Starting phenix.real_space_refine on Mon Dec 30 15:56:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fdu_29014/12_2024/8fdu_29014.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fdu_29014/12_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/cci-nas-00/data/ceres_data/8fdu_29014/12_2024/8fdu_29014.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fdu_29014/12_2024/8fdu_29014.map" model { file = "/net/cci-nas-00/data/ceres_data/8fdu_29014/12_2024/8fdu_29014.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fdu_29014/12_2024/8fdu_29014.cif" } 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. Time to flip 39 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.27, per 1000 atoms: 0.63 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 - 3.00 Amino acid : True - 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: 3.38 Conformation dependent library (CDL) restraints added in 1.8 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... Secondary structure from input PDB file: 45 helices and 20 sheets defined 39.9% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 1116 through 1132 removed outlier: 3.525A pdb=" N GLU A1132 " --> pdb=" O THR A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1157 removed outlier: 3.668A pdb=" N ALA A1156 " --> pdb=" O SER A1152 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A1157 " --> pdb=" O ALA A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1184 removed outlier: 4.262A pdb=" N LEU A1176 " --> pdb=" O THR A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1234 Processing helix chain 'A' and resid 1269 through 1274 removed outlier: 3.618A pdb=" N ARG A1274 " --> pdb=" O HIS A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1301 removed outlier: 3.621A pdb=" N PHE A1296 " --> pdb=" O ILE A1292 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1304 No H-bonds generated for 'chain 'A' and resid 1302 through 1304' Processing helix chain 'A' and resid 1307 through 1309 No H-bonds generated for 'chain 'A' and resid 1307 through 1309' Processing helix chain 'A' and resid 1310 through 1329 removed outlier: 3.577A pdb=" N ALA A1316 " --> pdb=" O GLU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1355 removed outlier: 3.809A pdb=" N MET A1344 " --> pdb=" O SER A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1379 Processing helix chain 'A' and resid 1384 through 1403 removed outlier: 3.512A pdb=" N ARG A1388 " --> pdb=" O GLU A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1412 Processing helix chain 'A' and resid 1430 through 1449 removed outlier: 3.613A pdb=" N GLU A1447 " --> pdb=" O LYS A1443 " (cutoff:3.500A) Processing helix chain 'A' and resid 1457 through 1473 removed outlier: 3.584A pdb=" N GLN A1473 " --> pdb=" O ARG A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1499 Processing helix chain 'A' and resid 1513 through 1529 Processing helix chain 'A' and resid 1546 through 1560 removed outlier: 3.667A pdb=" N LEU A1550 " --> pdb=" O ASP A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1586 Processing helix chain 'A' and resid 1591 through 1606 Processing helix chain 'A' and resid 1618 through 1627 removed outlier: 3.858A pdb=" N ASP A1622 " --> pdb=" O GLU A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1633 Processing helix chain 'A' and resid 1643 through 1655 Processing helix chain 'A' and resid 1683 through 1709 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 1717 through 1765 removed outlier: 3.632A pdb=" N TYR A1721 " --> pdb=" O THR A1717 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1980 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) Processing helix chain 'A' and resid 1980 through 1994 removed outlier: 3.553A pdb=" N ASP A1984 " --> pdb=" O THR A1980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1999 through 2017 Processing helix chain 'A' and resid 2026 through 2032 Processing helix chain 'A' and resid 2033 through 2043 removed outlier: 3.564A pdb=" N ARG A2039 " --> pdb=" O ASP A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2048 through 2060 Processing helix chain 'A' and resid 2072 through 2082 removed outlier: 3.562A pdb=" N GLU A2076 " --> pdb=" O GLY A2072 " (cutoff:3.500A) Processing helix chain 'A' and resid 2083 through 2086 Processing helix chain 'A' and resid 2096 through 2108 Processing helix chain 'A' and resid 2115 through 2119 removed outlier: 3.532A pdb=" N SER A2118 " --> pdb=" O ASP A2115 " (cutoff:3.500A) Processing helix chain 'A' and resid 2120 through 2122 No H-bonds generated for 'chain 'A' and resid 2120 through 2122' Processing helix chain 'A' and resid 2123 through 2129 Processing helix chain 'A' and resid 2167 through 2172 removed outlier: 4.132A pdb=" N SER A2172 " --> pdb=" O PRO A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2182 through 2199 Processing helix chain 'A' and resid 2199 through 2234 Processing helix chain 'A' and resid 2240 through 2268 removed outlier: 3.920A pdb=" N ILE A2244 " --> pdb=" O ASP A2240 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A2245 " --> pdb=" O ASP A2241 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A2268 " --> pdb=" O GLU A2264 " (cutoff:3.500A) Processing helix chain 'A' and resid 2268 through 2278 removed outlier: 3.977A pdb=" N GLN A2278 " --> pdb=" O THR A2274 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 299 removed outlier: 3.514A pdb=" N TYR B 291 " --> pdb=" O PRO B 287 " (cutoff:3.500A) 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 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 290 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 1160 through 1166 removed outlier: 3.769A pdb=" N GLU A1161 " --> pdb=" O TRP A1203 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A1254 " --> pdb=" O LEU A1206 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A1136 " --> pdb=" O GLY A1255 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N CYS A1257 " --> pdb=" O LEU A1136 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A1138 " --> pdb=" O CYS A1257 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1193 through 1195 removed outlier: 6.887A pdb=" N VAL A1193 " --> pdb=" O LYS A1247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA4, first strand: chain 'A' and resid 1504 through 1505 removed outlier: 6.728A pdb=" N TYR A1504 " --> pdb=" O ILE A1538 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N ASP A1540 " --> pdb=" O TYR A1504 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N PHE A1537 " --> pdb=" O VAL A1610 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A1612 " --> pdb=" O PHE A1537 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET A1539 " --> pdb=" O THR A1612 " (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) Processing sheet with id=AA5, first strand: chain 'A' and resid 2088 through 2091 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: 6.088A pdb=" N LEU A2066 " --> pdb=" O VAL A2177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 2132 through 2133 removed outlier: 4.466A pdb=" N VAL A2138 " --> pdb=" O LEU A2149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 7.647A pdb=" N GLU B 101 " --> pdb=" O GLU B 409 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU B 409 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR B 103 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 386 " --> pdb=" O GLY B 399 " (cutoff:3.500A) Processing sheet with id=AA8, 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: 6.229A pdb=" N ILE B 133 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 146 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 135 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 154 through 159 removed outlier: 3.747A pdb=" N ASP B 156 " --> pdb=" O CYS B 169 " (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=AB1, 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) Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 243 removed outlier: 3.688A pdb=" N MET B 240 " --> pdb=" O CYS B 253 " (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=AB3, first strand: chain 'B' and resid 280 through 285 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=AB4, first strand: chain 'B' and resid 342 through 347 Processing sheet with id=AB5, first strand: chain 'C' and resid 97 through 106 removed outlier: 4.323A pdb=" N GLU C 409 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL C 407 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA C 104 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL C 405 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 112 through 117 removed outlier: 6.821A pdb=" N VAL C 135 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id=AB7, 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: 6.521A pdb=" N ILE C 175 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N THR C 188 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C 177 " --> pdb=" O ILE C 186 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 196 through 201 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: 6.149A pdb=" N ILE C 217 " --> pdb=" O THR C 230 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR C 230 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N MET C 219 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 243 removed outlier: 3.550A pdb=" N MET C 240 " --> pdb=" O CYS C 253 " (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=AC1, first strand: chain 'C' and resid 280 through 285 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=AC2, first strand: chain 'C' and resid 342 through 347 618 hydrogen bonds defined for protein. 1800 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: 6.22 Time building geometry restraints manager: 3.61 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: 0.00 - 2.58: 17960 2.58 - 5.16: 310 5.16 - 7.75: 30 7.75 - 10.33: 8 10.33 - 12.91: 5 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: 1586 2.75 - 3.29: 13470 3.29 - 3.82: 22663 3.82 - 4.36: 27127 4.36 - 4.90: 45737 Nonbonded interactions: 110583 Sorted by model distance: nonbonded pdb=" OE2 GLU A1101 " pdb=" NH2 ARG A1302 " model vdw 2.212 3.120 nonbonded pdb=" O ASN A1420 " pdb=" NZ LYS C 319 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR A1322 " pdb=" OE1 GLN A1326 " model vdw 2.221 3.040 nonbonded pdb=" OE2 GLU A1561 " pdb=" OH TYR A1596 " model vdw 2.247 3.040 nonbonded pdb=" NZ LYS B 102 " pdb=" OH TYR B 395 " model vdw 2.247 3.120 ... (remaining 110578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 3.870 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: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 33.540 Find NCS groups from input model: 0.230 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: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.500 ------------------------------------------------------------------------------- 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= 0.359 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 to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 1.564 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: 0.3019 time to fit residues: 83.2315 Evaluate side-chains 143 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 1.452 ------------------------------------------------------------------------------- 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: 0.0970 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 chunk 49 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1297 ASN A1733 HIS A2004 GLN ** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13503 Z= 0.249 Angle : 0.637 7.965 18313 Z= 0.322 Chirality : 0.044 0.150 2028 Planarity : 0.004 0.042 2342 Dihedral : 5.483 103.865 1804 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.96 % Allowed : 8.00 % Favored : 91.05 % 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: 0.19 (0.21), residues: 1625 helix: 1.58 (0.21), residues: 607 sheet: -0.44 (0.27), residues: 347 loop : -0.86 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 324 HIS 0.004 0.001 HIS B 192 PHE 0.014 0.001 PHE A2216 TYR 0.013 0.001 TYR A1426 ARG 0.014 0.001 ARG B 411 *********************** 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 165 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1213 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7916 (mm) REVERT: A 1346 ARG cc_start: 0.7899 (ptp-170) cc_final: 0.7681 (ttp-110) REVERT: A 1677 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8217 (mmtp) REVERT: A 1742 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 1949 LYS cc_start: 0.4372 (tttp) cc_final: 0.3950 (pttt) REVERT: B 268 GLU cc_start: 0.7044 (pm20) cc_final: 0.6788 (pm20) REVERT: C 145 ARG cc_start: 0.6880 (ttt90) cc_final: 0.6510 (ttt90) REVERT: C 179 ASP cc_start: 0.7671 (t0) cc_final: 0.7238 (t0) outliers start: 14 outliers final: 6 residues processed: 158 average time/residue: 0.3109 time to fit residues: 72.3108 Evaluate side-chains 146 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 1.724 ------------------------------------------------------------------------------- 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 1699 LEU Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 370 ASN 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: 9.9990 chunk 45 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13503 Z= 0.248 Angle : 0.608 7.688 18313 Z= 0.306 Chirality : 0.044 0.134 2028 Planarity : 0.004 0.046 2342 Dihedral : 5.232 92.962 1804 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.37 % Allowed : 10.66 % Favored : 87.97 % 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: 0.37 (0.21), residues: 1625 helix: 1.76 (0.21), residues: 607 sheet: -0.39 (0.28), residues: 359 loop : -0.77 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 220 HIS 0.003 0.001 HIS A1745 PHE 0.014 0.001 PHE B 183 TYR 0.013 0.001 TYR A1426 ARG 0.004 0.000 ARG B 145 *********************** 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 174 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1213 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7939 (mm) REVERT: A 1677 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8258 (mmtp) REVERT: A 1742 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8204 (tm-30) REVERT: A 1949 LYS cc_start: 0.4405 (tttp) cc_final: 0.3974 (pttt) REVERT: B 268 GLU cc_start: 0.7055 (pm20) cc_final: 0.6842 (pm20) REVERT: C 145 ARG cc_start: 0.6992 (ttt90) cc_final: 0.6543 (ttt90) REVERT: C 179 ASP cc_start: 0.7615 (t0) cc_final: 0.7224 (t0) REVERT: C 367 ASP cc_start: 0.6985 (t0) cc_final: 0.6735 (t0) outliers start: 20 outliers final: 13 residues processed: 167 average time/residue: 0.2665 time to fit residues: 65.7612 Evaluate side-chains 156 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 1444 VAL Chi-restraints excluded: chain A residue 1613 MET Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1954 THR Chi-restraints excluded: chain A residue 2223 LEU Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain B residue 128 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: 2.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 156 optimal weight: 0.0000 chunk 77 optimal weight: 3.9990 chunk 140 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.5790 ------------------------------------------------------------------------------- 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: 0.7757 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13503 Z= 0.253 Angle : 0.602 7.705 18313 Z= 0.304 Chirality : 0.044 0.201 2028 Planarity : 0.004 0.047 2342 Dihedral : 5.151 84.887 1804 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.91 % Allowed : 12.17 % Favored : 85.92 % 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: 0.44 (0.21), residues: 1625 helix: 1.78 (0.21), residues: 607 sheet: -0.34 (0.28), residues: 349 loop : -0.70 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 220 HIS 0.004 0.001 HIS A1745 PHE 0.012 0.001 PHE B 347 TYR 0.013 0.001 TYR A1293 ARG 0.003 0.000 ARG B 98 *********************** 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 180 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1213 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8004 (mm) REVERT: A 1677 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8383 (mmtp) REVERT: A 1742 GLN cc_start: 0.8480 (tm-30) cc_final: 0.8190 (tm-30) REVERT: A 1949 LYS cc_start: 0.4433 (tttp) cc_final: 0.3940 (pttt) REVERT: A 2000 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7413 (tt0) REVERT: A 2076 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7238 (pm20) REVERT: A 2254 GLU cc_start: 0.8628 (pp20) cc_final: 0.8356 (pp20) REVERT: B 268 GLU cc_start: 0.6986 (pm20) cc_final: 0.6736 (pm20) REVERT: C 145 ARG cc_start: 0.7102 (ttt90) cc_final: 0.6619 (ttt90) REVERT: C 179 ASP cc_start: 0.7712 (t0) cc_final: 0.7310 (t0) outliers start: 28 outliers final: 18 residues processed: 169 average time/residue: 0.2636 time to fit residues: 65.5430 Evaluate side-chains 162 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.541 ------------------------------------------------------------------------------- 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 1444 VAL Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1744 MET Chi-restraints excluded: chain A residue 1954 THR Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2078 ILE Chi-restraints excluded: chain A residue 2222 GLN Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 96 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 0.2980 chunk 88 optimal weight: 0.0060 chunk 2 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 140 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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** B 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13503 Z= 0.163 Angle : 0.575 6.899 18313 Z= 0.289 Chirality : 0.042 0.139 2028 Planarity : 0.004 0.042 2342 Dihedral : 4.981 76.692 1804 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.57 % Allowed : 13.33 % Favored : 85.10 % 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: 0.63 (0.21), residues: 1625 helix: 1.99 (0.21), residues: 601 sheet: -0.10 (0.28), residues: 337 loop : -0.72 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 178 HIS 0.002 0.000 HIS B 118 PHE 0.011 0.001 PHE A1457 TYR 0.015 0.001 TYR A1293 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 186 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1169 SER cc_start: 0.9228 (p) cc_final: 0.8956 (p) REVERT: A 1213 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7932 (mm) REVERT: A 1266 LYS cc_start: 0.8085 (ptpt) cc_final: 0.7714 (mtmt) REVERT: A 1677 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8480 (mmtp) REVERT: A 1742 GLN cc_start: 0.8405 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 1949 LYS cc_start: 0.4537 (tttp) cc_final: 0.3990 (pttt) REVERT: A 2000 GLN cc_start: 0.7627 (mm-40) cc_final: 0.7334 (tt0) REVERT: A 2076 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: A 2254 GLU cc_start: 0.8612 (pp20) cc_final: 0.8331 (pp20) REVERT: B 323 MET cc_start: 0.4456 (OUTLIER) cc_final: 0.4186 (ptm) REVERT: B 382 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7377 (t-90) REVERT: C 145 ARG cc_start: 0.7097 (ttt90) cc_final: 0.6683 (ttt90) REVERT: C 179 ASP cc_start: 0.7635 (t0) cc_final: 0.7265 (t0) outliers start: 23 outliers final: 12 residues processed: 177 average time/residue: 0.2654 time to fit residues: 69.7164 Evaluate side-chains 163 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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 1358 LEU Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2078 ILE Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 370 ASN Chi-restraints excluded: chain B residue 382 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 0.0020 chunk 141 optimal weight: 0.0370 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 156 optimal weight: 0.4980 chunk 130 optimal weight: 0.0020 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1258 ASN A1291 GLN A1559 ASN ** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13503 Z= 0.150 Angle : 0.573 8.118 18313 Z= 0.287 Chirality : 0.042 0.139 2028 Planarity : 0.004 0.041 2342 Dihedral : 4.890 73.124 1804 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.12 % Allowed : 13.94 % 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: 0.73 (0.21), residues: 1625 helix: 2.08 (0.21), residues: 601 sheet: 0.04 (0.29), residues: 333 loop : -0.70 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 178 HIS 0.003 0.000 HIS A1336 PHE 0.012 0.001 PHE A1457 TYR 0.015 0.001 TYR A1293 ARG 0.006 0.000 ARG B 239 *********************** 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 to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1169 SER cc_start: 0.9195 (p) cc_final: 0.8916 (p) REVERT: A 1213 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7903 (mm) REVERT: A 1481 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7968 (mp) REVERT: A 1575 MET cc_start: 0.8035 (mtt) cc_final: 0.7835 (mtp) REVERT: A 1733 HIS cc_start: 0.7344 (t-90) cc_final: 0.7046 (t70) REVERT: A 1742 GLN cc_start: 0.8451 (tm-30) cc_final: 0.8187 (tm-30) REVERT: A 1949 LYS cc_start: 0.4530 (tttp) cc_final: 0.3991 (pttt) REVERT: A 2000 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7299 (tt0) REVERT: A 2076 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7092 (pm20) REVERT: A 2254 GLU cc_start: 0.8543 (pp20) cc_final: 0.8236 (pp20) REVERT: B 323 MET cc_start: 0.4413 (OUTLIER) cc_final: 0.4147 (ptm) REVERT: B 382 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.7388 (t-90) REVERT: C 145 ARG cc_start: 0.7187 (ttt90) cc_final: 0.6778 (ttt90) REVERT: C 179 ASP cc_start: 0.7687 (t0) cc_final: 0.7330 (t0) REVERT: C 374 MET cc_start: 0.8363 (tpp) cc_final: 0.8095 (tpp) outliers start: 31 outliers final: 19 residues processed: 183 average time/residue: 0.2555 time to fit residues: 69.9088 Evaluate side-chains 172 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 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 1545 LEU Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2076 GLU Chi-restraints excluded: chain A residue 2078 ILE Chi-restraints excluded: chain A residue 2257 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 136 TRP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 382 HIS Chi-restraints excluded: chain C residue 96 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 89 optimal weight: 0.0470 chunk 114 optimal weight: 6.9990 chunk 88 optimal weight: 40.0000 chunk 131 optimal weight: 0.0010 chunk 87 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.1888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1291 GLN ** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2100 ASN ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13503 Z= 0.220 Angle : 0.606 9.343 18313 Z= 0.303 Chirality : 0.043 0.161 2028 Planarity : 0.004 0.042 2342 Dihedral : 4.921 74.184 1804 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.32 % Allowed : 14.97 % Favored : 82.71 % 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: 0.69 (0.21), residues: 1625 helix: 2.06 (0.21), residues: 601 sheet: 0.01 (0.28), residues: 333 loop : -0.74 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 178 HIS 0.003 0.001 HIS A1696 PHE 0.010 0.001 PHE B 347 TYR 0.013 0.001 TYR A1293 ARG 0.004 0.000 ARG A1493 *********************** 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 181 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1169 SER cc_start: 0.9184 (p) cc_final: 0.8920 (p) REVERT: A 1213 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7607 (mm) REVERT: A 1481 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7987 (mp) REVERT: A 1742 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8134 (tm-30) REVERT: A 1949 LYS cc_start: 0.4586 (tttp) cc_final: 0.3992 (pttt) REVERT: A 2031 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8867 (mm) REVERT: A 2076 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: A 2254 GLU cc_start: 0.8572 (pp20) cc_final: 0.8253 (pp20) REVERT: B 323 MET cc_start: 0.4181 (OUTLIER) cc_final: 0.3910 (ptm) REVERT: B 382 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7460 (t-90) REVERT: C 145 ARG cc_start: 0.7244 (ttt90) cc_final: 0.6805 (ttt90) REVERT: C 179 ASP cc_start: 0.7731 (t0) cc_final: 0.7405 (t0) REVERT: C 374 MET cc_start: 0.8253 (tpp) cc_final: 0.8051 (tpp) outliers start: 34 outliers final: 20 residues processed: 171 average time/residue: 0.2526 time to fit residues: 64.6586 Evaluate side-chains 167 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 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 1545 LEU Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 1744 MET Chi-restraints excluded: chain A residue 2028 THR Chi-restraints excluded: chain A residue 2031 LEU 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 2257 GLU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 382 HIS Chi-restraints excluded: chain C residue 96 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1509 HIS ** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13503 Z= 0.303 Angle : 0.643 11.852 18313 Z= 0.326 Chirality : 0.045 0.201 2028 Planarity : 0.004 0.044 2342 Dihedral : 5.135 80.163 1804 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.19 % Allowed : 15.04 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.21), residues: 1625 helix: 1.82 (0.21), residues: 601 sheet: -0.13 (0.28), residues: 325 loop : -0.80 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 178 HIS 0.004 0.001 HIS A1745 PHE 0.013 0.001 PHE A2156 TYR 0.016 0.002 TYR B 103 ARG 0.003 0.000 ARG A2237 *********************** REFINEMENT MACRO_CYCLE 8 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 176 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1213 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8065 (mm) REVERT: A 1481 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7984 (mp) REVERT: A 1677 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8375 (mmtp) REVERT: A 1742 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8116 (tm-30) REVERT: A 1949 LYS cc_start: 0.4559 (tttp) cc_final: 0.3887 (pttt) REVERT: A 2000 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7389 (tt0) REVERT: A 2076 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7317 (pm20) REVERT: A 2254 GLU cc_start: 0.8599 (pp20) cc_final: 0.8272 (pp20) REVERT: B 323 MET cc_start: 0.4252 (OUTLIER) cc_final: 0.3947 (ptm) REVERT: B 382 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7464 (t-90) REVERT: C 145 ARG cc_start: 0.7328 (ttt90) cc_final: 0.6763 (ttt90) REVERT: C 179 ASP cc_start: 0.7803 (t0) cc_final: 0.7425 (t0) REVERT: C 202 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8051 (mmp) outliers start: 32 outliers final: 21 residues processed: 169 average time/residue: 0.2538 time to fit residues: 64.2200 Evaluate side-chains 164 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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 1276 VAL 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 1545 LEU Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 2028 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 2257 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 382 HIS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 202 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.2980 chunk 136 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13503 Z= 0.223 Angle : 0.624 11.214 18313 Z= 0.312 Chirality : 0.044 0.180 2028 Planarity : 0.004 0.043 2342 Dihedral : 5.058 76.970 1804 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.05 % Allowed : 15.52 % Favored : 82.43 % 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: 0.50 (0.21), residues: 1625 helix: 1.83 (0.21), residues: 602 sheet: -0.11 (0.28), residues: 325 loop : -0.76 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 178 HIS 0.002 0.001 HIS C 207 PHE 0.010 0.001 PHE A1694 TYR 0.016 0.001 TYR B 291 ARG 0.004 0.000 ARG A1414 *********************** REFINEMENT MACRO_CYCLE 9 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 171 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1169 SER cc_start: 0.9328 (p) cc_final: 0.9034 (p) REVERT: A 1213 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8071 (mm) REVERT: A 1481 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7925 (mp) REVERT: A 1677 LYS cc_start: 0.8702 (mmtp) cc_final: 0.8456 (mmtp) REVERT: A 1742 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 1949 LYS cc_start: 0.4533 (tttp) cc_final: 0.3905 (pttt) REVERT: A 2000 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7288 (tt0) REVERT: A 2076 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: A 2254 GLU cc_start: 0.8602 (pp20) cc_final: 0.8283 (pp20) REVERT: B 323 MET cc_start: 0.4215 (OUTLIER) cc_final: 0.3916 (ptm) REVERT: B 382 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.7304 (t-90) REVERT: C 145 ARG cc_start: 0.7331 (ttt90) cc_final: 0.6814 (ttt90) REVERT: C 179 ASP cc_start: 0.7794 (t0) cc_final: 0.7438 (t0) outliers start: 30 outliers final: 20 residues processed: 164 average time/residue: 0.2568 time to fit residues: 63.0723 Evaluate side-chains 164 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 1276 VAL 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 1545 LEU Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 2028 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 B residue 120 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 382 HIS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 128 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2330 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= 0.233 Angle : 0.632 11.118 18313 Z= 0.316 Chirality : 0.044 0.177 2028 Planarity : 0.004 0.043 2342 Dihedral : 5.067 77.165 1804 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.85 % Allowed : 15.93 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1625 helix: 1.74 (0.21), residues: 610 sheet: -0.04 (0.29), residues: 321 loop : -0.76 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 178 HIS 0.002 0.001 HIS A1745 PHE 0.009 0.001 PHE A1694 TYR 0.024 0.001 TYR B 291 ARG 0.003 0.000 ARG A1414 ********************** REFINEMENT MACRO_CYCLE 10 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 170 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1213 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8065 (mm) REVERT: A 1481 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.7951 (mp) REVERT: A 1592 HIS cc_start: 0.7393 (m-70) cc_final: 0.7159 (t-90) REVERT: A 1677 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8447 (mmtp) REVERT: A 1742 GLN cc_start: 0.8410 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 1949 LYS cc_start: 0.4675 (tttp) cc_final: 0.3998 (pttt) REVERT: A 2076 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7325 (pm20) REVERT: A 2139 LEU cc_start: 0.6388 (mm) cc_final: 0.6157 (mt) REVERT: A 2253 ARG cc_start: 0.7902 (tpt90) cc_final: 0.7702 (tpt90) REVERT: A 2254 GLU cc_start: 0.8648 (pp20) cc_final: 0.8333 (pp20) REVERT: B 219 MET cc_start: 0.5583 (tpt) cc_final: 0.4956 (tpt) REVERT: B 382 HIS cc_start: 0.7747 (OUTLIER) cc_final: 0.7323 (t-90) REVERT: C 145 ARG cc_start: 0.7357 (ttt90) cc_final: 0.6816 (ttt90) REVERT: C 179 ASP cc_start: 0.7800 (t0) cc_final: 0.7428 (t0) outliers start: 27 outliers final: 20 residues processed: 165 average time/residue: 0.2638 time to fit residues: 65.2348 Evaluate side-chains 163 residues out of total 1463 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 1276 VAL Chi-restraints excluded: chain A residue 1481 ILE Chi-restraints excluded: chain A residue 1544 VAL Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1635 VAL Chi-restraints excluded: chain A residue 2028 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 B residue 120 VAL Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 382 HIS Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain C residue 366 TRP Chi-restraints excluded: chain C residue 385 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.110638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.086288 restraints weight = 33200.208| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.14 r_work: 0.3248 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13503 Z= 0.313 Angle : 0.667 10.865 18313 Z= 0.336 Chirality : 0.045 0.171 2028 Planarity : 0.004 0.045 2342 Dihedral : 5.240 82.595 1804 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.85 % Allowed : 16.06 % Favored : 82.09 % 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: 0.31 (0.21), residues: 1625 helix: 1.58 (0.21), residues: 608 sheet: -0.21 (0.29), residues: 325 loop : -0.79 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 178 HIS 0.004 0.001 HIS A1745 PHE 0.011 0.002 PHE A2156 TYR 0.021 0.002 TYR B 291 ARG 0.004 0.000 ARG A1493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2893.83 seconds wall clock time: 54 minutes 40.30 seconds (3280.30 seconds total)