GLU A 780 " ideal model delta sigma weight residual 112.60 128.64 -16.04 1.70e+00 3.46e-01 8.91e+01 angle pdb=" C GLU G 852 " pdb=" CA GLU G 852 " pdb=" CB GLU G 852 " ideal model delta sigma weight residual 108.76 117.68 -8.92 1.37e+00 5.33e-01 4.24e+01 angle pdb=" CB GLU A1317 " pdb=" CG GLU A1317 " pdb=" CD GLU A1317 " ideal model delta sigma weight residual 112.60 123.21 -10.61 1.70e+00 3.46e-01 3.89e+01 angle pdb=" C GLY G 662 " pdb=" N ILE G 663 " pdb=" CA ILE G 663 " ideal model delta sigma weight residual 120.33 125.20 -4.87 8.00e-01 1.56e+00 3.70e+01 ... (remaining 41055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.65: 16789 19.65 - 39.30: 1210 39.30 - 58.95: 215 58.95 - 78.59: 62 78.59 - 98.24: 21 Dihedral angle restraints: 18297 sinusoidal: 7358 harmonic: 10939 Sorted by residual: dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual 93.00 10.67 82.33 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CA GLY A 892 " pdb=" C GLY A 892 " pdb=" N VAL A 893 " pdb=" CA VAL A 893 " ideal model delta harmonic sigma weight residual 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ILE G1503 " pdb=" C ILE G1503 " pdb=" N VAL G1504 " pdb=" CA VAL G1504 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 18294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2774 0.082 - 0.165: 1580 0.165 - 0.247: 240 0.247 - 0.330: 19 0.330 - 0.412: 1 Chirality restraints: 4614 Sorted by residual: chirality pdb=" CA GLU A 841 " pdb=" N GLU A 841 " pdb=" C GLU A 841 " pdb=" CB GLU A 841 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA ILE A1403 " pdb=" N ILE A1403 " pdb=" C ILE A1403 " pdb=" CB ILE A1403 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLN A1389 " pdb=" N GLN A1389 " pdb=" C GLN A1389 " pdb=" CB GLN A1389 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 4611 not shown) Planarity restraints: 5299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 PNS B1901 " 0.086 2.00e-02 2.50e+03 8.79e-02 9.66e+01 pdb=" C34 PNS B1901 " -0.051 2.00e-02 2.50e+03 pdb=" C37 PNS B1901 " 0.107 2.00e-02 2.50e+03 pdb=" N36 PNS B1901 " -0.131 2.00e-02 2.50e+03 pdb=" O35 PNS B1901 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.000 2.00e-02 2.50e+03 3.19e-02 4.83e+01 pdb=" C10 FMN G2101 " 0.008 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.034 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.009 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.019 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.060 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.036 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.016 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.072 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.016 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.028 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.012 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.047 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.020 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.028 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.034 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.038 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.012 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PNS B1901 " 0.008 2.00e-02 2.50e+03 4.90e-02 3.01e+01 pdb=" C39 PNS B1901 " 0.024 2.00e-02 2.50e+03 pdb=" C42 PNS B1901 " -0.056 2.00e-02 2.50e+03 pdb=" N41 PNS B1901 " 0.075 2.00e-02 2.50e+03 pdb=" O40 PNS B1901 " -0.051 2.00e-02 2.50e+03 ... (remaining 5296 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 636 2.69 - 3.24: 28830 3.24 - 3.79: 46206 3.79 - 4.35: 66358 4.35 - 4.90: 106322 Nonbonded interactions: 248352 Sorted by model distance: nonbonded pdb=" OH TYR A 89 " pdb=" OD2 ASP G1791 " model vdw 2.135 2.440 nonbonded pdb=" O3P FMN G2101 " pdb=" O4' FMN G2101 " model vdw 2.138 2.440 nonbonded pdb=" O GLY G 161 " pdb=" NE2 GLN G 245 " model vdw 2.252 2.520 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.286 2.440 nonbonded pdb=" O PRO G1975 " pdb=" OG SER G1978 " model vdw 2.292 2.440 ... (remaining 248347 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: 0.650 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: 4.900 Check model and map are aligned: 0.440 Set scattering table: 0.280 Process input model: 81.610 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 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 0.136 30314 Z= 0.883 Angle : 1.858 19.826 41060 Z= 1.360 Chirality : 0.091 0.412 4614 Planarity : 0.007 0.088 5299 Dihedral : 14.798 98.243 11252 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.53 % Favored : 94.15 % Rotamer: Outliers : 0.89 % Allowed : 4.06 % Favored : 95.05 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.12), residues: 3776 helix: -2.60 (0.09), residues: 1667 sheet: -1.94 (0.20), residues: 538 loop : -1.31 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.009 TRP A1286 HIS 0.026 0.004 HIS G1581 PHE 0.061 0.006 PHE G 799 TYR 0.060 0.007 TYR A 722 ARG 0.014 0.001 ARG A1680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 385 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8146 (mp0) REVERT: A 56 MET cc_start: 0.8995 (mtt) cc_final: 0.8776 (mtt) REVERT: A 492 ASP cc_start: 0.7994 (t0) cc_final: 0.7765 (t0) REVERT: A 505 LYS cc_start: 0.8200 (ptmm) cc_final: 0.7994 (tttm) REVERT: A 691 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8576 (mm-30) REVERT: A 780 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6493 (mm-30) REVERT: A 788 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8851 (m) REVERT: A 841 GLU cc_start: 0.7232 (tp30) cc_final: 0.5610 (tp30) REVERT: A 881 ASN cc_start: 0.7873 (m-40) cc_final: 0.7575 (m110) REVERT: A 945 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8491 (ttpt) REVERT: A 1283 MET cc_start: 0.8905 (mpp) cc_final: 0.8678 (mpt) REVERT: A 1317 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6886 (tm-30) REVERT: A 1391 ASP cc_start: 0.8824 (t70) cc_final: 0.8617 (t0) REVERT: A 1437 LYS cc_start: 0.5036 (pttt) cc_final: 0.4724 (pttt) REVERT: A 1468 GLU cc_start: 0.8662 (mm-30) cc_final: 0.7894 (tp30) REVERT: A 1749 THR cc_start: 0.7421 (m) cc_final: 0.7138 (m) REVERT: A 1790 ASN cc_start: 0.7587 (m-40) cc_final: 0.7235 (t0) REVERT: B 211 GLU cc_start: 0.7869 (pt0) cc_final: 0.7663 (pt0) REVERT: B 237 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.5659 (mpt) REVERT: B 243 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.7020 (pt) REVERT: B 251 GLN cc_start: 0.6821 (tp40) cc_final: 0.6566 (tp40) REVERT: B 276 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5192 (mmm160) REVERT: G 13 HIS cc_start: 0.5881 (t70) cc_final: 0.5546 (t-90) REVERT: G 38 ASN cc_start: 0.7782 (t0) cc_final: 0.7560 (t0) REVERT: G 80 PHE cc_start: 0.6657 (m-80) cc_final: 0.6245 (m-80) REVERT: G 82 GLN cc_start: 0.7842 (mp-120) cc_final: 0.7417 (mp-120) REVERT: G 85 ASN cc_start: 0.7015 (m-40) cc_final: 0.6446 (m-40) REVERT: G 116 LEU cc_start: 0.8101 (mm) cc_final: 0.7863 (mm) REVERT: G 117 VAL cc_start: 0.8560 (m) cc_final: 0.8052 (p) REVERT: G 121 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7555 (mt-10) REVERT: G 181 HIS cc_start: 0.8772 (p90) cc_final: 0.8568 (p90) REVERT: G 217 GLU cc_start: 0.7574 (tp30) cc_final: 0.7216 (tp30) REVERT: G 539 ASP cc_start: 0.8039 (t0) cc_final: 0.7805 (t0) REVERT: G 753 MET cc_start: 0.9231 (mmm) cc_final: 0.8943 (mmm) REVERT: G 1011 MET cc_start: 0.8319 (mtp) cc_final: 0.8101 (mtp) REVERT: G 1079 ASP cc_start: 0.8546 (m-30) cc_final: 0.8321 (m-30) REVERT: G 1134 ASP cc_start: 0.8216 (t70) cc_final: 0.7890 (t70) REVERT: G 1276 ASN cc_start: 0.8735 (t0) cc_final: 0.8510 (t0) REVERT: G 1364 LYS cc_start: 0.8635 (pttm) cc_final: 0.8130 (mppt) REVERT: G 1433 MET cc_start: 0.9140 (mtm) cc_final: 0.8619 (mtp) REVERT: G 1492 GLU cc_start: 0.8282 (tt0) cc_final: 0.7985 (mm-30) REVERT: G 1609 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8726 (p) REVERT: G 1673 GLU cc_start: 0.8126 (pm20) cc_final: 0.7838 (pm20) REVERT: G 1838 MET cc_start: 0.8867 (mmt) cc_final: 0.8609 (mmm) REVERT: G 1849 ARG cc_start: 0.7129 (ptt-90) cc_final: 0.6665 (ptm-80) REVERT: G 1880 LYS cc_start: 0.8443 (mptt) cc_final: 0.8001 (mppt) outliers start: 29 outliers final: 5 residues processed: 410 average time/residue: 1.6743 time to fit residues: 793.4306 Evaluate side-chains 286 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 275 time to evaluate : 4.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1397 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1759 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 192 optimal weight: 7.9990 chunk 152 optimal weight: 0.0050 chunk 295 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 342 optimal weight: 0.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 422 HIS A 618 ASN A 987 ASN A 989 GLN A1239 HIS A1432 HIS A1507 GLN A1748 ASN B 292 GLN G 155 GLN G 331 ASN G 440 ASN G 517 HIS G 718 ASN G 993 GLN G1202 GLN G1241 ASN G1355 ASN G1451 GLN G1514 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1595 ASN G1619 ASN G1697 HIS G1716 ASN G1890 ASN G1912 ASN G2020 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30314 Z= 0.206 Angle : 0.557 8.124 41060 Z= 0.292 Chirality : 0.042 0.169 4614 Planarity : 0.004 0.031 5299 Dihedral : 5.723 97.078 4069 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.04 % Favored : 97.88 % Rotamer: Outliers : 1.57 % Allowed : 8.61 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.13), residues: 3776 helix: 0.03 (0.12), residues: 1677 sheet: -1.18 (0.20), residues: 536 loop : -0.29 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 732 HIS 0.010 0.001 HIS A1689 PHE 0.022 0.002 PHE A 35 TYR 0.018 0.002 TYR A 417 ARG 0.004 0.001 ARG A1180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 285 time to evaluate : 4.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 LYS cc_start: 0.8113 (ptmm) cc_final: 0.7886 (tttm) REVERT: A 750 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7941 (tm-30) REVERT: A 780 GLU cc_start: 0.6656 (tp30) cc_final: 0.6409 (mm-30) REVERT: A 841 GLU cc_start: 0.6094 (tp30) cc_final: 0.4501 (mp0) REVERT: A 881 ASN cc_start: 0.7924 (m-40) cc_final: 0.7605 (m110) REVERT: A 901 MET cc_start: 0.9193 (tpt) cc_final: 0.8974 (tpt) REVERT: A 945 LYS cc_start: 0.8771 (ttpp) cc_final: 0.8430 (ttpt) REVERT: A 1162 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: A 1498 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: A 1681 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: A 1790 ASN cc_start: 0.7408 (m-40) cc_final: 0.7206 (t0) REVERT: B 236 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.6165 (mptp) REVERT: B 237 MET cc_start: 0.6106 (mmt) cc_final: 0.5794 (mpt) REVERT: B 243 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6718 (pt) REVERT: B 279 SER cc_start: 0.5776 (t) cc_final: 0.5448 (p) REVERT: B 280 GLU cc_start: 0.5129 (tm-30) cc_final: 0.4791 (tm-30) REVERT: G 82 GLN cc_start: 0.7871 (mp-120) cc_final: 0.7563 (mp-120) REVERT: G 85 ASN cc_start: 0.6617 (m-40) cc_final: 0.6123 (m-40) REVERT: G 117 VAL cc_start: 0.8400 (m) cc_final: 0.7959 (p) REVERT: G 121 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7543 (mt-10) REVERT: G 168 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7992 (p0) REVERT: G 447 ASN cc_start: 0.8145 (m-40) cc_final: 0.7891 (m-40) REVERT: G 753 MET cc_start: 0.9132 (mmm) cc_final: 0.8788 (mmm) REVERT: G 1011 MET cc_start: 0.8347 (mtp) cc_final: 0.8135 (mtp) REVERT: G 1079 ASP cc_start: 0.8485 (m-30) cc_final: 0.8254 (m-30) REVERT: G 1134 ASP cc_start: 0.7928 (t70) cc_final: 0.7611 (t0) REVERT: G 1276 ASN cc_start: 0.8800 (t0) cc_final: 0.8507 (t0) REVERT: G 1673 GLU cc_start: 0.7857 (pm20) cc_final: 0.7565 (pm20) REVERT: G 1678 MET cc_start: 0.8578 (mmm) cc_final: 0.7963 (mmp) REVERT: G 1849 ARG cc_start: 0.7235 (ptt-90) cc_final: 0.6509 (ptm-80) REVERT: G 1880 LYS cc_start: 0.8435 (mptt) cc_final: 0.8030 (mppt) REVERT: G 1986 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8047 (tmmt) outliers start: 51 outliers final: 13 residues processed: 317 average time/residue: 1.6677 time to fit residues: 616.3842 Evaluate side-chains 272 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 251 time to evaluate : 4.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1162 GLU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1681 GLU Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 168 ASP Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1397 SER Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1759 SER Chi-restraints excluded: chain G residue 1986 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 284 optimal weight: 0.0270 chunk 233 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 342 optimal weight: 2.9990 chunk 370 optimal weight: 9.9990 chunk 305 optimal weight: 5.9990 chunk 340 optimal weight: 7.9990 chunk 116 optimal weight: 8.9990 chunk 275 optimal weight: 8.9990 overall best weight: 2.9844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1063 HIS A1482 GLN ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 181 HIS ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1716 ASN G1851 ASN G1912 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30314 Z= 0.232 Angle : 0.520 7.813 41060 Z= 0.269 Chirality : 0.042 0.148 4614 Planarity : 0.004 0.034 5299 Dihedral : 5.152 92.515 4056 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.49 % Favored : 97.43 % Rotamer: Outliers : 1.97 % Allowed : 9.81 % Favored : 88.22 % 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: 0.25 (0.14), residues: 3776 helix: 0.80 (0.13), residues: 1690 sheet: -0.79 (0.21), residues: 539 loop : 0.01 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G1138 HIS 0.012 0.001 HIS G 181 PHE 0.024 0.002 PHE A 35 TYR 0.019 0.002 TYR B 294 ARG 0.004 0.001 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 274 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: A 370 GLU cc_start: 0.8810 (tt0) cc_final: 0.8576 (tm-30) REVERT: A 505 LYS cc_start: 0.8109 (ptmm) cc_final: 0.7888 (tttm) REVERT: A 750 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: A 754 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7989 (t0) REVERT: A 841 GLU cc_start: 0.6279 (tp30) cc_final: 0.4605 (mp0) REVERT: A 945 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8400 (ttpt) REVERT: A 1094 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: A 1162 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: A 1484 GLU cc_start: 0.6947 (tm-30) cc_final: 0.5665 (tp30) REVERT: A 1498 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: A 1790 ASN cc_start: 0.7448 (m-40) cc_final: 0.7165 (t0) REVERT: B 237 MET cc_start: 0.6006 (mmt) cc_final: 0.5800 (mpt) REVERT: B 279 SER cc_start: 0.5914 (t) cc_final: 0.5667 (p) REVERT: B 280 GLU cc_start: 0.5247 (tm-30) cc_final: 0.4888 (tm-30) REVERT: G 82 GLN cc_start: 0.7909 (mp-120) cc_final: 0.7585 (mp-120) REVERT: G 85 ASN cc_start: 0.6544 (m-40) cc_final: 0.6030 (m-40) REVERT: G 117 VAL cc_start: 0.8463 (m) cc_final: 0.7905 (p) REVERT: G 121 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7579 (mt-10) REVERT: G 447 ASN cc_start: 0.8219 (m-40) cc_final: 0.7987 (m-40) REVERT: G 539 ASP cc_start: 0.8277 (t0) cc_final: 0.7562 (t0) REVERT: G 753 MET cc_start: 0.9121 (mmm) cc_final: 0.8831 (mmm) REVERT: G 913 ASP cc_start: 0.8472 (t70) cc_final: 0.8079 (m-30) REVERT: G 1011 MET cc_start: 0.8362 (mtp) cc_final: 0.8154 (mtp) REVERT: G 1079 ASP cc_start: 0.8580 (m-30) cc_final: 0.8375 (m-30) REVERT: G 1276 ASN cc_start: 0.8842 (t0) cc_final: 0.8530 (t0) REVERT: G 1673 GLU cc_start: 0.7913 (pm20) cc_final: 0.7613 (pm20) REVERT: G 1678 MET cc_start: 0.8601 (mmm) cc_final: 0.8040 (mmp) REVERT: G 1847 LEU cc_start: 0.7694 (mp) cc_final: 0.7306 (mm) REVERT: G 1849 ARG cc_start: 0.7331 (ptt-90) cc_final: 0.6604 (ptm-80) REVERT: G 1962 ARG cc_start: 0.6792 (tmm-80) cc_final: 0.6546 (tmm-80) REVERT: G 1986 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8125 (tmmt) outliers start: 64 outliers final: 27 residues processed: 313 average time/residue: 1.6253 time to fit residues: 599.0899 Evaluate side-chains 288 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 254 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1162 GLU Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1397 SER Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1759 SER Chi-restraints excluded: chain G residue 1943 ILE Chi-restraints excluded: chain G residue 1986 LYS Chi-restraints excluded: chain G residue 2033 THR 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: 8.9990 chunk 177 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 163 optimal weight: 30.0000 chunk 230 optimal weight: 0.1980 chunk 344 optimal weight: 5.9990 chunk 364 optimal weight: 6.9990 chunk 179 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1380 GLN ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 181 HIS ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30314 Z= 0.281 Angle : 0.531 8.345 41060 Z= 0.273 Chirality : 0.043 0.149 4614 Planarity : 0.004 0.036 5299 Dihedral : 5.113 93.924 4054 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.28 % Favored : 97.64 % Rotamer: Outliers : 2.18 % Allowed : 11.10 % Favored : 86.71 % 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: 0.43 (0.14), residues: 3776 helix: 0.90 (0.13), residues: 1693 sheet: -0.64 (0.21), residues: 534 loop : 0.12 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 865 HIS 0.014 0.001 HIS G 181 PHE 0.025 0.002 PHE A 35 TYR 0.018 0.002 TYR B 294 ARG 0.004 0.000 ARG A1489 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 269 time to evaluate : 3.936 Fit side-chains revert: symmetry clash REVERT: A 341 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: A 370 GLU cc_start: 0.8828 (tt0) cc_final: 0.8589 (tm-30) REVERT: A 750 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: A 754 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8044 (t0) REVERT: A 841 GLU cc_start: 0.6286 (tp30) cc_final: 0.4687 (OUTLIER) REVERT: A 1066 ASN cc_start: 0.7831 (t0) cc_final: 0.7498 (t0) REVERT: A 1298 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8553 (tp) REVERT: A 1498 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: A 1751 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7224 (mm-30) REVERT: A 1790 ASN cc_start: 0.7605 (m-40) cc_final: 0.7120 (t0) REVERT: B 208 GLU cc_start: 0.8247 (mp0) cc_final: 0.7666 (mp0) REVERT: B 224 GLN cc_start: 0.7603 (tp40) cc_final: 0.7292 (tp40) REVERT: B 236 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.6084 (mptt) REVERT: B 237 MET cc_start: 0.6064 (mmt) cc_final: 0.5816 (mpt) REVERT: B 279 SER cc_start: 0.5863 (t) cc_final: 0.5662 (p) REVERT: B 280 GLU cc_start: 0.5391 (tm-30) cc_final: 0.4992 (tm-30) REVERT: G 80 PHE cc_start: 0.6494 (m-80) cc_final: 0.6255 (m-80) REVERT: G 82 GLN cc_start: 0.8031 (mp-120) cc_final: 0.7579 (mp-120) REVERT: G 85 ASN cc_start: 0.6570 (m-40) cc_final: 0.6071 (m-40) REVERT: G 117 VAL cc_start: 0.8527 (m) cc_final: 0.7911 (p) REVERT: G 121 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7578 (mt-10) REVERT: G 168 ASP cc_start: 0.8310 (p0) cc_final: 0.7944 (p0) REVERT: G 753 MET cc_start: 0.9116 (mmm) cc_final: 0.8777 (mmm) REVERT: G 913 ASP cc_start: 0.8469 (t70) cc_final: 0.8028 (m-30) REVERT: G 1011 MET cc_start: 0.8371 (mtp) cc_final: 0.8166 (mtp) REVERT: G 1079 ASP cc_start: 0.8575 (m-30) cc_final: 0.8356 (m-30) REVERT: G 1276 ASN cc_start: 0.8838 (t0) cc_final: 0.8535 (t0) REVERT: G 1673 GLU cc_start: 0.7925 (pm20) cc_final: 0.7622 (pm20) REVERT: G 1678 MET cc_start: 0.8585 (mmm) cc_final: 0.8032 (mmp) REVERT: G 1847 LEU cc_start: 0.7795 (mp) cc_final: 0.7562 (mm) outliers start: 71 outliers final: 31 residues processed: 316 average time/residue: 1.7165 time to fit residues: 636.7895 Evaluate side-chains 290 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 254 time to evaluate : 3.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 553 ASN Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1759 SER Chi-restraints excluded: chain G residue 1940 LEU Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 0.4980 chunk 206 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 271 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 310 optimal weight: 10.0000 chunk 251 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 chunk 327 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 181 HIS G1202 GLN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30314 Z= 0.137 Angle : 0.470 8.587 41060 Z= 0.241 Chirality : 0.040 0.146 4614 Planarity : 0.003 0.034 5299 Dihedral : 4.718 88.346 4053 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.91 % Rotamer: Outliers : 1.69 % Allowed : 12.27 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.14), residues: 3776 helix: 1.18 (0.13), residues: 1679 sheet: -0.47 (0.21), residues: 529 loop : 0.22 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 661 HIS 0.014 0.001 HIS G 181 PHE 0.024 0.001 PHE A 35 TYR 0.019 0.001 TYR B 294 ARG 0.003 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 275 time to evaluate : 3.783 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8673 (tppp) REVERT: A 348 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8500 (ttp-110) REVERT: A 370 GLU cc_start: 0.8804 (tt0) cc_final: 0.8563 (tm-30) REVERT: A 505 LYS cc_start: 0.8262 (ptmm) cc_final: 0.7898 (tttm) REVERT: A 750 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7840 (tm-30) REVERT: A 754 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8000 (t0) REVERT: A 841 GLU cc_start: 0.6158 (tp30) cc_final: 0.4820 (OUTLIER) REVERT: A 945 LYS cc_start: 0.8713 (ttpp) cc_final: 0.8389 (ttpt) REVERT: A 1066 ASN cc_start: 0.7660 (t0) cc_final: 0.7436 (t0) REVERT: A 1162 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7284 (tt0) REVERT: A 1484 GLU cc_start: 0.6888 (tm-30) cc_final: 0.5545 (tp30) REVERT: A 1681 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8649 (tm-30) REVERT: A 1751 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7212 (mm-30) REVERT: A 1755 MET cc_start: 0.7026 (mtp) cc_final: 0.6668 (mtm) REVERT: A 1790 ASN cc_start: 0.7497 (m-40) cc_final: 0.6979 (t0) REVERT: B 208 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: B 224 GLN cc_start: 0.7572 (tp40) cc_final: 0.7290 (tp40) REVERT: B 237 MET cc_start: 0.6180 (mmt) cc_final: 0.5862 (mpt) REVERT: B 279 SER cc_start: 0.6000 (t) cc_final: 0.5794 (p) REVERT: B 280 GLU cc_start: 0.5506 (tm-30) cc_final: 0.5133 (tm-30) REVERT: G 48 PHE cc_start: 0.6581 (m-80) cc_final: 0.6357 (m-80) REVERT: G 80 PHE cc_start: 0.6472 (m-80) cc_final: 0.6207 (m-80) REVERT: G 82 GLN cc_start: 0.7837 (mp-120) cc_final: 0.7467 (mp-120) REVERT: G 85 ASN cc_start: 0.6694 (m-40) cc_final: 0.6222 (m110) REVERT: G 117 VAL cc_start: 0.8508 (m) cc_final: 0.7829 (p) REVERT: G 118 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7379 (ttpt) REVERT: G 121 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7559 (mt-10) REVERT: G 168 ASP cc_start: 0.8299 (p0) cc_final: 0.7864 (p0) REVERT: G 753 MET cc_start: 0.9112 (mmm) cc_final: 0.8853 (mmm) REVERT: G 913 ASP cc_start: 0.8426 (t70) cc_final: 0.8010 (m-30) REVERT: G 1011 MET cc_start: 0.8337 (mtp) cc_final: 0.8131 (mtp) REVERT: G 1079 ASP cc_start: 0.8522 (m-30) cc_final: 0.8292 (m-30) REVERT: G 1216 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7307 (tp30) REVERT: G 1276 ASN cc_start: 0.8816 (t0) cc_final: 0.8513 (t0) REVERT: G 1673 GLU cc_start: 0.7926 (pm20) cc_final: 0.7621 (pm20) REVERT: G 1678 MET cc_start: 0.8649 (mmm) cc_final: 0.7870 (mmp) REVERT: G 1708 ASP cc_start: 0.8366 (t70) cc_final: 0.8138 (t0) outliers start: 55 outliers final: 22 residues processed: 311 average time/residue: 1.5797 time to fit residues: 574.8491 Evaluate side-chains 284 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 256 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1162 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 118 LYS Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1743 ASP Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 3.9990 chunk 328 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 364 optimal weight: 4.9990 chunk 302 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1380 GLN A1873 HIS ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 181 HIS G1186 ASN G1202 GLN G1226 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30314 Z= 0.215 Angle : 0.499 9.779 41060 Z= 0.255 Chirality : 0.041 0.146 4614 Planarity : 0.004 0.037 5299 Dihedral : 4.709 88.103 4052 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.33 % Favored : 97.64 % Rotamer: Outliers : 1.81 % Allowed : 13.23 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3776 helix: 1.15 (0.13), residues: 1689 sheet: -0.32 (0.22), residues: 519 loop : 0.30 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 661 HIS 0.013 0.001 HIS G 181 PHE 0.024 0.001 PHE A 35 TYR 0.026 0.001 TYR B 294 ARG 0.004 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 266 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8253 (mt0) REVERT: A 348 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8516 (ttp-110) REVERT: A 370 GLU cc_start: 0.8846 (tt0) cc_final: 0.8612 (tm-30) REVERT: A 435 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8153 (tp30) REVERT: A 750 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: A 754 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7993 (t0) REVERT: A 841 GLU cc_start: 0.6349 (tp30) cc_final: 0.4489 (mm-30) REVERT: A 945 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8393 (ttpt) REVERT: A 1180 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.5814 (mtt90) REVERT: A 1298 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8502 (tp) REVERT: A 1484 GLU cc_start: 0.6987 (tm-30) cc_final: 0.5647 (tp30) REVERT: A 1751 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7227 (mm-30) REVERT: A 1755 MET cc_start: 0.7037 (mtp) cc_final: 0.6641 (mtm) REVERT: A 1790 ASN cc_start: 0.7626 (m-40) cc_final: 0.7141 (t0) REVERT: B 208 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: B 224 GLN cc_start: 0.7570 (tp40) cc_final: 0.7265 (tp-100) REVERT: B 237 MET cc_start: 0.6057 (mmt) cc_final: 0.5826 (mpt) REVERT: B 279 SER cc_start: 0.5988 (t) cc_final: 0.5758 (p) REVERT: B 280 GLU cc_start: 0.5505 (tm-30) cc_final: 0.5116 (tm-30) REVERT: G 80 PHE cc_start: 0.6468 (m-80) cc_final: 0.6209 (m-80) REVERT: G 82 GLN cc_start: 0.7947 (mp-120) cc_final: 0.7475 (mp-120) REVERT: G 85 ASN cc_start: 0.6790 (m-40) cc_final: 0.6321 (m110) REVERT: G 117 VAL cc_start: 0.8539 (m) cc_final: 0.7834 (p) REVERT: G 121 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7573 (mt-10) REVERT: G 168 ASP cc_start: 0.8313 (p0) cc_final: 0.7874 (p0) REVERT: G 753 MET cc_start: 0.9105 (mmm) cc_final: 0.8789 (mmm) REVERT: G 913 ASP cc_start: 0.8430 (t70) cc_final: 0.8021 (m-30) REVERT: G 1079 ASP cc_start: 0.8541 (m-30) cc_final: 0.8305 (m-30) REVERT: G 1216 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7283 (tp30) REVERT: G 1276 ASN cc_start: 0.8826 (t0) cc_final: 0.8525 (t0) REVERT: G 1505 ASP cc_start: 0.8345 (t70) cc_final: 0.8140 (t0) REVERT: G 1673 GLU cc_start: 0.7921 (pm20) cc_final: 0.7630 (pm20) REVERT: G 1678 MET cc_start: 0.8663 (mmm) cc_final: 0.8156 (mmp) REVERT: G 1708 ASP cc_start: 0.8382 (t70) cc_final: 0.8162 (t0) REVERT: G 1849 ARG cc_start: 0.7400 (ptt90) cc_final: 0.6807 (ptm-80) outliers start: 59 outliers final: 29 residues processed: 307 average time/residue: 1.6391 time to fit residues: 591.2472 Evaluate side-chains 297 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1743 ASP Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 307 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 363 optimal weight: 8.9990 chunk 227 optimal weight: 0.0370 chunk 221 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 overall best weight: 3.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1380 GLN A1873 HIS G 38 ASN G 181 HIS G 331 ASN G1202 GLN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30314 Z= 0.244 Angle : 0.515 10.197 41060 Z= 0.263 Chirality : 0.042 0.146 4614 Planarity : 0.004 0.038 5299 Dihedral : 4.752 89.003 4052 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 2.06 % Allowed : 13.66 % Favored : 84.28 % 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: 0.77 (0.14), residues: 3776 helix: 1.11 (0.13), residues: 1689 sheet: -0.28 (0.22), residues: 529 loop : 0.33 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 661 HIS 0.014 0.001 HIS G 181 PHE 0.024 0.001 PHE A 35 TYR 0.021 0.002 TYR B 294 ARG 0.004 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 260 time to evaluate : 3.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8259 (mt0) REVERT: A 370 GLU cc_start: 0.8846 (tt0) cc_final: 0.8618 (tm-30) REVERT: A 435 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8139 (tp30) REVERT: A 750 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: A 754 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7991 (t0) REVERT: A 841 GLU cc_start: 0.6398 (tp30) cc_final: 0.4508 (mm-30) REVERT: A 945 LYS cc_start: 0.8737 (ttpp) cc_final: 0.8397 (ttpt) REVERT: A 1180 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.5795 (mtt90) REVERT: A 1298 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8506 (tp) REVERT: A 1498 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: A 1751 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7228 (mm-30) REVERT: A 1755 MET cc_start: 0.7051 (mtp) cc_final: 0.6623 (mtm) REVERT: A 1790 ASN cc_start: 0.7598 (m-40) cc_final: 0.7095 (t0) REVERT: B 208 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: B 224 GLN cc_start: 0.7558 (tp40) cc_final: 0.7249 (tp-100) REVERT: B 237 MET cc_start: 0.6099 (mmt) cc_final: 0.5800 (mpt) REVERT: B 279 SER cc_start: 0.6066 (t) cc_final: 0.5833 (p) REVERT: B 280 GLU cc_start: 0.5502 (tm-30) cc_final: 0.5113 (tm-30) REVERT: G 80 PHE cc_start: 0.6478 (m-80) cc_final: 0.6224 (m-80) REVERT: G 82 GLN cc_start: 0.7953 (mp-120) cc_final: 0.7469 (mp-120) REVERT: G 85 ASN cc_start: 0.6784 (m-40) cc_final: 0.6323 (m110) REVERT: G 117 VAL cc_start: 0.8560 (m) cc_final: 0.7814 (p) REVERT: G 121 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7656 (mt-10) REVERT: G 168 ASP cc_start: 0.8325 (p0) cc_final: 0.7894 (p0) REVERT: G 753 MET cc_start: 0.9105 (mmm) cc_final: 0.8805 (mmm) REVERT: G 913 ASP cc_start: 0.8427 (t70) cc_final: 0.8022 (m-30) REVERT: G 1011 MET cc_start: 0.8344 (mtp) cc_final: 0.8139 (mtp) REVERT: G 1079 ASP cc_start: 0.8548 (m-30) cc_final: 0.8310 (m-30) REVERT: G 1216 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7298 (tp30) REVERT: G 1276 ASN cc_start: 0.8786 (t0) cc_final: 0.8535 (t0) REVERT: G 1673 GLU cc_start: 0.7948 (pm20) cc_final: 0.7660 (pm20) REVERT: G 1678 MET cc_start: 0.8639 (mmm) cc_final: 0.8137 (mmp) REVERT: G 1708 ASP cc_start: 0.8392 (t70) cc_final: 0.8178 (t0) outliers start: 67 outliers final: 37 residues processed: 303 average time/residue: 1.5995 time to fit residues: 569.5790 Evaluate side-chains 298 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 254 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 181 HIS Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 553 ASN Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1465 THR Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1743 ASP Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 217 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.0980 chunk 231 optimal weight: 5.9990 chunk 247 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 285 optimal weight: 0.0570 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1873 HIS G 38 ASN G 181 HIS G 723 HIS G1186 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30314 Z= 0.125 Angle : 0.477 10.020 41060 Z= 0.241 Chirality : 0.040 0.228 4614 Planarity : 0.003 0.036 5299 Dihedral : 4.476 83.902 4052 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.01 % Favored : 97.96 % Rotamer: Outliers : 1.29 % Allowed : 14.24 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3776 helix: 1.27 (0.13), residues: 1686 sheet: -0.22 (0.22), residues: 537 loop : 0.39 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 661 HIS 0.023 0.001 HIS G 181 PHE 0.028 0.001 PHE G 37 TYR 0.023 0.001 TYR B 294 ARG 0.004 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 269 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7243 (mtp85) REVERT: A 62 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8668 (tppp) REVERT: A 333 LYS cc_start: 0.8944 (tppp) cc_final: 0.8614 (ttpp) REVERT: A 370 GLU cc_start: 0.8822 (tt0) cc_final: 0.8587 (tm-30) REVERT: A 750 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7810 (tm-30) REVERT: A 754 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7958 (t0) REVERT: A 841 GLU cc_start: 0.6382 (tp30) cc_final: 0.4935 (mm-30) REVERT: A 945 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8428 (ttpt) REVERT: A 1180 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.5804 (mtt90) REVERT: A 1708 ASP cc_start: 0.8812 (m-30) cc_final: 0.8569 (t0) REVERT: A 1751 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7217 (mm-30) REVERT: A 1755 MET cc_start: 0.6969 (mtp) cc_final: 0.6597 (mtm) REVERT: A 1790 ASN cc_start: 0.7469 (m-40) cc_final: 0.6926 (t0) REVERT: B 208 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: B 224 GLN cc_start: 0.7641 (tp40) cc_final: 0.7342 (tp40) REVERT: B 237 MET cc_start: 0.6152 (mmt) cc_final: 0.5832 (mpt) REVERT: B 280 GLU cc_start: 0.5511 (tm-30) cc_final: 0.5193 (tm-30) REVERT: G 80 PHE cc_start: 0.6471 (m-80) cc_final: 0.6225 (m-80) REVERT: G 82 GLN cc_start: 0.7987 (mp-120) cc_final: 0.7509 (mp-120) REVERT: G 85 ASN cc_start: 0.6802 (m-40) cc_final: 0.6329 (m110) REVERT: G 117 VAL cc_start: 0.8535 (m) cc_final: 0.7745 (p) REVERT: G 121 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7611 (mt-10) REVERT: G 168 ASP cc_start: 0.8300 (p0) cc_final: 0.7861 (p0) REVERT: G 753 MET cc_start: 0.9098 (mmm) cc_final: 0.8796 (mmm) REVERT: G 913 ASP cc_start: 0.8394 (t70) cc_final: 0.8002 (m-30) REVERT: G 1079 ASP cc_start: 0.8476 (m-30) cc_final: 0.8261 (m-30) REVERT: G 1216 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7264 (tp30) REVERT: G 1276 ASN cc_start: 0.8768 (t0) cc_final: 0.8509 (t0) REVERT: G 1673 GLU cc_start: 0.7936 (pm20) cc_final: 0.7701 (pm20) REVERT: G 1678 MET cc_start: 0.8624 (mmm) cc_final: 0.7880 (mmp) REVERT: G 1708 ASP cc_start: 0.8404 (t70) cc_final: 0.8180 (t0) outliers start: 42 outliers final: 19 residues processed: 299 average time/residue: 1.6286 time to fit residues: 572.4041 Evaluate side-chains 284 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 260 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1465 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1743 ASP Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 0.0270 chunk 348 optimal weight: 0.0670 chunk 317 optimal weight: 0.9990 chunk 338 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 305 optimal weight: 0.9990 chunk 320 optimal weight: 6.9990 chunk 337 optimal weight: 5.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1873 HIS G 38 ASN G1186 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 30314 Z= 0.161 Angle : 0.486 10.814 41060 Z= 0.246 Chirality : 0.041 0.211 4614 Planarity : 0.003 0.036 5299 Dihedral : 4.436 81.362 4051 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.36 % Favored : 97.62 % Rotamer: Outliers : 1.26 % Allowed : 14.58 % Favored : 84.16 % 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: 0.98 (0.14), residues: 3776 helix: 1.29 (0.13), residues: 1688 sheet: -0.13 (0.22), residues: 525 loop : 0.40 (0.16), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 661 HIS 0.005 0.001 HIS A1689 PHE 0.025 0.001 PHE G 37 TYR 0.023 0.001 TYR B 294 ARG 0.004 0.000 ARG A 632 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 270 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7232 (mtp85) REVERT: A 62 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8667 (tppp) REVERT: A 333 LYS cc_start: 0.8935 (tppp) cc_final: 0.8606 (ttpp) REVERT: A 341 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: A 370 GLU cc_start: 0.8824 (tt0) cc_final: 0.8587 (tm-30) REVERT: A 750 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: A 754 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7950 (t0) REVERT: A 841 GLU cc_start: 0.6207 (tp30) cc_final: 0.4561 (mm-30) REVERT: A 945 LYS cc_start: 0.8678 (ttpp) cc_final: 0.8394 (ttpt) REVERT: A 1162 GLU cc_start: 0.7550 (tp30) cc_final: 0.6967 (tt0) REVERT: A 1180 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.5816 (mtt90) REVERT: A 1681 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8679 (tm-30) REVERT: A 1708 ASP cc_start: 0.8809 (m-30) cc_final: 0.8572 (t0) REVERT: A 1751 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7213 (mm-30) REVERT: A 1755 MET cc_start: 0.7025 (mtp) cc_final: 0.6657 (mtm) REVERT: A 1790 ASN cc_start: 0.7450 (m-40) cc_final: 0.6898 (t0) REVERT: B 183 GLN cc_start: 0.8361 (tt0) cc_final: 0.8118 (tt0) REVERT: B 208 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7852 (mp0) REVERT: B 224 GLN cc_start: 0.7614 (tp40) cc_final: 0.7308 (tp40) REVERT: B 280 GLU cc_start: 0.5624 (tm-30) cc_final: 0.5295 (tm-30) REVERT: G 80 PHE cc_start: 0.6511 (m-80) cc_final: 0.6251 (m-80) REVERT: G 82 GLN cc_start: 0.7982 (mp-120) cc_final: 0.7504 (mp-120) REVERT: G 85 ASN cc_start: 0.6709 (m-40) cc_final: 0.6259 (m110) REVERT: G 117 VAL cc_start: 0.8552 (m) cc_final: 0.7747 (p) REVERT: G 121 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7618 (mt-10) REVERT: G 168 ASP cc_start: 0.8290 (p0) cc_final: 0.7854 (p0) REVERT: G 753 MET cc_start: 0.9090 (mmm) cc_final: 0.8792 (mmm) REVERT: G 913 ASP cc_start: 0.8411 (t70) cc_final: 0.8010 (m-30) REVERT: G 1216 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7275 (tp30) REVERT: G 1276 ASN cc_start: 0.8774 (t0) cc_final: 0.8511 (t0) REVERT: G 1673 GLU cc_start: 0.7963 (pm20) cc_final: 0.7727 (pm20) REVERT: G 1678 MET cc_start: 0.8624 (mmm) cc_final: 0.7897 (mmp) REVERT: G 1708 ASP cc_start: 0.8386 (t70) cc_final: 0.8166 (t0) outliers start: 41 outliers final: 24 residues processed: 295 average time/residue: 1.6382 time to fit residues: 572.0109 Evaluate side-chains 290 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 259 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1486 LEU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1465 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1743 ASP Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 0.9990 chunk 358 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 169 optimal weight: 0.2980 chunk 248 optimal weight: 2.9990 chunk 375 optimal weight: 2.9990 chunk 345 optimal weight: 0.9990 chunk 299 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 231 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1873 HIS G 38 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30314 Z= 0.129 Angle : 0.476 10.763 41060 Z= 0.239 Chirality : 0.040 0.197 4614 Planarity : 0.003 0.035 5299 Dihedral : 4.294 76.381 4051 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.17 % Allowed : 14.73 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.14), residues: 3776 helix: 1.42 (0.13), residues: 1667 sheet: -0.08 (0.22), residues: 534 loop : 0.47 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 661 HIS 0.006 0.001 HIS G 13 PHE 0.023 0.001 PHE A 35 TYR 0.031 0.001 TYR B 294 ARG 0.005 0.000 ARG A 632 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 264 time to evaluate : 4.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8665 (tppp) REVERT: A 333 LYS cc_start: 0.8962 (tppp) cc_final: 0.8623 (ttpp) REVERT: A 341 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8261 (mt0) REVERT: A 352 MET cc_start: 0.7913 (ttm) cc_final: 0.7572 (ttp) REVERT: A 370 GLU cc_start: 0.8826 (tt0) cc_final: 0.8587 (tm-30) REVERT: A 750 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7790 (tm-30) REVERT: A 754 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7928 (t0) REVERT: A 841 GLU cc_start: 0.6187 (tp30) cc_final: 0.4710 (mm-30) REVERT: A 945 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8402 (ttpt) REVERT: A 1162 GLU cc_start: 0.7608 (tp30) cc_final: 0.6970 (tt0) REVERT: A 1180 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.5801 (mtt90) REVERT: A 1681 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8693 (tm-30) REVERT: A 1708 ASP cc_start: 0.8800 (m-30) cc_final: 0.8547 (t0) REVERT: A 1751 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7223 (mm-30) REVERT: A 1755 MET cc_start: 0.6902 (mtp) cc_final: 0.6586 (mtm) REVERT: A 1790 ASN cc_start: 0.7465 (m-40) cc_final: 0.6913 (t0) REVERT: B 208 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: B 224 GLN cc_start: 0.7611 (tp40) cc_final: 0.7302 (tp40) REVERT: B 237 MET cc_start: 0.5138 (mmp) cc_final: 0.4577 (mpt) REVERT: B 280 GLU cc_start: 0.5746 (tm-30) cc_final: 0.5369 (tm-30) REVERT: G 80 PHE cc_start: 0.6482 (m-80) cc_final: 0.6219 (m-80) REVERT: G 82 GLN cc_start: 0.7981 (mp-120) cc_final: 0.7501 (mp-120) REVERT: G 85 ASN cc_start: 0.6846 (m-40) cc_final: 0.6361 (m110) REVERT: G 117 VAL cc_start: 0.8530 (m) cc_final: 0.7705 (p) REVERT: G 121 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7577 (mt-10) REVERT: G 168 ASP cc_start: 0.8244 (p0) cc_final: 0.7849 (p0) REVERT: G 753 MET cc_start: 0.9083 (mmm) cc_final: 0.8716 (mmm) REVERT: G 913 ASP cc_start: 0.8388 (t70) cc_final: 0.8003 (m-30) REVERT: G 1216 GLU cc_start: 0.7569 (tm-30) cc_final: 0.7251 (tp30) REVERT: G 1276 ASN cc_start: 0.8753 (t0) cc_final: 0.8477 (t0) REVERT: G 1673 GLU cc_start: 0.7967 (pm20) cc_final: 0.7735 (pm20) REVERT: G 1678 MET cc_start: 0.8647 (mmm) cc_final: 0.7902 (mmp) outliers start: 38 outliers final: 17 residues processed: 288 average time/residue: 1.6737 time to fit residues: 565.1217 Evaluate side-chains 273 residues out of total 3252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 251 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain G residue 538 ASP Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1465 THR Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1743 ASP Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 9.9990 chunk 318 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 275 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 307 optimal weight: 10.0000 chunk 37 optimal weight: 0.0470 chunk 55 optimal weight: 6.9990 overall best weight: 2.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1380 GLN A1873 HIS G 38 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.079412 restraints weight = 52613.057| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.91 r_work: 0.2868 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30314 Z= 0.180 Angle : 0.496 10.503 41060 Z= 0.249 Chirality : 0.041 0.200 4614 Planarity : 0.003 0.036 5299 Dihedral : 4.353 74.439 4051 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.14 % Allowed : 15.04 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.14), residues: 3776 helix: 1.33 (0.13), residues: 1688 sheet: -0.03 (0.22), residues: 538 loop : 0.51 (0.17), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 661 HIS 0.006 0.001 HIS G 13 PHE 0.033 0.001 PHE G 37 TYR 0.028 0.001 TYR B 294 ARG 0.006 0.000 ARG A 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10490.06 seconds wall clock time: 191 minutes 12.44 seconds (11472.44 seconds total)