Starting phenix.real_space_refine on Wed May 21 19:56:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ui7_42287/05_2025/8ui7_42287.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ui7_42287/05_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_42287/05_2025/8ui7_42287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ui7_42287/05_2025/8ui7_42287.map" model { file = "/net/cci-nas-00/data/ceres_data/8ui7_42287/05_2025/8ui7_42287.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ui7_42287/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 12.40, per 1000 atoms: 0.57 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: 5.39 Conformation dependent library (CDL) restraints added in 2.9 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: 2.21 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: 8.25 Time building geometry restraints manager: 6.33 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 48.620 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.130 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.170 ------------------------------------------------------------------------------- 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 : 2.363 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: 0.3488 time to fit residues: 210.0627 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 : 2.333 ------------------------------------------------------------------------------- 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 = 56)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065684 restraints weight = 120365.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.067219 restraints weight = 91219.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.068058 restraints weight = 75919.627| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 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 : 2.653 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: 0.9005 (ppp) cc_final: 0.8419 (ppp) REVERT: A 1664 THR cc_start: 0.7856 (p) cc_final: 0.7392 (t) REVERT: A 1708 LEU cc_start: 0.9284 (mt) cc_final: 0.9071 (mt) REVERT: A 1709 LYS cc_start: 0.9093 (ptpp) cc_final: 0.8790 (pttt) REVERT: A 1790 ARG cc_start: 0.8974 (ptp90) cc_final: 0.8640 (ptp90) REVERT: B 171 CYS cc_start: 0.6544 (m) cc_final: 0.6227 (m) REVERT: C 108 PHE cc_start: 0.9515 (t80) cc_final: 0.8888 (t80) REVERT: C 120 LYS cc_start: 0.9580 (mtmt) cc_final: 0.9367 (mtmt) REVERT: C 155 CYS cc_start: 0.8300 (t) cc_final: 0.7934 (t) REVERT: E 126 GLN cc_start: 0.2260 (OUTLIER) cc_final: 0.1249 (tm-30) REVERT: E 139 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8844 (mmmt) REVERT: E 318 TYR cc_start: 0.8883 (m-10) cc_final: 0.8675 (m-10) REVERT: E 335 PHE cc_start: 0.9253 (t80) cc_final: 0.8707 (t80) REVERT: E 339 PHE cc_start: 0.9307 (t80) cc_final: 0.9052 (t80) REVERT: E 340 MET cc_start: 0.9279 (mmp) cc_final: 0.8870 (mmt) REVERT: F 139 MET cc_start: 0.9224 (ptt) cc_final: 0.8992 (ptm) REVERT: F 215 PHE cc_start: 0.9194 (m-80) cc_final: 0.8979 (m-80) REVERT: F 229 MET cc_start: 0.8115 (tmm) cc_final: 0.7665 (tmm) REVERT: F 248 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8259 (mmtm) REVERT: G 68 MET cc_start: 0.8765 (pmm) cc_final: 0.8472 (pmm) REVERT: G 116 MET cc_start: 0.6237 (tpt) cc_final: 0.5896 (tpp) REVERT: G 215 PHE cc_start: 0.9303 (m-80) cc_final: 0.9099 (m-80) REVERT: G 247 LEU cc_start: 0.9207 (tp) cc_final: 0.8692 (tp) REVERT: H 119 MET cc_start: 0.7240 (ppp) cc_final: 0.6922 (ppp) outliers start: 3 outliers final: 0 residues processed: 345 average time/residue: 0.3494 time to fit residues: 185.0234 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 : 2.600 ------------------------------------------------------------------------------- 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: 2.9990 chunk 235 optimal weight: 1.9990 chunk 263 optimal weight: 30.0000 chunk 173 optimal weight: 5.9990 chunk 254 optimal weight: 20.0000 chunk 111 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.102572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.075781 restraints weight = 107635.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.077309 restraints weight = 81011.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.078386 restraints weight = 67304.991| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22182 Z= 0.127 Angle : 0.636 8.484 29984 Z= 0.319 Chirality : 0.043 0.166 3479 Planarity : 0.004 0.062 3815 Dihedral : 7.565 149.436 3027 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.08 % Allowed : 3.70 % Favored : 96.22 % 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: -0.37 (0.15), residues: 2734 helix: 0.41 (0.14), residues: 1305 sheet: -0.27 (0.23), residues: 478 loop : -0.99 (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 0.030 0.002 PHE G 215 TYR 0.026 0.002 TYR B 322 ARG 0.007 0.001 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 1148) hydrogen bonds : angle 5.12467 ( 3276) covalent geometry : bond 0.00273 (22182) covalent geometry : angle 0.63591 (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 383 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 381 time to evaluate : 2.722 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: symmetry clash REVERT: A 1052 MET cc_start: 0.9124 (ppp) cc_final: 0.8543 (ppp) REVERT: A 1644 HIS cc_start: 0.8616 (m90) cc_final: 0.8230 (m90) REVERT: B 87 LEU cc_start: 0.9694 (tp) cc_final: 0.9461 (pp) REVERT: B 100 ASP cc_start: 0.8488 (m-30) cc_final: 0.8222 (m-30) REVERT: B 171 CYS cc_start: 0.7180 (m) cc_final: 0.6786 (m) REVERT: B 203 MET cc_start: 0.9177 (ptp) cc_final: 0.8866 (ptt) REVERT: C 56 LEU cc_start: 0.9281 (mt) cc_final: 0.8979 (mt) REVERT: C 108 PHE cc_start: 0.9443 (t80) cc_final: 0.8619 (t80) REVERT: C 120 LYS cc_start: 0.9470 (mtmt) cc_final: 0.9164 (ttmt) REVERT: C 148 ASN cc_start: 0.8834 (t0) cc_final: 0.8415 (t0) REVERT: C 155 CYS cc_start: 0.8079 (t) cc_final: 0.7823 (t) REVERT: D 109 ASN cc_start: 0.7512 (p0) cc_final: 0.7207 (p0) REVERT: E 99 ASP cc_start: 0.8723 (p0) cc_final: 0.8462 (p0) REVERT: E 139 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8811 (mmmt) REVERT: E 161 LEU cc_start: 0.8398 (pp) cc_final: 0.8128 (pp) REVERT: E 314 MET cc_start: 0.9116 (ptt) cc_final: 0.8863 (ptt) REVERT: E 318 TYR cc_start: 0.8790 (m-10) cc_final: 0.8583 (m-10) REVERT: E 335 PHE cc_start: 0.9213 (t80) cc_final: 0.8739 (t80) REVERT: E 339 PHE cc_start: 0.9371 (t80) cc_final: 0.9053 (t80) REVERT: E 340 MET cc_start: 0.9281 (mmp) cc_final: 0.9032 (mmt) REVERT: F 40 MET cc_start: 0.8565 (ttt) cc_final: 0.8094 (ttt) REVERT: F 114 TYR cc_start: 0.9063 (m-80) cc_final: 0.8860 (m-10) REVERT: F 215 PHE cc_start: 0.9083 (m-80) cc_final: 0.8807 (m-80) REVERT: G 116 MET cc_start: 0.6377 (tpt) cc_final: 0.5963 (tpp) REVERT: G 139 MET cc_start: 0.8400 (tmm) cc_final: 0.8191 (tmm) REVERT: G 215 PHE cc_start: 0.9310 (m-80) cc_final: 0.8971 (m-80) REVERT: G 247 LEU cc_start: 0.9141 (tp) cc_final: 0.8715 (tp) REVERT: G 251 LEU cc_start: 0.9679 (tp) cc_final: 0.9383 (tp) outliers start: 2 outliers final: 0 residues processed: 382 average time/residue: 0.3417 time to fit residues: 199.7471 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 : 2.518 ------------------------------------------------------------------------------- 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: 20.0000 chunk 9 optimal weight: 50.0000 chunk 101 optimal weight: 30.0000 chunk 247 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 181 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.091993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065422 restraints weight = 121139.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.066895 restraints weight = 91637.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.067849 restraints weight = 76308.104| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 22182 Z= 0.296 Angle : 0.767 12.263 29984 Z= 0.393 Chirality : 0.044 0.200 3479 Planarity : 0.005 0.057 3815 Dihedral : 7.715 148.998 3027 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 2734 helix: 0.17 (0.14), residues: 1309 sheet: -0.39 (0.23), residues: 479 loop : -1.09 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 22 HIS 0.010 0.002 HIS C 289 PHE 0.036 0.003 PHE C 151 TYR 0.022 0.002 TYR A1823 ARG 0.007 0.001 ARG A1802 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 1148) hydrogen bonds : angle 5.46652 ( 3276) covalent geometry : bond 0.00604 (22182) covalent geometry : angle 0.76730 (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 343 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 2.523 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: 0.9130 (ppp) cc_final: 0.8521 (ppp) REVERT: A 1506 PHE cc_start: 0.8694 (t80) cc_final: 0.8371 (t80) REVERT: A 1644 HIS cc_start: 0.8747 (m90) cc_final: 0.8330 (m90) REVERT: B 102 MET cc_start: 0.8907 (tmm) cc_final: 0.8334 (tmm) REVERT: B 171 CYS cc_start: 0.6669 (m) cc_final: 0.6258 (m) REVERT: C 56 LEU cc_start: 0.9324 (mt) cc_final: 0.8875 (pp) REVERT: C 58 LEU cc_start: 0.8881 (mp) cc_final: 0.8593 (mp) REVERT: C 144 LYS cc_start: 0.9528 (tmmt) cc_final: 0.9168 (tppt) REVERT: C 148 ASN cc_start: 0.9049 (t0) cc_final: 0.8687 (t0) REVERT: D 109 ASN cc_start: 0.7539 (p0) cc_final: 0.7258 (p0) REVERT: D 356 MET cc_start: 0.8487 (tpt) cc_final: 0.8278 (tpt) REVERT: E 99 ASP cc_start: 0.8583 (p0) cc_final: 0.8157 (p0) REVERT: E 139 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8799 (mmmt) REVERT: E 314 MET cc_start: 0.9137 (ptt) cc_final: 0.8563 (ptp) REVERT: E 318 TYR cc_start: 0.8771 (m-10) cc_final: 0.8362 (m-10) REVERT: E 335 PHE cc_start: 0.9168 (t80) cc_final: 0.8486 (t80) REVERT: E 339 PHE cc_start: 0.9267 (t80) cc_final: 0.8818 (t80) REVERT: E 340 MET cc_start: 0.9296 (mmp) cc_final: 0.8849 (mmt) REVERT: F 139 MET cc_start: 0.9193 (ptt) cc_final: 0.8977 (ptt) REVERT: F 148 CYS cc_start: 0.8941 (m) cc_final: 0.8648 (m) REVERT: F 199 MET cc_start: 0.6590 (ppp) cc_final: 0.5659 (ppp) REVERT: F 215 PHE cc_start: 0.9215 (m-80) cc_final: 0.9000 (m-80) REVERT: F 229 MET cc_start: 0.7997 (tmm) cc_final: 0.7570 (tmm) REVERT: G 68 MET cc_start: 0.8682 (pmm) cc_final: 0.8456 (pmm) REVERT: G 116 MET cc_start: 0.6280 (tpt) cc_final: 0.5845 (tpp) REVERT: G 174 GLU cc_start: 0.8625 (tp30) cc_final: 0.8423 (tp30) REVERT: G 215 PHE cc_start: 0.9309 (m-80) cc_final: 0.9029 (m-80) REVERT: G 247 LEU cc_start: 0.9183 (tp) cc_final: 0.8630 (tp) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.3413 time to fit residues: 179.6571 Evaluate side-chains 270 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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: 5.9990 chunk 269 optimal weight: 30.0000 chunk 78 optimal weight: 0.9980 chunk 216 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 229 optimal weight: 30.0000 chunk 244 optimal weight: 6.9990 chunk 2 optimal weight: 40.0000 chunk 65 optimal weight: 0.0170 chunk 242 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 overall best weight: 2.8024 ------------------------------------------------------------------------------- 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** 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 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 361 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** 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** G 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.102305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.074793 restraints weight = 106319.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076258 restraints weight = 82798.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.077133 restraints weight = 70069.355| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22182 Z= 0.153 Angle : 0.643 8.703 29984 Z= 0.326 Chirality : 0.043 0.158 3479 Planarity : 0.004 0.053 3815 Dihedral : 7.629 149.864 3027 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.08 % Allowed : 2.26 % 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: -0.36 (0.16), residues: 2734 helix: 0.42 (0.14), residues: 1315 sheet: -0.29 (0.23), residues: 476 loop : -0.98 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1083 HIS 0.007 0.001 HIS B 287 PHE 0.030 0.002 PHE C 151 TYR 0.020 0.002 TYR B 322 ARG 0.005 0.001 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.03536 ( 1148) hydrogen bonds : angle 5.12582 ( 3276) covalent geometry : bond 0.00330 (22182) covalent geometry : angle 0.64281 (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 368 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 366 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.8997 (ppp) cc_final: 0.8489 (ppp) REVERT: A 1365 TYR cc_start: 0.9569 (t80) cc_final: 0.9305 (t80) REVERT: A 1506 PHE cc_start: 0.8327 (t80) cc_final: 0.8054 (t80) REVERT: A 1644 HIS cc_start: 0.8729 (m90) cc_final: 0.8319 (m90) REVERT: A 1709 LYS cc_start: 0.9228 (ptpp) cc_final: 0.8780 (pttt) REVERT: B 102 MET cc_start: 0.8829 (tmm) cc_final: 0.8198 (tmm) REVERT: B 156 ARG cc_start: 0.8968 (tpt170) cc_final: 0.8376 (tpm170) REVERT: B 171 CYS cc_start: 0.6766 (m) cc_final: 0.6500 (m) REVERT: B 203 MET cc_start: 0.9195 (ptp) cc_final: 0.8945 (ptt) REVERT: B 308 MET cc_start: 0.8970 (ppp) cc_final: 0.8734 (ppp) REVERT: C 56 LEU cc_start: 0.9195 (mt) cc_final: 0.8804 (pp) REVERT: C 86 MET cc_start: 0.7571 (mtt) cc_final: 0.7339 (mtt) REVERT: C 120 LYS cc_start: 0.9372 (mtmt) cc_final: 0.8992 (mtmm) REVERT: C 148 ASN cc_start: 0.8748 (t0) cc_final: 0.8320 (t0) REVERT: C 152 CYS cc_start: 0.8188 (m) cc_final: 0.7942 (m) REVERT: C 160 LYS cc_start: 0.8583 (tmtt) cc_final: 0.8081 (tmtt) REVERT: D 109 ASN cc_start: 0.7503 (p0) cc_final: 0.7182 (p0) REVERT: D 356 MET cc_start: 0.8260 (tpt) cc_final: 0.8048 (tpt) REVERT: E 139 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8834 (mmmt) REVERT: E 161 LEU cc_start: 0.8468 (pp) cc_final: 0.8148 (pp) REVERT: E 314 MET cc_start: 0.9046 (ptt) cc_final: 0.8689 (ptt) REVERT: E 318 TYR cc_start: 0.8665 (m-10) cc_final: 0.8344 (m-10) REVERT: E 335 PHE cc_start: 0.9087 (t80) cc_final: 0.8643 (t80) REVERT: E 339 PHE cc_start: 0.9212 (t80) cc_final: 0.8746 (t80) REVERT: E 340 MET cc_start: 0.9310 (mmp) cc_final: 0.8903 (mmt) REVERT: F 148 CYS cc_start: 0.8809 (m) cc_final: 0.8525 (m) REVERT: F 199 MET cc_start: 0.6166 (ppp) cc_final: 0.5223 (ppp) REVERT: F 215 PHE cc_start: 0.9286 (m-80) cc_final: 0.9082 (m-80) REVERT: F 229 MET cc_start: 0.8068 (tmm) cc_final: 0.7598 (tmm) REVERT: G 68 MET cc_start: 0.8549 (pmm) cc_final: 0.8312 (pmm) REVERT: G 116 MET cc_start: 0.6467 (tpt) cc_final: 0.5773 (tpp) REVERT: G 215 PHE cc_start: 0.9286 (m-80) cc_final: 0.9029 (m-80) REVERT: G 244 MET cc_start: 0.8079 (mmm) cc_final: 0.7874 (mmm) REVERT: G 247 LEU cc_start: 0.9063 (tp) cc_final: 0.8659 (tp) outliers start: 2 outliers final: 1 residues processed: 368 average time/residue: 0.3588 time to fit residues: 201.4373 Evaluate side-chains 285 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 3.207 ------------------------------------------------------------------------------- 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: 8.9990 chunk 159 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 251 optimal weight: 0.0770 chunk 3 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 overall best weight: 2.2146 ------------------------------------------------------------------------------- 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** B 118 ASN ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN C 241 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 246 GLN D 361 GLN E 72 GLN E 323 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.101702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.074619 restraints weight = 109004.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076128 restraints weight = 83373.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.077127 restraints weight = 69810.082| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22182 Z= 0.141 Angle : 0.639 11.555 29984 Z= 0.325 Chirality : 0.042 0.180 3479 Planarity : 0.004 0.056 3815 Dihedral : 7.477 147.290 3027 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: -0.22 (0.23), residues: 480 loop : -0.94 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 28 HIS 0.012 0.001 HIS E 37 PHE 0.022 0.002 PHE G 144 TYR 0.021 0.002 TYR B 322 ARG 0.005 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 1148) hydrogen bonds : angle 5.00641 ( 3276) covalent geometry : bond 0.00304 (22182) covalent geometry : angle 0.63937 (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 363 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 2.374 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: 0.9116 (ppp) cc_final: 0.8562 (ppp) REVERT: A 1365 TYR cc_start: 0.9579 (t80) cc_final: 0.9351 (t80) REVERT: A 1506 PHE cc_start: 0.8454 (t80) cc_final: 0.8166 (t80) REVERT: A 1644 HIS cc_start: 0.8720 (m90) cc_final: 0.8303 (m90) REVERT: A 1709 LYS cc_start: 0.9194 (ptpp) cc_final: 0.8762 (pttt) REVERT: A 1790 ARG cc_start: 0.8994 (mtm-85) cc_final: 0.8441 (mtm-85) REVERT: A 1797 TYR cc_start: 0.8868 (m-10) cc_final: 0.8498 (m-80) REVERT: B 156 ARG cc_start: 0.9039 (tpt170) cc_final: 0.8474 (tpm170) REVERT: B 171 CYS cc_start: 0.6854 (m) cc_final: 0.6548 (m) REVERT: B 203 MET cc_start: 0.9212 (ptp) cc_final: 0.8947 (ptt) REVERT: C 56 LEU cc_start: 0.9284 (mt) cc_final: 0.8868 (pp) REVERT: C 58 LEU cc_start: 0.8938 (mp) cc_final: 0.8727 (mp) REVERT: C 86 MET cc_start: 0.7742 (mtt) cc_final: 0.7460 (mtt) REVERT: C 148 ASN cc_start: 0.8789 (t0) cc_final: 0.8477 (t0) REVERT: C 152 CYS cc_start: 0.8330 (m) cc_final: 0.7930 (m) REVERT: C 160 LYS cc_start: 0.8651 (tmtt) cc_final: 0.8140 (tmtt) REVERT: C 166 GLN cc_start: 0.9379 (mt0) cc_final: 0.9115 (mt0) REVERT: C 330 GLN cc_start: 0.8670 (mm-40) cc_final: 0.7500 (tm-30) REVERT: D 109 ASN cc_start: 0.7574 (p0) cc_final: 0.7205 (p0) REVERT: D 356 MET cc_start: 0.8354 (tpt) cc_final: 0.8110 (tpt) REVERT: E 139 LYS cc_start: 0.9146 (mmtm) cc_final: 0.8823 (mmmt) REVERT: E 314 MET cc_start: 0.9095 (ptt) cc_final: 0.8677 (ptp) REVERT: E 318 TYR cc_start: 0.8793 (m-10) cc_final: 0.8444 (m-10) REVERT: E 335 PHE cc_start: 0.9213 (t80) cc_final: 0.8662 (t80) REVERT: E 339 PHE cc_start: 0.9318 (t80) cc_final: 0.8803 (t80) REVERT: E 340 MET cc_start: 0.9373 (mmp) cc_final: 0.8930 (mmt) REVERT: F 199 MET cc_start: 0.6055 (ppp) cc_final: 0.4901 (ppp) REVERT: F 215 PHE cc_start: 0.9319 (m-80) cc_final: 0.9070 (m-80) REVERT: F 229 MET cc_start: 0.8085 (tmm) cc_final: 0.7577 (tmm) REVERT: G 68 MET cc_start: 0.8658 (pmm) cc_final: 0.8404 (pmm) REVERT: G 116 MET cc_start: 0.6368 (tpt) cc_final: 0.5689 (tpp) REVERT: G 215 PHE cc_start: 0.9384 (m-80) cc_final: 0.9136 (m-80) REVERT: G 247 LEU cc_start: 0.9119 (tp) cc_final: 0.8667 (tp) REVERT: H 119 MET cc_start: 0.7220 (ppp) cc_final: 0.6836 (ppp) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3345 time to fit residues: 187.2198 Evaluate side-chains 294 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 294 time to evaluate : 2.482 ------------------------------------------------------------------------------- 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: 6.9990 chunk 172 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 161 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 overall best weight: 2.4384 ------------------------------------------------------------------------------- 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** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 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 357 GLN ** D 361 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 ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.106987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.079149 restraints weight = 110597.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.080794 restraints weight = 82379.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.081815 restraints weight = 67897.634| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22182 Z= 0.144 Angle : 0.639 9.328 29984 Z= 0.323 Chirality : 0.043 0.176 3479 Planarity : 0.004 0.055 3815 Dihedral : 7.377 146.086 3027 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2734 helix: 0.66 (0.14), residues: 1315 sheet: -0.18 (0.24), residues: 472 loop : -0.89 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 28 HIS 0.009 0.001 HIS E 331 PHE 0.029 0.002 PHE B 123 TYR 0.020 0.002 TYR E 330 ARG 0.006 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 1148) hydrogen bonds : angle 4.97299 ( 3276) covalent geometry : bond 0.00315 (22182) covalent geometry : angle 0.63857 (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 364 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 2.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1052 MET cc_start: 0.9060 (ppp) cc_final: 0.8436 (ppp) REVERT: A 1365 TYR cc_start: 0.9551 (t80) cc_final: 0.9285 (t80) REVERT: A 1506 PHE cc_start: 0.8607 (t80) cc_final: 0.8248 (t80) REVERT: A 1644 HIS cc_start: 0.8754 (m90) cc_final: 0.8276 (m90) REVERT: A 1709 LYS cc_start: 0.9128 (ptpp) cc_final: 0.8755 (pttt) REVERT: B 102 MET cc_start: 0.8900 (tmm) cc_final: 0.8533 (tmm) REVERT: B 121 LYS cc_start: 0.9406 (ttmt) cc_final: 0.8852 (mttt) REVERT: B 156 ARG cc_start: 0.9018 (tpt170) cc_final: 0.8485 (tpm170) REVERT: B 171 CYS cc_start: 0.6790 (m) cc_final: 0.6473 (m) REVERT: B 203 MET cc_start: 0.9102 (ptp) cc_final: 0.8848 (ptt) REVERT: C 56 LEU cc_start: 0.9264 (mt) cc_final: 0.8820 (pp) REVERT: C 58 LEU cc_start: 0.8878 (mp) cc_final: 0.8530 (mp) REVERT: C 108 PHE cc_start: 0.9273 (t80) cc_final: 0.8688 (t80) REVERT: C 148 ASN cc_start: 0.8818 (t0) cc_final: 0.8529 (t0) REVERT: C 152 CYS cc_start: 0.8625 (m) cc_final: 0.8309 (m) REVERT: C 166 GLN cc_start: 0.9400 (mt0) cc_final: 0.9099 (mt0) REVERT: C 307 ASP cc_start: 0.9458 (m-30) cc_final: 0.9257 (m-30) REVERT: C 330 GLN cc_start: 0.8585 (mm-40) cc_final: 0.7400 (tm-30) REVERT: D 109 ASN cc_start: 0.7611 (p0) cc_final: 0.7287 (p0) REVERT: E 139 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8814 (mmmt) REVERT: E 161 LEU cc_start: 0.8725 (pp) cc_final: 0.8404 (pp) REVERT: E 335 PHE cc_start: 0.9081 (t80) cc_final: 0.8838 (t80) REVERT: F 199 MET cc_start: 0.6130 (ppp) cc_final: 0.4701 (ppp) REVERT: F 229 MET cc_start: 0.8237 (tmm) cc_final: 0.7716 (tmm) REVERT: G 68 MET cc_start: 0.8476 (pmm) cc_final: 0.8219 (pmm) REVERT: G 116 MET cc_start: 0.6503 (tpt) cc_final: 0.5773 (tpp) REVERT: G 215 PHE cc_start: 0.9322 (m-80) cc_final: 0.9050 (m-80) REVERT: G 247 LEU cc_start: 0.9181 (tp) cc_final: 0.8698 (tp) REVERT: G 251 LEU cc_start: 0.9633 (tp) cc_final: 0.9432 (tp) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3584 time to fit residues: 204.9373 Evaluate side-chains 284 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 2.524 ------------------------------------------------------------------------------- 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: 1.9990 chunk 179 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 205 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 225 optimal weight: 0.4980 chunk 153 optimal weight: 5.9990 chunk 267 optimal weight: 30.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 361 GLN ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 184 GLN ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3991 r_free = 0.3991 target = 0.108806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080418 restraints weight = 111046.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.082144 restraints weight = 83202.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.083380 restraints weight = 68489.852| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22182 Z= 0.135 Angle : 0.658 9.860 29984 Z= 0.331 Chirality : 0.043 0.189 3479 Planarity : 0.004 0.057 3815 Dihedral : 7.337 145.260 3027 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: -0.07 (0.16), residues: 2734 helix: 0.67 (0.14), residues: 1312 sheet: -0.15 (0.23), residues: 476 loop : -0.87 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 28 HIS 0.008 0.001 HIS E 331 PHE 0.040 0.002 PHE F 214 TYR 0.021 0.002 TYR E 330 ARG 0.012 0.000 ARG F 61 Details of bonding type rmsd hydrogen bonds : bond 0.03417 ( 1148) hydrogen bonds : angle 5.00010 ( 3276) covalent geometry : bond 0.00299 (22182) covalent geometry : angle 0.65842 (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 363 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 2.336 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: 0.9109 (ppp) cc_final: 0.8480 (ppp) REVERT: A 1325 MET cc_start: 0.9383 (pmm) cc_final: 0.9149 (pmm) REVERT: A 1365 TYR cc_start: 0.9539 (t80) cc_final: 0.9270 (t80) REVERT: A 1506 PHE cc_start: 0.8669 (t80) cc_final: 0.8296 (t80) REVERT: A 1644 HIS cc_start: 0.8742 (m90) cc_final: 0.8281 (m90) REVERT: A 1709 LYS cc_start: 0.9130 (ptpp) cc_final: 0.8788 (pttt) REVERT: B 102 MET cc_start: 0.8910 (tmm) cc_final: 0.8588 (tmm) REVERT: B 121 LYS cc_start: 0.9410 (ttmt) cc_final: 0.8923 (mttt) REVERT: B 156 ARG cc_start: 0.8988 (tpt170) cc_final: 0.8385 (tpm170) REVERT: B 171 CYS cc_start: 0.6795 (m) cc_final: 0.6488 (m) REVERT: B 203 MET cc_start: 0.9118 (ptp) cc_final: 0.8886 (ptt) REVERT: C 56 LEU cc_start: 0.9242 (mt) cc_final: 0.8800 (pp) REVERT: C 58 LEU cc_start: 0.8899 (mp) cc_final: 0.8573 (mp) REVERT: C 148 ASN cc_start: 0.8835 (t0) cc_final: 0.8541 (t0) REVERT: C 152 CYS cc_start: 0.8504 (m) cc_final: 0.8192 (m) REVERT: C 166 GLN cc_start: 0.9398 (mt0) cc_final: 0.9054 (mt0) REVERT: D 109 ASN cc_start: 0.7603 (p0) cc_final: 0.7268 (p0) REVERT: D 356 MET cc_start: 0.7980 (tpt) cc_final: 0.7473 (tpt) REVERT: E 99 ASP cc_start: 0.8431 (p0) cc_final: 0.8223 (p0) REVERT: E 139 LYS cc_start: 0.9129 (mmtm) cc_final: 0.8805 (mmmt) REVERT: E 156 MET cc_start: 0.8704 (pmm) cc_final: 0.8451 (pmm) REVERT: E 314 MET cc_start: 0.8954 (ptp) cc_final: 0.8547 (ptt) REVERT: E 335 PHE cc_start: 0.9010 (t80) cc_final: 0.8635 (t80) REVERT: F 77 LYS cc_start: 0.8862 (tttt) cc_final: 0.8520 (tttt) REVERT: F 229 MET cc_start: 0.8180 (tmm) cc_final: 0.7671 (tmm) REVERT: G 68 MET cc_start: 0.8447 (pmm) cc_final: 0.8193 (pmm) REVERT: G 116 MET cc_start: 0.6524 (tpt) cc_final: 0.5786 (tpp) REVERT: G 215 PHE cc_start: 0.9340 (m-80) cc_final: 0.9067 (m-80) REVERT: G 247 LEU cc_start: 0.9195 (tp) cc_final: 0.8671 (tp) REVERT: G 251 LEU cc_start: 0.9623 (tp) cc_final: 0.9405 (tp) REVERT: H 119 MET cc_start: 0.7630 (ppp) cc_final: 0.7325 (ppp) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3445 time to fit residues: 193.7575 Evaluate side-chains 292 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 2.731 ------------------------------------------------------------------------------- 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: 9.9990 chunk 193 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 246 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 203 optimal weight: 0.9990 chunk 247 optimal weight: 6.9990 chunk 223 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 361 GLN ** E 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.103435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.076530 restraints weight = 113851.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.078222 restraints weight = 82846.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.079397 restraints weight = 67405.579| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22182 Z= 0.143 Angle : 0.654 10.493 29984 Z= 0.330 Chirality : 0.043 0.169 3479 Planarity : 0.004 0.057 3815 Dihedral : 7.279 144.165 3027 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.16), residues: 2734 helix: 0.70 (0.14), residues: 1319 sheet: -0.23 (0.23), residues: 499 loop : -0.82 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 28 HIS 0.008 0.001 HIS E 331 PHE 0.030 0.002 PHE A1324 TYR 0.022 0.002 TYR E 330 ARG 0.006 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 1148) hydrogen bonds : angle 4.96880 ( 3276) covalent geometry : bond 0.00314 (22182) covalent geometry : angle 0.65369 (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 364 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 2.480 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: 0.9108 (ppp) cc_final: 0.8473 (ppp) REVERT: A 1365 TYR cc_start: 0.9527 (t80) cc_final: 0.9262 (t80) REVERT: A 1501 MET cc_start: 0.4488 (mmm) cc_final: 0.4274 (mmm) REVERT: A 1506 PHE cc_start: 0.8649 (t80) cc_final: 0.8300 (t80) REVERT: A 1644 HIS cc_start: 0.8729 (m90) cc_final: 0.8210 (m90) REVERT: A 1709 LYS cc_start: 0.9107 (ptpp) cc_final: 0.8875 (mtmt) REVERT: A 1797 TYR cc_start: 0.8827 (m-10) cc_final: 0.8470 (m-80) REVERT: B 102 MET cc_start: 0.8896 (tmm) cc_final: 0.8027 (tmm) REVERT: B 156 ARG cc_start: 0.9033 (tpt170) cc_final: 0.8452 (tpm170) REVERT: B 203 MET cc_start: 0.9182 (ptp) cc_final: 0.8944 (ptt) REVERT: B 308 MET cc_start: 0.8930 (ppp) cc_final: 0.8655 (ppp) REVERT: C 56 LEU cc_start: 0.9247 (mt) cc_final: 0.8814 (pp) REVERT: C 58 LEU cc_start: 0.8905 (mp) cc_final: 0.8608 (mp) REVERT: C 136 ASN cc_start: 0.9072 (t0) cc_final: 0.8726 (t0) REVERT: C 152 CYS cc_start: 0.8325 (m) cc_final: 0.7900 (m) REVERT: C 166 GLN cc_start: 0.9401 (mt0) cc_final: 0.9054 (mt0) REVERT: C 330 GLN cc_start: 0.8563 (mm-40) cc_final: 0.7666 (tm-30) REVERT: D 109 ASN cc_start: 0.7614 (p0) cc_final: 0.7267 (p0) REVERT: E 99 ASP cc_start: 0.8423 (p0) cc_final: 0.8170 (p0) REVERT: E 134 LEU cc_start: 0.9558 (mt) cc_final: 0.9124 (pp) REVERT: E 136 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7149 (mt-10) REVERT: E 139 LYS cc_start: 0.9092 (mmtm) cc_final: 0.8762 (mmmt) REVERT: E 335 PHE cc_start: 0.9125 (t80) cc_final: 0.8905 (t80) REVERT: E 339 PHE cc_start: 0.9353 (t80) cc_final: 0.9071 (t80) REVERT: E 340 MET cc_start: 0.9374 (mmt) cc_final: 0.9114 (mmm) REVERT: F 77 LYS cc_start: 0.8862 (tttt) cc_final: 0.8543 (tttt) REVERT: F 199 MET cc_start: 0.6122 (ppp) cc_final: 0.5264 (ppp) REVERT: F 229 MET cc_start: 0.8213 (tmm) cc_final: 0.7707 (tmm) REVERT: G 68 MET cc_start: 0.8513 (pmm) cc_final: 0.8213 (pmm) REVERT: G 116 MET cc_start: 0.6447 (tpt) cc_final: 0.5903 (tpp) REVERT: G 185 THR cc_start: 0.9166 (p) cc_final: 0.8818 (t) REVERT: G 215 PHE cc_start: 0.9331 (m-80) cc_final: 0.9096 (m-80) REVERT: G 247 LEU cc_start: 0.9203 (tp) cc_final: 0.8721 (tp) REVERT: G 251 LEU cc_start: 0.9658 (tp) cc_final: 0.9429 (tp) REVERT: H 119 MET cc_start: 0.7686 (ppp) cc_final: 0.7353 (ppp) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3339 time to fit residues: 188.9040 Evaluate side-chains 288 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 2.664 ------------------------------------------------------------------------------- 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: 0.9980 chunk 74 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 2 optimal weight: 0.0070 chunk 4 optimal weight: 0.1980 chunk 139 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** 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 361 GLN E 323 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** H 213 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.100841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.072684 restraints weight = 102190.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.074198 restraints weight = 77313.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.075408 restraints weight = 64358.185| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3246 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= 0.117 Angle : 0.660 10.818 29984 Z= 0.328 Chirality : 0.043 0.171 3479 Planarity : 0.004 0.060 3815 Dihedral : 7.193 141.043 3027 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2734 helix: 0.77 (0.14), residues: 1299 sheet: -0.15 (0.23), residues: 496 loop : -0.74 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP G 28 HIS 0.007 0.001 HIS B 287 PHE 0.043 0.002 PHE F 214 TYR 0.023 0.001 TYR E 343 ARG 0.006 0.000 ARG C 264 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 1148) hydrogen bonds : angle 4.87379 ( 3276) covalent geometry : bond 0.00257 (22182) covalent geometry : angle 0.65996 (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 364 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 2.646 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: 0.9088 (ppp) cc_final: 0.8466 (ppp) REVERT: A 1333 ILE cc_start: 0.9687 (mt) cc_final: 0.9257 (tp) REVERT: A 1365 TYR cc_start: 0.9489 (t80) cc_final: 0.9208 (t80) REVERT: A 1501 MET cc_start: 0.4574 (mmm) cc_final: 0.4348 (mmm) REVERT: A 1506 PHE cc_start: 0.8379 (t80) cc_final: 0.8159 (t80) REVERT: A 1644 HIS cc_start: 0.8744 (m90) cc_final: 0.8400 (m170) REVERT: A 1707 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8752 (mt-10) REVERT: A 1709 LYS cc_start: 0.9154 (ptpp) cc_final: 0.8769 (pttt) REVERT: A 1797 TYR cc_start: 0.8808 (m-10) cc_final: 0.8455 (m-80) REVERT: B 102 MET cc_start: 0.8478 (tmm) cc_final: 0.8190 (tmm) REVERT: B 121 LYS cc_start: 0.9388 (ttmt) cc_final: 0.9041 (mmtp) REVERT: B 156 ARG cc_start: 0.9074 (tpt170) cc_final: 0.8563 (tpm170) REVERT: B 177 ILE cc_start: 0.9156 (mm) cc_final: 0.8870 (mm) REVERT: B 203 MET cc_start: 0.9202 (ptp) cc_final: 0.8963 (ptt) REVERT: C 56 LEU cc_start: 0.9199 (mt) cc_final: 0.8756 (pp) REVERT: C 58 LEU cc_start: 0.8892 (mp) cc_final: 0.8631 (mp) REVERT: C 86 MET cc_start: 0.8058 (mtt) cc_final: 0.7701 (mtt) REVERT: C 136 ASN cc_start: 0.8909 (t0) cc_final: 0.8574 (t0) REVERT: C 152 CYS cc_start: 0.8092 (m) cc_final: 0.7629 (m) REVERT: C 166 GLN cc_start: 0.9372 (mt0) cc_final: 0.8990 (mt0) REVERT: C 330 GLN cc_start: 0.8570 (mm-40) cc_final: 0.7439 (tm-30) REVERT: D 109 ASN cc_start: 0.7636 (p0) cc_final: 0.7278 (p0) REVERT: E 99 ASP cc_start: 0.8253 (p0) cc_final: 0.7965 (p0) REVERT: E 136 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6978 (mt-10) REVERT: E 139 LYS cc_start: 0.9127 (mmtm) cc_final: 0.8745 (mmmt) REVERT: E 323 GLN cc_start: 0.8970 (mp10) cc_final: 0.8677 (mp10) REVERT: E 335 PHE cc_start: 0.9126 (t80) cc_final: 0.8887 (t80) REVERT: E 339 PHE cc_start: 0.9287 (t80) cc_final: 0.9061 (t80) REVERT: F 77 LYS cc_start: 0.8888 (tttt) cc_final: 0.8604 (tttt) REVERT: F 139 MET cc_start: 0.9338 (ptt) cc_final: 0.9105 (ptm) REVERT: F 199 MET cc_start: 0.6051 (ppp) cc_final: 0.4957 (ppp) REVERT: F 229 MET cc_start: 0.8099 (tmm) cc_final: 0.7567 (tmm) REVERT: G 1 MET cc_start: 0.8513 (mmm) cc_final: 0.8160 (tpt) REVERT: G 68 MET cc_start: 0.8524 (pmm) cc_final: 0.8244 (pmm) REVERT: G 116 MET cc_start: 0.6379 (tpt) cc_final: 0.5782 (tpp) REVERT: G 147 ILE cc_start: 0.9422 (pt) cc_final: 0.9157 (pt) REVERT: G 185 THR cc_start: 0.9073 (p) cc_final: 0.8685 (t) REVERT: G 247 LEU cc_start: 0.9145 (tp) cc_final: 0.8649 (tp) REVERT: G 251 LEU cc_start: 0.9622 (tp) cc_final: 0.9375 (tp) REVERT: H 119 MET cc_start: 0.7321 (ppp) cc_final: 0.6975 (ppp) REVERT: H 249 TYR cc_start: 0.8832 (m-10) cc_final: 0.8588 (m-10) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.3409 time to fit residues: 192.2686 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 : 2.252 ------------------------------------------------------------------------------- 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: 4.9990 chunk 183 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 267 optimal weight: 10.0000 chunk 119 optimal weight: 0.0970 chunk 26 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 148 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 361 GLN ** F 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.104941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.077691 restraints weight = 114892.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.079396 restraints weight = 84986.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.080520 restraints weight = 69668.275| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22182 Z= 0.181 Angle : 0.691 9.336 29984 Z= 0.351 Chirality : 0.044 0.176 3479 Planarity : 0.004 0.057 3815 Dihedral : 7.196 141.421 3027 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2734 helix: 0.72 (0.14), residues: 1310 sheet: -0.17 (0.23), residues: 492 loop : -0.77 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 28 HIS 0.007 0.001 HIS B 287 PHE 0.036 0.002 PHE G 215 TYR 0.021 0.002 TYR B 322 ARG 0.009 0.001 ARG C 333 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 1148) hydrogen bonds : angle 5.07102 ( 3276) covalent geometry : bond 0.00390 (22182) covalent geometry : angle 0.69111 (29984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7503.56 seconds wall clock time: 132 minutes 52.91 seconds (7972.91 seconds total)