Starting phenix.real_space_refine on Sun Aug 24 12:28:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ui8_42288/08_2025/8ui8_42288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ui8_42288/08_2025/8ui8_42288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ui8_42288/08_2025/8ui8_42288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ui8_42288/08_2025/8ui8_42288.map" model { file = "/net/cci-nas-00/data/ceres_data/8ui8_42288/08_2025/8ui8_42288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ui8_42288/08_2025/8ui8_42288.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 129 5.16 5 C 12489 2.51 5 N 3381 2.21 5 O 3807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19822 Number of models: 1 Model: "" Number of chains: 12 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: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.86, per 1000 atoms: 0.25 Number of scatterers: 19822 At special positions: 0 Unit cell: (107.64, 128.34, 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 129 16.00 P 13 15.00 Mg 3 11.99 O 3807 8.00 N 3381 7.00 C 12489 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: 2.07 Conformation dependent library (CDL) restraints added in 989.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4758 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 12 sheets defined 55.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 940 through 955 Processing helix chain 'A' and resid 963 through 972 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 1150 Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 6.241A pdb=" N GLU A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1327 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: 3.687A 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: 3.525A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A1463 " --> pdb=" O ALA A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1468 Processing helix chain 'A' and resid 1474 through 1481 removed outlier: 3.663A pdb=" N HIS A1481 " --> pdb=" O SER A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1501 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 1663 removed outlier: 3.574A pdb=" N LEU A1663 " --> pdb=" O LEU A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1730 removed outlier: 4.316A pdb=" N SER A1705 " --> pdb=" O THR A1701 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR A1730 " --> pdb=" O LYS A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1738 removed outlier: 3.605A pdb=" N CYS A1734 " --> pdb=" O THR A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1746 Processing helix chain 'A' and resid 1750 through 1755 Processing helix chain 'A' and resid 1764 through 1780 Processing helix chain 'A' and resid 1781 through 1787 removed outlier: 3.546A pdb=" N LEU A1785 " --> pdb=" O ARG A1782 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR A1786 " --> pdb=" O SER A1783 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A1787 " --> pdb=" O LEU A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 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 removed outlier: 3.838A pdb=" N ILE B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.067A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.934A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.874A 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 Processing helix chain 'B' and resid 194 through 207 Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 4.025A 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: 3.562A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 11 Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.973A pdb=" N TYR C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 removed outlier: 3.947A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.792A 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 98 through 103 removed outlier: 4.020A pdb=" N ARG C 102 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 127 through 130 Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.795A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.580A pdb=" N LYS C 160 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.624A pdb=" N CYS C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.707A pdb=" N MET C 182 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 183 " --> pdb=" O PRO C 179 " (cutoff:3.500A) Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.985A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) 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 removed outlier: 3.545A pdb=" N GLN C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 274 removed outlier: 3.504A pdb=" N ALA C 262 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 289 removed outlier: 3.867A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 314 removed outlier: 3.805A pdb=" N VAL C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 339 removed outlier: 3.698A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 5.113A 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 removed outlier: 3.903A pdb=" N GLY D 68 " --> pdb=" O LYS D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 97 through 104 removed outlier: 4.018A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.843A pdb=" N LEU D 129 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 removed outlier: 3.877A pdb=" N MET D 155 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.771A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 203 through 219 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.505A pdb=" N GLY D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.667A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 298 removed outlier: 3.604A pdb=" N LEU D 289 " --> pdb=" O SER D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 361 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.742A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.795A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.889A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS E 66 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 3.592A pdb=" N GLY E 101 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 4.258A pdb=" N GLU E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS E 113 " --> pdb=" O GLN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 204 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.830A 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: 4.299A pdb=" N GLY E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 349 removed outlier: 4.308A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP E 349 " --> pdb=" O LYS E 345 " (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 141 through 155 Processing helix chain 'F' and resid 208 through 217 removed outlier: 3.578A pdb=" N LEU F 212 " --> pdb=" O ALA F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 222 removed outlier: 3.646A pdb=" N LEU F 221 " --> pdb=" O ALA F 218 " (cutoff:3.500A) removed outlier: 3.621A 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: 4.055A pdb=" N LEU G 12 " --> pdb=" O GLN G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 removed outlier: 3.904A pdb=" N LEU G 221 " --> pdb=" O ALA G 218 " (cutoff:3.500A) removed outlier: 3.743A 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 sheet with id=AA1, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.294A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.530A 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: 5.774A pdb=" N LYS A1152 " --> pdb=" O LEU A1301 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A1303 " --> pdb=" O LYS A1152 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N PHE A1154 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLU A1305 " --> pdb=" O PHE A1154 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL A1156 " --> pdb=" O GLU A1305 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ILE A1333 " --> pdb=" O SER A1300 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE A1302 " --> pdb=" O ILE A1333 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N THR A1335 " --> pdb=" O ILE A1302 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A1304 " --> pdb=" O THR A1335 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR A1127 " --> pdb=" O GLU A1350 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ILE A1352 " --> pdb=" O THR A1127 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU A1129 " --> pdb=" O ILE A1352 " (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: 6.154A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.043A 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 91 removed outlier: 6.439A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.716A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 68 through 74 removed outlier: 6.655A pdb=" N LEU E 93 " --> pdb=" O LEU E 133 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N THR E 135 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL E 95 " --> pdb=" O THR E 135 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 62 removed outlier: 3.601A pdb=" N ILE F 87 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.371A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR F 196 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 177 through 180 Processing sheet with id=AB2, first strand: chain 'G' and resid 61 through 62 removed outlier: 3.514A pdb=" N GLU G 3 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.417A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3003 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 6505 1.34 - 1.49: 4824 1.49 - 1.65: 8628 1.65 - 1.80: 90 1.80 - 1.95: 100 Bond restraints: 20147 Sorted by residual: bond pdb=" CA ALA B 342 " pdb=" CB ALA B 342 " ideal model delta sigma weight residual 1.528 1.461 0.067 1.56e-02 4.11e+03 1.87e+01 bond pdb=" C LEU B 341 " pdb=" O LEU B 341 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.15e-02 7.56e+03 1.52e+01 bond pdb=" C LEU B 340 " pdb=" O LEU B 340 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.16e-02 7.43e+03 1.18e+01 bond pdb=" C ALA B 342 " pdb=" O ALA B 342 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.34e+00 bond pdb=" N LEU F 209 " pdb=" CA LEU F 209 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 9.04e+00 ... (remaining 20142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 26723 2.68 - 5.36: 424 5.36 - 8.04: 70 8.04 - 10.73: 17 10.73 - 13.41: 1 Bond angle restraints: 27235 Sorted by residual: angle pdb=" C GLU C 2 " pdb=" CA GLU C 2 " pdb=" CB GLU C 2 " ideal model delta sigma weight residual 116.54 108.92 7.62 1.15e+00 7.56e-01 4.39e+01 angle pdb=" N LEU B 341 " pdb=" CA LEU B 341 " pdb=" C LEU B 341 " ideal model delta sigma weight residual 111.11 104.56 6.55 1.20e+00 6.94e-01 2.98e+01 angle pdb=" N PRO G 234 " pdb=" CA PRO G 234 " pdb=" C PRO G 234 " ideal model delta sigma weight residual 110.40 118.86 -8.46 1.61e+00 3.86e-01 2.76e+01 angle pdb=" CA GLU C 50 " pdb=" CB GLU C 50 " pdb=" CG GLU C 50 " ideal model delta sigma weight residual 114.10 124.21 -10.11 2.00e+00 2.50e-01 2.56e+01 angle pdb=" N ILE C 17 " pdb=" CA ILE C 17 " pdb=" C ILE C 17 " ideal model delta sigma weight residual 113.71 108.97 4.74 9.50e-01 1.11e+00 2.49e+01 ... (remaining 27230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.40: 11827 33.40 - 66.80: 546 66.80 - 100.20: 34 100.20 - 133.60: 0 133.60 - 167.00: 2 Dihedral angle restraints: 12409 sinusoidal: 5105 harmonic: 7304 Sorted by residual: dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 133.00 167.00 1 2.00e+01 2.50e-03 4.74e+01 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 75.29 -135.29 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" CA LEU G 247 " pdb=" C LEU G 247 " pdb=" N LYS G 248 " pdb=" CA LYS G 248 " ideal model delta harmonic sigma weight residual -180.00 -154.66 -25.34 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 12406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2238 0.046 - 0.092: 686 0.092 - 0.139: 189 0.139 - 0.185: 39 0.185 - 0.231: 4 Chirality restraints: 3156 Sorted by residual: chirality pdb=" CA ALA G 242 " pdb=" N ALA G 242 " pdb=" C ALA G 242 " pdb=" CB ALA G 242 " both_signs ideal model delta sigma weight residual False 2.48 2.72 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE G 87 " pdb=" CA ILE G 87 " pdb=" CG1 ILE G 87 " pdb=" CG2 ILE G 87 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA LYS G 248 " pdb=" N LYS G 248 " pdb=" C LYS G 248 " pdb=" CB LYS G 248 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 3153 not shown) Planarity restraints: 3459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 215 " 0.013 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE F 215 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE F 215 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 PHE F 215 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 215 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE F 215 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE F 215 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 249 " -0.035 2.00e-02 2.50e+03 2.29e-02 1.04e+01 pdb=" CG TYR F 249 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR F 249 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR F 249 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR F 249 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR F 249 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 249 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 249 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1082 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.58e+00 pdb=" CG ASP A1082 " 0.054 2.00e-02 2.50e+03 pdb=" OD1 ASP A1082 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP A1082 " -0.019 2.00e-02 2.50e+03 ... (remaining 3456 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 203 2.58 - 3.16: 15618 3.16 - 3.74: 32055 3.74 - 4.32: 42842 4.32 - 4.90: 71795 Nonbonded interactions: 162513 Sorted by model distance: nonbonded pdb=" OE2 GLU A1305 " pdb="MG MG A2001 " model vdw 2.003 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.018 2.170 nonbonded pdb=" OG1 THR A1139 " pdb="MG MG A2001 " model vdw 2.042 2.170 nonbonded pdb="MG MG A2001 " pdb=" O1B AGS A2002 " model vdw 2.057 2.170 nonbonded pdb="MG MG C 401 " pdb=" O1B AGS C 402 " model vdw 2.062 2.170 ... (remaining 162508 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' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.090 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.830 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20147 Z= 0.243 Angle : 0.851 13.407 27235 Z= 0.463 Chirality : 0.049 0.231 3156 Planarity : 0.006 0.073 3459 Dihedral : 17.828 166.999 7651 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.91 % Allowed : 25.48 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.16), residues: 2475 helix: -0.33 (0.13), residues: 1235 sheet: -0.65 (0.25), residues: 379 loop : -1.03 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 91 TYR 0.052 0.003 TYR F 249 PHE 0.043 0.002 PHE F 215 TRP 0.019 0.002 TRP A1769 HIS 0.013 0.002 HIS E 301 Details of bonding type rmsd covalent geometry : bond 0.00494 (20147) covalent geometry : angle 0.85106 (27235) hydrogen bonds : bond 0.14087 ( 1044) hydrogen bonds : angle 6.04671 ( 3003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 315 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 923 LEU cc_start: 0.4495 (OUTLIER) cc_final: 0.4267 (mt) REVERT: A 1375 PHE cc_start: 0.7822 (m-80) cc_final: 0.7618 (m-80) REVERT: F 84 ASN cc_start: 0.7351 (m-40) cc_final: 0.6841 (p0) REVERT: G 72 LEU cc_start: 0.7707 (pt) cc_final: 0.7218 (mt) outliers start: 20 outliers final: 10 residues processed: 326 average time/residue: 0.1383 time to fit residues: 69.1815 Evaluate side-chains 307 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 296 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 4.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A1147 GLN A1490 HIS A1751 GLN A1755 ASN ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.162715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116722 restraints weight = 30340.230| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.76 r_work: 0.3158 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 20147 Z= 0.307 Angle : 0.700 8.408 27235 Z= 0.361 Chirality : 0.046 0.215 3156 Planarity : 0.005 0.064 3459 Dihedral : 8.357 165.763 2771 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.40 % Allowed : 21.58 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.17), residues: 2475 helix: 0.43 (0.14), residues: 1242 sheet: -0.69 (0.25), residues: 392 loop : -0.76 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 5 TYR 0.040 0.003 TYR F 249 PHE 0.023 0.002 PHE A1779 TRP 0.010 0.002 TRP G 28 HIS 0.009 0.002 HIS C 278 Details of bonding type rmsd covalent geometry : bond 0.00722 (20147) covalent geometry : angle 0.70005 (27235) hydrogen bonds : bond 0.04756 ( 1044) hydrogen bonds : angle 4.81147 ( 3003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 313 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1129 LEU cc_start: 0.9116 (tt) cc_final: 0.8813 (tt) REVERT: A 1324 PHE cc_start: 0.8921 (OUTLIER) cc_final: 0.8257 (t80) REVERT: A 1489 TRP cc_start: 0.8353 (t-100) cc_final: 0.8148 (t-100) REVERT: B 158 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8458 (ttp) REVERT: C 89 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: C 212 ASP cc_start: 0.8443 (t0) cc_final: 0.8234 (t0) outliers start: 97 outliers final: 52 residues processed: 377 average time/residue: 0.1315 time to fit residues: 76.8077 Evaluate side-chains 350 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 295 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 89 GLU Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 206 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 116 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A1147 GLN A1490 HIS ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN G 246 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.164828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.120158 restraints weight = 30510.196| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.61 r_work: 0.3207 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20147 Z= 0.168 Angle : 0.583 7.069 27235 Z= 0.298 Chirality : 0.042 0.166 3156 Planarity : 0.004 0.063 3459 Dihedral : 7.906 165.796 2761 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.49 % Allowed : 22.67 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.17), residues: 2475 helix: 0.85 (0.15), residues: 1243 sheet: -0.61 (0.25), residues: 380 loop : -0.66 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 5 TYR 0.022 0.002 TYR F 249 PHE 0.041 0.001 PHE F 214 TRP 0.009 0.001 TRP G 28 HIS 0.005 0.001 HIS A1490 Details of bonding type rmsd covalent geometry : bond 0.00395 (20147) covalent geometry : angle 0.58269 (27235) hydrogen bonds : bond 0.03924 ( 1044) hydrogen bonds : angle 4.53379 ( 3003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 321 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1489 TRP cc_start: 0.8232 (t-100) cc_final: 0.7996 (t-100) REVERT: A 1498 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: B 146 MET cc_start: 0.9282 (tpp) cc_final: 0.9062 (mmm) REVERT: B 158 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8359 (ttp) REVERT: C 202 MET cc_start: 0.8959 (tpp) cc_final: 0.8727 (tpp) REVERT: C 212 ASP cc_start: 0.8408 (t0) cc_final: 0.8192 (t0) REVERT: E 333 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: F 238 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7075 (mm-30) REVERT: F 248 LYS cc_start: 0.7406 (mtpt) cc_final: 0.7199 (mtpt) REVERT: G 72 LEU cc_start: 0.7668 (pt) cc_final: 0.6990 (mt) REVERT: G 114 TYR cc_start: 0.5306 (m-80) cc_final: 0.5076 (m-80) outliers start: 77 outliers final: 48 residues processed: 370 average time/residue: 0.1381 time to fit residues: 79.3032 Evaluate side-chains 352 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1709 LYS Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 179 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 152 optimal weight: 0.1980 chunk 181 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A1490 HIS ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.166771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117744 restraints weight = 30669.311| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.74 r_work: 0.3221 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20147 Z= 0.113 Angle : 0.544 10.843 27235 Z= 0.276 Chirality : 0.040 0.270 3156 Planarity : 0.004 0.064 3459 Dihedral : 7.571 166.649 2759 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.26 % Allowed : 22.48 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2475 helix: 1.15 (0.15), residues: 1249 sheet: -0.55 (0.25), residues: 381 loop : -0.54 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 5 TYR 0.018 0.001 TYR A1823 PHE 0.033 0.001 PHE F 214 TRP 0.009 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 Details of bonding type rmsd covalent geometry : bond 0.00255 (20147) covalent geometry : angle 0.54443 (27235) hydrogen bonds : bond 0.03369 ( 1044) hydrogen bonds : angle 4.33308 ( 3003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 321 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8873 (pt) cc_final: 0.8542 (mm) REVERT: A 1368 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7495 (mpp) REVERT: A 1488 GLU cc_start: 0.7780 (pm20) cc_final: 0.7304 (pm20) REVERT: A 1489 TRP cc_start: 0.8214 (t-100) cc_final: 0.7984 (t-100) REVERT: A 1498 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6510 (tm-30) REVERT: A 1786 TYR cc_start: 0.7969 (m-10) cc_final: 0.7489 (m-80) REVERT: B 91 ARG cc_start: 0.8439 (ttm-80) cc_final: 0.8115 (ttm110) REVERT: B 146 MET cc_start: 0.9251 (tpp) cc_final: 0.9036 (mmm) REVERT: C 180 GLU cc_start: 0.8605 (pp20) cc_final: 0.8369 (mp0) REVERT: C 212 ASP cc_start: 0.8439 (t0) cc_final: 0.8205 (t0) REVERT: F 238 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7085 (mm-30) REVERT: G 5 ARG cc_start: 0.7872 (tpt90) cc_final: 0.7525 (tpt90) REVERT: G 72 LEU cc_start: 0.7671 (pt) cc_final: 0.7058 (mt) REVERT: G 165 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6983 (p0) outliers start: 72 outliers final: 43 residues processed: 366 average time/residue: 0.1467 time to fit residues: 82.2091 Evaluate side-chains 355 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 308 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1694 LEU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1812 GLU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 333 GLU Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 231 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 208 optimal weight: 7.9990 chunk 148 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A1490 HIS ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 257 GLN D 308 ASN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.164156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.114136 restraints weight = 30399.128| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.61 r_work: 0.3193 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 20147 Z= 0.206 Angle : 0.602 12.885 27235 Z= 0.305 Chirality : 0.043 0.331 3156 Planarity : 0.004 0.064 3459 Dihedral : 7.587 167.243 2759 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.58 % Allowed : 22.30 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.17), residues: 2475 helix: 1.14 (0.15), residues: 1245 sheet: -0.55 (0.25), residues: 385 loop : -0.55 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 146 TYR 0.022 0.002 TYR A1823 PHE 0.016 0.001 PHE A1779 TRP 0.009 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 Details of bonding type rmsd covalent geometry : bond 0.00494 (20147) covalent geometry : angle 0.60245 (27235) hydrogen bonds : bond 0.03887 ( 1044) hydrogen bonds : angle 4.39583 ( 3003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 310 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8887 (pt) cc_final: 0.8541 (mm) REVERT: A 1368 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7444 (mpp) REVERT: A 1488 GLU cc_start: 0.7794 (pm20) cc_final: 0.7465 (pm20) REVERT: A 1653 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7975 (mtt) REVERT: A 1786 TYR cc_start: 0.7959 (m-10) cc_final: 0.7526 (m-80) REVERT: A 1830 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5478 (p0) REVERT: B 91 ARG cc_start: 0.8445 (ttm-80) cc_final: 0.8129 (ttm110) REVERT: B 146 MET cc_start: 0.9278 (tpp) cc_final: 0.9043 (mmm) REVERT: B 158 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8380 (ttp) REVERT: D 36 LYS cc_start: 0.5650 (OUTLIER) cc_final: 0.5379 (tptm) REVERT: D 102 ARG cc_start: 0.8346 (mmt180) cc_final: 0.7664 (tmm160) REVERT: D 318 ASN cc_start: 0.8278 (p0) cc_final: 0.8054 (p0) REVERT: E 201 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8557 (mmtt) REVERT: F 238 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: G 72 LEU cc_start: 0.7617 (pt) cc_final: 0.7022 (mt) REVERT: G 154 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7447 (mt) outliers start: 101 outliers final: 67 residues processed: 381 average time/residue: 0.1394 time to fit residues: 80.8954 Evaluate side-chains 372 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 297 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1066 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1653 MET Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1830 ASP Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 349 ILE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 201 LYS Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 188 optimal weight: 2.9990 chunk 218 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN ** E 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.164012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118726 restraints weight = 30429.091| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.06 r_work: 0.3154 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20147 Z= 0.196 Angle : 0.604 13.973 27235 Z= 0.304 Chirality : 0.043 0.351 3156 Planarity : 0.004 0.066 3459 Dihedral : 7.512 165.467 2757 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.17 % Allowed : 23.25 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.17), residues: 2475 helix: 1.16 (0.15), residues: 1244 sheet: -0.60 (0.26), residues: 385 loop : -0.56 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 210 TYR 0.026 0.002 TYR A1823 PHE 0.015 0.001 PHE A1779 TRP 0.008 0.001 TRP F 28 HIS 0.005 0.001 HIS A1490 Details of bonding type rmsd covalent geometry : bond 0.00466 (20147) covalent geometry : angle 0.60393 (27235) hydrogen bonds : bond 0.03810 ( 1044) hydrogen bonds : angle 4.38494 ( 3003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 303 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8896 (pt) cc_final: 0.8585 (mm) REVERT: A 1368 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7975 (mmm) REVERT: A 1488 GLU cc_start: 0.7864 (pm20) cc_final: 0.7528 (pm20) REVERT: A 1489 TRP cc_start: 0.8292 (t-100) cc_final: 0.8038 (t-100) REVERT: A 1786 TYR cc_start: 0.7898 (m-10) cc_final: 0.7529 (m-80) REVERT: A 1830 ASP cc_start: 0.5867 (OUTLIER) cc_final: 0.5522 (p0) REVERT: B 91 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8183 (ttm110) REVERT: B 146 MET cc_start: 0.9276 (tpp) cc_final: 0.9033 (mmm) REVERT: B 158 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8403 (ttp) REVERT: D 36 LYS cc_start: 0.5627 (OUTLIER) cc_final: 0.5351 (tptm) REVERT: D 102 ARG cc_start: 0.8395 (mmt180) cc_final: 0.7645 (tmm160) REVERT: D 318 ASN cc_start: 0.8338 (p0) cc_final: 0.8110 (p0) REVERT: E 35 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.8032 (p90) REVERT: E 51 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.7498 (mtt90) REVERT: F 238 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: G 5 ARG cc_start: 0.7985 (tpt90) cc_final: 0.7498 (tpt90) REVERT: G 72 LEU cc_start: 0.7605 (pt) cc_final: 0.7001 (mt) REVERT: G 154 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7506 (mt) REVERT: G 199 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6842 (ppp) outliers start: 92 outliers final: 68 residues processed: 365 average time/residue: 0.1392 time to fit residues: 76.8416 Evaluate side-chains 360 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1830 ASP Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 35 PHE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 82 ILE Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain F residue 249 TYR Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 199 MET Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 201 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN E 194 HIS ** G 49 GLN ** 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 = 0.4065 r_free = 0.4065 target = 0.165773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.124811 restraints weight = 30787.652| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.66 r_work: 0.3224 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20147 Z= 0.143 Angle : 0.582 14.813 27235 Z= 0.292 Chirality : 0.042 0.360 3156 Planarity : 0.004 0.062 3459 Dihedral : 7.366 165.597 2757 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.99 % Allowed : 23.30 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.17), residues: 2475 helix: 1.26 (0.15), residues: 1251 sheet: -0.50 (0.26), residues: 377 loop : -0.57 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 146 TYR 0.019 0.001 TYR A1823 PHE 0.013 0.001 PHE F 144 TRP 0.008 0.001 TRP F 28 HIS 0.005 0.001 HIS A1490 Details of bonding type rmsd covalent geometry : bond 0.00338 (20147) covalent geometry : angle 0.58214 (27235) hydrogen bonds : bond 0.03494 ( 1044) hydrogen bonds : angle 4.29656 ( 3003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 303 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8911 (pt) cc_final: 0.8655 (mm) REVERT: A 1489 TRP cc_start: 0.8185 (t-100) cc_final: 0.7936 (t-100) REVERT: A 1498 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6683 (tm-30) REVERT: B 91 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8048 (ttm110) REVERT: B 146 MET cc_start: 0.9201 (tpp) cc_final: 0.8992 (mmm) REVERT: B 158 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8243 (ttp) REVERT: C 76 GLN cc_start: 0.7401 (pt0) cc_final: 0.7191 (pt0) REVERT: D 36 LYS cc_start: 0.5638 (OUTLIER) cc_final: 0.5391 (tptm) REVERT: D 102 ARG cc_start: 0.8274 (mmt180) cc_final: 0.7606 (tmm160) REVERT: D 318 ASN cc_start: 0.8227 (p0) cc_final: 0.8024 (p0) REVERT: E 51 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.7365 (mtt90) REVERT: F 238 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7296 (mm-30) REVERT: G 5 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7366 (tpt90) REVERT: G 72 LEU cc_start: 0.7604 (pt) cc_final: 0.7149 (mt) REVERT: G 154 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7521 (mt) REVERT: G 199 MET cc_start: 0.6974 (tmm) cc_final: 0.6669 (ppp) outliers start: 88 outliers final: 62 residues processed: 367 average time/residue: 0.1360 time to fit residues: 75.3848 Evaluate side-chains 366 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 297 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 36 LYS Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 161 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 177 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A1490 HIS A1644 HIS ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 308 ASN E 90 ASN E 194 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.167237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126491 restraints weight = 30665.862| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.71 r_work: 0.3259 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20147 Z= 0.110 Angle : 0.567 15.035 27235 Z= 0.283 Chirality : 0.041 0.342 3156 Planarity : 0.004 0.071 3459 Dihedral : 7.169 166.903 2757 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.49 % Allowed : 24.03 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.17), residues: 2475 helix: 1.43 (0.15), residues: 1250 sheet: -0.46 (0.26), residues: 374 loop : -0.52 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 146 TYR 0.016 0.001 TYR F 249 PHE 0.012 0.001 PHE D 54 TRP 0.010 0.001 TRP A1083 HIS 0.005 0.001 HIS E 331 Details of bonding type rmsd covalent geometry : bond 0.00251 (20147) covalent geometry : angle 0.56709 (27235) hydrogen bonds : bond 0.03156 ( 1044) hydrogen bonds : angle 4.19762 ( 3003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 318 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8800 (pt) cc_final: 0.8595 (mm) REVERT: A 1489 TRP cc_start: 0.8190 (t-100) cc_final: 0.7947 (t-100) REVERT: A 1498 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6691 (tm-30) REVERT: A 1830 ASP cc_start: 0.5775 (OUTLIER) cc_final: 0.5436 (p0) REVERT: B 91 ARG cc_start: 0.8432 (ttm-80) cc_final: 0.8101 (ttm110) REVERT: D 102 ARG cc_start: 0.8294 (mmt180) cc_final: 0.7622 (tmm160) REVERT: E 51 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.7314 (mtt90) REVERT: E 66 LYS cc_start: 0.7700 (pptt) cc_final: 0.7494 (pptt) REVERT: F 80 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8040 (tptt) REVERT: F 213 ASN cc_start: 0.8569 (m-40) cc_final: 0.8092 (m-40) REVERT: F 238 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: G 72 LEU cc_start: 0.7721 (pt) cc_final: 0.7169 (mt) outliers start: 77 outliers final: 56 residues processed: 369 average time/residue: 0.1510 time to fit residues: 84.0352 Evaluate side-chains 349 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 289 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1830 ASP Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 4 optimal weight: 0.6980 chunk 175 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 174 optimal weight: 0.7980 chunk 186 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS A1644 HIS ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN D 308 ASN E 194 HIS G 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.167462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126849 restraints weight = 30719.787| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.56 r_work: 0.3274 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20147 Z= 0.114 Angle : 0.580 15.048 27235 Z= 0.289 Chirality : 0.041 0.366 3156 Planarity : 0.004 0.069 3459 Dihedral : 7.123 167.907 2757 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.99 % Allowed : 24.30 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.17), residues: 2475 helix: 1.49 (0.15), residues: 1248 sheet: -0.46 (0.26), residues: 375 loop : -0.49 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 146 TYR 0.032 0.001 TYR F 249 PHE 0.015 0.001 PHE F 215 TRP 0.009 0.001 TRP A1083 HIS 0.006 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00264 (20147) covalent geometry : angle 0.57974 (27235) hydrogen bonds : bond 0.03151 ( 1044) hydrogen bonds : angle 4.16129 ( 3003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 307 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1489 TRP cc_start: 0.8163 (t-100) cc_final: 0.7946 (t-100) REVERT: A 1498 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6692 (tm-30) REVERT: A 1786 TYR cc_start: 0.8041 (m-10) cc_final: 0.7810 (m-10) REVERT: A 1830 ASP cc_start: 0.5750 (OUTLIER) cc_final: 0.5420 (p0) REVERT: B 91 ARG cc_start: 0.8435 (ttm-80) cc_final: 0.8109 (ttm110) REVERT: B 203 MET cc_start: 0.8750 (mmm) cc_final: 0.8523 (mmm) REVERT: D 102 ARG cc_start: 0.8302 (mmt180) cc_final: 0.7629 (tmm160) REVERT: E 51 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.7320 (mtt90) REVERT: F 238 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7142 (mm-30) REVERT: G 5 ARG cc_start: 0.7691 (tpt90) cc_final: 0.7453 (tpt90) REVERT: G 72 LEU cc_start: 0.7715 (pt) cc_final: 0.7154 (mt) REVERT: G 154 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7367 (mt) outliers start: 66 outliers final: 57 residues processed: 351 average time/residue: 0.1400 time to fit residues: 74.9029 Evaluate side-chains 356 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 294 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1360 LEU Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1812 GLU Chi-restraints excluded: chain A residue 1830 ASP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 204 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 chunk 101 optimal weight: 0.0170 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 132 optimal weight: 0.3980 chunk 242 optimal weight: 4.9990 chunk 110 optimal weight: 0.1980 overall best weight: 0.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS A1644 HIS ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 GLN D 308 ASN E 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.119222 restraints weight = 30490.947| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.75 r_work: 0.3233 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20147 Z= 0.109 Angle : 0.587 15.164 27235 Z= 0.292 Chirality : 0.041 0.361 3156 Planarity : 0.004 0.067 3459 Dihedral : 7.061 168.531 2757 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.72 % Allowed : 24.57 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.17), residues: 2475 helix: 1.51 (0.15), residues: 1248 sheet: -0.45 (0.26), residues: 375 loop : -0.49 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 146 TYR 0.024 0.001 TYR F 249 PHE 0.015 0.001 PHE D 101 TRP 0.011 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 Details of bonding type rmsd covalent geometry : bond 0.00249 (20147) covalent geometry : angle 0.58678 (27235) hydrogen bonds : bond 0.03083 ( 1044) hydrogen bonds : angle 4.14482 ( 3003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4950 Ramachandran restraints generated. 2475 Oldfield, 0 Emsley, 2475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 311 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1489 TRP cc_start: 0.8096 (t-100) cc_final: 0.7894 (t-100) REVERT: A 1498 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6727 (tm-30) REVERT: A 1786 TYR cc_start: 0.7953 (m-10) cc_final: 0.7720 (m-10) REVERT: A 1830 ASP cc_start: 0.5772 (OUTLIER) cc_final: 0.5418 (p0) REVERT: B 91 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8181 (ttm110) REVERT: B 203 MET cc_start: 0.8834 (mmm) cc_final: 0.8587 (mmm) REVERT: D 102 ARG cc_start: 0.8377 (mmt180) cc_final: 0.7634 (tmm160) REVERT: E 51 ARG cc_start: 0.9333 (OUTLIER) cc_final: 0.7301 (mtt90) REVERT: F 238 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7170 (mm-30) REVERT: G 5 ARG cc_start: 0.7829 (tpt90) cc_final: 0.7563 (tpt90) REVERT: G 72 LEU cc_start: 0.7684 (pt) cc_final: 0.7126 (mt) REVERT: G 154 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7420 (mt) outliers start: 60 outliers final: 50 residues processed: 352 average time/residue: 0.1448 time to fit residues: 76.9718 Evaluate side-chains 354 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 299 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 LEU Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain A residue 1167 ILE Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 PHE Chi-restraints excluded: chain A residue 1195 SER Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1411 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1812 GLU Chi-restraints excluded: chain A residue 1830 ASP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 248 LYS Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 83 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 169 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 226 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 224 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS A1644 HIS ** A1803 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.166570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118982 restraints weight = 30486.282| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.69 r_work: 0.3238 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20147 Z= 0.121 Angle : 0.591 14.277 27235 Z= 0.294 Chirality : 0.042 0.367 3156 Planarity : 0.004 0.066 3459 Dihedral : 7.064 169.398 2757 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.04 % Allowed : 24.48 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.17), residues: 2475 helix: 1.52 (0.15), residues: 1250 sheet: -0.40 (0.26), residues: 375 loop : -0.45 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 146 TYR 0.022 0.001 TYR F 249 PHE 0.016 0.001 PHE F 215 TRP 0.012 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 Details of bonding type rmsd covalent geometry : bond 0.00286 (20147) covalent geometry : angle 0.59122 (27235) hydrogen bonds : bond 0.03155 ( 1044) hydrogen bonds : angle 4.12043 ( 3003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4631.45 seconds wall clock time: 80 minutes 24.99 seconds (4824.99 seconds total)