Starting phenix.real_space_refine on Thu Jun 19 00:36:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ui7_42287/06_2025/8ui7_42287.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ui7_42287/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ui7_42287/06_2025/8ui7_42287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ui7_42287/06_2025/8ui7_42287.map" model { file = "/net/cci-nas-00/data/ceres_data/8ui7_42287/06_2025/8ui7_42287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ui7_42287/06_2025/8ui7_42287.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.08, per 1000 atoms: 0.55 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: 4.84 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.32 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: 7.27 Time building geometry restraints manager: 5.78 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 46.080 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.970 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (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 TRP 0.051 0.003 TRP C 22 HIS 0.015 0.002 HIS A1644 PHE 0.071 0.003 PHE G 215 TYR 0.030 0.003 TYR G 249 ARG 0.020 0.001 ARG C 333 Details of bonding type rmsd hydrogen bonds : bond 0.13970 ( 1148) hydrogen bonds : angle 6.38254 ( 3276) covalent geometry : bond 0.00439 (22182) covalent geometry : angle 0.96874 (29984) *********************** 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 : 2.557 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: 0.3451 time to fit residues: 207.7018 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 : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 40.0000 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 247 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- 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** A1751 GLN B 237 GLN ** B 284 HIS ** 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 GLN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3900 r_free = 0.3900 target = 0.092501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065701 restraints weight = 120365.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.067241 restraints weight = 91106.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.068201 restraints weight = 75710.291| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 22182 Z= 0.325 Angle : 0.810 10.862 29984 Z= 0.420 Chirality : 0.045 0.178 3479 Planarity : 0.006 0.085 3815 Dihedral : 7.839 150.253 3027 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.12 % Allowed : 6.04 % Favored : 93.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2734 helix: -0.00 (0.14), residues: 1286 sheet: -0.38 (0.23), residues: 483 loop : -1.05 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 22 HIS 0.010 0.002 HIS C 289 PHE 0.029 0.003 PHE F 215 TYR 0.028 0.002 TYR B 322 ARG 0.025 0.001 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.04619 ( 1148) hydrogen bonds : angle 5.62794 ( 3276) covalent geometry : bond 0.00652 (22182) covalent geometry : angle 0.81033 (29984) *********************** 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 345 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 342 time to evaluate : 2.397 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: 0.9002 (ppp) cc_final: 0.8416 (ppp) REVERT: A 1664 THR cc_start: 0.7854 (p) cc_final: 0.7387 (t) REVERT: A 1708 LEU cc_start: 0.9286 (mt) cc_final: 0.9074 (mt) REVERT: A 1709 LYS cc_start: 0.9089 (ptpp) cc_final: 0.8787 (pttt) REVERT: A 1790 ARG cc_start: 0.8977 (ptp90) cc_final: 0.8640 (ptp90) REVERT: B 171 CYS cc_start: 0.6550 (m) cc_final: 0.6228 (m) REVERT: C 108 PHE cc_start: 0.9507 (t80) cc_final: 0.8882 (t80) REVERT: C 120 LYS cc_start: 0.9578 (mtmt) cc_final: 0.9365 (mtmt) REVERT: C 155 CYS cc_start: 0.8294 (t) cc_final: 0.7930 (t) REVERT: E 126 GLN cc_start: 0.2246 (OUTLIER) cc_final: 0.1240 (tm-30) REVERT: E 139 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8841 (mmmt) REVERT: E 318 TYR cc_start: 0.8883 (m-10) cc_final: 0.8675 (m-10) REVERT: E 335 PHE cc_start: 0.9249 (t80) cc_final: 0.8707 (t80) REVERT: E 339 PHE cc_start: 0.9305 (t80) cc_final: 0.9048 (t80) REVERT: E 340 MET cc_start: 0.9279 (mmp) cc_final: 0.8867 (mmt) REVERT: F 139 MET cc_start: 0.9214 (ptt) cc_final: 0.8982 (ptm) REVERT: F 215 PHE cc_start: 0.9191 (m-80) cc_final: 0.8977 (m-80) REVERT: F 229 MET cc_start: 0.8106 (tmm) cc_final: 0.7656 (tmm) REVERT: F 248 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8261 (mmtm) REVERT: G 68 MET cc_start: 0.8763 (pmm) cc_final: 0.8470 (pmm) REVERT: G 116 MET cc_start: 0.6243 (tpt) cc_final: 0.5901 (tpp) REVERT: G 215 PHE cc_start: 0.9296 (m-80) cc_final: 0.9096 (m-80) REVERT: G 247 LEU cc_start: 0.9202 (tp) cc_final: 0.8687 (tp) REVERT: H 119 MET cc_start: 0.7227 (ppp) cc_final: 0.6908 (ppp) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.3607 time to fit residues: 191.2888 Evaluate side-chains 271 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 270 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 94 optimal weight: 0.9990 chunk 235 optimal weight: 4.9990 chunk 263 optimal weight: 30.0000 chunk 173 optimal weight: 6.9990 chunk 254 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1644 HIS ** B 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** C 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 289 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.102829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.075962 restraints weight = 107510.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077476 restraints weight = 80929.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078611 restraints weight = 67135.016| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22182 Z= 0.124 Angle : 0.635 8.585 29984 Z= 0.318 Chirality : 0.043 0.167 3479 Planarity : 0.004 0.058 3815 Dihedral : 7.555 149.283 3027 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 2734 helix: 0.40 (0.14), residues: 1305 sheet: -0.26 (0.23), residues: 478 loop : -0.98 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 28 HIS 0.010 0.001 HIS A1644 PHE 0.029 0.002 PHE G 215 TYR 0.026 0.002 TYR B 322 ARG 0.010 0.001 ARG F 146 Details of bonding type rmsd hydrogen bonds : bond 0.03742 ( 1148) hydrogen bonds : angle 5.11379 ( 3276) covalent geometry : bond 0.00267 (22182) covalent geometry : angle 0.63511 (29984) *********************** 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 388 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 2.591 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: symmetry clash REVERT: A 1052 MET cc_start: 0.9107 (ppp) cc_final: 0.8537 (ppp) REVERT: A 1644 HIS cc_start: 0.8614 (m90) cc_final: 0.8229 (m90) REVERT: B 87 LEU cc_start: 0.9697 (tp) cc_final: 0.9461 (pp) REVERT: B 100 ASP cc_start: 0.8477 (m-30) cc_final: 0.8213 (m-30) REVERT: B 171 CYS cc_start: 0.7183 (m) cc_final: 0.6778 (m) REVERT: B 203 MET cc_start: 0.9174 (ptp) cc_final: 0.8860 (ptt) REVERT: C 56 LEU cc_start: 0.9283 (mt) cc_final: 0.8989 (mt) REVERT: C 108 PHE cc_start: 0.9442 (t80) cc_final: 0.8616 (t80) REVERT: C 120 LYS cc_start: 0.9469 (mtmt) cc_final: 0.9162 (ttmt) REVERT: C 148 ASN cc_start: 0.8856 (t0) cc_final: 0.8432 (t0) REVERT: C 155 CYS cc_start: 0.8088 (t) cc_final: 0.7829 (t) REVERT: D 109 ASN cc_start: 0.7626 (p0) cc_final: 0.7304 (p0) REVERT: E 139 LYS cc_start: 0.9118 (mmtm) cc_final: 0.8812 (mmmt) REVERT: E 161 LEU cc_start: 0.8377 (pp) cc_final: 0.8126 (pp) REVERT: E 314 MET cc_start: 0.9109 (ptt) cc_final: 0.8847 (ptt) REVERT: E 318 TYR cc_start: 0.8779 (m-10) cc_final: 0.8572 (m-10) REVERT: E 335 PHE cc_start: 0.9220 (t80) cc_final: 0.8746 (t80) REVERT: E 339 PHE cc_start: 0.9366 (t80) cc_final: 0.9054 (t80) REVERT: E 340 MET cc_start: 0.9270 (mmp) cc_final: 0.9029 (mmt) REVERT: F 40 MET cc_start: 0.8543 (ttt) cc_final: 0.8099 (ttt) REVERT: F 45 VAL cc_start: 0.9087 (m) cc_final: 0.8830 (p) REVERT: F 61 ARG cc_start: 0.8606 (mpp-170) cc_final: 0.7950 (mtm-85) REVERT: F 114 TYR cc_start: 0.9060 (m-80) cc_final: 0.8852 (m-10) REVERT: F 215 PHE cc_start: 0.9067 (m-80) cc_final: 0.8791 (m-80) REVERT: G 116 MET cc_start: 0.6364 (tpt) cc_final: 0.5952 (tpp) REVERT: G 215 PHE cc_start: 0.9305 (m-80) cc_final: 0.8966 (m-80) REVERT: G 247 LEU cc_start: 0.9150 (tp) cc_final: 0.8719 (tp) REVERT: G 251 LEU cc_start: 0.9676 (tp) cc_final: 0.9380 (tp) outliers start: 2 outliers final: 0 residues processed: 387 average time/residue: 0.3620 time to fit residues: 213.6642 Evaluate side-chains 295 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 259 optimal weight: 10.0000 chunk 9 optimal weight: 40.0000 chunk 101 optimal weight: 30.0000 chunk 247 optimal weight: 30.0000 chunk 179 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1094 ASN ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1500 GLN B 126 GLN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 ASN ** 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 D 347 GLN ** E 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.090944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064658 restraints weight = 122948.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.066050 restraints weight = 93064.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.066991 restraints weight = 77757.964| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 22182 Z= 0.349 Angle : 0.832 11.462 29984 Z= 0.428 Chirality : 0.046 0.200 3479 Planarity : 0.005 0.057 3815 Dihedral : 7.829 149.337 3027 Min Nonbonded Distance : 1.645 Molprobity Statistics. All-atom Clashscore : 24.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2734 helix: 0.03 (0.14), residues: 1312 sheet: -0.41 (0.23), residues: 479 loop : -1.10 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 22 HIS 0.008 0.002 HIS E 331 PHE 0.036 0.003 PHE C 151 TYR 0.023 0.002 TYR A1823 ARG 0.016 0.001 ARG E 176 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 1148) hydrogen bonds : angle 5.62597 ( 3276) covalent geometry : bond 0.00709 (22182) covalent geometry : angle 0.83174 (29984) *********************** 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 341 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 2.733 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: symmetry clash REVERT: A 1052 MET cc_start: 0.9139 (ppp) cc_final: 0.8531 (ppp) REVERT: A 1506 PHE cc_start: 0.8684 (t80) cc_final: 0.8353 (t80) REVERT: A 1644 HIS cc_start: 0.8757 (m90) cc_final: 0.8341 (m90) REVERT: B 102 MET cc_start: 0.8948 (tmm) cc_final: 0.8357 (tmm) REVERT: B 154 LEU cc_start: 0.9825 (tt) cc_final: 0.9572 (tt) REVERT: B 171 CYS cc_start: 0.6466 (m) cc_final: 0.6079 (m) REVERT: B 266 MET cc_start: 0.8345 (mmt) cc_final: 0.7885 (mmt) REVERT: C 56 LEU cc_start: 0.9316 (mt) cc_final: 0.8871 (pp) REVERT: C 58 LEU cc_start: 0.8912 (mp) cc_final: 0.8619 (mp) REVERT: C 148 ASN cc_start: 0.9031 (t0) cc_final: 0.8641 (t0) REVERT: D 109 ASN cc_start: 0.7559 (p0) cc_final: 0.7289 (p0) REVERT: D 356 MET cc_start: 0.8529 (tpt) cc_final: 0.8327 (tpt) REVERT: E 139 LYS cc_start: 0.9103 (mmtm) cc_final: 0.8823 (mmmt) REVERT: E 335 PHE cc_start: 0.9174 (t80) cc_final: 0.8927 (t80) REVERT: E 339 PHE cc_start: 0.9258 (t80) cc_final: 0.8787 (t80) REVERT: E 340 MET cc_start: 0.9307 (mmp) cc_final: 0.8855 (mmt) REVERT: F 75 MET cc_start: 0.9237 (mtm) cc_final: 0.9037 (mtm) REVERT: F 139 MET cc_start: 0.9194 (ptt) cc_final: 0.8959 (ptt) REVERT: F 148 CYS cc_start: 0.8991 (m) cc_final: 0.8684 (m) REVERT: F 199 MET cc_start: 0.6611 (ppp) cc_final: 0.5805 (ppp) REVERT: F 215 PHE cc_start: 0.9234 (m-80) cc_final: 0.9025 (m-80) REVERT: F 229 MET cc_start: 0.7990 (tmm) cc_final: 0.7552 (tmm) REVERT: G 68 MET cc_start: 0.8718 (pmm) cc_final: 0.8448 (pmm) REVERT: G 116 MET cc_start: 0.6339 (tpt) cc_final: 0.5734 (tpp) REVERT: G 119 MET cc_start: 0.4756 (tmm) cc_final: 0.4549 (tmm) REVERT: G 174 GLU cc_start: 0.8636 (tp30) cc_final: 0.8424 (tp30) REVERT: G 215 PHE cc_start: 0.9320 (m-80) cc_final: 0.9043 (m-80) REVERT: G 247 LEU cc_start: 0.9171 (tp) cc_final: 0.8627 (tp) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.3711 time to fit residues: 194.4278 Evaluate side-chains 260 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 201 optimal weight: 1.9990 chunk 269 optimal weight: 30.0000 chunk 78 optimal weight: 0.7980 chunk 216 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 229 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 2 optimal weight: 40.0000 chunk 65 optimal weight: 0.0770 chunk 242 optimal weight: 9.9990 chunk 234 optimal weight: 2.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- 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** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** 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** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.105592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.078641 restraints weight = 113726.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.080447 restraints weight = 82921.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.081661 restraints weight = 67121.170| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22182 Z= 0.127 Angle : 0.644 8.354 29984 Z= 0.324 Chirality : 0.043 0.161 3479 Planarity : 0.004 0.054 3815 Dihedral : 7.634 149.755 3027 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.04 % Allowed : 2.30 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.16), residues: 2734 helix: 0.46 (0.14), residues: 1311 sheet: -0.26 (0.23), residues: 477 loop : -0.95 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1083 HIS 0.008 0.001 HIS B 287 PHE 0.028 0.002 PHE G 144 TYR 0.023 0.002 TYR B 322 ARG 0.006 0.001 ARG C 168 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 1148) hydrogen bonds : angle 5.08480 ( 3276) covalent geometry : bond 0.00277 (22182) covalent geometry : angle 0.64422 (29984) *********************** 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 374 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 4.899 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: 0.8972 (ppp) cc_final: 0.8466 (ppp) REVERT: A 1365 TYR cc_start: 0.9579 (t80) cc_final: 0.9294 (t80) REVERT: A 1506 PHE cc_start: 0.8603 (t80) cc_final: 0.8265 (t80) REVERT: A 1644 HIS cc_start: 0.8743 (m90) cc_final: 0.8255 (m90) REVERT: A 1709 LYS cc_start: 0.9223 (ptpp) cc_final: 0.8866 (pttt) REVERT: A 1790 ARG cc_start: 0.8992 (mtm-85) cc_final: 0.8537 (mtt180) REVERT: B 102 MET cc_start: 0.8872 (tmm) cc_final: 0.8620 (tmm) REVERT: B 123 PHE cc_start: 0.9380 (t80) cc_final: 0.9170 (t80) REVERT: B 171 CYS cc_start: 0.6904 (m) cc_final: 0.6635 (m) REVERT: B 203 MET cc_start: 0.9139 (ptp) cc_final: 0.8885 (ptt) REVERT: B 295 ILE cc_start: 0.9012 (mt) cc_final: 0.8802 (mt) REVERT: C 56 LEU cc_start: 0.9332 (mt) cc_final: 0.8896 (pp) REVERT: C 58 LEU cc_start: 0.8923 (mp) cc_final: 0.8613 (mp) REVERT: C 86 MET cc_start: 0.7718 (mtt) cc_final: 0.7485 (mtt) REVERT: C 120 LYS cc_start: 0.9451 (mtmt) cc_final: 0.9112 (mtmm) REVERT: C 148 ASN cc_start: 0.8864 (t0) cc_final: 0.8349 (t0) REVERT: C 152 CYS cc_start: 0.8677 (m) cc_final: 0.8459 (m) REVERT: C 160 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8173 (tmtt) REVERT: C 305 MET cc_start: 0.8866 (mtm) cc_final: 0.8650 (mtm) REVERT: D 109 ASN cc_start: 0.7596 (p0) cc_final: 0.7282 (p0) REVERT: D 356 MET cc_start: 0.8277 (tpt) cc_final: 0.8053 (tpt) REVERT: E 139 LYS cc_start: 0.9154 (mmtm) cc_final: 0.8841 (mmmt) REVERT: E 161 LEU cc_start: 0.8806 (pp) cc_final: 0.8503 (pp) REVERT: E 339 PHE cc_start: 0.9327 (t80) cc_final: 0.8887 (t80) REVERT: E 340 MET cc_start: 0.9351 (mmp) cc_final: 0.8935 (mmt) REVERT: F 114 TYR cc_start: 0.9060 (m-80) cc_final: 0.8789 (m-10) REVERT: F 199 MET cc_start: 0.6038 (ppp) cc_final: 0.5288 (ppp) REVERT: F 214 PHE cc_start: 0.9280 (m-80) cc_final: 0.9070 (m-80) REVERT: F 215 PHE cc_start: 0.9282 (m-80) cc_final: 0.9057 (m-80) REVERT: F 229 MET cc_start: 0.8086 (tmm) cc_final: 0.7647 (tmm) REVERT: G 68 MET cc_start: 0.8559 (pmm) cc_final: 0.8317 (pmm) REVERT: G 116 MET cc_start: 0.6325 (tpt) cc_final: 0.5835 (tpp) REVERT: G 119 MET cc_start: 0.5676 (tmm) cc_final: 0.5321 (tmm) REVERT: G 215 PHE cc_start: 0.9375 (m-80) cc_final: 0.9111 (m-80) REVERT: G 247 LEU cc_start: 0.9251 (tp) cc_final: 0.8823 (tp) REVERT: G 251 LEU cc_start: 0.9663 (tp) cc_final: 0.9441 (tp) outliers start: 1 outliers final: 0 residues processed: 374 average time/residue: 0.6268 time to fit residues: 363.6568 Evaluate side-chains 289 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 55 optimal weight: 30.0000 chunk 159 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 251 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 GLN ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 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 221 GLN C 241 HIS ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.093506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.066849 restraints weight = 119673.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.068446 restraints weight = 88236.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.069521 restraints weight = 72359.316| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22182 Z= 0.188 Angle : 0.662 11.373 29984 Z= 0.338 Chirality : 0.043 0.178 3479 Planarity : 0.004 0.056 3815 Dihedral : 7.542 147.904 3027 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.04 % Allowed : 1.81 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2734 helix: 0.50 (0.14), residues: 1318 sheet: -0.28 (0.23), residues: 477 loop : -0.96 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP G 28 HIS 0.012 0.002 HIS E 37 PHE 0.019 0.002 PHE G 144 TYR 0.021 0.002 TYR E 330 ARG 0.006 0.001 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.03535 ( 1148) hydrogen bonds : angle 5.12618 ( 3276) covalent geometry : bond 0.00398 (22182) covalent geometry : angle 0.66231 (29984) *********************** 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 356 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 3.647 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: 0.9039 (ppp) cc_final: 0.8450 (ppp) REVERT: A 1506 PHE cc_start: 0.8674 (t80) cc_final: 0.8352 (t80) REVERT: A 1644 HIS cc_start: 0.8767 (m90) cc_final: 0.8328 (m90) REVERT: A 1709 LYS cc_start: 0.9194 (ptpp) cc_final: 0.8825 (pttt) REVERT: B 102 MET cc_start: 0.8831 (tmm) cc_final: 0.8399 (tmm) REVERT: B 156 ARG cc_start: 0.9014 (tpt170) cc_final: 0.8455 (tpm170) REVERT: B 171 CYS cc_start: 0.6620 (m) cc_final: 0.6382 (m) REVERT: B 203 MET cc_start: 0.9150 (ptp) cc_final: 0.8910 (ptt) REVERT: B 337 MET cc_start: 0.8815 (mmt) cc_final: 0.8500 (mmt) REVERT: C 56 LEU cc_start: 0.9275 (mt) cc_final: 0.8850 (pp) REVERT: C 58 LEU cc_start: 0.8889 (mp) cc_final: 0.8567 (mp) REVERT: C 108 PHE cc_start: 0.9341 (t80) cc_final: 0.8868 (t80) REVERT: C 144 LYS cc_start: 0.9407 (tmtt) cc_final: 0.9126 (tppt) REVERT: C 148 ASN cc_start: 0.8826 (t0) cc_final: 0.8562 (t0) REVERT: C 152 CYS cc_start: 0.8656 (m) cc_final: 0.8261 (m) REVERT: C 305 MET cc_start: 0.8864 (mtm) cc_final: 0.8566 (mtm) REVERT: D 109 ASN cc_start: 0.7545 (p0) cc_final: 0.7232 (p0) REVERT: D 356 MET cc_start: 0.8404 (tpt) cc_final: 0.8148 (tpt) REVERT: E 139 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8811 (mmmt) REVERT: E 339 PHE cc_start: 0.9146 (t80) cc_final: 0.8682 (t80) REVERT: E 340 MET cc_start: 0.9171 (mmp) cc_final: 0.8803 (mmt) REVERT: F 148 CYS cc_start: 0.8884 (m) cc_final: 0.8644 (m) REVERT: F 199 MET cc_start: 0.6261 (ppp) cc_final: 0.5181 (ppp) REVERT: F 229 MET cc_start: 0.8142 (tmm) cc_final: 0.7613 (tmm) REVERT: G 68 MET cc_start: 0.8630 (pmm) cc_final: 0.8325 (pmm) REVERT: G 116 MET cc_start: 0.6351 (tpt) cc_final: 0.5800 (tpp) REVERT: G 119 MET cc_start: 0.6056 (tmm) cc_final: 0.5724 (tmm) REVERT: G 247 LEU cc_start: 0.9044 (tp) cc_final: 0.8594 (tp) outliers start: 1 outliers final: 0 residues processed: 356 average time/residue: 0.3506 time to fit residues: 193.1554 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 : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 157 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 172 optimal weight: 0.0270 chunk 130 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 161 optimal weight: 20.0000 chunk 209 optimal weight: 7.9990 chunk 48 optimal weight: 0.0670 chunk 14 optimal weight: 0.8980 overall best weight: 1.1980 ------------------------------------------------------------------------------- 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** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** 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 241 HIS ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN E 72 GLN F 107 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.109841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.080573 restraints weight = 109087.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.082157 restraints weight = 83096.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.083272 restraints weight = 69590.865| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22182 Z= 0.124 Angle : 0.644 9.521 29984 Z= 0.324 Chirality : 0.043 0.176 3479 Planarity : 0.004 0.058 3815 Dihedral : 7.396 146.287 3027 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2734 helix: 0.57 (0.14), residues: 1317 sheet: -0.17 (0.23), residues: 480 loop : -0.90 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 28 HIS 0.008 0.001 HIS E 331 PHE 0.060 0.002 PHE G 215 TYR 0.021 0.002 TYR E 317 ARG 0.006 0.001 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.03333 ( 1148) hydrogen bonds : angle 4.95006 ( 3276) covalent geometry : bond 0.00277 (22182) covalent geometry : angle 0.64423 (29984) *********************** 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 362 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 3.006 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: 0.9045 (ppp) cc_final: 0.8449 (ppp) REVERT: A 1365 TYR cc_start: 0.9550 (t80) cc_final: 0.9287 (t80) REVERT: A 1501 MET cc_start: 0.4092 (mmm) cc_final: 0.3875 (mmm) REVERT: A 1506 PHE cc_start: 0.8668 (t80) cc_final: 0.8326 (t80) REVERT: A 1644 HIS cc_start: 0.8689 (m90) cc_final: 0.8290 (m90) REVERT: A 1709 LYS cc_start: 0.9159 (ptpp) cc_final: 0.8841 (pttt) REVERT: B 102 MET cc_start: 0.8832 (tmm) cc_final: 0.8014 (tmm) REVERT: B 121 LYS cc_start: 0.9467 (ttmt) cc_final: 0.9106 (mttt) REVERT: B 156 ARG cc_start: 0.9027 (tpt170) cc_final: 0.8477 (tpm170) REVERT: B 171 CYS cc_start: 0.6798 (m) cc_final: 0.6566 (m) REVERT: B 203 MET cc_start: 0.9100 (ptp) cc_final: 0.8857 (ptt) REVERT: B 337 MET cc_start: 0.9003 (mmt) cc_final: 0.8721 (mmt) REVERT: C 56 LEU cc_start: 0.9249 (mt) cc_final: 0.8821 (pp) REVERT: C 58 LEU cc_start: 0.8913 (mp) cc_final: 0.8559 (mp) REVERT: C 88 LEU cc_start: 0.9152 (tp) cc_final: 0.8940 (tp) REVERT: C 148 ASN cc_start: 0.8864 (t0) cc_final: 0.8546 (t0) REVERT: C 152 CYS cc_start: 0.8613 (m) cc_final: 0.8409 (m) REVERT: C 305 MET cc_start: 0.8815 (mtm) cc_final: 0.8509 (mtm) REVERT: D 109 ASN cc_start: 0.7623 (p0) cc_final: 0.7281 (p0) REVERT: E 139 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8800 (mmmt) REVERT: E 156 MET cc_start: 0.8632 (pmm) cc_final: 0.8400 (pmm) REVERT: E 161 LEU cc_start: 0.8609 (pp) cc_final: 0.8313 (pp) REVERT: E 339 PHE cc_start: 0.9268 (t80) cc_final: 0.8777 (t80) REVERT: E 340 MET cc_start: 0.9284 (mmp) cc_final: 0.8903 (mmt) REVERT: F 199 MET cc_start: 0.6092 (ppp) cc_final: 0.4851 (ppp) REVERT: F 229 MET cc_start: 0.8055 (tmm) cc_final: 0.7574 (tmm) REVERT: G 68 MET cc_start: 0.8510 (pmm) cc_final: 0.8197 (pmm) REVERT: G 116 MET cc_start: 0.6468 (tpt) cc_final: 0.5897 (tpp) REVERT: G 119 MET cc_start: 0.6299 (tmm) cc_final: 0.6002 (tmm) REVERT: G 247 LEU cc_start: 0.9201 (tp) cc_final: 0.8674 (tp) REVERT: G 251 LEU cc_start: 0.9588 (tp) cc_final: 0.9379 (tp) REVERT: H 119 MET cc_start: 0.7773 (ppp) cc_final: 0.7478 (ppp) REVERT: H 244 MET cc_start: 0.8425 (mmm) cc_final: 0.8168 (mmm) outliers start: 0 outliers final: 0 residues processed: 362 average time/residue: 0.4613 time to fit residues: 263.8324 Evaluate side-chains 293 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 208 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 225 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 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** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN 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** F 213 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.104481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075533 restraints weight = 98451.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076727 restraints weight = 79226.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.077462 restraints weight = 69341.560| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22182 Z= 0.179 Angle : 0.665 11.044 29984 Z= 0.339 Chirality : 0.043 0.183 3479 Planarity : 0.004 0.055 3815 Dihedral : 7.350 145.492 3027 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2734 helix: 0.60 (0.14), residues: 1327 sheet: -0.22 (0.23), residues: 483 loop : -0.90 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 28 HIS 0.009 0.001 HIS G 44 PHE 0.032 0.002 PHE A1324 TYR 0.024 0.002 TYR E 330 ARG 0.015 0.001 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.03464 ( 1148) hydrogen bonds : angle 5.05544 ( 3276) covalent geometry : bond 0.00384 (22182) covalent geometry : angle 0.66530 (29984) *********************** 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 353 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 2.618 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: 0.9108 (ppp) cc_final: 0.8490 (ppp) REVERT: A 1489 TRP cc_start: 0.7293 (t60) cc_final: 0.6930 (t60) REVERT: A 1506 PHE cc_start: 0.8400 (t80) cc_final: 0.8121 (t80) REVERT: A 1644 HIS cc_start: 0.8709 (m90) cc_final: 0.8321 (m90) REVERT: A 1709 LYS cc_start: 0.9139 (ptpp) cc_final: 0.8875 (mtmt) REVERT: A 1790 ARG cc_start: 0.9163 (mtm-85) cc_final: 0.8946 (mtm-85) REVERT: B 121 LYS cc_start: 0.9395 (ttmt) cc_final: 0.8890 (mttm) REVERT: B 156 ARG cc_start: 0.9013 (tpt170) cc_final: 0.8442 (tpm170) REVERT: B 171 CYS cc_start: 0.6637 (m) cc_final: 0.6392 (m) REVERT: B 203 MET cc_start: 0.9181 (ptp) cc_final: 0.8929 (ptt) REVERT: B 337 MET cc_start: 0.8785 (mmt) cc_final: 0.8470 (mmt) REVERT: C 56 LEU cc_start: 0.9127 (mt) cc_final: 0.8852 (mt) REVERT: C 130 MET cc_start: 0.7980 (mmp) cc_final: 0.7735 (mmp) REVERT: C 136 ASN cc_start: 0.9136 (t0) cc_final: 0.8758 (t0) REVERT: C 144 LYS cc_start: 0.9382 (tmtt) cc_final: 0.9132 (tppt) REVERT: C 218 ASN cc_start: 0.9082 (t0) cc_final: 0.8878 (t0) REVERT: D 109 ASN cc_start: 0.7521 (p0) cc_final: 0.7183 (p0) REVERT: D 356 MET cc_start: 0.8027 (tpt) cc_final: 0.7539 (tpt) REVERT: E 99 ASP cc_start: 0.8458 (p0) cc_final: 0.8181 (p0) REVERT: E 139 LYS cc_start: 0.9126 (mmtm) cc_final: 0.8811 (mmmt) REVERT: E 335 PHE cc_start: 0.9197 (t80) cc_final: 0.8920 (t80) REVERT: E 339 PHE cc_start: 0.9231 (t80) cc_final: 0.8721 (t80) REVERT: E 340 MET cc_start: 0.9393 (mmp) cc_final: 0.8886 (mmt) REVERT: F 77 LYS cc_start: 0.8766 (tttt) cc_final: 0.8503 (tttt) REVERT: F 229 MET cc_start: 0.8189 (tmm) cc_final: 0.7677 (tmm) REVERT: G 68 MET cc_start: 0.8582 (pmm) cc_final: 0.8242 (pmm) REVERT: G 116 MET cc_start: 0.6489 (tpt) cc_final: 0.5934 (tpp) REVERT: G 119 MET cc_start: 0.6296 (tmm) cc_final: 0.5996 (tmm) REVERT: G 247 LEU cc_start: 0.9083 (tp) cc_final: 0.8608 (tp) REVERT: H 119 MET cc_start: 0.7234 (ppp) cc_final: 0.6805 (ppp) REVERT: H 249 TYR cc_start: 0.8929 (m-10) cc_final: 0.8698 (m-10) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.3438 time to fit residues: 188.2263 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 : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 44 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 246 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 24 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 43 optimal weight: 0.5980 chunk 203 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 223 optimal weight: 20.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 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 117 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** ** F 246 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.103049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074908 restraints weight = 103861.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076081 restraints weight = 82857.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076846 restraints weight = 71482.022| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22182 Z= 0.184 Angle : 0.689 10.550 29984 Z= 0.350 Chirality : 0.044 0.205 3479 Planarity : 0.004 0.055 3815 Dihedral : 7.397 147.258 3027 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2734 helix: 0.58 (0.14), residues: 1317 sheet: -0.29 (0.23), residues: 500 loop : -0.90 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 28 HIS 0.009 0.001 HIS G 44 PHE 0.036 0.002 PHE C 108 TYR 0.024 0.002 TYR E 330 ARG 0.007 0.001 ARG C 333 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 1148) hydrogen bonds : angle 5.13187 ( 3276) covalent geometry : bond 0.00393 (22182) covalent geometry : angle 0.68855 (29984) *********************** 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 356 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 2.594 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: 0.9172 (ppp) cc_final: 0.8539 (ppp) REVERT: A 1365 TYR cc_start: 0.9590 (t80) cc_final: 0.9368 (t80) REVERT: A 1489 TRP cc_start: 0.7310 (t60) cc_final: 0.6912 (t60) REVERT: A 1506 PHE cc_start: 0.8479 (t80) cc_final: 0.8184 (t80) REVERT: A 1644 HIS cc_start: 0.8685 (m90) cc_final: 0.8297 (m90) REVERT: A 1709 LYS cc_start: 0.9117 (ptpp) cc_final: 0.8848 (mtmt) REVERT: A 1790 ARG cc_start: 0.9177 (mtm-85) cc_final: 0.8564 (mtm-85) REVERT: B 102 MET cc_start: 0.8983 (tmm) cc_final: 0.8664 (tpt) REVERT: B 121 LYS cc_start: 0.9436 (ttmt) cc_final: 0.8906 (mttm) REVERT: B 156 ARG cc_start: 0.9088 (tpt170) cc_final: 0.8486 (tpm170) REVERT: B 171 CYS cc_start: 0.6730 (m) cc_final: 0.6473 (m) REVERT: B 203 MET cc_start: 0.9204 (ptp) cc_final: 0.8955 (ptt) REVERT: B 337 MET cc_start: 0.8880 (mmt) cc_final: 0.8578 (mmt) REVERT: C 56 LEU cc_start: 0.9198 (mt) cc_final: 0.8816 (pp) REVERT: C 108 PHE cc_start: 0.9039 (t80) cc_final: 0.8833 (t80) REVERT: C 136 ASN cc_start: 0.9138 (t0) cc_final: 0.8752 (t0) REVERT: C 144 LYS cc_start: 0.9405 (tmtt) cc_final: 0.9156 (tppt) REVERT: C 148 ASN cc_start: 0.8949 (t0) cc_final: 0.8719 (t0) REVERT: C 152 CYS cc_start: 0.8071 (m) cc_final: 0.7590 (m) REVERT: D 109 ASN cc_start: 0.7589 (p0) cc_final: 0.7076 (p0) REVERT: E 99 ASP cc_start: 0.8431 (p0) cc_final: 0.8149 (p0) REVERT: E 139 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8798 (mmmt) REVERT: E 179 CYS cc_start: 0.9209 (m) cc_final: 0.8777 (t) REVERT: E 335 PHE cc_start: 0.9216 (t80) cc_final: 0.8899 (t80) REVERT: F 77 LYS cc_start: 0.8888 (tttt) cc_final: 0.8639 (tttt) REVERT: F 199 MET cc_start: 0.6158 (ppp) cc_final: 0.5440 (ppp) REVERT: F 215 PHE cc_start: 0.9025 (m-80) cc_final: 0.8773 (m-80) REVERT: F 229 MET cc_start: 0.8115 (tmm) cc_final: 0.7604 (tmm) REVERT: G 68 MET cc_start: 0.8595 (pmm) cc_final: 0.8218 (pmm) REVERT: G 116 MET cc_start: 0.6423 (tpt) cc_final: 0.5865 (tpp) REVERT: G 119 MET cc_start: 0.6165 (tmm) cc_final: 0.5558 (tmm) REVERT: G 215 PHE cc_start: 0.9356 (m-80) cc_final: 0.9113 (m-80) REVERT: G 247 LEU cc_start: 0.9093 (tp) cc_final: 0.8605 (tp) REVERT: H 119 MET cc_start: 0.7736 (ppp) cc_final: 0.7463 (ppp) REVERT: H 244 MET cc_start: 0.8438 (mmm) cc_final: 0.8183 (mmm) REVERT: H 247 LEU cc_start: 0.9542 (mp) cc_final: 0.9335 (tt) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.3643 time to fit residues: 202.2866 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 : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 139 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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** ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1490 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN ** 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.099979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073162 restraints weight = 110596.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074619 restraints weight = 84528.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075586 restraints weight = 70606.615| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22182 Z= 0.187 Angle : 0.704 10.885 29984 Z= 0.356 Chirality : 0.044 0.182 3479 Planarity : 0.004 0.055 3815 Dihedral : 7.423 148.107 3027 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2734 helix: 0.57 (0.14), residues: 1308 sheet: -0.29 (0.23), residues: 491 loop : -0.83 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 28 HIS 0.007 0.001 HIS B 287 PHE 0.035 0.002 PHE G 215 TYR 0.027 0.002 TYR E 330 ARG 0.007 0.001 ARG C 333 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 1148) hydrogen bonds : angle 5.20704 ( 3276) covalent geometry : bond 0.00399 (22182) covalent geometry : angle 0.70443 (29984) ********************** 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 351 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 3.579 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: A 1052 MET cc_start: 0.9205 (ppp) cc_final: 0.8556 (ppp) REVERT: A 1365 TYR cc_start: 0.9563 (t80) cc_final: 0.9308 (t80) REVERT: A 1489 TRP cc_start: 0.7425 (t60) cc_final: 0.7043 (t60) REVERT: A 1501 MET cc_start: 0.4158 (mmm) cc_final: 0.3887 (mmm) REVERT: A 1644 HIS cc_start: 0.8735 (m90) cc_final: 0.8383 (m170) REVERT: A 1709 LYS cc_start: 0.9105 (ptpp) cc_final: 0.8855 (mtmt) REVERT: A 1790 ARG cc_start: 0.9171 (mtm-85) cc_final: 0.8550 (mtm-85) REVERT: A 1797 TYR cc_start: 0.8871 (m-10) cc_final: 0.8513 (m-80) REVERT: B 102 MET cc_start: 0.8994 (tmm) cc_final: 0.8403 (tmm) REVERT: B 121 LYS cc_start: 0.9430 (ttmt) cc_final: 0.8941 (mttm) REVERT: B 156 ARG cc_start: 0.9063 (tpt170) cc_final: 0.8494 (tpm170) REVERT: B 171 CYS cc_start: 0.6739 (m) cc_final: 0.6528 (m) REVERT: B 203 MET cc_start: 0.9237 (ptp) cc_final: 0.9002 (ptt) REVERT: B 337 MET cc_start: 0.8869 (mmt) cc_final: 0.8566 (mmt) REVERT: C 56 LEU cc_start: 0.9195 (mt) cc_final: 0.8805 (pp) REVERT: C 58 LEU cc_start: 0.8934 (mp) cc_final: 0.8695 (mp) REVERT: C 108 PHE cc_start: 0.8999 (t80) cc_final: 0.8706 (t80) REVERT: C 136 ASN cc_start: 0.9086 (t0) cc_final: 0.8806 (t0) REVERT: C 144 LYS cc_start: 0.9397 (tmtt) cc_final: 0.9053 (tppt) REVERT: C 148 ASN cc_start: 0.8965 (t0) cc_final: 0.8755 (t0) REVERT: C 152 CYS cc_start: 0.8120 (m) cc_final: 0.7605 (m) REVERT: D 109 ASN cc_start: 0.7682 (p0) cc_final: 0.7132 (p0) REVERT: E 139 LYS cc_start: 0.9092 (mmtm) cc_final: 0.8766 (mmmt) REVERT: E 179 CYS cc_start: 0.9169 (m) cc_final: 0.8670 (t) REVERT: E 180 LEU cc_start: 0.8259 (tt) cc_final: 0.7240 (mp) REVERT: E 335 PHE cc_start: 0.9206 (t80) cc_final: 0.8909 (t80) REVERT: E 339 PHE cc_start: 0.9271 (t80) cc_final: 0.8995 (t80) REVERT: E 340 MET cc_start: 0.9332 (mmt) cc_final: 0.9044 (mmm) REVERT: F 77 LYS cc_start: 0.8919 (tttt) cc_final: 0.8581 (tttt) REVERT: F 199 MET cc_start: 0.6162 (ppp) cc_final: 0.5315 (ppp) REVERT: F 215 PHE cc_start: 0.9097 (m-80) cc_final: 0.8781 (m-80) REVERT: F 229 MET cc_start: 0.8141 (tmm) cc_final: 0.7632 (tmm) REVERT: G 116 MET cc_start: 0.6335 (tpt) cc_final: 0.5770 (tpp) REVERT: G 119 MET cc_start: 0.6242 (tmm) cc_final: 0.5722 (tmm) REVERT: G 215 PHE cc_start: 0.9316 (m-80) cc_final: 0.8979 (m-80) REVERT: G 247 LEU cc_start: 0.9060 (tp) cc_final: 0.8498 (tp) REVERT: G 251 LEU cc_start: 0.9627 (tp) cc_final: 0.9413 (tp) REVERT: H 119 MET cc_start: 0.7612 (ppp) cc_final: 0.7308 (ppp) REVERT: H 244 MET cc_start: 0.8487 (mmm) cc_final: 0.8257 (mmm) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.4984 time to fit residues: 275.4262 Evaluate side-chains 278 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 4.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 147 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 267 optimal weight: 30.0000 chunk 119 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 148 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1186 ASN B 231 GLN ** 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** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 323 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** 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 = 0.3929 r_free = 0.3929 target = 0.098315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.071901 restraints weight = 115701.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073339 restraints weight = 87216.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074449 restraints weight = 72371.488| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22182 Z= 0.204 Angle : 0.720 10.705 29984 Z= 0.366 Chirality : 0.044 0.176 3479 Planarity : 0.004 0.058 3815 Dihedral : 7.473 149.127 3027 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2734 helix: 0.48 (0.14), residues: 1313 sheet: -0.29 (0.24), residues: 477 loop : -0.85 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 28 HIS 0.008 0.001 HIS G 44 PHE 0.035 0.002 PHE B 123 TYR 0.027 0.002 TYR E 330 ARG 0.007 0.001 ARG C 333 Details of bonding type rmsd hydrogen bonds : bond 0.03617 ( 1148) hydrogen bonds : angle 5.27671 ( 3276) covalent geometry : bond 0.00433 (22182) covalent geometry : angle 0.72035 (29984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9129.35 seconds wall clock time: 167 minutes 27.52 seconds (10047.52 seconds total)