Starting phenix.real_space_refine on Sat Mar 16 00:23:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdu_29014/03_2024/8fdu_29014_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdu_29014/03_2024/8fdu_29014.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdu_29014/03_2024/8fdu_29014.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdu_29014/03_2024/8fdu_29014.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdu_29014/03_2024/8fdu_29014_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fdu_29014/03_2024/8fdu_29014_updated.pdb" } resolution = 3.3 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= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 76 5.16 5 C 8326 2.51 5 N 2317 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A GLU 1343": "OE1" <-> "OE2" Residue "A ASP 1380": "OD1" <-> "OD2" Residue "A GLU 1447": "OE1" <-> "OE2" Residue "A GLU 1448": "OE1" <-> "OE2" Residue "A PHE 1457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1459": "OE1" <-> "OE2" Residue "A ASP 1462": "OD1" <-> "OD2" Residue "A GLU 1551": "OE1" <-> "OE2" Residue "A PHE 1732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1738": "OE1" <-> "OE2" Residue "A GLU 1755": "OE1" <-> "OE2" Residue "A PHE 1998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1999": "OD1" <-> "OD2" Residue "A PHE 2156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2161": "OD1" <-> "OD2" Residue "A GLU 2249": "OE1" <-> "OE2" Residue "A GLU 2254": "OE1" <-> "OE2" Residue "A GLU 2271": "OE1" <-> "OE2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B GLU 296": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "B PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C ASP 193": "OD1" <-> "OD2" Residue "C ASP 325": "OD1" <-> "OD2" Residue "C ASP 359": "OD1" <-> "OD2" Residue "C TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 388": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13193 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 8141 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 50, 'TRANS': 950} Chain breaks: 1 Chain: "B" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2499 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain: "C" Number of atoms: 2499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2499 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.21, per 1000 atoms: 0.55 Number of scatterers: 13193 At special positions: 0 Unit cell: (96.516, 147.072, 122.943, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 4 15.00 O 2470 8.00 N 2317 7.00 C 8326 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: 5.00 Conformation dependent library (CDL) restraints added in 2.3 seconds 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3100 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 19 sheets defined 35.3% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 1117 through 1131 Processing helix chain 'A' and resid 1146 through 1156 removed outlier: 3.668A pdb=" N ALA A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1173 through 1183 Processing helix chain 'A' and resid 1223 through 1233 Processing helix chain 'A' and resid 1270 through 1273 No H-bonds generated for 'chain 'A' and resid 1270 through 1273' Processing helix chain 'A' and resid 1286 through 1303 removed outlier: 3.621A pdb=" N PHE A1296 " --> pdb=" O ILE A1292 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A1302 " --> pdb=" O ARG A1298 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU A1303 " --> pdb=" O ALA A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1328 removed outlier: 4.328A pdb=" N GLU A1312 " --> pdb=" O THR A1309 " (cutoff:3.500A) Proline residue: A1313 - end of helix removed outlier: 3.990A pdb=" N ARG A1328 " --> pdb=" O SER A1325 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1355 Processing helix chain 'A' and resid 1363 through 1378 Processing helix chain 'A' and resid 1385 through 1402 Processing helix chain 'A' and resid 1408 through 1411 No H-bonds generated for 'chain 'A' and resid 1408 through 1411' Processing helix chain 'A' and resid 1431 through 1448 removed outlier: 3.613A pdb=" N GLU A1447 " --> pdb=" O LYS A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1472 Processing helix chain 'A' and resid 1488 through 1498 Processing helix chain 'A' and resid 1514 through 1528 Processing helix chain 'A' and resid 1547 through 1559 Processing helix chain 'A' and resid 1569 through 1585 Processing helix chain 'A' and resid 1592 through 1605 Processing helix chain 'A' and resid 1619 through 1626 Processing helix chain 'A' and resid 1628 through 1632 Processing helix chain 'A' and resid 1644 through 1656 Processing helix chain 'A' and resid 1684 through 1708 removed outlier: 3.685A pdb=" N ASN A1690 " --> pdb=" O GLU A1686 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS A1700 " --> pdb=" O HIS A1696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1718 through 1764 Processing helix chain 'A' and resid 1951 through 1994 removed outlier: 3.841A pdb=" N GLU A1963 " --> pdb=" O SER A1959 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG A1966 " --> pdb=" O ALA A1962 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LYS A1975 " --> pdb=" O SER A1971 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN A1976 " --> pdb=" O GLU A1972 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA A1982 " --> pdb=" O MET A1978 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N GLY A1983 " --> pdb=" O SER A1979 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP A1984 " --> pdb=" O THR A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 2000 through 2016 Processing helix chain 'A' and resid 2027 through 2031 Processing helix chain 'A' and resid 2034 through 2042 removed outlier: 3.564A pdb=" N ARG A2039 " --> pdb=" O ASP A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2049 through 2059 Processing helix chain 'A' and resid 2073 through 2081 Processing helix chain 'A' and resid 2083 through 2085 No H-bonds generated for 'chain 'A' and resid 2083 through 2085' Processing helix chain 'A' and resid 2095 through 2107 removed outlier: 4.094A pdb=" N ARG A2098 " --> pdb=" O ASP A2095 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN A2100 " --> pdb=" O PHE A2097 " (cutoff:3.500A) Processing helix chain 'A' and resid 2121 through 2128 Proline residue: A2125 - end of helix Processing helix chain 'A' and resid 2168 through 2171 No H-bonds generated for 'chain 'A' and resid 2168 through 2171' Processing helix chain 'A' and resid 2183 through 2198 Processing helix chain 'A' and resid 2200 through 2233 Processing helix chain 'A' and resid 2241 through 2267 removed outlier: 3.761A pdb=" N ILE A2245 " --> pdb=" O ASP A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2269 through 2277 Processing helix chain 'B' and resid 288 through 298 removed outlier: 4.235A pdb=" N SER B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 298 removed outlier: 4.853A pdb=" N SER C 292 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 1277 through 1280 removed outlier: 3.652A pdb=" N VAL A1254 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU A1161 " --> pdb=" O TRP A1203 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1193 through 1195 removed outlier: 3.933A pdb=" N VAL A1193 " --> pdb=" O TRP A1245 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1536 through 1540 removed outlier: 6.334A pdb=" N HIS A1608 " --> pdb=" O PHE A1537 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N MET A1539 " --> pdb=" O HIS A1608 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A1610 " --> pdb=" O MET A1539 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A1478 " --> pdb=" O PHE A1611 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N MET A1613 " --> pdb=" O LEU A1478 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N LEU A1480 " --> pdb=" O MET A1613 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL A1635 " --> pdb=" O LEU A1479 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE A1481 " --> pdb=" O VAL A1635 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN A1637 " --> pdb=" O ILE A1481 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 2175 through 2178 removed outlier: 7.800A pdb=" N ILE A2155 " --> pdb=" O PRO A2065 " (cutoff:3.500A) removed outlier: 8.922A pdb=" N ILE A2067 " --> pdb=" O ILE A2155 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU A2157 " --> pdb=" O ILE A2067 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A2111 " --> pdb=" O PHE A2156 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N SER A2158 " --> pdb=" O LEU A2111 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A2113 " --> pdb=" O SER A2158 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR A2088 " --> pdb=" O LEU A2112 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLN A2114 " --> pdb=" O THR A2088 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N THR A2090 " --> pdb=" O GLN A2114 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 2138 through 2142 removed outlier: 4.466A pdb=" N VAL A2138 " --> pdb=" O LEU A2149 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 112 through 117 removed outlier: 6.681A pdb=" N ALA B 127 " --> pdb=" O THR B 113 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL B 115 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 125 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASP B 137 " --> pdb=" O PHE B 143 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE B 143 " --> pdb=" O ASP B 137 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 154 through 159 removed outlier: 6.907A pdb=" N CYS B 169 " --> pdb=" O GLN B 155 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 157 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA B 167 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE B 159 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU B 165 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER B 170 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 187 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP B 179 " --> pdb=" O CYS B 185 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N CYS B 185 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 196 through 201 removed outlier: 6.592A pdb=" N ALA B 211 " --> pdb=" O SER B 197 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N VAL B 199 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL B 209 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ILE B 201 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N HIS B 207 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER B 212 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR B 216 " --> pdb=" O SER B 212 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 229 " --> pdb=" O MET B 219 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLU B 221 " --> pdb=" O CYS B 227 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N CYS B 227 " --> pdb=" O GLU B 221 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 238 through 243 removed outlier: 6.722A pdb=" N CYS B 253 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 241 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA B 251 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B 249 " --> pdb=" O PRO B 243 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 263 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS B 269 " --> pdb=" O VAL B 263 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 280 through 285 removed outlier: 6.814A pdb=" N GLY B 315 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE B 283 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 313 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N TRP B 285 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE B 311 " --> pdb=" O TRP B 285 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 316 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N THR B 320 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP B 325 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N CYS B 331 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 374 through 377 Processing sheet with id= L, first strand: chain 'B' and resid 101 through 105 removed outlier: 6.859A pdb=" N VAL B 407 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ALA B 104 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N VAL B 405 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 386 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 112 through 117 removed outlier: 6.815A pdb=" N ALA C 127 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL C 115 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 125 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ASP C 137 " --> pdb=" O PHE C 143 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE C 143 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 154 through 159 removed outlier: 6.933A pdb=" N CYS C 169 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE C 157 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA C 167 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE C 159 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU C 165 " --> pdb=" O PHE C 159 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 187 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP C 179 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N CYS C 185 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 196 through 201 removed outlier: 6.295A pdb=" N ALA C 211 " --> pdb=" O SER C 197 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 199 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL C 209 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ILE C 201 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N HIS C 207 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 212 " --> pdb=" O THR C 216 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR C 216 " --> pdb=" O SER C 212 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS C 229 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU C 221 " --> pdb=" O CYS C 227 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS C 227 " --> pdb=" O GLU C 221 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 238 through 243 removed outlier: 6.847A pdb=" N CYS C 253 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL C 241 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA C 251 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU C 249 " --> pdb=" O PRO C 243 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL C 263 " --> pdb=" O CYS C 269 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N CYS C 269 " --> pdb=" O VAL C 263 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 280 through 285 removed outlier: 6.889A pdb=" N GLY C 315 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ILE C 283 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU C 313 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N TRP C 285 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N PHE C 311 " --> pdb=" O TRP C 285 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER C 316 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR C 320 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP C 325 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N CYS C 331 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.408A pdb=" N THR C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 358 " --> pdb=" O THR C 362 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 387 through 389 removed outlier: 6.347A pdb=" N GLU C 409 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU C 101 " --> pdb=" O GLU C 409 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.25 Time building geometry restraints manager: 5.46 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: 3571 1.33 - 1.45: 2459 1.45 - 1.57: 7347 1.57 - 1.69: 6 1.69 - 1.81: 120 Bond restraints: 13503 Sorted by residual: bond pdb=" C4 ADP A3201 " pdb=" C5 ADP A3201 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4 ADP A3202 " pdb=" C5 ADP A3202 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" N ARG B 98 " pdb=" CA ARG B 98 " ideal model delta sigma weight residual 1.455 1.491 -0.035 7.00e-03 2.04e+04 2.57e+01 bond pdb=" N VAL B 120 " pdb=" CA VAL B 120 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.83e+01 bond pdb=" CA PRO A1141 " pdb=" C PRO A1141 " ideal model delta sigma weight residual 1.514 1.537 -0.022 5.50e-03 3.31e+04 1.67e+01 ... (remaining 13498 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.08: 334 106.08 - 113.11: 7391 113.11 - 120.14: 4844 120.14 - 127.18: 5549 127.18 - 134.21: 195 Bond angle restraints: 18313 Sorted by residual: angle pdb=" N VAL A1674 " pdb=" CA VAL A1674 " pdb=" C VAL A1674 " ideal model delta sigma weight residual 111.62 106.52 5.10 7.90e-01 1.60e+00 4.17e+01 angle pdb=" N PRO C 99 " pdb=" CA PRO C 99 " pdb=" C PRO C 99 " ideal model delta sigma weight residual 110.70 118.42 -7.72 1.22e+00 6.72e-01 4.00e+01 angle pdb=" N PRO B 99 " pdb=" CA PRO B 99 " pdb=" C PRO B 99 " ideal model delta sigma weight residual 110.70 117.54 -6.84 1.22e+00 6.72e-01 3.14e+01 angle pdb=" PA ADP A3202 " pdb=" O3A ADP A3202 " pdb=" PB ADP A3202 " ideal model delta sigma weight residual 120.50 133.41 -12.91 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CA PRO C 99 " pdb=" C PRO C 99 " pdb=" N PRO C 100 " ideal model delta sigma weight residual 117.93 123.06 -5.13 1.20e+00 6.94e-01 1.83e+01 ... (remaining 18308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.27: 7631 22.27 - 44.54: 428 44.54 - 66.81: 42 66.81 - 89.09: 8 89.09 - 111.36: 4 Dihedral angle restraints: 8113 sinusoidal: 3340 harmonic: 4773 Sorted by residual: dihedral pdb=" C5' ADP A3201 " pdb=" O5' ADP A3201 " pdb=" PA ADP A3201 " pdb=" O2A ADP A3201 " ideal model delta sinusoidal sigma weight residual -60.00 -171.35 111.36 1 2.00e+01 2.50e-03 3.27e+01 dihedral pdb=" CA HIS B 192 " pdb=" C HIS B 192 " pdb=" N ASP B 193 " pdb=" CA ASP B 193 " ideal model delta harmonic sigma weight residual -180.00 -161.32 -18.68 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA PRO B 99 " pdb=" C PRO B 99 " pdb=" N PRO B 100 " pdb=" CA PRO B 100 " ideal model delta harmonic sigma weight residual -180.00 -162.01 -17.99 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 8110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1436 0.046 - 0.091: 413 0.091 - 0.137: 143 0.137 - 0.182: 31 0.182 - 0.228: 5 Chirality restraints: 2028 Sorted by residual: chirality pdb=" CA LEU C 177 " pdb=" N LEU C 177 " pdb=" C LEU C 177 " pdb=" CB LEU C 177 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C3' ADP A3202 " pdb=" C2' ADP A3202 " pdb=" C4' ADP A3202 " pdb=" O3' ADP A3202 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL A1674 " pdb=" N VAL A1674 " pdb=" C VAL A1674 " pdb=" CB VAL A1674 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2025 not shown) Planarity restraints: 2342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1318 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C MET A1318 " 0.031 2.00e-02 2.50e+03 pdb=" O MET A1318 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A1319 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A1671 " 0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A1672 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A1672 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1672 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1320 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.10e+00 pdb=" C GLU A1320 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU A1320 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A1321 " 0.010 2.00e-02 2.50e+03 ... (remaining 2339 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1602 2.75 - 3.29: 13513 3.29 - 3.82: 22680 3.82 - 4.36: 27295 4.36 - 4.90: 45765 Nonbonded interactions: 110855 Sorted by model distance: nonbonded pdb=" OE2 GLU A1101 " pdb=" NH2 ARG A1302 " model vdw 2.212 2.520 nonbonded pdb=" O ASN A1420 " pdb=" NZ LYS C 319 " model vdw 2.213 2.520 nonbonded pdb=" OH TYR A1322 " pdb=" OE1 GLN A1326 " model vdw 2.221 2.440 nonbonded pdb=" OE2 GLU A1561 " pdb=" OH TYR A1596 " model vdw 2.247 2.440 nonbonded pdb=" NZ LYS B 102 " pdb=" OH TYR B 395 " model vdw 2.247 2.520 ... (remaining 110850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.850 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: 10.280 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 37.520 Find NCS groups from input model: 0.510 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 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 : 0.005 0.108 13503 Z= 0.360 Angle : 0.830 12.911 18313 Z= 0.498 Chirality : 0.050 0.228 2028 Planarity : 0.004 0.052 2342 Dihedral : 13.461 111.356 5013 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 0.21 % Allowed : 0.82 % Favored : 98.97 % 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: -0.29 (0.21), residues: 1625 helix: 1.05 (0.21), residues: 604 sheet: -0.66 (0.27), residues: 365 loop : -1.02 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1967 HIS 0.007 0.001 HIS B 382 PHE 0.018 0.002 PHE B 347 TYR 0.018 0.002 TYR A1426 ARG 0.010 0.000 ARG A2260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 192 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1257 CYS cc_start: 0.7274 (p) cc_final: 0.7037 (p) REVERT: B 206 ASP cc_start: 0.8571 (m-30) cc_final: 0.8367 (m-30) REVERT: C 179 ASP cc_start: 0.7667 (t0) cc_final: 0.7393 (t0) outliers start: 3 outliers final: 0 residues processed: 194 average time/residue: 0.2797 time to fit residues: 76.6884 Evaluate side-chains 143 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 6.9990 chunk 122 optimal weight: 0.3980 chunk 68 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 82 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 49 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 147 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13503 Z= 0.419 Angle : 0.706 9.101 18313 Z= 0.359 Chirality : 0.047 0.144 2028 Planarity : 0.005 0.050 2342 Dihedral : 5.708 111.251 1804 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.50 % Allowed : 10.59 % Favored : 87.90 % 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: -0.36 (0.20), residues: 1625 helix: 0.99 (0.21), residues: 599 sheet: -0.69 (0.27), residues: 342 loop : -1.03 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 220 HIS 0.007 0.001 HIS C 278 PHE 0.019 0.002 PHE A2216 TYR 0.017 0.002 TYR A1426 ARG 0.007 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 1.637 Fit side-chains revert: symmetry clash REVERT: A 1213 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8048 (mm) REVERT: A 1346 ARG cc_start: 0.7907 (ptp-170) cc_final: 0.7700 (ttp-110) REVERT: A 1575 MET cc_start: 0.7867 (mmt) cc_final: 0.7597 (mmt) REVERT: A 1677 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8366 (mmtp) REVERT: A 1742 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 1949 LYS cc_start: 0.4432 (tttp) cc_final: 0.3928 (pttt) REVERT: B 268 GLU cc_start: 0.7029 (pm20) cc_final: 0.6776 (pm20) REVERT: C 145 ARG cc_start: 0.6901 (ttt90) cc_final: 0.6461 (ttt90) REVERT: C 179 ASP cc_start: 0.7768 (t0) cc_final: 0.7553 (t0) REVERT: C 388 ASP cc_start: 0.7970 (t0) cc_final: 0.7706 (t0) outliers start: 22 outliers final: 13 residues processed: 166 average time/residue: 0.2605 time to fit residues: 62.9961 Evaluate side-chains 154 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 2078 ILE Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2184 SER Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 334 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 147 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13503 Z= 0.192 Angle : 0.581 6.990 18313 Z= 0.292 Chirality : 0.043 0.135 2028 Planarity : 0.004 0.044 2342 Dihedral : 5.266 96.322 1804 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.57 % Allowed : 12.71 % Favored : 85.71 % 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: -0.09 (0.21), residues: 1625 helix: 1.23 (0.21), residues: 606 sheet: -0.63 (0.27), residues: 365 loop : -0.86 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1370 HIS 0.003 0.001 HIS C 278 PHE 0.016 0.001 PHE B 183 TYR 0.013 0.001 TYR A1426 ARG 0.003 0.000 ARG A2173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1213 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7898 (mm) REVERT: A 1654 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7959 (t80) REVERT: A 1677 LYS cc_start: 0.8818 (mmtp) cc_final: 0.8541 (mmtp) REVERT: A 1742 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8148 (tm-30) REVERT: A 1949 LYS cc_start: 0.4433 (tttp) cc_final: 0.3942 (pttt) REVERT: A 2139 LEU cc_start: 0.6975 (mt) cc_final: 0.6759 (mt) REVERT: C 145 ARG cc_start: 0.6908 (ttt90) cc_final: 0.6498 (ttt90) outliers start: 23 outliers final: 16 residues processed: 171 average time/residue: 0.2682 time to fit residues: 66.5184 Evaluate side-chains 159 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1257 CYS Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1654 PHE Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 2078 ILE Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 136 TRP Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 0.0770 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13503 Z= 0.250 Angle : 0.600 7.806 18313 Z= 0.301 Chirality : 0.043 0.147 2028 Planarity : 0.004 0.047 2342 Dihedral : 5.228 91.547 1804 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.80 % Allowed : 13.26 % Favored : 83.94 % 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: -0.05 (0.21), residues: 1625 helix: 1.26 (0.21), residues: 607 sheet: -0.56 (0.27), residues: 359 loop : -0.88 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 366 HIS 0.004 0.001 HIS A1592 PHE 0.013 0.001 PHE B 347 TYR 0.012 0.001 TYR A1426 ARG 0.004 0.000 ARG A1493 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 151 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1213 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8036 (mm) REVERT: A 1654 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.8013 (t80) REVERT: A 1677 LYS cc_start: 0.8858 (mmtp) cc_final: 0.8648 (mmtp) REVERT: A 1742 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8158 (tm-30) REVERT: A 1949 LYS cc_start: 0.4501 (tttp) cc_final: 0.3960 (pttt) REVERT: A 1999 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7921 (p0) REVERT: A 2000 GLN cc_start: 0.7619 (mm110) cc_final: 0.7339 (tt0) REVERT: A 2076 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: A 2254 GLU cc_start: 0.8625 (pp20) cc_final: 0.8345 (pp20) REVERT: B 150 HIS cc_start: 0.7111 (OUTLIER) cc_final: 0.6046 (t-90) REVERT: B 382 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.7125 (t-90) REVERT: C 145 ARG cc_start: 0.7016 (ttt90) cc_final: 0.6743 (ttt90) outliers start: 41 outliers final: 27 residues processed: 177 average time/residue: 0.2484 time to fit residues: 65.2867 Evaluate side-chains 169 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 136 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1257 CYS Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1612 THR Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1654 PHE Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1744 MET Chi-restraints excluded: chain A residue 1999 ASP Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2078 ILE Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 136 TRP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 HIS Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 382 HIS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13503 Z= 0.229 Angle : 0.592 8.077 18313 Z= 0.297 Chirality : 0.043 0.137 2028 Planarity : 0.004 0.044 2342 Dihedral : 5.182 89.271 1804 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.08 % Allowed : 14.08 % Favored : 82.84 % 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: -0.01 (0.21), residues: 1625 helix: 1.26 (0.21), residues: 606 sheet: -0.49 (0.28), residues: 349 loop : -0.83 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 178 HIS 0.003 0.001 HIS A1745 PHE 0.010 0.001 PHE A1694 TYR 0.013 0.001 TYR B 291 ARG 0.003 0.000 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 149 time to evaluate : 1.467 Fit side-chains revert: symmetry clash REVERT: A 1169 SER cc_start: 0.9284 (p) cc_final: 0.9004 (p) REVERT: A 1213 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8076 (mm) REVERT: A 1481 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7700 (mp) REVERT: A 1654 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8035 (t80) REVERT: A 1742 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 1949 LYS cc_start: 0.4605 (tttp) cc_final: 0.4019 (pttt) REVERT: A 2076 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7293 (pm20) REVERT: A 2254 GLU cc_start: 0.8624 (pp20) cc_final: 0.8339 (pp20) outliers start: 45 outliers final: 31 residues processed: 182 average time/residue: 0.2467 time to fit residues: 66.5817 Evaluate side-chains 171 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 136 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1257 CYS Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1444 VAL Chi-restraints excluded: chain A residue 1481 ILE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1612 THR Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1654 PHE Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1744 MET Chi-restraints excluded: chain A residue 1973 THR Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2078 ILE Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 136 TRP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13503 Z= 0.193 Angle : 0.577 7.038 18313 Z= 0.287 Chirality : 0.042 0.144 2028 Planarity : 0.004 0.044 2342 Dihedral : 5.095 86.461 1804 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.21 % Allowed : 14.83 % Favored : 81.95 % 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: 0.10 (0.21), residues: 1625 helix: 1.38 (0.21), residues: 603 sheet: -0.42 (0.28), residues: 349 loop : -0.81 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 178 HIS 0.003 0.001 HIS C 207 PHE 0.010 0.001 PHE A1694 TYR 0.023 0.001 TYR B 291 ARG 0.006 0.000 ARG C 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 147 time to evaluate : 1.612 Fit side-chains revert: symmetry clash REVERT: A 1169 SER cc_start: 0.9281 (p) cc_final: 0.9007 (p) REVERT: A 1213 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8101 (mm) REVERT: A 1481 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7643 (mp) REVERT: A 1654 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.8084 (t80) REVERT: A 1742 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 1949 LYS cc_start: 0.4628 (tttp) cc_final: 0.4038 (pttt) REVERT: A 2000 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7336 (tt0) REVERT: A 2076 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: A 2130 GLU cc_start: 0.8053 (tt0) cc_final: 0.7726 (tm-30) REVERT: A 2254 GLU cc_start: 0.8625 (pp20) cc_final: 0.8322 (pp20) REVERT: B 150 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6199 (t-90) REVERT: C 145 ARG cc_start: 0.7076 (ttt90) cc_final: 0.6815 (ttt90) outliers start: 47 outliers final: 34 residues processed: 182 average time/residue: 0.2483 time to fit residues: 67.2021 Evaluate side-chains 175 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 136 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1206 LEU Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1257 CYS Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1481 ILE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1612 THR Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1654 PHE Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1744 MET Chi-restraints excluded: chain A residue 1973 THR Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2078 ILE Chi-restraints excluded: chain A residue 2084 ASP Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2222 GLN Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 136 TRP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 150 HIS Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 114 optimal weight: 0.0970 chunk 88 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1291 GLN ** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2004 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13503 Z= 0.153 Angle : 0.558 11.206 18313 Z= 0.277 Chirality : 0.042 0.137 2028 Planarity : 0.004 0.043 2342 Dihedral : 4.952 81.635 1804 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.60 % Allowed : 15.52 % Favored : 81.89 % 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 (0.21), residues: 1625 helix: 1.52 (0.21), residues: 604 sheet: -0.30 (0.28), residues: 349 loop : -0.74 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 178 HIS 0.003 0.001 HIS C 207 PHE 0.011 0.001 PHE A1457 TYR 0.025 0.001 TYR B 291 ARG 0.006 0.000 ARG C 145 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3250 Ramachandran restraints generated. 1625 Oldfield, 0 Emsley, 1625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1169 SER cc_start: 0.9262 (p) cc_final: 0.9004 (p) REVERT: A 1213 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8039 (mm) REVERT: A 1481 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7625 (mp) REVERT: A 1654 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8109 (t80) REVERT: A 1677 LYS cc_start: 0.8865 (mmtp) cc_final: 0.8665 (mmtp) REVERT: A 1742 GLN cc_start: 0.8344 (tm-30) cc_final: 0.8086 (tm-30) REVERT: A 1949 LYS cc_start: 0.4615 (tttp) cc_final: 0.4009 (pttt) REVERT: A 2000 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7347 (tt0) REVERT: A 2076 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: A 2254 GLU cc_start: 0.8564 (pp20) cc_final: 0.8239 (pp20) REVERT: B 150 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6150 (t-90) REVERT: C 145 ARG cc_start: 0.7048 (ttt90) cc_final: 0.6837 (ttt90) REVERT: C 220 TRP cc_start: 0.8562 (OUTLIER) cc_final: 0.8006 (m100) outliers start: 38 outliers final: 27 residues processed: 181 average time/residue: 0.2536 time to fit residues: 67.3867 Evaluate side-chains 173 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 140 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1113 VAL Chi-restraints excluded: chain A residue 1198 VAL Chi-restraints excluded: chain A residue 1213 LEU Chi-restraints excluded: chain A residue 1257 CYS Chi-restraints excluded: chain A residue 1276 VAL Chi-restraints excluded: chain A residue 1279 VAL Chi-restraints excluded: chain A residue 1358 LEU Chi-restraints excluded: chain A residue 1481 ILE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1654 PHE Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1973 THR Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2078 ILE Chi-restraints excluded: chain A residue 2126 VAL Chi-restraints excluded: chain A residue 2222 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 136 TRP Chi-restraints excluded: chain B residue 150 HIS Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 333 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 220 TRP Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 366 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.9892 > 50: distance: 49 - 54: 34.186 distance: 55 - 56: 57.587 distance: 56 - 57: 40.461 distance: 56 - 58: 16.345 distance: 58 - 59: 40.026 distance: 59 - 60: 33.815 distance: 60 - 61: 39.744 distance: 60 - 66: 41.087 distance: 62 - 63: 41.328 distance: 63 - 64: 39.144 distance: 63 - 65: 43.533 distance: 66 - 67: 32.430 distance: 67 - 68: 21.362 distance: 67 - 70: 45.645 distance: 68 - 77: 11.439 distance: 70 - 71: 39.363 distance: 71 - 72: 41.066 distance: 71 - 73: 38.921 distance: 72 - 74: 40.602 distance: 73 - 75: 10.515 distance: 74 - 76: 40.317 distance: 75 - 76: 11.920 distance: 77 - 78: 26.527 distance: 78 - 79: 46.657 distance: 78 - 81: 56.971 distance: 79 - 80: 12.707 distance: 79 - 86: 14.732 distance: 81 - 82: 56.562 distance: 83 - 84: 39.928 distance: 83 - 85: 40.179 distance: 86 - 87: 40.817 distance: 87 - 88: 57.546 distance: 88 - 90: 69.052 distance: 91 - 94: 42.112 distance: 92 - 93: 29.758 distance: 92 - 98: 39.884 distance: 93 - 124: 30.289 distance: 94 - 95: 51.626 distance: 95 - 96: 57.002 distance: 98 - 99: 40.830 distance: 99 - 100: 64.503 distance: 99 - 102: 33.823 distance: 100 - 101: 40.038 distance: 101 - 131: 29.692 distance: 102 - 103: 47.834 distance: 104 - 105: 35.489 distance: 104 - 106: 56.550 distance: 107 - 108: 47.998 distance: 108 - 109: 60.927 distance: 108 - 111: 39.087 distance: 109 - 110: 47.526 distance: 109 - 119: 56.856 distance: 110 - 139: 27.379 distance: 111 - 112: 14.433 distance: 112 - 113: 27.212 distance: 112 - 114: 28.711 distance: 113 - 115: 59.060 distance: 114 - 116: 70.657 distance: 115 - 117: 13.475 distance: 116 - 117: 40.674 distance: 117 - 118: 68.772 distance: 119 - 120: 55.187 distance: 120 - 121: 63.866 distance: 120 - 123: 39.299 distance: 121 - 122: 56.615 distance: 121 - 124: 40.618 distance: 122 - 147: 36.452 distance: 124 - 125: 6.773 distance: 125 - 126: 43.042 distance: 125 - 128: 25.649 distance: 126 - 127: 46.520 distance: 126 - 131: 17.841 distance: 127 - 154: 28.931 distance: 128 - 129: 41.347 distance: 128 - 130: 49.119