Starting phenix.real_space_refine on Sat Feb 17 23:30:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2024/6wge_21663_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2024/6wge_21663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2024/6wge_21663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2024/6wge_21663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2024/6wge_21663_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2024/6wge_21663_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 92 5.49 5 Mg 2 5.21 5 S 106 5.16 5 C 12574 2.51 5 N 3470 2.21 5 O 3950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 131": "NH1" <-> "NH2" Residue "A ARG 151": "NH1" <-> "NH2" Residue "A GLU 157": "OE1" <-> "OE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 171": "NH1" <-> "NH2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1038": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1040": "OE1" <-> "OE2" Residue "A PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1066": "NH1" <-> "NH2" Residue "A ARG 1069": "NH1" <-> "NH2" Residue "A TYR 1107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1109": "OD1" <-> "OD2" Residue "A ARG 1121": "NH1" <-> "NH2" Residue "A ASP 1159": "OD1" <-> "OD2" Residue "A ASP 1163": "OD1" <-> "OD2" Residue "A TYR 1173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1191": "OE1" <-> "OE2" Residue "A ASP 1209": "OD1" <-> "OD2" Residue "B TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 51": "OD1" <-> "OD2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 99": "NH1" <-> "NH2" Residue "B ASP 107": "OD1" <-> "OD2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B ARG 199": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B TYR 957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 988": "OD1" <-> "OD2" Residue "B ARG 1009": "NH1" <-> "NH2" Residue "B GLU 1022": "OE1" <-> "OE2" Residue "B ARG 1024": "NH1" <-> "NH2" Residue "B PHE 1102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1143": "OD1" <-> "OD2" Residue "B ARG 1176": "NH1" <-> "NH2" Residue "B ASP 1213": "OD1" <-> "OD2" Residue "C TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C ARG 559": "NH1" <-> "NH2" Residue "C ARG 569": "NH1" <-> "NH2" Residue "C ARG 586": "NH1" <-> "NH2" Residue "C TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 619": "OD1" <-> "OD2" Residue "E PHE 1199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1207": "OE1" <-> "OE2" Residue "E ASP 1275": "OD1" <-> "OD2" Residue "E ARG 1294": "NH1" <-> "NH2" Residue "E TYR 1328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1335": "NH1" <-> "NH2" Residue "E TYR 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1357": "NH1" <-> "NH2" Residue "E ASP 1392": "OD1" <-> "OD2" Residue "E GLU 1425": "OE1" <-> "OE2" Residue "E ARG 1444": "NH1" <-> "NH2" Residue "E GLU 1446": "OE1" <-> "OE2" Residue "E ARG 1462": "NH1" <-> "NH2" Residue "E ARG 1471": "NH1" <-> "NH2" Residue "E ARG 1536": "NH1" <-> "NH2" Residue "E PHE 1545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1559": "NH1" <-> "NH2" Residue "E ASP 1568": "OD1" <-> "OD2" Residue "E ARG 1590": "NH1" <-> "NH2" Residue "E ARG 1606": "NH1" <-> "NH2" Residue "E ARG 1621": "NH1" <-> "NH2" Residue "E TYR 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1664": "OE1" <-> "OE2" Residue "E ASP 1666": "OD1" <-> "OD2" Residue "E ARG 1719": "NH1" <-> "NH2" Residue "E ARG 1723": "NH1" <-> "NH2" Residue "E ASP 1752": "OD1" <-> "OD2" Residue "E TYR 1759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1779": "NH1" <-> "NH2" Residue "E ARG 1809": "NH1" <-> "NH2" Residue "E ARG 1814": "NH1" <-> "NH2" Residue "E ARG 1819": "NH1" <-> "NH2" Residue "E ARG 1837": "NH1" <-> "NH2" Residue "E ARG 1842": "NH1" <-> "NH2" Residue "E ASP 1859": "OD1" <-> "OD2" Residue "E ARG 1873": "NH1" <-> "NH2" Residue "E ASP 1874": "OD1" <-> "OD2" Residue "E PHE 1882": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1894": "NH1" <-> "NH2" Residue "E ASP 1898": "OD1" <-> "OD2" Residue "E ASP 1935": "OD1" <-> "OD2" Residue "E ASP 1961": "OD1" <-> "OD2" Residue "E GLU 1980": "OE1" <-> "OE2" Residue "E ARG 2001": "NH1" <-> "NH2" Residue "E ARG 2016": "NH1" <-> "NH2" Residue "E PHE 2103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 2112": "NH1" <-> "NH2" Residue "E ARG 2142": "NH1" <-> "NH2" Residue "E ARG 2152": "NH1" <-> "NH2" Residue "E PHE 2156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 2185": "OD1" <-> "OD2" Residue "E GLU 2243": "OE1" <-> "OE2" Residue "E GLU 2262": "OE1" <-> "OE2" Residue "E ARG 2298": "NH1" <-> "NH2" Residue "E ARG 2335": "NH1" <-> "NH2" Residue "E ARG 2400": "NH1" <-> "NH2" Residue "E ARG 2407": "NH1" <-> "NH2" Residue "E ASP 2424": "OD1" <-> "OD2" Residue "E TYR 2440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 2454": "OD1" <-> "OD2" Residue "E GLU 2535": "OE1" <-> "OE2" Residue "E GLU 2571": "OE1" <-> "OE2" Residue "E ASP 2577": "OD1" <-> "OD2" Residue "E ASP 2620": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20194 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3099 Classifications: {'peptide': 390} Link IDs: {'PTRANS': 14, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 4008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 4008 Classifications: {'peptide': 490} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 478} Chain breaks: 2 Chain: "C" Number of atoms: 1395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1395 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain breaks: 2 Chain: "E" Number of atoms: 9865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1226, 9865 Classifications: {'peptide': 1226} Link IDs: {'PTRANS': 35, 'TRANS': 1190} Chain breaks: 11 Chain: "F" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 903 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "G" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 860 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.84, per 1000 atoms: 0.54 Number of scatterers: 20194 At special positions: 0 Unit cell: (147.4, 142.04, 172.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 106 16.00 P 92 15.00 Mg 2 11.99 O 3950 8.00 N 3470 7.00 C 12574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.54 Conformation dependent library (CDL) restraints added in 3.2 seconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4376 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 11 sheets defined 61.7% alpha, 4.8% beta 35 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 9.46 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 114 through 124 Processing helix chain 'A' and resid 139 through 144 removed outlier: 4.061A pdb=" N ALA A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 165 through 198 Processing helix chain 'A' and resid 1035 through 1088 removed outlier: 3.914A pdb=" N GLN A1057 " --> pdb=" O LYS A1053 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA A1058 " --> pdb=" O LYS A1054 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1130 through 1147 removed outlier: 3.679A pdb=" N VAL A1135 " --> pdb=" O GLY A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1178 Processing helix chain 'A' and resid 1191 through 1194 No H-bonds generated for 'chain 'A' and resid 1191 through 1194' Processing helix chain 'B' and resid 39 through 49 removed outlier: 3.536A pdb=" N LEU B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 152 through 163 Processing helix chain 'B' and resid 167 through 235 removed outlier: 4.342A pdb=" N SER B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 935 through 946 Processing helix chain 'B' and resid 964 through 978 Processing helix chain 'B' and resid 986 through 1047 Processing helix chain 'B' and resid 1117 through 1134 Processing helix chain 'B' and resid 1145 through 1147 No H-bonds generated for 'chain 'B' and resid 1145 through 1147' Processing helix chain 'B' and resid 1151 through 1166 removed outlier: 5.039A pdb=" N VAL B1166 " --> pdb=" O MET B1162 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1181 Processing helix chain 'B' and resid 1203 through 1211 removed outlier: 3.793A pdb=" N GLU B1211 " --> pdb=" O LYS B1207 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 22 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.906A pdb=" N PHE C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 29 through 34' Processing helix chain 'C' and resid 38 through 47 removed outlier: 4.198A pdb=" N SER C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 46 " --> pdb=" O GLU C 42 " (cutoff:3.500A) Proline residue: C 47 - end of helix Processing helix chain 'C' and resid 53 through 85 Processing helix chain 'C' and resid 559 through 571 Processing helix chain 'C' and resid 581 through 584 No H-bonds generated for 'chain 'C' and resid 581 through 584' Processing helix chain 'C' and resid 590 through 606 removed outlier: 3.772A pdb=" N GLN C 606 " --> pdb=" O VAL C 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 1199 through 1215 Processing helix chain 'E' and resid 1235 through 1246 Processing helix chain 'E' and resid 1248 through 1252 removed outlier: 4.039A pdb=" N MET E1251 " --> pdb=" O ILE E1248 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY E1252 " --> pdb=" O LYS E1249 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1248 through 1252' Processing helix chain 'E' and resid 1258 through 1274 removed outlier: 4.058A pdb=" N GLN E1274 " --> pdb=" O GLU E1270 " (cutoff:3.500A) Processing helix chain 'E' and resid 1295 through 1318 removed outlier: 3.761A pdb=" N MET E1318 " --> pdb=" O THR E1314 " (cutoff:3.500A) Processing helix chain 'E' and resid 1330 through 1352 removed outlier: 5.621A pdb=" N TYR E1349 " --> pdb=" O GLN E1345 " (cutoff:3.500A) Proline residue: E1350 - end of helix Processing helix chain 'E' and resid 1381 through 1403 Processing helix chain 'E' and resid 1408 through 1423 removed outlier: 3.846A pdb=" N GLN E1413 " --> pdb=" O THR E1409 " (cutoff:3.500A) Proline residue: E1421 - end of helix Processing helix chain 'E' and resid 1428 through 1444 Processing helix chain 'E' and resid 1449 through 1457 Processing helix chain 'E' and resid 1490 through 1500 Processing helix chain 'E' and resid 1525 through 1550 Processing helix chain 'E' and resid 1559 through 1572 Processing helix chain 'E' and resid 1581 through 1596 Processing helix chain 'E' and resid 1604 through 1627 Processing helix chain 'E' and resid 1647 through 1665 removed outlier: 3.590A pdb=" N GLU E1664 " --> pdb=" O ASP E1660 " (cutoff:3.500A) Processing helix chain 'E' and resid 1669 through 1689 Processing helix chain 'E' and resid 1709 through 1727 Processing helix chain 'E' and resid 1750 through 1763 Processing helix chain 'E' and resid 1767 through 1780 removed outlier: 4.386A pdb=" N PHE E1770 " --> pdb=" O ALA E1767 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ASP E1771 " --> pdb=" O GLN E1768 " (cutoff:3.500A) Processing helix chain 'E' and resid 1786 through 1802 Processing helix chain 'E' and resid 1810 through 1821 Processing helix chain 'E' and resid 1825 through 1841 Processing helix chain 'E' and resid 1850 through 1857 removed outlier: 4.275A pdb=" N ARG E1856 " --> pdb=" O MET E1852 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE E1857 " --> pdb=" O LEU E1853 " (cutoff:3.500A) Processing helix chain 'E' and resid 1863 through 1878 Processing helix chain 'E' and resid 1883 through 1897 removed outlier: 4.544A pdb=" N THR E1886 " --> pdb=" O PRO E1883 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU E1887 " --> pdb=" O LYS E1884 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET E1892 " --> pdb=" O CYS E1889 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN E1897 " --> pdb=" O ARG E1894 " (cutoff:3.500A) Processing helix chain 'E' and resid 1901 through 1913 Processing helix chain 'E' and resid 1923 through 1940 Processing helix chain 'E' and resid 1946 through 1957 Processing helix chain 'E' and resid 1963 through 1985 Proline residue: E1966 - end of helix removed outlier: 4.036A pdb=" N LYS E1969 " --> pdb=" O PRO E1966 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP E1976 " --> pdb=" O GLN E1973 " (cutoff:3.500A) Processing helix chain 'E' and resid 1999 through 2015 Processing helix chain 'E' and resid 2018 through 2020 No H-bonds generated for 'chain 'E' and resid 2018 through 2020' Processing helix chain 'E' and resid 2024 through 2032 Proline residue: E2029 - end of helix removed outlier: 3.824A pdb=" N THR E2032 " --> pdb=" O GLN E2028 " (cutoff:3.500A) Processing helix chain 'E' and resid 2038 through 2057 Proline residue: E2056 - end of helix Processing helix chain 'E' and resid 2063 through 2079 removed outlier: 3.834A pdb=" N LYS E2079 " --> pdb=" O LYS E2075 " (cutoff:3.500A) Processing helix chain 'E' and resid 2082 through 2098 removed outlier: 4.043A pdb=" N CYS E2091 " --> pdb=" O HIS E2087 " (cutoff:3.500A) Processing helix chain 'E' and resid 2103 through 2125 Processing helix chain 'E' and resid 2133 through 2153 Proline residue: E2138 - end of helix Processing helix chain 'E' and resid 2159 through 2162 No H-bonds generated for 'chain 'E' and resid 2159 through 2162' Processing helix chain 'E' and resid 2169 through 2181 Processing helix chain 'E' and resid 2187 through 2202 removed outlier: 3.801A pdb=" N GLN E2202 " --> pdb=" O PHE E2198 " (cutoff:3.500A) Processing helix chain 'E' and resid 2204 through 2208 Processing helix chain 'E' and resid 2210 through 2219 Processing helix chain 'E' and resid 2228 through 2252 Processing helix chain 'E' and resid 2259 through 2261 No H-bonds generated for 'chain 'E' and resid 2259 through 2261' Processing helix chain 'E' and resid 2273 through 2290 removed outlier: 4.245A pdb=" N ILE E2278 " --> pdb=" O SER E2275 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEU E2283 " --> pdb=" O GLN E2280 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N LYS E2284 " --> pdb=" O LEU E2281 " (cutoff:3.500A) Processing helix chain 'E' and resid 2296 through 2311 removed outlier: 3.750A pdb=" N ASN E2310 " --> pdb=" O ALA E2306 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLN E2311 " --> pdb=" O LEU E2307 " (cutoff:3.500A) Processing helix chain 'E' and resid 2321 through 2327 removed outlier: 4.338A pdb=" N GLY E2327 " --> pdb=" O LEU E2323 " (cutoff:3.500A) Processing helix chain 'E' and resid 2332 through 2348 removed outlier: 3.774A pdb=" N LYS E2348 " --> pdb=" O GLU E2344 " (cutoff:3.500A) Processing helix chain 'E' and resid 2352 through 2355 No H-bonds generated for 'chain 'E' and resid 2352 through 2355' Processing helix chain 'E' and resid 2358 through 2371 Processing helix chain 'E' and resid 2393 through 2399 Processing helix chain 'E' and resid 2403 through 2417 Processing helix chain 'E' and resid 2425 through 2437 removed outlier: 3.638A pdb=" N LEU E2429 " --> pdb=" O VAL E2425 " (cutoff:3.500A) Processing helix chain 'E' and resid 2444 through 2470 Processing helix chain 'E' and resid 2534 through 2557 Processing helix chain 'E' and resid 2561 through 2566 Processing helix chain 'E' and resid 2589 through 2600 removed outlier: 3.623A pdb=" N ASP E2600 " --> pdb=" O PHE E2596 " (cutoff:3.500A) Processing helix chain 'E' and resid 2608 through 2626 Processing sheet with id= A, first strand: chain 'A' and resid 8 through 10 removed outlier: 3.802A pdb=" N ILE A 9 " --> pdb=" O GLN A 19 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 19 " --> pdb=" O ILE A 9 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.836A pdb=" N ALA A1184 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE A1185 " --> pdb=" O PHE A1153 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 77 through 81 removed outlier: 3.687A pdb=" N ALA A 78 " --> pdb=" O ILE A 98 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 98 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A 80 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 106 " --> pdb=" O ALA A 95 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 84 through 86 removed outlier: 4.425A pdb=" N GLU A 86 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1096 through 1100 Processing sheet with id= F, first strand: chain 'A' and resid 1199 through 1206 Processing sheet with id= G, first strand: chain 'B' and resid 28 through 30 Processing sheet with id= H, first strand: chain 'B' and resid 107 through 111 removed outlier: 3.798A pdb=" N VAL B 78 " --> pdb=" O ARG B 100 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1052 through 1057 Processing sheet with id= J, first strand: chain 'B' and resid 1188 through 1192 Processing sheet with id= K, first strand: chain 'C' and resid 609 through 612 1054 hydrogen bonds defined for protein. 2985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 70 hydrogen bonds 140 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 10.45 Time building geometry restraints manager: 9.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4746 1.33 - 1.45: 4470 1.45 - 1.58: 11132 1.58 - 1.70: 181 1.70 - 1.82: 179 Bond restraints: 20708 Sorted by residual: bond pdb=" N3B ANP B2000 " pdb=" PG ANP B2000 " ideal model delta sigma weight residual 1.795 1.618 0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N3B ANP A2000 " pdb=" PG ANP A2000 " ideal model delta sigma weight residual 1.795 1.627 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" O3A ANP B2000 " pdb=" PB ANP B2000 " ideal model delta sigma weight residual 1.700 1.591 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" O3A ANP A2000 " pdb=" PB ANP A2000 " ideal model delta sigma weight residual 1.700 1.601 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" N3B ANP B2000 " pdb=" PB ANP B2000 " ideal model delta sigma weight residual 1.669 1.610 0.059 2.00e-02 2.50e+03 8.79e+00 ... (remaining 20703 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.89: 783 105.89 - 113.06: 11090 113.06 - 120.22: 8057 120.22 - 127.39: 8045 127.39 - 134.55: 271 Bond angle restraints: 28246 Sorted by residual: angle pdb=" PB ANP B2000 " pdb=" N3B ANP B2000 " pdb=" PG ANP B2000 " ideal model delta sigma weight residual 126.95 111.83 15.12 3.00e+00 1.11e-01 2.54e+01 angle pdb=" CA LEU E2413 " pdb=" CB LEU E2413 " pdb=" CG LEU E2413 " ideal model delta sigma weight residual 116.30 131.57 -15.27 3.50e+00 8.16e-02 1.90e+01 angle pdb=" C LYS A 59 " pdb=" N THR A 60 " pdb=" CA THR A 60 " ideal model delta sigma weight residual 121.54 129.76 -8.22 1.91e+00 2.74e-01 1.85e+01 angle pdb=" N3B ANP B2000 " pdb=" PG ANP B2000 " pdb=" O2G ANP B2000 " ideal model delta sigma weight residual 101.05 113.11 -12.06 3.00e+00 1.11e-01 1.62e+01 angle pdb=" CA LEU C 155 " pdb=" CB LEU C 155 " pdb=" CG LEU C 155 " ideal model delta sigma weight residual 116.30 130.03 -13.73 3.50e+00 8.16e-02 1.54e+01 ... (remaining 28241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 11844 35.30 - 70.59: 728 70.59 - 105.89: 40 105.89 - 141.19: 0 141.19 - 176.49: 2 Dihedral angle restraints: 12614 sinusoidal: 5905 harmonic: 6709 Sorted by residual: dihedral pdb=" CA GLU B1111 " pdb=" C GLU B1111 " pdb=" N MET B1112 " pdb=" CA MET B1112 " ideal model delta harmonic sigma weight residual -180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA VAL E2317 " pdb=" C VAL E2317 " pdb=" N GLN E2318 " pdb=" CA GLN E2318 " ideal model delta harmonic sigma weight residual 180.00 153.03 26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA GLY E2351 " pdb=" C GLY E2351 " pdb=" N PHE E2352 " pdb=" CA PHE E2352 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 12611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2693 0.076 - 0.152: 451 0.152 - 0.228: 44 0.228 - 0.304: 5 0.304 - 0.380: 2 Chirality restraints: 3195 Sorted by residual: chirality pdb=" C3' ANP A2000 " pdb=" C2' ANP A2000 " pdb=" C4' ANP A2000 " pdb=" O3' ANP A2000 " both_signs ideal model delta sigma weight residual False -2.36 -2.74 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" C3' ANP B2000 " pdb=" C2' ANP B2000 " pdb=" C4' ANP B2000 " pdb=" O3' ANP B2000 " both_signs ideal model delta sigma weight residual False -2.36 -2.71 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB ILE B1098 " pdb=" CA ILE B1098 " pdb=" CG1 ILE B1098 " pdb=" CG2 ILE B1098 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3192 not shown) Planarity restraints: 3284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E1986 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.64e+00 pdb=" C GLU E1986 " 0.051 2.00e-02 2.50e+03 pdb=" O GLU E1986 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU E1987 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E2408 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ALA E2408 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA E2408 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE E2409 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A1117 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO A1118 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A1118 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A1118 " -0.034 5.00e-02 4.00e+02 ... (remaining 3281 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 146 2.52 - 3.11: 15217 3.11 - 3.71: 31136 3.71 - 4.30: 41127 4.30 - 4.90: 66005 Nonbonded interactions: 153631 Sorted by model distance: nonbonded pdb=" NE2 GLN B 141 " pdb="MG MG B2001 " model vdw 1.921 2.250 nonbonded pdb=" O3G ANP B2000 " pdb="MG MG B2001 " model vdw 1.924 2.170 nonbonded pdb=" OE1 GLN B 141 " pdb="MG MG B2001 " model vdw 2.059 2.170 nonbonded pdb=" NE2 GLN A 137 " pdb="MG MG A2001 " model vdw 2.160 2.250 nonbonded pdb=" O ILE E1315 " pdb=" OG1 THR E1319 " model vdw 2.184 2.440 ... (remaining 153626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.010 Extract box with map and model: 4.240 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 61.770 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.007 0.177 20708 Z= 0.468 Angle : 0.995 15.265 28246 Z= 0.548 Chirality : 0.057 0.380 3195 Planarity : 0.006 0.060 3284 Dihedral : 19.791 176.485 8238 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.35 % Favored : 91.61 % Rotamer: Outliers : 0.15 % Allowed : 4.03 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.35 (0.16), residues: 2240 helix: -0.67 (0.12), residues: 1382 sheet: -2.45 (0.39), residues: 157 loop : -3.01 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 18 HIS 0.020 0.002 HIS B 66 PHE 0.032 0.003 PHE E2161 TYR 0.026 0.003 TYR C 67 ARG 0.016 0.001 ARG E2407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 221 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1108 LEU cc_start: 0.9202 (tp) cc_final: 0.8823 (tp) REVERT: B 62 LEU cc_start: 0.9557 (tt) cc_final: 0.9315 (tp) REVERT: B 946 LEU cc_start: 0.8502 (mt) cc_final: 0.8272 (mt) REVERT: C 33 PHE cc_start: 0.8524 (t80) cc_final: 0.8022 (t80) REVERT: C 44 ILE cc_start: 0.8040 (mm) cc_final: 0.7742 (mm) REVERT: C 80 GLU cc_start: 0.8781 (tp30) cc_final: 0.8490 (tp30) REVERT: C 163 PHE cc_start: 0.8165 (m-80) cc_final: 0.7942 (m-80) REVERT: C 563 MET cc_start: 0.7167 (tpp) cc_final: 0.6725 (tpp) REVERT: C 583 GLU cc_start: 0.8317 (tp30) cc_final: 0.8062 (tp30) REVERT: E 1193 MET cc_start: 0.6705 (mtp) cc_final: 0.5866 (mtm) REVERT: E 1254 MET cc_start: 0.7620 (ptp) cc_final: 0.7093 (tpp) REVERT: E 1312 LEU cc_start: 0.9340 (mm) cc_final: 0.9065 (mm) REVERT: E 1859 ASP cc_start: 0.7552 (t0) cc_final: 0.7346 (t0) REVERT: E 2025 MET cc_start: 0.8667 (mpp) cc_final: 0.8081 (mtt) REVERT: E 2207 MET cc_start: 0.8982 (mmt) cc_final: 0.8533 (mmt) REVERT: E 2624 LEU cc_start: 0.8581 (mt) cc_final: 0.7916 (mt) outliers start: 3 outliers final: 1 residues processed: 224 average time/residue: 0.3379 time to fit residues: 116.0801 Evaluate side-chains 152 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 151 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 2424 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 0.9990 chunk 178 optimal weight: 0.0020 chunk 98 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 20.0000 chunk 137 optimal weight: 0.7980 chunk 213 optimal weight: 0.9980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 187 HIS A1114 ASN A1166 ASN B 134 ASN B 229 ASN B 958 GLN B1113 GLN ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 587 ASN C 613 GLN E1343 HIS E1539 GLN E1567 GLN E1598 ASN E1649 GLN E1813 GLN E2023 HIS E2086 GLN E2111 ASN E2124 HIS E2153 HIS E2224 ASN E2236 ASN E2292 HIS E2294 GLN E2315 HIS E2372 ASN E2434 ASN E2551 GLN ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20708 Z= 0.167 Angle : 0.570 11.135 28246 Z= 0.311 Chirality : 0.038 0.188 3195 Planarity : 0.003 0.042 3284 Dihedral : 19.757 179.280 3545 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.03 % Allowed : 14.19 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2240 helix: 1.10 (0.14), residues: 1389 sheet: -1.73 (0.41), residues: 155 loop : -2.44 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E2255 HIS 0.007 0.001 HIS E2394 PHE 0.015 0.001 PHE E2110 TYR 0.017 0.001 TYR B 137 ARG 0.004 0.000 ARG B1110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 195 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7469 (tmm) cc_final: 0.7240 (tmm) REVERT: A 1108 LEU cc_start: 0.9203 (tp) cc_final: 0.8902 (tp) REVERT: B 946 LEU cc_start: 0.8499 (mt) cc_final: 0.8185 (mt) REVERT: C 33 PHE cc_start: 0.8429 (t80) cc_final: 0.7875 (t80) REVERT: C 163 PHE cc_start: 0.8156 (m-80) cc_final: 0.7866 (m-80) REVERT: C 583 GLU cc_start: 0.8273 (tp30) cc_final: 0.7952 (tp30) REVERT: E 1193 MET cc_start: 0.6270 (mtp) cc_final: 0.5714 (mtm) REVERT: E 1251 MET cc_start: 0.8167 (mpp) cc_final: 0.7875 (mpp) REVERT: E 1254 MET cc_start: 0.7722 (ptp) cc_final: 0.7202 (tpp) REVERT: E 1312 LEU cc_start: 0.9318 (mm) cc_final: 0.8992 (mm) REVERT: E 1323 MET cc_start: 0.8232 (mtp) cc_final: 0.7938 (mtp) REVERT: E 1570 LEU cc_start: 0.8062 (mt) cc_final: 0.7842 (mt) REVERT: E 1666 ASP cc_start: 0.7424 (t0) cc_final: 0.7138 (t0) REVERT: E 1900 GLU cc_start: 0.6802 (pm20) cc_final: 0.6418 (tp30) REVERT: E 2025 MET cc_start: 0.8621 (mpp) cc_final: 0.8061 (mtt) REVERT: E 2207 MET cc_start: 0.8954 (mmt) cc_final: 0.8666 (mmt) REVERT: E 2361 MET cc_start: 0.8883 (mmm) cc_final: 0.8446 (tpp) outliers start: 21 outliers final: 8 residues processed: 208 average time/residue: 0.2892 time to fit residues: 98.1756 Evaluate side-chains 171 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain B residue 940 MET Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain E residue 2621 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1061 GLN ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 134 ASN B 229 ASN B 964 GLN B 973 ASN E1343 HIS ** E2280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20708 Z= 0.346 Angle : 0.642 8.474 28246 Z= 0.346 Chirality : 0.040 0.178 3195 Planarity : 0.004 0.043 3284 Dihedral : 19.636 177.456 3543 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.50 % Allowed : 19.00 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.18), residues: 2240 helix: 1.34 (0.14), residues: 1386 sheet: -1.49 (0.41), residues: 155 loop : -2.41 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E2107 HIS 0.009 0.001 HIS E2394 PHE 0.019 0.002 PHE E2409 TYR 0.026 0.002 TYR B 2 ARG 0.005 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 154 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7528 (tmm) cc_final: 0.7313 (tmm) REVERT: B 946 LEU cc_start: 0.8427 (mt) cc_final: 0.8092 (mt) REVERT: C 33 PHE cc_start: 0.8439 (t80) cc_final: 0.7914 (t80) REVERT: C 163 PHE cc_start: 0.8338 (m-80) cc_final: 0.8119 (m-80) REVERT: C 583 GLU cc_start: 0.8317 (tp30) cc_final: 0.8012 (tp30) REVERT: E 1193 MET cc_start: 0.6288 (mtp) cc_final: 0.5643 (mtm) REVERT: E 1251 MET cc_start: 0.8161 (mpp) cc_final: 0.7744 (mpp) REVERT: E 1254 MET cc_start: 0.7647 (ptp) cc_final: 0.7085 (tpp) REVERT: E 1312 LEU cc_start: 0.9339 (mm) cc_final: 0.9041 (mm) REVERT: E 1323 MET cc_start: 0.8505 (mtp) cc_final: 0.8286 (mtp) REVERT: E 1666 ASP cc_start: 0.7469 (t0) cc_final: 0.7157 (t0) REVERT: E 1858 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8087 (mt) REVERT: E 1900 GLU cc_start: 0.7024 (pm20) cc_final: 0.6733 (tp30) REVERT: E 2025 MET cc_start: 0.8767 (mpp) cc_final: 0.8163 (mtt) REVERT: E 2339 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7955 (t70) outliers start: 51 outliers final: 31 residues processed: 196 average time/residue: 0.2866 time to fit residues: 93.6716 Evaluate side-chains 183 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1210 VAL Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain E residue 1298 ASP Chi-restraints excluded: chain E residue 1343 HIS Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1437 LEU Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1858 LEU Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 2015 ILE Chi-restraints excluded: chain E residue 2039 ASN Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2308 THR Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2553 LEU Chi-restraints excluded: chain E residue 2597 LEU Chi-restraints excluded: chain E residue 2621 PHE Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 143 optimal weight: 0.3980 chunk 214 optimal weight: 0.9980 chunk 227 optimal weight: 20.0000 chunk 112 optimal weight: 0.0060 chunk 203 optimal weight: 0.5980 chunk 61 optimal weight: 10.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1080 ASN A1166 ASN B 134 ASN B 229 ASN E1343 HIS E2452 HIS ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20708 Z= 0.145 Angle : 0.527 14.357 28246 Z= 0.287 Chirality : 0.036 0.178 3195 Planarity : 0.003 0.043 3284 Dihedral : 19.249 178.118 3543 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.96 % Allowed : 19.98 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.18), residues: 2240 helix: 1.91 (0.14), residues: 1382 sheet: -1.02 (0.43), residues: 153 loop : -2.19 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E2255 HIS 0.033 0.001 HIS E1343 PHE 0.013 0.001 PHE B 77 TYR 0.018 0.001 TYR B 2 ARG 0.004 0.000 ARG B1110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 180 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7429 (tmm) cc_final: 0.7189 (tmm) REVERT: B 946 LEU cc_start: 0.8367 (mt) cc_final: 0.8049 (mt) REVERT: C 33 PHE cc_start: 0.8318 (t80) cc_final: 0.7896 (t80) REVERT: C 163 PHE cc_start: 0.8246 (m-80) cc_final: 0.8006 (m-80) REVERT: C 583 GLU cc_start: 0.8254 (tp30) cc_final: 0.7932 (tp30) REVERT: E 1193 MET cc_start: 0.6318 (mtp) cc_final: 0.5723 (mtm) REVERT: E 1251 MET cc_start: 0.7996 (mpp) cc_final: 0.7654 (mpp) REVERT: E 1254 MET cc_start: 0.7797 (ptp) cc_final: 0.7233 (tpp) REVERT: E 1312 LEU cc_start: 0.9316 (mm) cc_final: 0.9002 (mm) REVERT: E 1402 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8388 (tm-30) REVERT: E 1497 LEU cc_start: 0.9503 (mt) cc_final: 0.9280 (mt) REVERT: E 1570 LEU cc_start: 0.8054 (mt) cc_final: 0.7727 (mt) REVERT: E 1666 ASP cc_start: 0.7379 (t0) cc_final: 0.6908 (t0) REVERT: E 2082 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7664 (mtp) REVERT: E 2339 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7939 (t70) outliers start: 40 outliers final: 24 residues processed: 211 average time/residue: 0.2763 time to fit residues: 97.3108 Evaluate side-chains 190 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 164 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1343 HIS Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 1967 VAL Chi-restraints excluded: chain E residue 2082 MET Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2201 ILE Chi-restraints excluded: chain E residue 2227 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2307 LEU Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2424 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 0.6980 chunk 128 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 203 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B 229 ASN E1343 HIS E2394 HIS ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20708 Z= 0.232 Angle : 0.563 12.194 28246 Z= 0.303 Chirality : 0.038 0.196 3195 Planarity : 0.003 0.039 3284 Dihedral : 19.225 176.810 3543 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.70 % Allowed : 21.65 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2240 helix: 1.89 (0.14), residues: 1398 sheet: -0.96 (0.43), residues: 154 loop : -2.28 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E1680 HIS 0.014 0.001 HIS E1343 PHE 0.021 0.001 PHE E2290 TYR 0.017 0.001 TYR B 2 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 157 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 MET cc_start: 0.7469 (tmm) cc_final: 0.7242 (tmm) REVERT: B 946 LEU cc_start: 0.8425 (mt) cc_final: 0.8096 (mt) REVERT: C 33 PHE cc_start: 0.8335 (t80) cc_final: 0.7931 (t80) REVERT: C 163 PHE cc_start: 0.8282 (m-80) cc_final: 0.8035 (m-80) REVERT: E 1193 MET cc_start: 0.6385 (mtp) cc_final: 0.5772 (mtm) REVERT: E 1251 MET cc_start: 0.7996 (mpp) cc_final: 0.7580 (mpp) REVERT: E 1254 MET cc_start: 0.7708 (ptp) cc_final: 0.7205 (tpp) REVERT: E 1301 MET cc_start: 0.7096 (mtt) cc_final: 0.6827 (mpp) REVERT: E 1312 LEU cc_start: 0.9323 (mm) cc_final: 0.9015 (mm) REVERT: E 1858 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8113 (mt) REVERT: E 1864 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8317 (p) REVERT: E 2339 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7784 (t70) REVERT: E 2349 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: E 2625 MET cc_start: 0.8188 (mmt) cc_final: 0.7913 (mmm) outliers start: 55 outliers final: 43 residues processed: 201 average time/residue: 0.2762 time to fit residues: 93.3952 Evaluate side-chains 195 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 148 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 939 CYS Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain E residue 1203 THR Chi-restraints excluded: chain E residue 1298 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1343 HIS Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1437 LEU Chi-restraints excluded: chain E residue 1491 THR Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1726 PHE Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1858 LEU Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 1967 VAL Chi-restraints excluded: chain E residue 1975 VAL Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2307 LEU Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2349 TYR Chi-restraints excluded: chain E residue 2424 ASP Chi-restraints excluded: chain E residue 2586 VAL Chi-restraints excluded: chain E residue 2597 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 188 optimal weight: 0.0010 chunk 105 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN A1177 GLN B 229 ASN B 992 ASN E1343 HIS ** E2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20708 Z= 0.205 Angle : 0.547 11.871 28246 Z= 0.295 Chirality : 0.037 0.173 3195 Planarity : 0.003 0.041 3284 Dihedral : 19.142 176.251 3543 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.53 % Allowed : 21.50 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2240 helix: 1.98 (0.14), residues: 1398 sheet: -0.85 (0.43), residues: 154 loop : -2.26 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E1680 HIS 0.015 0.001 HIS E1343 PHE 0.038 0.001 PHE B 993 TYR 0.017 0.001 TYR B 2 ARG 0.003 0.000 ARG B1110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 153 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 946 LEU cc_start: 0.8456 (mt) cc_final: 0.8173 (mt) REVERT: C 33 PHE cc_start: 0.8343 (t80) cc_final: 0.7880 (t80) REVERT: C 51 MET cc_start: 0.7710 (tpt) cc_final: 0.7458 (tpp) REVERT: C 163 PHE cc_start: 0.8261 (m-80) cc_final: 0.8003 (m-80) REVERT: C 620 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8696 (mm) REVERT: E 1193 MET cc_start: 0.6383 (mtp) cc_final: 0.5767 (mtm) REVERT: E 1251 MET cc_start: 0.8021 (mpp) cc_final: 0.7618 (mpp) REVERT: E 1254 MET cc_start: 0.7726 (ptp) cc_final: 0.7227 (tpp) REVERT: E 1312 LEU cc_start: 0.9324 (mm) cc_final: 0.9013 (mm) REVERT: E 1858 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8117 (mt) REVERT: E 1864 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8293 (p) REVERT: E 2339 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7673 (t70) REVERT: E 2349 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8038 (m-80) outliers start: 72 outliers final: 47 residues processed: 212 average time/residue: 0.2676 time to fit residues: 95.5854 Evaluate side-chains 202 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 150 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1014 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain E residue 1203 THR Chi-restraints excluded: chain E residue 1298 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1343 HIS Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1491 THR Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1603 MET Chi-restraints excluded: chain E residue 1625 VAL Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1858 LEU Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 1967 VAL Chi-restraints excluded: chain E residue 1975 VAL Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2227 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2307 LEU Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2349 TYR Chi-restraints excluded: chain E residue 2424 ASP Chi-restraints excluded: chain E residue 2586 VAL Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 128 optimal weight: 0.0670 chunk 191 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 104 optimal weight: 10.0000 overall best weight: 0.9920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B 134 ASN B 229 ASN ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1343 HIS ** E2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 20708 Z= 0.161 Angle : 0.534 11.410 28246 Z= 0.287 Chirality : 0.036 0.169 3195 Planarity : 0.003 0.039 3284 Dihedral : 18.987 175.816 3543 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.24 % Allowed : 22.24 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.18), residues: 2240 helix: 2.12 (0.14), residues: 1401 sheet: -0.66 (0.43), residues: 153 loop : -2.25 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E1680 HIS 0.020 0.001 HIS E1343 PHE 0.029 0.001 PHE E2110 TYR 0.015 0.001 TYR B 137 ARG 0.002 0.000 ARG E2407 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 169 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 946 LEU cc_start: 0.8344 (mt) cc_final: 0.8031 (mt) REVERT: C 33 PHE cc_start: 0.8358 (t80) cc_final: 0.7905 (t80) REVERT: C 79 ASN cc_start: 0.8631 (m-40) cc_final: 0.8407 (m-40) REVERT: C 163 PHE cc_start: 0.8192 (m-80) cc_final: 0.7844 (m-80) REVERT: C 583 GLU cc_start: 0.8248 (tp30) cc_final: 0.7939 (tp30) REVERT: C 620 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8685 (mm) REVERT: E 1193 MET cc_start: 0.6330 (mtp) cc_final: 0.5734 (mtm) REVERT: E 1210 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6671 (mm) REVERT: E 1251 MET cc_start: 0.8013 (mpp) cc_final: 0.7574 (mpp) REVERT: E 1254 MET cc_start: 0.7636 (ptp) cc_final: 0.7188 (tpp) REVERT: E 1312 LEU cc_start: 0.9296 (mm) cc_final: 0.8985 (mm) REVERT: E 1427 VAL cc_start: 0.8293 (m) cc_final: 0.8026 (m) REVERT: E 1864 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8254 (p) REVERT: E 2326 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8172 (tpp) REVERT: E 2339 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7561 (t70) REVERT: E 2349 TYR cc_start: 0.8570 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: E 2625 MET cc_start: 0.7933 (mmt) cc_final: 0.7693 (mmm) outliers start: 66 outliers final: 42 residues processed: 223 average time/residue: 0.2753 time to fit residues: 102.8160 Evaluate side-chains 207 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 159 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain E residue 1203 THR Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1298 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1343 HIS Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1625 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 1967 VAL Chi-restraints excluded: chain E residue 1975 VAL Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2039 ASN Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2156 PHE Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2201 ILE Chi-restraints excluded: chain E residue 2227 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2326 MET Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2349 TYR Chi-restraints excluded: chain E residue 2424 ASP Chi-restraints excluded: chain E residue 2586 VAL Chi-restraints excluded: chain E residue 2597 LEU Chi-restraints excluded: chain E residue 2621 PHE Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B 229 ASN E1343 HIS ** E2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20708 Z= 0.221 Angle : 0.566 11.281 28246 Z= 0.302 Chirality : 0.038 0.169 3195 Planarity : 0.003 0.040 3284 Dihedral : 18.991 175.043 3543 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.19 % Allowed : 22.63 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.18), residues: 2240 helix: 2.13 (0.14), residues: 1402 sheet: -0.68 (0.43), residues: 154 loop : -2.27 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E1680 HIS 0.011 0.001 HIS E1343 PHE 0.024 0.001 PHE E2110 TYR 0.016 0.001 TYR B 137 ARG 0.004 0.000 ARG B1110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 153 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 946 LEU cc_start: 0.8446 (mt) cc_final: 0.8110 (mt) REVERT: B 1108 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6222 (mt-10) REVERT: C 33 PHE cc_start: 0.8344 (t80) cc_final: 0.7894 (t80) REVERT: C 163 PHE cc_start: 0.8195 (m-80) cc_final: 0.7942 (m-80) REVERT: C 583 GLU cc_start: 0.8266 (tp30) cc_final: 0.7952 (tp30) REVERT: C 620 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8663 (mm) REVERT: E 1193 MET cc_start: 0.6337 (mtp) cc_final: 0.5765 (mtm) REVERT: E 1210 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6652 (mm) REVERT: E 1251 MET cc_start: 0.7992 (mpp) cc_final: 0.7560 (mpp) REVERT: E 1254 MET cc_start: 0.7411 (ptp) cc_final: 0.7060 (tpp) REVERT: E 1312 LEU cc_start: 0.9303 (mm) cc_final: 0.8993 (mm) REVERT: E 1427 VAL cc_start: 0.8324 (m) cc_final: 0.8073 (m) REVERT: E 1864 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8293 (p) REVERT: E 2339 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7777 (t70) REVERT: E 2349 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7908 (m-80) REVERT: E 2625 MET cc_start: 0.7919 (mmt) cc_final: 0.7649 (mmm) outliers start: 65 outliers final: 51 residues processed: 208 average time/residue: 0.2817 time to fit residues: 97.9963 Evaluate side-chains 208 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 152 time to evaluate : 2.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1154 VAL Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1043 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1149 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 612 THR Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain E residue 1203 THR Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1298 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1437 LEU Chi-restraints excluded: chain E residue 1491 THR Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1625 VAL Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 1967 VAL Chi-restraints excluded: chain E residue 1974 LEU Chi-restraints excluded: chain E residue 1975 VAL Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2039 ASN Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2156 PHE Chi-restraints excluded: chain E residue 2160 ASP Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2227 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2307 LEU Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2349 TYR Chi-restraints excluded: chain E residue 2424 ASP Chi-restraints excluded: chain E residue 2586 VAL Chi-restraints excluded: chain E residue 2621 PHE Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 211 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 190 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B 229 ASN ** E2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20708 Z= 0.167 Angle : 0.541 11.450 28246 Z= 0.287 Chirality : 0.037 0.168 3195 Planarity : 0.003 0.038 3284 Dihedral : 18.829 174.689 3543 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.99 % Allowed : 22.78 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.18), residues: 2240 helix: 2.29 (0.14), residues: 1395 sheet: -0.21 (0.46), residues: 140 loop : -2.29 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E1680 HIS 0.012 0.001 HIS E2627 PHE 0.022 0.001 PHE E2110 TYR 0.015 0.001 TYR B 137 ARG 0.002 0.000 ARG B1110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 167 time to evaluate : 2.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 946 LEU cc_start: 0.8361 (mt) cc_final: 0.8031 (mt) REVERT: C 33 PHE cc_start: 0.8332 (t80) cc_final: 0.7874 (t80) REVERT: C 163 PHE cc_start: 0.8104 (m-80) cc_final: 0.7862 (m-80) REVERT: C 583 GLU cc_start: 0.8248 (tp30) cc_final: 0.7939 (tp30) REVERT: C 620 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8639 (mm) REVERT: E 1193 MET cc_start: 0.6313 (mtp) cc_final: 0.5771 (mtm) REVERT: E 1210 LEU cc_start: 0.6808 (OUTLIER) cc_final: 0.6564 (mm) REVERT: E 1251 MET cc_start: 0.8047 (mpp) cc_final: 0.7597 (mpp) REVERT: E 1254 MET cc_start: 0.7577 (ptp) cc_final: 0.7127 (tpp) REVERT: E 1312 LEU cc_start: 0.9296 (mm) cc_final: 0.8988 (mm) REVERT: E 1864 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8250 (p) REVERT: E 2339 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7784 (t70) REVERT: E 2349 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7793 (m-80) outliers start: 61 outliers final: 46 residues processed: 218 average time/residue: 0.2908 time to fit residues: 105.2161 Evaluate side-chains 212 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 161 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain E residue 1203 THR Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1298 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1435 ILE Chi-restraints excluded: chain E residue 1437 LEU Chi-restraints excluded: chain E residue 1491 THR Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1625 VAL Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1810 LEU Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 1967 VAL Chi-restraints excluded: chain E residue 1974 LEU Chi-restraints excluded: chain E residue 1975 VAL Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2156 PHE Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2227 VAL Chi-restraints excluded: chain E residue 2274 MET Chi-restraints excluded: chain E residue 2307 LEU Chi-restraints excluded: chain E residue 2326 MET Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2349 TYR Chi-restraints excluded: chain E residue 2586 VAL Chi-restraints excluded: chain E residue 2597 LEU Chi-restraints excluded: chain E residue 2621 PHE Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 136 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 186 optimal weight: 0.6980 chunk 19 optimal weight: 0.1980 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN B 229 ASN ** E2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20708 Z= 0.166 Angle : 0.550 11.624 28246 Z= 0.290 Chirality : 0.037 0.166 3195 Planarity : 0.003 0.038 3284 Dihedral : 18.735 173.866 3543 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.80 % Allowed : 22.73 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.18), residues: 2240 helix: 2.32 (0.14), residues: 1398 sheet: -0.29 (0.46), residues: 145 loop : -2.24 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E1680 HIS 0.029 0.001 HIS E2627 PHE 0.021 0.001 PHE E2110 TYR 0.015 0.001 TYR B 137 ARG 0.006 0.000 ARG B1110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 163 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8932 (mt) cc_final: 0.8674 (tp) REVERT: B 946 LEU cc_start: 0.8479 (mt) cc_final: 0.8097 (mt) REVERT: C 33 PHE cc_start: 0.8128 (t80) cc_final: 0.7865 (t80) REVERT: C 583 GLU cc_start: 0.8242 (tp30) cc_final: 0.7989 (tp30) REVERT: C 620 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8623 (mm) REVERT: E 1193 MET cc_start: 0.6259 (mtp) cc_final: 0.5762 (mtm) REVERT: E 1210 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6583 (mm) REVERT: E 1251 MET cc_start: 0.8074 (mpp) cc_final: 0.7673 (mpp) REVERT: E 1254 MET cc_start: 0.7562 (ptp) cc_final: 0.7118 (tpp) REVERT: E 1312 LEU cc_start: 0.9293 (mm) cc_final: 0.8978 (mm) REVERT: E 1864 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8245 (p) REVERT: E 2334 MET cc_start: 0.8231 (mmm) cc_final: 0.7819 (mtp) REVERT: E 2339 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7780 (t70) REVERT: E 2349 TYR cc_start: 0.8532 (OUTLIER) cc_final: 0.7741 (m-80) REVERT: E 2628 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6265 (mt) outliers start: 57 outliers final: 42 residues processed: 213 average time/residue: 0.2742 time to fit residues: 97.6496 Evaluate side-chains 208 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 160 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 945 GLU Chi-restraints excluded: chain B residue 960 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 620 ILE Chi-restraints excluded: chain E residue 1203 THR Chi-restraints excluded: chain E residue 1210 LEU Chi-restraints excluded: chain E residue 1298 ASP Chi-restraints excluded: chain E residue 1320 SER Chi-restraints excluded: chain E residue 1491 THR Chi-restraints excluded: chain E residue 1501 VAL Chi-restraints excluded: chain E residue 1568 ASP Chi-restraints excluded: chain E residue 1625 VAL Chi-restraints excluded: chain E residue 1670 VAL Chi-restraints excluded: chain E residue 1747 THR Chi-restraints excluded: chain E residue 1864 VAL Chi-restraints excluded: chain E residue 1877 ILE Chi-restraints excluded: chain E residue 1916 THR Chi-restraints excluded: chain E residue 1956 LEU Chi-restraints excluded: chain E residue 1967 VAL Chi-restraints excluded: chain E residue 1975 VAL Chi-restraints excluded: chain E residue 2037 THR Chi-restraints excluded: chain E residue 2084 VAL Chi-restraints excluded: chain E residue 2085 VAL Chi-restraints excluded: chain E residue 2156 PHE Chi-restraints excluded: chain E residue 2160 ASP Chi-restraints excluded: chain E residue 2167 VAL Chi-restraints excluded: chain E residue 2188 VAL Chi-restraints excluded: chain E residue 2227 VAL Chi-restraints excluded: chain E residue 2307 LEU Chi-restraints excluded: chain E residue 2308 THR Chi-restraints excluded: chain E residue 2326 MET Chi-restraints excluded: chain E residue 2339 ASP Chi-restraints excluded: chain E residue 2344 GLU Chi-restraints excluded: chain E residue 2349 TYR Chi-restraints excluded: chain E residue 2586 VAL Chi-restraints excluded: chain E residue 2597 LEU Chi-restraints excluded: chain E residue 2621 PHE Chi-restraints excluded: chain E residue 2628 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1166 ASN ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN B 229 ASN ** E2434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2552 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 = 0.3487 r_free = 0.3487 target = 0.094371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.071233 restraints weight = 54884.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.071734 restraints weight = 41705.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.072324 restraints weight = 31824.249| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20708 Z= 0.273 Angle : 0.602 12.152 28246 Z= 0.319 Chirality : 0.039 0.167 3195 Planarity : 0.003 0.039 3284 Dihedral : 18.833 172.933 3543 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.70 % Allowed : 22.93 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.18), residues: 2240 helix: 2.20 (0.14), residues: 1390 sheet: -0.36 (0.47), residues: 146 loop : -2.29 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E2107 HIS 0.018 0.001 HIS E2627 PHE 0.019 0.002 PHE E2110 TYR 0.017 0.001 TYR B 137 ARG 0.007 0.000 ARG B1110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3159.33 seconds wall clock time: 59 minutes 34.01 seconds (3574.01 seconds total)