Starting phenix.real_space_refine on Sun Aug 24 18:08:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ui7_42287/08_2025/8ui7_42287.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ui7_42287/08_2025/8ui7_42287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ui7_42287/08_2025/8ui7_42287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ui7_42287/08_2025/8ui7_42287.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ui7_42287/08_2025/8ui7_42287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ui7_42287/08_2025/8ui7_42287.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.001 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 3 5.21 5 S 145 5.16 5 C 13746 2.51 5 N 3709 2.21 5 O 4215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21831 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5134 Classifications: {'peptide': 643} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 621} Chain breaks: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2697 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} Chain: "D" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2536 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.24, per 1000 atoms: 0.19 Number of scatterers: 21831 At special positions: 0 Unit cell: (137.448, 129.168, 141.588, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 145 16.00 P 13 15.00 Mg 3 11.99 O 4215 8.00 N 3709 7.00 C 13746 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: 1.73 Conformation dependent library (CDL) restraints added in 695.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 14 sheets defined 51.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 940 through 955 Processing helix chain 'A' and resid 959 through 972 removed outlier: 4.172A pdb=" N TYR A 963 " --> pdb=" O SER A 959 " (cutoff:3.500A) Proline residue: A 965 - end of helix Processing helix chain 'A' and resid 1053 through 1058 Processing helix chain 'A' and resid 1062 through 1066 Processing helix chain 'A' and resid 1069 through 1098 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 6.204A pdb=" N GLU A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1328 Processing helix chain 'A' and resid 1340 through 1345 Processing helix chain 'A' and resid 1358 through 1373 Processing helix chain 'A' and resid 1378 through 1389 removed outlier: 3.955A pdb=" N PHE A1382 " --> pdb=" O ASP A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1406 Processing helix chain 'A' and resid 1457 through 1463 removed outlier: 3.648A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1468 Processing helix chain 'A' and resid 1474 through 1481 removed outlier: 3.669A pdb=" N HIS A1481 " --> pdb=" O SER A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1502 removed outlier: 4.125A pdb=" N ARG A1502 " --> pdb=" O GLU A1498 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1510 Processing helix chain 'A' and resid 1510 through 1515 Processing helix chain 'A' and resid 1633 through 1662 Processing helix chain 'A' and resid 1699 through 1730 removed outlier: 4.165A pdb=" N SER A1705 " --> pdb=" O THR A1701 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR A1730 " --> pdb=" O LYS A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1737 Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 4.328A pdb=" N ASN A1743 " --> pdb=" O ASP A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1750 through 1755 Processing helix chain 'A' and resid 1764 through 1779 Processing helix chain 'A' and resid 1789 through 1814 Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1817 through 1822 Processing helix chain 'A' and resid 1824 through 1828 Processing helix chain 'A' and resid 1832 through 1840 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 96 through 100 removed outlier: 4.270A pdb=" N LYS B 99 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.995A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.723A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.599A pdb=" N GLN B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 Processing helix chain 'B' and resid 214 through 224 Processing helix chain 'B' and resid 228 through 243 removed outlier: 3.629A pdb=" N ALA B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 289 removed outlier: 3.916A pdb=" N ALA B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.524A pdb=" N ILE B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.860A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 removed outlier: 3.660A pdb=" N LYS C 7 " --> pdb=" O THR C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.767A pdb=" N TYR C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.608A pdb=" N MET C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 82 through 86' Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 131 through 144 removed outlier: 4.079A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 Processing helix chain 'C' and resid 178 through 194 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 212 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 289 removed outlier: 3.634A pdb=" N ILE C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 315 removed outlier: 3.603A pdb=" N SER C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 339 removed outlier: 3.823A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 56 through 68 Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 97 through 104 removed outlier: 4.094A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 removed outlier: 4.236A pdb=" N VAL D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.726A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.538A pdb=" N THR D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 218 removed outlier: 3.809A pdb=" N GLN D 207 " --> pdb=" O SER D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 237 through 253 Processing helix chain 'D' and resid 258 through 264 removed outlier: 3.676A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.670A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 316 removed outlier: 3.957A pdb=" N GLU D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 363 removed outlier: 4.144A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS D 363 " --> pdb=" O LEU D 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 33 removed outlier: 3.612A pdb=" N ALA E 23 " --> pdb=" O HIS E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.613A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS E 66 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 4.113A pdb=" N ASP E 99 " --> pdb=" O ASN E 96 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 3.671A pdb=" N GLN E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 153 Processing helix chain 'E' and resid 172 through 179 removed outlier: 3.576A pdb=" N ARG E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS E 179 " --> pdb=" O ILE E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.521A pdb=" N ALA E 212 " --> pdb=" O PRO E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.695A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 287 through 300 Processing helix chain 'E' and resid 304 through 325 removed outlier: 4.004A pdb=" N GLY E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 348 removed outlier: 4.442A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 79 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.535A pdb=" N ALA F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.872A pdb=" N LEU F 221 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER F 222 " --> pdb=" O THR F 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 218 through 222' Processing helix chain 'G' and resid 8 through 19 removed outlier: 4.213A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 4.025A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 removed outlier: 3.632A pdb=" N LEU G 221 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 222 " --> pdb=" O THR G 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 218 through 222' Processing helix chain 'H' and resid 11 through 19 removed outlier: 4.038A pdb=" N GLU H 17 " --> pdb=" O LYS H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 217 through 222 Proline residue: H 220 - end of helix No H-bonds generated for 'chain 'H' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.284A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1151 through 1156 removed outlier: 5.685A pdb=" N LYS A1152 " --> pdb=" O LEU A1301 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A1303 " --> pdb=" O LYS A1152 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N PHE A1154 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N GLU A1305 " --> pdb=" O PHE A1154 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A1156 " --> pdb=" O GLU A1305 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ILE A1333 " --> pdb=" O SER A1300 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A1302 " --> pdb=" O ILE A1333 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR A1335 " --> pdb=" O ILE A1302 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A1304 " --> pdb=" O THR A1335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1519 through 1521 Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.634A pdb=" N LEU B 103 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.142A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 68 through 74 Processing sheet with id=AA7, first strand: chain 'F' and resid 60 through 62 removed outlier: 4.659A pdb=" N ILE F 87 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU F 104 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.308A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 177 through 183 removed outlier: 4.976A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 60 through 62 Processing sheet with id=AB2, first strand: chain 'G' and resid 66 through 71 removed outlier: 7.397A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY G 245 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS G 138 " --> pdb=" O THR G 196 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR G 196 " --> pdb=" O LYS G 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 60 through 61 removed outlier: 3.592A pdb=" N ARG H 61 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU H 3 " --> pdb=" O ARG H 61 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.352A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR H 51 " --> pdb=" O HIS H 246 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS H 246 " --> pdb=" O THR H 51 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR H 196 " --> pdb=" O LYS H 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 178 through 182 removed outlier: 3.827A pdb=" N GLY H 178 " --> pdb=" O ALA H 171 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA H 171 " --> pdb=" O GLY H 178 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) 1148 hydrogen bonds defined for protein. 3276 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: 3.53 Time building geometry restraints manager: 2.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 7201 1.35 - 1.50: 5441 1.50 - 1.65: 9324 1.65 - 1.80: 115 1.80 - 1.95: 101 Bond restraints: 22182 Sorted by residual: bond pdb=" N MET F 139 " pdb=" CA MET F 139 " ideal model delta sigma weight residual 1.453 1.486 -0.033 9.20e-03 1.18e+04 1.29e+01 bond pdb=" N ARG B 155 " pdb=" CA ARG B 155 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.17e-02 7.31e+03 9.32e+00 bond pdb=" N ASP D 50 " pdb=" CA ASP D 50 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.62e+00 bond pdb=" N MET E 229 " pdb=" CA MET E 229 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.79e+00 bond pdb=" C VAL C 183 " pdb=" N PRO C 184 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.23e-02 6.61e+03 3.55e+00 ... (remaining 22177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 29212 2.61 - 5.21: 619 5.21 - 7.82: 115 7.82 - 10.43: 33 10.43 - 13.04: 5 Bond angle restraints: 29984 Sorted by residual: angle pdb=" N LEU E 161 " pdb=" CA LEU E 161 " pdb=" C LEU E 161 " ideal model delta sigma weight residual 108.13 118.01 -9.88 1.72e+00 3.38e-01 3.30e+01 angle pdb=" N GLN E 313 " pdb=" CA GLN E 313 " pdb=" CB GLN E 313 " ideal model delta sigma weight residual 110.28 118.97 -8.69 1.55e+00 4.16e-01 3.14e+01 angle pdb=" C ASN H 107 " pdb=" N GLN H 108 " pdb=" CA GLN H 108 " ideal model delta sigma weight residual 121.54 130.53 -8.99 1.91e+00 2.74e-01 2.21e+01 angle pdb=" CB MET A1656 " pdb=" CG MET A1656 " pdb=" SD MET A1656 " ideal model delta sigma weight residual 112.70 125.74 -13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" CA GLN E 313 " pdb=" CB GLN E 313 " pdb=" CG GLN E 313 " ideal model delta sigma weight residual 114.10 122.40 -8.30 2.00e+00 2.50e-01 1.72e+01 ... (remaining 29979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.08: 13195 29.08 - 58.15: 433 58.15 - 87.23: 36 87.23 - 116.30: 1 116.30 - 145.38: 2 Dihedral angle restraints: 13667 sinusoidal: 5602 harmonic: 8065 Sorted by residual: dihedral pdb=" O2A ADP D2000 " pdb=" O3A ADP D2000 " pdb=" PA ADP D2000 " pdb=" PB ADP D2000 " ideal model delta sinusoidal sigma weight residual -60.00 85.38 -145.38 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 163.45 136.55 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" CA LEU A1662 " pdb=" C LEU A1662 " pdb=" N LEU A1663 " pdb=" CA LEU A1663 " ideal model delta harmonic sigma weight residual 180.00 150.25 29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 13664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2809 0.065 - 0.130: 583 0.130 - 0.195: 73 0.195 - 0.260: 11 0.260 - 0.325: 3 Chirality restraints: 3479 Sorted by residual: chirality pdb=" CG LEU C 255 " pdb=" CB LEU C 255 " pdb=" CD1 LEU C 255 " pdb=" CD2 LEU C 255 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CG LEU G 209 " pdb=" CB LEU G 209 " pdb=" CD1 LEU G 209 " pdb=" CD2 LEU G 209 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL H 123 " pdb=" CA VAL H 123 " pdb=" CG1 VAL H 123 " pdb=" CG2 VAL H 123 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 3476 not shown) Planarity restraints: 3815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS F 138 " 0.024 2.00e-02 2.50e+03 4.80e-02 2.31e+01 pdb=" C LYS F 138 " -0.083 2.00e-02 2.50e+03 pdb=" O LYS F 138 " 0.032 2.00e-02 2.50e+03 pdb=" N MET F 139 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 215 " -0.017 2.00e-02 2.50e+03 3.24e-02 1.84e+01 pdb=" CG PHE G 215 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE G 215 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE G 215 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE G 215 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE G 215 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 215 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 22 " 0.019 2.00e-02 2.50e+03 2.09e-02 1.10e+01 pdb=" CG TRP C 22 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP C 22 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP C 22 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 22 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP C 22 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 22 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 22 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 22 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 22 " 0.006 2.00e-02 2.50e+03 ... (remaining 3812 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 245 2.57 - 3.16: 17518 3.16 - 3.74: 36785 3.74 - 4.32: 48215 4.32 - 4.90: 77757 Nonbonded interactions: 180520 Sorted by model distance: nonbonded pdb="MG MG B 401 " pdb=" O3G AGS B 402 " model vdw 1.992 2.170 nonbonded pdb="MG MG B 401 " pdb=" O1B AGS B 402 " model vdw 2.010 2.170 nonbonded pdb="MG MG C 401 " pdb=" O1B AGS C 402 " model vdw 2.031 2.170 nonbonded pdb="MG MG A2001 " pdb=" O3G AGS A2002 " model vdw 2.040 2.170 nonbonded pdb="MG MG A2001 " pdb=" O1B AGS A2002 " model vdw 2.051 2.170 ... (remaining 180515 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 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.330 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 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 : 0.004 0.059 22182 Z= 0.210 Angle : 0.969 13.037 29984 Z= 0.499 Chirality : 0.053 0.325 3479 Planarity : 0.006 0.063 3815 Dihedral : 14.142 145.377 8415 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 0.04 % Allowed : 0.49 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.15), residues: 2734 helix: -0.67 (0.13), residues: 1278 sheet: -0.48 (0.22), residues: 495 loop : -1.22 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 333 TYR 0.030 0.003 TYR G 249 PHE 0.071 0.003 PHE G 215 TRP 0.051 0.003 TRP C 22 HIS 0.015 0.002 HIS A1644 Details of bonding type rmsd covalent geometry : bond 0.00439 (22182) covalent geometry : angle 0.96874 (29984) hydrogen bonds : bond 0.13970 ( 1148) hydrogen bonds : angle 6.38254 ( 3276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 394 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.8837 (ppp) cc_final: 0.8605 (ppp) REVERT: A 1317 PHE cc_start: 0.7703 (t80) cc_final: 0.7452 (t80) REVERT: A 1334 LEU cc_start: 0.9428 (mp) cc_final: 0.9194 (mt) REVERT: A 1506 PHE cc_start: 0.8109 (t80) cc_final: 0.7900 (t80) REVERT: A 1707 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8856 (mt-10) REVERT: A 1709 LYS cc_start: 0.9074 (ptpp) cc_final: 0.8823 (mtmm) REVERT: B 100 ASP cc_start: 0.8531 (m-30) cc_final: 0.8071 (m-30) REVERT: B 121 LYS cc_start: 0.9361 (ttmt) cc_final: 0.9078 (mttp) REVERT: B 123 PHE cc_start: 0.9406 (t80) cc_final: 0.9118 (t80) REVERT: B 293 GLU cc_start: 0.8916 (mp0) cc_final: 0.8589 (mp0) REVERT: B 308 MET cc_start: 0.9053 (ppp) cc_final: 0.8769 (ppp) REVERT: B 316 PHE cc_start: 0.9257 (m-10) cc_final: 0.9049 (m-80) REVERT: C 120 LYS cc_start: 0.9398 (mtmt) cc_final: 0.9013 (ttmt) REVERT: C 121 LEU cc_start: 0.9471 (tp) cc_final: 0.9265 (tp) REVERT: C 133 ASP cc_start: 0.9090 (m-30) cc_final: 0.8817 (m-30) REVERT: C 155 CYS cc_start: 0.7954 (t) cc_final: 0.7683 (t) REVERT: C 168 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7628 (tpp80) REVERT: E 139 LYS cc_start: 0.9169 (mmtm) cc_final: 0.8876 (mmmt) REVERT: E 313 GLN cc_start: 0.9090 (pm20) cc_final: 0.8500 (mp10) REVERT: E 314 MET cc_start: 0.9081 (ptp) cc_final: 0.8711 (ptt) REVERT: G 116 MET cc_start: 0.6136 (tpt) cc_final: 0.4942 (mpp) REVERT: G 215 PHE cc_start: 0.9293 (m-80) cc_final: 0.9001 (m-80) REVERT: G 247 LEU cc_start: 0.9324 (tp) cc_final: 0.8846 (tp) REVERT: G 249 TYR cc_start: 0.8883 (m-80) cc_final: 0.8674 (m-80) REVERT: G 251 LEU cc_start: 0.9647 (tp) cc_final: 0.9366 (tp) outliers start: 1 outliers final: 0 residues processed: 394 average time/residue: 0.1500 time to fit residues: 91.1915 Evaluate side-chains 298 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1644 HIS A1751 GLN ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 HIS ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN D 309 GLN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.095259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068219 restraints weight = 117486.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.069827 restraints weight = 87510.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.070935 restraints weight = 71949.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.071683 restraints weight = 63071.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.072163 restraints weight = 57708.123| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22182 Z= 0.231 Angle : 0.690 10.802 29984 Z= 0.358 Chirality : 0.042 0.164 3479 Planarity : 0.005 0.089 3815 Dihedral : 7.642 149.557 3027 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.08 % Allowed : 5.22 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.15), residues: 2734 helix: 0.22 (0.14), residues: 1293 sheet: -0.32 (0.23), residues: 489 loop : -0.99 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 61 TYR 0.030 0.002 TYR B 322 PHE 0.029 0.002 PHE F 215 TRP 0.013 0.002 TRP C 22 HIS 0.007 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00471 (22182) covalent geometry : angle 0.68973 (29984) hydrogen bonds : bond 0.04089 ( 1148) hydrogen bonds : angle 5.35109 ( 3276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 363 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.8932 (ppp) cc_final: 0.8333 (ppp) REVERT: A 1317 PHE cc_start: 0.7961 (t80) cc_final: 0.7742 (t80) REVERT: A 1708 LEU cc_start: 0.9265 (mt) cc_final: 0.9050 (mt) REVERT: B 100 ASP cc_start: 0.8595 (m-30) cc_final: 0.8295 (m-30) REVERT: B 171 CYS cc_start: 0.7008 (m) cc_final: 0.6744 (m) REVERT: B 223 PHE cc_start: 0.9496 (t80) cc_final: 0.9264 (t80) REVERT: B 293 GLU cc_start: 0.9056 (mp0) cc_final: 0.8840 (mp0) REVERT: C 120 LYS cc_start: 0.9539 (mtmt) cc_final: 0.9023 (mttt) REVERT: C 135 GLN cc_start: 0.8574 (mt0) cc_final: 0.8195 (mt0) REVERT: C 155 CYS cc_start: 0.8147 (t) cc_final: 0.7867 (t) REVERT: C 254 MET cc_start: 0.9153 (ptp) cc_final: 0.8942 (ptp) REVERT: C 330 GLN cc_start: 0.8741 (mm-40) cc_final: 0.7414 (tm-30) REVERT: E 139 LYS cc_start: 0.9156 (mmtm) cc_final: 0.8825 (mmmt) REVERT: E 317 TYR cc_start: 0.9162 (t80) cc_final: 0.8926 (t80) REVERT: E 335 PHE cc_start: 0.9150 (t80) cc_final: 0.8944 (t80) REVERT: E 340 MET cc_start: 0.9154 (mmp) cc_final: 0.8870 (mmm) REVERT: F 139 MET cc_start: 0.9095 (ptt) cc_final: 0.8887 (ptm) REVERT: F 248 LYS cc_start: 0.8585 (mmtt) cc_final: 0.8363 (mptt) REVERT: G 68 MET cc_start: 0.8643 (pmm) cc_final: 0.8404 (pmm) REVERT: G 247 LEU cc_start: 0.9102 (tp) cc_final: 0.8563 (tp) REVERT: G 251 LEU cc_start: 0.9649 (tp) cc_final: 0.9443 (tp) outliers start: 2 outliers final: 0 residues processed: 364 average time/residue: 0.1369 time to fit residues: 77.8850 Evaluate side-chains 284 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 126 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 232 optimal weight: 0.0870 chunk 97 optimal weight: 7.9990 chunk 104 optimal weight: 0.1980 chunk 188 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 196 optimal weight: 0.3980 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1644 HIS B 231 GLN ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.103814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.076469 restraints weight = 107441.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.078159 restraints weight = 81218.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.078987 restraints weight = 67064.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.079782 restraints weight = 59880.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.080340 restraints weight = 55051.325| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22182 Z= 0.125 Angle : 0.617 8.572 29984 Z= 0.311 Chirality : 0.042 0.171 3479 Planarity : 0.004 0.055 3815 Dihedral : 7.419 147.994 3027 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.04 % Allowed : 3.62 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.16), residues: 2734 helix: 0.50 (0.14), residues: 1317 sheet: -0.25 (0.23), residues: 481 loop : -0.95 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 149 TYR 0.025 0.002 TYR B 322 PHE 0.016 0.001 PHE A1324 TRP 0.019 0.001 TRP C 22 HIS 0.010 0.001 HIS A1644 Details of bonding type rmsd covalent geometry : bond 0.00268 (22182) covalent geometry : angle 0.61746 (29984) hydrogen bonds : bond 0.03622 ( 1148) hydrogen bonds : angle 5.03833 ( 3276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 384 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9022 (ppp) cc_final: 0.8459 (ppp) REVERT: A 1644 HIS cc_start: 0.8627 (m90) cc_final: 0.8222 (m90) REVERT: B 100 ASP cc_start: 0.8575 (m-30) cc_final: 0.8199 (m-30) REVERT: B 171 CYS cc_start: 0.7160 (m) cc_final: 0.6775 (m) REVERT: B 223 PHE cc_start: 0.9553 (t80) cc_final: 0.9227 (t80) REVERT: B 293 GLU cc_start: 0.8889 (mp0) cc_final: 0.8576 (mp0) REVERT: C 56 LEU cc_start: 0.9249 (mt) cc_final: 0.8946 (mt) REVERT: C 108 PHE cc_start: 0.9414 (t80) cc_final: 0.8575 (t80) REVERT: C 120 LYS cc_start: 0.9457 (mtmt) cc_final: 0.8983 (ttmt) REVERT: C 330 GLN cc_start: 0.8664 (mm-40) cc_final: 0.7755 (tm-30) REVERT: E 99 ASP cc_start: 0.8677 (p0) cc_final: 0.8327 (p0) REVERT: E 139 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8826 (mmmt) REVERT: E 161 LEU cc_start: 0.8388 (pp) cc_final: 0.8160 (pp) REVERT: F 40 MET cc_start: 0.8545 (ttt) cc_final: 0.8010 (ttt) REVERT: F 45 VAL cc_start: 0.9042 (m) cc_final: 0.8798 (p) REVERT: F 214 PHE cc_start: 0.9283 (m-80) cc_final: 0.9072 (m-80) REVERT: G 116 MET cc_start: 0.6839 (tpp) cc_final: 0.4676 (mpp) REVERT: G 139 MET cc_start: 0.8463 (tmm) cc_final: 0.8259 (tmm) REVERT: G 247 LEU cc_start: 0.9113 (tp) cc_final: 0.8708 (tp) REVERT: G 251 LEU cc_start: 0.9669 (tp) cc_final: 0.9414 (tp) outliers start: 1 outliers final: 0 residues processed: 384 average time/residue: 0.1418 time to fit residues: 84.4725 Evaluate side-chains 296 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 134 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 48 optimal weight: 0.0270 chunk 49 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 69 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 217 optimal weight: 20.0000 chunk 192 optimal weight: 9.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1500 GLN B 231 GLN B 235 ASN B 237 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN E 206 ASN E 323 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.093891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.067172 restraints weight = 116955.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.068698 restraints weight = 86973.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.069651 restraints weight = 71723.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.070403 restraints weight = 63513.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.070773 restraints weight = 58222.324| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22182 Z= 0.241 Angle : 0.706 9.113 29984 Z= 0.359 Chirality : 0.043 0.169 3479 Planarity : 0.005 0.072 3815 Dihedral : 7.426 147.313 3027 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.16), residues: 2734 helix: 0.45 (0.14), residues: 1305 sheet: -0.33 (0.23), residues: 487 loop : -0.94 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 61 TYR 0.022 0.002 TYR B 322 PHE 0.032 0.002 PHE C 151 TRP 0.038 0.002 TRP G 28 HIS 0.007 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00497 (22182) covalent geometry : angle 0.70617 (29984) hydrogen bonds : bond 0.03824 ( 1148) hydrogen bonds : angle 5.22090 ( 3276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 354 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9078 (ppp) cc_final: 0.8427 (ppp) REVERT: A 1644 HIS cc_start: 0.8753 (m90) cc_final: 0.8315 (m90) REVERT: B 121 LYS cc_start: 0.9329 (ttmt) cc_final: 0.9012 (mttp) REVERT: B 171 CYS cc_start: 0.6739 (m) cc_final: 0.6444 (m) REVERT: B 231 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8818 (mm-40) REVERT: C 56 LEU cc_start: 0.9259 (mt) cc_final: 0.8819 (pp) REVERT: C 58 LEU cc_start: 0.8910 (mp) cc_final: 0.8686 (mp) REVERT: C 86 MET cc_start: 0.7814 (mtt) cc_final: 0.7601 (mtt) REVERT: C 108 PHE cc_start: 0.9456 (t80) cc_final: 0.8795 (t80) REVERT: C 135 GLN cc_start: 0.8426 (mt0) cc_final: 0.7948 (mp10) REVERT: C 144 LYS cc_start: 0.9535 (tmmt) cc_final: 0.9182 (tppt) REVERT: C 148 ASN cc_start: 0.8918 (t0) cc_final: 0.8600 (t0) REVERT: D 356 MET cc_start: 0.8370 (tpt) cc_final: 0.8124 (tpt) REVERT: E 99 ASP cc_start: 0.8557 (p0) cc_final: 0.8123 (p0) REVERT: E 139 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8836 (mmmt) REVERT: E 161 LEU cc_start: 0.8599 (pp) cc_final: 0.8308 (pp) REVERT: E 335 PHE cc_start: 0.9174 (t80) cc_final: 0.8811 (t80) REVERT: E 339 PHE cc_start: 0.9210 (t80) cc_final: 0.9003 (t80) REVERT: E 340 MET cc_start: 0.9199 (mmp) cc_final: 0.8830 (mmt) REVERT: F 148 CYS cc_start: 0.8843 (m) cc_final: 0.8559 (m) REVERT: G 116 MET cc_start: 0.6959 (tpp) cc_final: 0.5206 (mpp) REVERT: G 247 LEU cc_start: 0.9050 (tp) cc_final: 0.8556 (tp) outliers start: 2 outliers final: 0 residues processed: 356 average time/residue: 0.1402 time to fit residues: 77.4381 Evaluate side-chains 277 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 261 optimal weight: 40.0000 chunk 157 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 8 optimal weight: 30.0000 chunk 253 optimal weight: 6.9990 chunk 263 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 143 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.095068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.068538 restraints weight = 118456.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.070144 restraints weight = 87331.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.071192 restraints weight = 71662.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.071902 restraints weight = 63066.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.072375 restraints weight = 57972.272| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22182 Z= 0.170 Angle : 0.645 8.836 29984 Z= 0.328 Chirality : 0.043 0.157 3479 Planarity : 0.004 0.054 3815 Dihedral : 7.376 148.580 3027 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.16), residues: 2734 helix: 0.55 (0.14), residues: 1312 sheet: -0.32 (0.23), residues: 490 loop : -0.95 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 5 TYR 0.021 0.002 TYR B 322 PHE 0.044 0.002 PHE G 215 TRP 0.023 0.002 TRP C 22 HIS 0.009 0.001 HIS E 37 Details of bonding type rmsd covalent geometry : bond 0.00360 (22182) covalent geometry : angle 0.64459 (29984) hydrogen bonds : bond 0.03516 ( 1148) hydrogen bonds : angle 5.05589 ( 3276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.8894 (ppp) cc_final: 0.8405 (ppp) REVERT: A 1644 HIS cc_start: 0.8744 (m90) cc_final: 0.8298 (m90) REVERT: B 100 ASP cc_start: 0.8382 (m-30) cc_final: 0.8165 (m-30) REVERT: B 171 CYS cc_start: 0.6911 (m) cc_final: 0.6643 (m) REVERT: C 56 LEU cc_start: 0.9273 (mt) cc_final: 0.8803 (pp) REVERT: C 58 LEU cc_start: 0.8897 (mp) cc_final: 0.8634 (mp) REVERT: C 108 PHE cc_start: 0.9292 (t80) cc_final: 0.8884 (t80) REVERT: C 148 ASN cc_start: 0.8867 (t0) cc_final: 0.8590 (t0) REVERT: D 327 ILE cc_start: 0.9270 (mt) cc_final: 0.9050 (mt) REVERT: D 356 MET cc_start: 0.8219 (tpt) cc_final: 0.8015 (tpt) REVERT: E 99 ASP cc_start: 0.8524 (p0) cc_final: 0.8234 (p0) REVERT: E 134 LEU cc_start: 0.9545 (mt) cc_final: 0.9099 (pp) REVERT: E 139 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8812 (mmmt) REVERT: E 339 PHE cc_start: 0.9149 (t80) cc_final: 0.8896 (t80) REVERT: E 340 MET cc_start: 0.9173 (mmp) cc_final: 0.8799 (mmt) REVERT: F 40 MET cc_start: 0.8400 (ttt) cc_final: 0.7893 (ttt) REVERT: F 148 CYS cc_start: 0.8815 (m) cc_final: 0.8553 (m) REVERT: F 199 MET cc_start: 0.6236 (ppp) cc_final: 0.5045 (ppp) REVERT: F 214 PHE cc_start: 0.9415 (m-80) cc_final: 0.9167 (m-80) REVERT: G 116 MET cc_start: 0.6951 (tpp) cc_final: 0.5212 (mpp) REVERT: G 215 PHE cc_start: 0.9287 (m-80) cc_final: 0.9051 (m-80) REVERT: G 247 LEU cc_start: 0.9060 (tp) cc_final: 0.8646 (tp) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1512 time to fit residues: 85.9179 Evaluate side-chains 281 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 211 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 221 optimal weight: 8.9990 chunk 175 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 323 GLN E 323 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.105517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.076136 restraints weight = 97913.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.077270 restraints weight = 78523.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.078223 restraints weight = 68642.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 16)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.078568 restraints weight = 62342.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.079050 restraints weight = 59195.181| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 22182 Z= 0.152 Angle : 0.646 11.375 29984 Z= 0.327 Chirality : 0.042 0.172 3479 Planarity : 0.004 0.061 3815 Dihedral : 7.336 147.323 3027 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.16), residues: 2734 helix: 0.63 (0.14), residues: 1318 sheet: -0.33 (0.23), residues: 492 loop : -0.85 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 112 TYR 0.020 0.002 TYR B 322 PHE 0.037 0.002 PHE G 215 TRP 0.030 0.002 TRP A 883 HIS 0.008 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00332 (22182) covalent geometry : angle 0.64602 (29984) hydrogen bonds : bond 0.03422 ( 1148) hydrogen bonds : angle 4.99152 ( 3276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9065 (ppp) cc_final: 0.8505 (ppp) REVERT: A 1365 TYR cc_start: 0.9592 (t80) cc_final: 0.9352 (t80) REVERT: A 1508 TYR cc_start: 0.8658 (t80) cc_final: 0.8366 (t80) REVERT: A 1644 HIS cc_start: 0.8660 (m90) cc_final: 0.8277 (m90) REVERT: A 1709 LYS cc_start: 0.9200 (ptpp) cc_final: 0.8772 (pttt) REVERT: A 1790 ARG cc_start: 0.8913 (mtm-85) cc_final: 0.8556 (mtt180) REVERT: B 102 MET cc_start: 0.8973 (tmm) cc_final: 0.8154 (tmm) REVERT: B 121 LYS cc_start: 0.9406 (ttmt) cc_final: 0.8916 (mttp) REVERT: B 156 ARG cc_start: 0.8996 (tpt170) cc_final: 0.8441 (tpm170) REVERT: B 171 CYS cc_start: 0.7024 (m) cc_final: 0.6747 (m) REVERT: C 56 LEU cc_start: 0.9241 (mt) cc_final: 0.8854 (pp) REVERT: C 87 VAL cc_start: 0.8855 (t) cc_final: 0.8636 (m) REVERT: C 88 LEU cc_start: 0.8901 (tp) cc_final: 0.8458 (tp) REVERT: C 121 LEU cc_start: 0.9006 (tp) cc_final: 0.8798 (tp) REVERT: C 135 GLN cc_start: 0.8389 (mt0) cc_final: 0.7972 (mp10) REVERT: C 152 CYS cc_start: 0.8090 (m) cc_final: 0.7845 (m) REVERT: D 327 ILE cc_start: 0.9339 (mt) cc_final: 0.9112 (mt) REVERT: D 356 MET cc_start: 0.8162 (tpt) cc_final: 0.7846 (tpt) REVERT: E 99 ASP cc_start: 0.8505 (p0) cc_final: 0.8256 (p0) REVERT: E 134 LEU cc_start: 0.9478 (mt) cc_final: 0.9062 (pp) REVERT: E 139 LYS cc_start: 0.9144 (mmtm) cc_final: 0.8842 (mmmt) REVERT: E 161 LEU cc_start: 0.8371 (pp) cc_final: 0.8106 (pp) REVERT: E 335 PHE cc_start: 0.9084 (t80) cc_final: 0.8742 (t80) REVERT: E 339 PHE cc_start: 0.9215 (t80) cc_final: 0.8857 (t80) REVERT: E 340 MET cc_start: 0.9301 (mmp) cc_final: 0.8870 (mmt) REVERT: F 40 MET cc_start: 0.8546 (ttt) cc_final: 0.7828 (ttt) REVERT: F 77 LYS cc_start: 0.8771 (tttt) cc_final: 0.8449 (tttt) REVERT: F 114 TYR cc_start: 0.9212 (m-80) cc_final: 0.9011 (m-10) REVERT: F 148 CYS cc_start: 0.8762 (m) cc_final: 0.8532 (m) REVERT: F 199 MET cc_start: 0.6044 (ppp) cc_final: 0.4670 (ppp) REVERT: G 116 MET cc_start: 0.7072 (tpp) cc_final: 0.4446 (mpp) REVERT: G 215 PHE cc_start: 0.9358 (m-80) cc_final: 0.9051 (m-80) REVERT: G 247 LEU cc_start: 0.9183 (tp) cc_final: 0.8745 (tp) REVERT: G 251 LEU cc_start: 0.9572 (tp) cc_final: 0.9341 (tp) REVERT: H 249 TYR cc_start: 0.8908 (m-10) cc_final: 0.8672 (m-10) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.1505 time to fit residues: 86.0160 Evaluate side-chains 287 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 170 optimal weight: 5.9990 chunk 138 optimal weight: 0.0370 chunk 248 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 236 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.109142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.079758 restraints weight = 109144.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.081320 restraints weight = 83821.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.082384 restraints weight = 70154.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.083130 restraints weight = 62668.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.083640 restraints weight = 57982.240| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22182 Z= 0.144 Angle : 0.640 9.239 29984 Z= 0.323 Chirality : 0.042 0.175 3479 Planarity : 0.004 0.056 3815 Dihedral : 7.291 145.905 3027 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.16), residues: 2734 helix: 0.68 (0.14), residues: 1325 sheet: -0.28 (0.23), residues: 494 loop : -0.85 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 112 TYR 0.023 0.002 TYR E 343 PHE 0.031 0.002 PHE C 108 TRP 0.054 0.002 TRP G 28 HIS 0.007 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00313 (22182) covalent geometry : angle 0.63989 (29984) hydrogen bonds : bond 0.03315 ( 1148) hydrogen bonds : angle 4.93127 ( 3276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9073 (ppp) cc_final: 0.8483 (ppp) REVERT: A 1365 TYR cc_start: 0.9525 (t80) cc_final: 0.9289 (t80) REVERT: A 1501 MET cc_start: 0.4000 (mmm) cc_final: 0.3781 (mmm) REVERT: A 1508 TYR cc_start: 0.8873 (t80) cc_final: 0.8516 (t80) REVERT: A 1644 HIS cc_start: 0.8732 (m90) cc_final: 0.8288 (m90) REVERT: A 1709 LYS cc_start: 0.9131 (ptpp) cc_final: 0.8897 (mtmm) REVERT: B 102 MET cc_start: 0.8563 (tmm) cc_final: 0.8033 (tmm) REVERT: B 121 LYS cc_start: 0.9491 (ttmt) cc_final: 0.8972 (mttp) REVERT: B 156 ARG cc_start: 0.8991 (tpt170) cc_final: 0.8427 (tpm170) REVERT: C 56 LEU cc_start: 0.9278 (mt) cc_final: 0.8859 (pp) REVERT: C 58 LEU cc_start: 0.8863 (mp) cc_final: 0.8546 (mp) REVERT: C 152 CYS cc_start: 0.8634 (m) cc_final: 0.8383 (m) REVERT: E 99 ASP cc_start: 0.8539 (p0) cc_final: 0.8041 (p0) REVERT: E 134 LEU cc_start: 0.9578 (mt) cc_final: 0.9092 (pp) REVERT: E 136 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7273 (mt-10) REVERT: E 139 LYS cc_start: 0.9127 (mmtm) cc_final: 0.8816 (mmmt) REVERT: E 156 MET cc_start: 0.8682 (pmm) cc_final: 0.8451 (pmm) REVERT: E 335 PHE cc_start: 0.9145 (t80) cc_final: 0.8847 (t80) REVERT: E 339 PHE cc_start: 0.9292 (t80) cc_final: 0.8874 (t80) REVERT: E 340 MET cc_start: 0.9295 (mmp) cc_final: 0.8923 (mmt) REVERT: F 40 MET cc_start: 0.8621 (ttt) cc_final: 0.8271 (ttt) REVERT: F 77 LYS cc_start: 0.8843 (tttt) cc_final: 0.8543 (tttt) REVERT: F 139 MET cc_start: 0.8823 (ppp) cc_final: 0.8620 (ppp) REVERT: F 199 MET cc_start: 0.6137 (ppp) cc_final: 0.4689 (ppp) REVERT: F 214 PHE cc_start: 0.9423 (m-80) cc_final: 0.9102 (m-80) REVERT: F 215 PHE cc_start: 0.9025 (m-80) cc_final: 0.8756 (m-80) REVERT: F 229 MET cc_start: 0.7869 (tmm) cc_final: 0.7304 (tmm) REVERT: G 28 TRP cc_start: 0.8976 (m100) cc_final: 0.8078 (m100) REVERT: G 247 LEU cc_start: 0.9209 (tp) cc_final: 0.8751 (tp) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1374 time to fit residues: 79.3260 Evaluate side-chains 285 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 170 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 chunk 74 optimal weight: 0.2980 chunk 108 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 269 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 206 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.105306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075844 restraints weight = 98933.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076985 restraints weight = 79728.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.077874 restraints weight = 69636.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.078255 restraints weight = 63904.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.078683 restraints weight = 60726.304| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 22182 Z= 0.162 Angle : 0.656 8.937 29984 Z= 0.332 Chirality : 0.043 0.174 3479 Planarity : 0.004 0.055 3815 Dihedral : 7.282 145.668 3027 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.16), residues: 2734 helix: 0.68 (0.14), residues: 1327 sheet: -0.35 (0.23), residues: 509 loop : -0.81 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1790 TYR 0.020 0.002 TYR E 343 PHE 0.027 0.002 PHE C 151 TRP 0.031 0.002 TRP G 28 HIS 0.007 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00353 (22182) covalent geometry : angle 0.65555 (29984) hydrogen bonds : bond 0.03348 ( 1148) hydrogen bonds : angle 4.96903 ( 3276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9116 (ppp) cc_final: 0.8517 (ppp) REVERT: A 1506 PHE cc_start: 0.8380 (t80) cc_final: 0.8125 (t80) REVERT: A 1508 TYR cc_start: 0.8691 (t80) cc_final: 0.8396 (t80) REVERT: A 1644 HIS cc_start: 0.8683 (m90) cc_final: 0.8272 (m90) REVERT: A 1653 MET cc_start: 0.9424 (mpp) cc_final: 0.9155 (mpp) REVERT: A 1709 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8733 (pttt) REVERT: B 156 ARG cc_start: 0.8973 (tpt170) cc_final: 0.8450 (tpm170) REVERT: C 56 LEU cc_start: 0.9208 (mt) cc_final: 0.8818 (pp) REVERT: C 121 LEU cc_start: 0.9208 (tp) cc_final: 0.8971 (tp) REVERT: C 152 CYS cc_start: 0.8037 (m) cc_final: 0.7521 (m) REVERT: C 218 ASN cc_start: 0.9090 (t0) cc_final: 0.8890 (t0) REVERT: E 99 ASP cc_start: 0.8450 (p0) cc_final: 0.8088 (p0) REVERT: E 134 LEU cc_start: 0.9512 (mt) cc_final: 0.9099 (pp) REVERT: E 139 LYS cc_start: 0.9101 (mmtm) cc_final: 0.8785 (mmmt) REVERT: E 335 PHE cc_start: 0.9136 (t80) cc_final: 0.8933 (t80) REVERT: E 339 PHE cc_start: 0.9227 (t80) cc_final: 0.8828 (t80) REVERT: E 340 MET cc_start: 0.9324 (mmp) cc_final: 0.8864 (mmt) REVERT: F 77 LYS cc_start: 0.8787 (tttt) cc_final: 0.8551 (tttt) REVERT: F 139 MET cc_start: 0.9155 (ppp) cc_final: 0.8901 (ppp) REVERT: F 148 CYS cc_start: 0.8782 (m) cc_final: 0.8504 (m) REVERT: F 214 PHE cc_start: 0.9386 (m-80) cc_final: 0.9071 (m-80) REVERT: G 28 TRP cc_start: 0.9126 (m100) cc_final: 0.8096 (m100) REVERT: G 68 MET cc_start: 0.8519 (pmm) cc_final: 0.8298 (pmm) REVERT: G 75 MET cc_start: 0.9645 (mmp) cc_final: 0.9347 (mmm) REVERT: G 116 MET cc_start: 0.6262 (tpt) cc_final: 0.5661 (tpp) REVERT: G 247 LEU cc_start: 0.9172 (tp) cc_final: 0.8768 (tp) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1448 time to fit residues: 82.0193 Evaluate side-chains 288 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 230 optimal weight: 0.1980 chunk 210 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 160 optimal weight: 9.9990 chunk 139 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1094 ASN A1170 GLN A1179 GLN ** A1490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.099809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.072954 restraints weight = 109400.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.074304 restraints weight = 83707.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.075257 restraints weight = 70486.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.075954 restraints weight = 62700.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.076228 restraints weight = 57741.840| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22182 Z= 0.202 Angle : 0.693 9.400 29984 Z= 0.354 Chirality : 0.044 0.176 3479 Planarity : 0.004 0.053 3815 Dihedral : 7.348 147.409 3027 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.04 % Allowed : 0.53 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2734 helix: 0.59 (0.14), residues: 1319 sheet: -0.39 (0.23), residues: 507 loop : -0.78 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1790 TYR 0.020 0.002 TYR E 343 PHE 0.041 0.002 PHE G 215 TRP 0.031 0.002 TRP G 28 HIS 0.008 0.001 HIS A1490 Details of bonding type rmsd covalent geometry : bond 0.00428 (22182) covalent geometry : angle 0.69310 (29984) hydrogen bonds : bond 0.03519 ( 1148) hydrogen bonds : angle 5.12487 ( 3276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 349 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9153 (ppp) cc_final: 0.8535 (ppp) REVERT: A 1506 PHE cc_start: 0.8349 (t80) cc_final: 0.8082 (t80) REVERT: A 1644 HIS cc_start: 0.8729 (m90) cc_final: 0.8257 (m90) REVERT: A 1709 LYS cc_start: 0.9088 (ptpp) cc_final: 0.8661 (pttt) REVERT: B 156 ARG cc_start: 0.9082 (tpt170) cc_final: 0.8507 (tpm170) REVERT: B 228 ASP cc_start: 0.9154 (p0) cc_final: 0.8855 (p0) REVERT: C 56 LEU cc_start: 0.9191 (mt) cc_final: 0.8804 (pp) REVERT: C 121 LEU cc_start: 0.9260 (tp) cc_final: 0.8991 (tp) REVERT: C 152 CYS cc_start: 0.8038 (m) cc_final: 0.7515 (m) REVERT: C 160 LYS cc_start: 0.8409 (tmtt) cc_final: 0.7636 (tmtt) REVERT: D 109 ASN cc_start: 0.7874 (p0) cc_final: 0.7527 (p0) REVERT: E 99 ASP cc_start: 0.8493 (p0) cc_final: 0.8211 (p0) REVERT: E 134 LEU cc_start: 0.9459 (mt) cc_final: 0.9064 (pp) REVERT: E 139 LYS cc_start: 0.9098 (mmtm) cc_final: 0.8791 (mmmt) REVERT: E 179 CYS cc_start: 0.9179 (m) cc_final: 0.8558 (t) REVERT: E 335 PHE cc_start: 0.9241 (t80) cc_final: 0.8913 (t80) REVERT: E 339 PHE cc_start: 0.9264 (t80) cc_final: 0.8826 (t80) REVERT: E 340 MET cc_start: 0.9353 (mmp) cc_final: 0.8853 (mmt) REVERT: F 5 ARG cc_start: 0.8639 (mpt90) cc_final: 0.8193 (mmt-90) REVERT: F 77 LYS cc_start: 0.8884 (tttt) cc_final: 0.8629 (tttt) REVERT: F 139 MET cc_start: 0.9154 (ppp) cc_final: 0.8874 (ppp) REVERT: F 148 CYS cc_start: 0.8847 (m) cc_final: 0.8571 (m) REVERT: F 199 MET cc_start: 0.6028 (ppp) cc_final: 0.5268 (ppp) REVERT: F 214 PHE cc_start: 0.9401 (m-80) cc_final: 0.9082 (m-80) REVERT: F 215 PHE cc_start: 0.9035 (m-80) cc_final: 0.8758 (m-80) REVERT: F 229 MET cc_start: 0.8036 (tmm) cc_final: 0.7519 (tmm) REVERT: G 28 TRP cc_start: 0.8917 (m100) cc_final: 0.7850 (m100) REVERT: G 75 MET cc_start: 0.9592 (mmp) cc_final: 0.9327 (mmm) REVERT: G 116 MET cc_start: 0.6063 (tpt) cc_final: 0.5451 (tpp) REVERT: G 215 PHE cc_start: 0.9276 (m-80) cc_final: 0.9051 (m-80) REVERT: G 247 LEU cc_start: 0.9102 (tp) cc_final: 0.8689 (tp) REVERT: G 248 LYS cc_start: 0.9383 (tttt) cc_final: 0.9069 (mmmt) REVERT: H 244 MET cc_start: 0.8454 (mmm) cc_final: 0.8171 (mmm) outliers start: 1 outliers final: 0 residues processed: 350 average time/residue: 0.1220 time to fit residues: 67.6054 Evaluate side-chains 283 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 105 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 230 optimal weight: 0.1980 chunk 149 optimal weight: 20.0000 chunk 239 optimal weight: 4.9990 chunk 257 optimal weight: 0.4980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1179 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 323 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.104332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.077271 restraints weight = 111310.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.078951 restraints weight = 81203.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.080105 restraints weight = 65910.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.080995 restraints weight = 57257.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.081485 restraints weight = 51798.750| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22182 Z= 0.136 Angle : 0.675 10.431 29984 Z= 0.338 Chirality : 0.043 0.194 3479 Planarity : 0.004 0.058 3815 Dihedral : 7.277 146.500 3027 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.04 % Allowed : 0.41 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.16), residues: 2734 helix: 0.72 (0.14), residues: 1313 sheet: -0.31 (0.23), residues: 513 loop : -0.75 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 264 TYR 0.018 0.002 TYR B 322 PHE 0.043 0.002 PHE G 215 TRP 0.030 0.002 TRP G 28 HIS 0.008 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00301 (22182) covalent geometry : angle 0.67497 (29984) hydrogen bonds : bond 0.03327 ( 1148) hydrogen bonds : angle 5.00289 ( 3276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9109 (ppp) cc_final: 0.8476 (ppp) REVERT: A 1365 TYR cc_start: 0.9532 (t80) cc_final: 0.9225 (t80) REVERT: A 1489 TRP cc_start: 0.7219 (t60) cc_final: 0.6867 (t60) REVERT: A 1506 PHE cc_start: 0.8567 (t80) cc_final: 0.8249 (t80) REVERT: A 1644 HIS cc_start: 0.8756 (m90) cc_final: 0.8300 (m90) REVERT: A 1707 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8686 (mt-10) REVERT: A 1709 LYS cc_start: 0.9062 (ptpp) cc_final: 0.8858 (mtmm) REVERT: A 1797 TYR cc_start: 0.8884 (m-10) cc_final: 0.8511 (m-80) REVERT: B 156 ARG cc_start: 0.9040 (tpt170) cc_final: 0.8466 (tpm170) REVERT: C 56 LEU cc_start: 0.9248 (mt) cc_final: 0.8822 (pp) REVERT: C 58 LEU cc_start: 0.8931 (mp) cc_final: 0.8642 (mp) REVERT: C 148 ASN cc_start: 0.9143 (t0) cc_final: 0.8852 (t0) REVERT: C 152 CYS cc_start: 0.8376 (m) cc_final: 0.7731 (m) REVERT: D 109 ASN cc_start: 0.7795 (p0) cc_final: 0.7467 (p0) REVERT: E 99 ASP cc_start: 0.8346 (p0) cc_final: 0.8016 (p0) REVERT: E 139 LYS cc_start: 0.9097 (mmtm) cc_final: 0.8775 (mmmt) REVERT: E 156 MET cc_start: 0.8748 (pmm) cc_final: 0.8540 (pmm) REVERT: E 339 PHE cc_start: 0.9303 (t80) cc_final: 0.8876 (t80) REVERT: E 340 MET cc_start: 0.9345 (mmp) cc_final: 0.8908 (mmt) REVERT: F 5 ARG cc_start: 0.8516 (mpt90) cc_final: 0.8123 (mmt-90) REVERT: F 77 LYS cc_start: 0.8841 (tttt) cc_final: 0.8589 (tttt) REVERT: F 139 MET cc_start: 0.8980 (ppp) cc_final: 0.8673 (ppp) REVERT: F 148 CYS cc_start: 0.8841 (m) cc_final: 0.8636 (m) REVERT: F 199 MET cc_start: 0.6155 (ppp) cc_final: 0.5102 (ppp) REVERT: F 214 PHE cc_start: 0.9361 (m-80) cc_final: 0.9025 (m-80) REVERT: F 215 PHE cc_start: 0.8997 (m-80) cc_final: 0.8704 (m-80) REVERT: F 229 MET cc_start: 0.8033 (tmm) cc_final: 0.7580 (tmm) REVERT: G 1 MET cc_start: 0.8465 (mmm) cc_final: 0.8143 (tpt) REVERT: G 28 TRP cc_start: 0.8938 (m100) cc_final: 0.8029 (m100) REVERT: G 68 MET cc_start: 0.8188 (pmm) cc_final: 0.7812 (pmm) REVERT: G 119 MET cc_start: 0.5784 (tmm) cc_final: 0.5162 (tmm) REVERT: G 215 PHE cc_start: 0.9261 (m-80) cc_final: 0.8916 (m-80) REVERT: G 247 LEU cc_start: 0.9181 (tp) cc_final: 0.8763 (tp) REVERT: G 248 LYS cc_start: 0.9434 (tttt) cc_final: 0.9066 (mmmt) REVERT: G 251 LEU cc_start: 0.9637 (tp) cc_final: 0.9302 (tp) REVERT: H 249 TYR cc_start: 0.8872 (m-10) cc_final: 0.8654 (m-10) outliers start: 1 outliers final: 0 residues processed: 355 average time/residue: 0.1291 time to fit residues: 72.3065 Evaluate side-chains 284 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 89 optimal weight: 4.9990 chunk 207 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 91 optimal weight: 7.9990 chunk 258 optimal weight: 0.1980 chunk 60 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 140 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 HIS ** 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 = 0.3967 r_free = 0.3967 target = 0.105686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.075551 restraints weight = 95487.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.076430 restraints weight = 80331.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077107 restraints weight = 72328.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.077315 restraints weight = 67460.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.077708 restraints weight = 65059.343| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 22182 Z= 0.184 Angle : 0.698 9.631 29984 Z= 0.354 Chirality : 0.044 0.195 3479 Planarity : 0.004 0.054 3815 Dihedral : 7.290 146.205 3027 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.16), residues: 2734 helix: 0.70 (0.14), residues: 1311 sheet: -0.35 (0.23), residues: 523 loop : -0.75 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1790 TYR 0.018 0.002 TYR A1399 PHE 0.034 0.002 PHE G 215 TRP 0.030 0.002 TRP G 28 HIS 0.006 0.001 HIS B 287 Details of bonding type rmsd covalent geometry : bond 0.00394 (22182) covalent geometry : angle 0.69785 (29984) hydrogen bonds : bond 0.03446 ( 1148) hydrogen bonds : angle 5.11773 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3766.41 seconds wall clock time: 66 minutes 18.97 seconds (3978.97 seconds total)