Starting phenix.real_space_refine (version: dev) on Thu Feb 23 12:30:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2023/6wge_21663_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2023/6wge_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_2023/6wge_21663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2023/6wge_21663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2023/6wge_21663_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wge_21663/02_2023/6wge_21663_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 11.64, per 1000 atoms: 0.58 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: 8.79 Conformation dependent library (CDL) restraints added in 2.8 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: 7.09 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: 8.96 Time building geometry restraints manager: 9.44 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: 11674 35.30 - 70.59: 690 70.59 - 105.89: 20 105.89 - 141.19: 0 141.19 - 176.49: 2 Dihedral angle restraints: 12386 sinusoidal: 5677 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 12383 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 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. 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.760 Check model and map are aligned: 0.320 Process input model: 59.510 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 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 : 18.973 176.485 8010 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 % 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 *********************** 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 : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 224 average time/residue: 0.3470 time to fit residues: 119.1997 Evaluate side-chains 149 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 2.218 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1928 time to fit residues: 3.8094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 60 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 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: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 E1316 ASN 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1451 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= 0.164 Angle : 0.567 11.389 28246 Z= 0.308 Chirality : 0.037 0.189 3195 Planarity : 0.003 0.043 3284 Dihedral : 18.969 179.390 3315 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 1.13 % 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: -0.22 (0.18), residues: 2240 helix: 1.12 (0.14), residues: 1390 sheet: -1.70 (0.41), residues: 155 loop : -2.42 (0.23), residues: 695 *********************** 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 218 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 2.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 209 average time/residue: 0.2931 time to fit residues: 99.6623 Evaluate side-chains 164 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 2.650 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1961 time to fit residues: 6.0624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 212 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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** A1039 GLN A1061 GLN A1080 ASN ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 GLN B 17 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 229 ASN B 964 GLN B 973 ASN B 992 ASN C 629 HIS E1343 HIS ** E2280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2434 ASN ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.056 20708 Z= 0.385 Angle : 0.674 8.865 28246 Z= 0.363 Chirality : 0.042 0.174 3195 Planarity : 0.004 0.044 3284 Dihedral : 19.111 176.600 3315 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer Outliers : 2.65 % 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: -0.06 (0.18), residues: 2240 helix: 1.28 (0.13), residues: 1386 sheet: -1.52 (0.41), residues: 155 loop : -2.45 (0.23), residues: 699 *********************** 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: 54 poor density : 151 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 31 residues processed: 193 average time/residue: 0.2904 time to fit residues: 92.9997 Evaluate side-chains 179 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 2.226 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.1825 time to fit residues: 13.9658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 203 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 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 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 229 ASN ** E1343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2434 ASN E2452 HIS ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 20708 Z= 0.164 Angle : 0.551 13.537 28246 Z= 0.298 Chirality : 0.037 0.177 3195 Planarity : 0.003 0.040 3284 Dihedral : 18.909 178.046 3315 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 1.87 % 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: 0.60 (0.18), residues: 2240 helix: 1.79 (0.14), residues: 1390 sheet: -1.05 (0.43), residues: 153 loop : -2.24 (0.23), residues: 697 *********************** 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 211 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 201 average time/residue: 0.2851 time to fit residues: 95.4869 Evaluate side-chains 175 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 154 time to evaluate : 2.199 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1940 time to fit residues: 10.8778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 9.9990 chunk 128 optimal weight: 0.3980 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 0.2980 chunk 93 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 157 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN E1343 HIS E2434 ASN ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 20708 Z= 0.264 Angle : 0.592 12.282 28246 Z= 0.317 Chirality : 0.038 0.201 3195 Planarity : 0.003 0.038 3284 Dihedral : 18.937 176.260 3315 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 1.42 % 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: 0.58 (0.18), residues: 2240 helix: 1.77 (0.14), residues: 1398 sheet: -1.01 (0.43), residues: 154 loop : -2.31 (0.23), residues: 688 *********************** 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 187 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 176 average time/residue: 0.2864 time to fit residues: 84.1376 Evaluate side-chains 162 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 2.561 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2160 time to fit residues: 9.1301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 227 optimal weight: 20.0000 chunk 188 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN E1343 HIS E1973 GLN E2434 ASN ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 20708 Z= 0.317 Angle : 0.625 12.100 28246 Z= 0.334 Chirality : 0.040 0.177 3195 Planarity : 0.003 0.040 3284 Dihedral : 18.963 175.579 3315 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 2.06 % 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: 0.53 (0.18), residues: 2240 helix: 1.76 (0.14), residues: 1388 sheet: -1.06 (0.43), residues: 154 loop : -2.33 (0.23), residues: 698 *********************** 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 193 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 184 average time/residue: 0.2874 time to fit residues: 88.6092 Evaluate side-chains 167 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 2.510 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1904 time to fit residues: 10.2392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 128 optimal weight: 0.0670 chunk 191 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 226 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 overall best weight: 2.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 229 ASN E1343 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: 0.8436 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 20708 Z= 0.211 Angle : 0.580 12.155 28246 Z= 0.309 Chirality : 0.038 0.171 3195 Planarity : 0.003 0.039 3284 Dihedral : 18.862 175.267 3315 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer Outliers : 1.18 % 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: 0.74 (0.18), residues: 2240 helix: 1.93 (0.14), residues: 1392 sheet: -0.98 (0.43), residues: 154 loop : -2.29 (0.23), residues: 694 *********************** 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 182 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 7 residues processed: 174 average time/residue: 0.2900 time to fit residues: 84.4350 Evaluate side-chains 157 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 150 time to evaluate : 2.490 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2055 time to fit residues: 5.9452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN E1343 HIS ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.080 20708 Z= 0.164 Angle : 0.570 11.376 28246 Z= 0.303 Chirality : 0.037 0.171 3195 Planarity : 0.003 0.038 3284 Dihedral : 18.683 174.771 3315 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer Outliers : 0.93 % 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: 0.98 (0.18), residues: 2240 helix: 2.11 (0.14), residues: 1399 sheet: -0.48 (0.44), residues: 147 loop : -2.30 (0.22), residues: 694 *********************** 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 196 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 191 average time/residue: 0.3076 time to fit residues: 96.8019 Evaluate side-chains 180 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 2.412 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1892 time to fit residues: 7.1103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 211 optimal weight: 0.0040 chunk 127 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 64 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- 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 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 20708 Z= 0.258 Angle : 0.618 13.503 28246 Z= 0.324 Chirality : 0.039 0.240 3195 Planarity : 0.003 0.040 3284 Dihedral : 18.709 173.803 3315 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.54 % 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: 0.95 (0.18), residues: 2240 helix: 2.09 (0.14), residues: 1396 sheet: -0.66 (0.43), residues: 153 loop : -2.28 (0.23), residues: 691 *********************** 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 165 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 154 time to evaluate : 2.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 163 average time/residue: 0.3040 time to fit residues: 81.8326 Evaluate side-chains 157 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 152 time to evaluate : 2.442 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1952 time to fit residues: 5.1177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 136 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 19 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN ** E2552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 20708 Z= 0.169 Angle : 0.576 13.777 28246 Z= 0.303 Chirality : 0.038 0.227 3195 Planarity : 0.003 0.038 3284 Dihedral : 18.586 173.739 3315 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.29 % 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: 1.14 (0.18), residues: 2240 helix: 2.22 (0.14), residues: 1396 sheet: -0.15 (0.47), residues: 139 loop : -2.24 (0.22), residues: 705 ********************** 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 174 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 2.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 172 average time/residue: 0.3132 time to fit residues: 88.9266 Evaluate side-chains 160 residues out of total 2037 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 2.438 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2286 time to fit residues: 3.6768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 1.9990 chunk 198 optimal weight: 0.0170 chunk 57 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 0.0970 chunk 78 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1166 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 ASN E1380 GLN ** 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 = 0.3549 r_free = 0.3549 target = 0.097969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.075060 restraints weight = 54930.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.075901 restraints weight = 39871.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.076282 restraints weight = 29232.975| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 20708 Z= 0.159 Angle : 0.574 13.488 28246 Z= 0.299 Chirality : 0.037 0.227 3195 Planarity : 0.003 0.038 3284 Dihedral : 18.489 172.761 3315 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 0.15 % 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: 1.26 (0.19), residues: 2240 helix: 2.33 (0.14), residues: 1397 sheet: -0.05 (0.46), residues: 139 loop : -2.23 (0.22), residues: 704 =============================================================================== Job complete usr+sys time: 2899.49 seconds wall clock time: 54 minutes 35.29 seconds (3275.29 seconds total)