Starting phenix.real_space_refine on Tue Jun 17 11:07:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ui8_42288/06_2025/8ui8_42288.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ui8_42288/06_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_42288/06_2025/8ui8_42288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ui8_42288/06_2025/8ui8_42288.map" model { file = "/net/cci-nas-00/data/ceres_data/8ui8_42288/06_2025/8ui8_42288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ui8_42288/06_2025/8ui8_42288.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.85, per 1000 atoms: 0.60 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: 4.99 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 2.19 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: 6.98 Time building geometry restraints manager: 5.90 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 46.360 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.660 ------------------------------------------------------------------------------- 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 : 7.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (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 TRP 0.019 0.002 TRP A1769 HIS 0.013 0.002 HIS E 301 PHE 0.043 0.002 PHE F 215 TYR 0.052 0.003 TYR F 249 ARG 0.011 0.001 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.14087 ( 1044) hydrogen bonds : angle 6.04671 ( 3003) covalent geometry : bond 0.00494 (20147) covalent geometry : angle 0.85106 (27235) *********************** 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 : 2.158 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: 0.3256 time to fit residues: 161.2271 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 : 2.173 ------------------------------------------------------------------------------- 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 207 optimal weight: 9.9990 chunk 186 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 63 optimal weight: 0.0870 chunk 125 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 223 optimal weight: 20.0000 overall best weight: 1.9562 ------------------------------------------------------------------------------- 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** ** 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 246 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.166492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122124 restraints weight = 30350.960| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.85 r_work: 0.3210 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20147 Z= 0.184 Angle : 0.602 8.045 27235 Z= 0.309 Chirality : 0.042 0.178 3156 Planarity : 0.005 0.065 3459 Dihedral : 8.207 166.755 2771 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.35 % Allowed : 22.21 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.17), residues: 2475 helix: 0.64 (0.15), residues: 1241 sheet: -0.54 (0.25), residues: 379 loop : -0.70 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.018 0.001 PHE F 214 TYR 0.041 0.002 TYR F 249 ARG 0.024 0.001 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 1044) hydrogen bonds : angle 4.68635 ( 3003) covalent geometry : bond 0.00431 (20147) covalent geometry : angle 0.60236 (27235) *********************** 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 397 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 323 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1324 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8186 (t80) REVERT: E 99 ASP cc_start: 0.8033 (m-30) cc_final: 0.7770 (m-30) REVERT: F 199 MET cc_start: 0.5452 (tmm) cc_final: 0.5096 (tmm) REVERT: G 165 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6921 (p0) outliers start: 74 outliers final: 40 residues processed: 372 average time/residue: 0.3086 time to fit residues: 178.1520 Evaluate side-chains 340 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 298 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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 1192 PHE Chi-restraints excluded: chain A residue 1324 PHE Chi-restraints excluded: chain A residue 1377 THR 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 C residue 23 VAL 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 206 ILE Chi-restraints excluded: chain D residue 220 VAL 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 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 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 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 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 233 VAL 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 124 optimal weight: 0.9980 chunk 138 optimal weight: 0.0010 chunk 150 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 58 optimal weight: 0.0000 chunk 74 optimal weight: 3.9990 chunk 75 optimal weight: 0.0010 chunk 86 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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** D 308 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.169307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.124691 restraints weight = 30519.314| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.74 r_work: 0.3252 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20147 Z= 0.103 Angle : 0.535 7.842 27235 Z= 0.272 Chirality : 0.040 0.158 3156 Planarity : 0.004 0.065 3459 Dihedral : 7.669 167.326 2760 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.72 % Allowed : 22.94 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2475 helix: 1.06 (0.15), residues: 1248 sheet: -0.41 (0.26), residues: 370 loop : -0.63 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.041 0.001 PHE F 214 TYR 0.019 0.001 TYR F 249 ARG 0.006 0.000 ARG G 5 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 1044) hydrogen bonds : angle 4.37859 ( 3003) covalent geometry : bond 0.00223 (20147) covalent geometry : angle 0.53456 (27235) *********************** 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 386 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 326 time to evaluate : 2.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1758 PHE cc_start: 0.8394 (p90) cc_final: 0.8167 (p90) REVERT: B 296 ILE cc_start: 0.9377 (tp) cc_final: 0.9162 (tp) REVERT: C 202 MET cc_start: 0.8965 (tpp) cc_final: 0.8736 (tpp) REVERT: F 36 ASN cc_start: 0.7803 (t0) cc_final: 0.7329 (t0) REVERT: F 49 GLN cc_start: 0.7253 (tm130) cc_final: 0.7046 (tm130) REVERT: F 139 MET cc_start: 0.7058 (ttm) cc_final: 0.6719 (ttt) REVERT: F 199 MET cc_start: 0.5384 (tmm) cc_final: 0.4810 (tmm) REVERT: F 238 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6838 (mm-30) REVERT: F 246 HIS cc_start: 0.8469 (p90) cc_final: 0.8195 (p90) REVERT: F 248 LYS cc_start: 0.7283 (mtpt) cc_final: 0.7001 (mtpt) REVERT: G 16 LEU cc_start: 0.8164 (tt) cc_final: 0.7781 (tt) REVERT: G 72 LEU cc_start: 0.7673 (pt) cc_final: 0.7174 (mt) REVERT: G 165 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6827 (p0) outliers start: 60 outliers final: 36 residues processed: 361 average time/residue: 0.3512 time to fit residues: 192.5667 Evaluate side-chains 344 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 306 time to evaluate : 3.287 ------------------------------------------------------------------------------- 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 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 B residue 158 MET Chi-restraints excluded: chain B residue 175 ASP 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 146 THR Chi-restraints excluded: chain C residue 195 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 222 ILE Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 219 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 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 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 196 THR 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 216 optimal weight: 10.0000 chunk 234 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 177 optimal weight: 0.0670 chunk 178 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 overall best weight: 1.9922 ------------------------------------------------------------------------------- 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 ** 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 = 0.4063 r_free = 0.4063 target = 0.166158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120277 restraints weight = 30524.992| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.90 r_work: 0.3194 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20147 Z= 0.183 Angle : 0.577 10.602 27235 Z= 0.293 Chirality : 0.042 0.244 3156 Planarity : 0.004 0.064 3459 Dihedral : 7.573 167.571 2759 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.58 % Allowed : 22.12 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.17), residues: 2475 helix: 1.16 (0.15), residues: 1245 sheet: -0.51 (0.25), residues: 383 loop : -0.58 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.037 0.001 PHE F 214 TYR 0.017 0.002 TYR E 318 ARG 0.005 0.000 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 1044) hydrogen bonds : angle 4.35299 ( 3003) covalent geometry : bond 0.00436 (20147) covalent geometry : angle 0.57736 (27235) *********************** 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: 79 poor density : 314 time to evaluate : 2.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8901 (pt) cc_final: 0.8533 (mm) REVERT: A 1758 PHE cc_start: 0.8499 (p90) cc_final: 0.8248 (p90) REVERT: C 202 MET cc_start: 0.8984 (tpp) cc_final: 0.8768 (tpp) REVERT: E 138 ASP cc_start: 0.8692 (p0) cc_final: 0.8476 (p0) REVERT: F 238 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7100 (mm-30) REVERT: F 248 LYS cc_start: 0.7473 (mtpt) cc_final: 0.7217 (mtpt) REVERT: G 72 LEU cc_start: 0.7709 (pt) cc_final: 0.7207 (mt) REVERT: G 165 ASP cc_start: 0.7203 (OUTLIER) cc_final: 0.6951 (p0) outliers start: 79 outliers final: 56 residues processed: 363 average time/residue: 0.3310 time to fit residues: 182.6108 Evaluate side-chains 356 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 298 time to evaluate : 2.456 ------------------------------------------------------------------------------- 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 1134 THR Chi-restraints excluded: chain A residue 1189 LYS Chi-restraints excluded: chain A residue 1192 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 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 249 GLU 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 314 VAL Chi-restraints excluded: chain C residue 333 ARG 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 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 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 46 SER Chi-restraints excluded: chain F residue 65 ASN 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 251 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 154 ILE Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 196 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 10 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 238 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** D 308 ASN E 194 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.166574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.125084 restraints weight = 30591.823| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.67 r_work: 0.3215 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20147 Z= 0.143 Angle : 0.551 10.753 27235 Z= 0.279 Chirality : 0.041 0.225 3156 Planarity : 0.004 0.065 3459 Dihedral : 7.345 166.391 2757 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.76 % Allowed : 21.85 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2475 helix: 1.28 (0.15), residues: 1246 sheet: -0.50 (0.25), residues: 384 loop : -0.52 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.018 0.001 PHE D 101 TYR 0.037 0.002 TYR F 249 ARG 0.006 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.03475 ( 1044) hydrogen bonds : angle 4.28689 ( 3003) covalent geometry : bond 0.00336 (20147) covalent geometry : angle 0.55109 (27235) *********************** 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 397 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 314 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8911 (pt) cc_final: 0.8602 (mm) REVERT: A 1368 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7567 (mpp) REVERT: A 1758 PHE cc_start: 0.8505 (p90) cc_final: 0.8292 (p90) REVERT: A 1830 ASP cc_start: 0.5901 (OUTLIER) cc_final: 0.5607 (p0) REVERT: B 91 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8128 (ttm110) REVERT: C 202 MET cc_start: 0.8997 (tpp) cc_final: 0.8781 (tpp) REVERT: E 105 ARG cc_start: 0.8530 (ptt90) cc_final: 0.8327 (ptm-80) REVERT: F 238 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7134 (mm-30) REVERT: F 248 LYS cc_start: 0.7351 (mtpt) cc_final: 0.7062 (mtpt) REVERT: G 72 LEU cc_start: 0.7715 (pt) cc_final: 0.7359 (mt) REVERT: G 165 ASP cc_start: 0.7231 (OUTLIER) cc_final: 0.6983 (p0) outliers start: 83 outliers final: 59 residues processed: 369 average time/residue: 0.3405 time to fit residues: 190.0375 Evaluate side-chains 362 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 299 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1368 MET Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1522 ILE 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 249 GLU 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 257 GLN Chi-restraints excluded: chain C residue 314 VAL 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 87 THR Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 82 ILE 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 40 MET Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 49 GLN Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 65 ASN 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 182 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 251 LEU 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 165 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 196 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 37 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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** D 308 ASN E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.164376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.119132 restraints weight = 30437.850| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.72 r_work: 0.3203 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1921 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= 0.193 Angle : 0.590 11.003 27235 Z= 0.299 Chirality : 0.042 0.209 3156 Planarity : 0.004 0.066 3459 Dihedral : 7.346 166.666 2755 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.31 % Allowed : 22.35 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2475 helix: 1.23 (0.15), residues: 1246 sheet: -0.50 (0.25), residues: 385 loop : -0.52 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.043 0.002 PHE F 214 TYR 0.026 0.002 TYR F 249 ARG 0.006 0.000 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 1044) hydrogen bonds : angle 4.34632 ( 3003) covalent geometry : bond 0.00461 (20147) covalent geometry : angle 0.59029 (27235) *********************** 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 405 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 310 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8881 (pt) cc_final: 0.8545 (mm) REVERT: A 1368 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7918 (mmm) REVERT: A 1758 PHE cc_start: 0.8548 (p90) cc_final: 0.8303 (p90) REVERT: A 1830 ASP cc_start: 0.5964 (OUTLIER) cc_final: 0.5661 (p0) REVERT: B 91 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8148 (ttm110) REVERT: B 146 MET cc_start: 0.9283 (tpp) cc_final: 0.9052 (mmm) REVERT: B 158 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8296 (ttp) REVERT: D 318 ASN cc_start: 0.8277 (p0) cc_final: 0.8051 (p0) REVERT: E 35 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7985 (p90) REVERT: E 99 ASP cc_start: 0.7938 (m-30) cc_final: 0.7577 (m-30) REVERT: F 238 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7092 (mm-30) REVERT: F 248 LYS cc_start: 0.7301 (mtpt) cc_final: 0.7052 (mtpt) REVERT: G 5 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7659 (tpt90) REVERT: G 72 LEU cc_start: 0.7829 (pt) cc_final: 0.7308 (mt) REVERT: G 154 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7349 (mt) REVERT: G 165 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.7082 (p0) outliers start: 95 outliers final: 65 residues processed: 373 average time/residue: 0.3367 time to fit residues: 190.9986 Evaluate side-chains 373 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 300 time to evaluate : 2.461 ------------------------------------------------------------------------------- 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 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 1522 ILE Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1772 ILE 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 218 LEU Chi-restraints excluded: chain B residue 249 GLU 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 314 VAL 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 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 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 35 PHE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 82 ILE 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 49 GLN 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 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 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 165 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 196 THR 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 160 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 172 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 223 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 884 HIS A 955 ASN 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** ** 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 = 0.4062 r_free = 0.4062 target = 0.166184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125731 restraints weight = 30253.364| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.69 r_work: 0.3223 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20147 Z= 0.118 Angle : 0.560 12.205 27235 Z= 0.281 Chirality : 0.041 0.229 3156 Planarity : 0.004 0.069 3459 Dihedral : 7.139 166.119 2755 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.26 % Allowed : 23.53 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2475 helix: 1.39 (0.15), residues: 1245 sheet: -0.36 (0.26), residues: 374 loop : -0.52 (0.22), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.016 0.001 PHE D 101 TYR 0.022 0.001 TYR E 343 ARG 0.007 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 1044) hydrogen bonds : angle 4.23313 ( 3003) covalent geometry : bond 0.00273 (20147) covalent geometry : angle 0.55952 (27235) *********************** 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 396 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 324 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8859 (pt) cc_final: 0.8603 (mm) REVERT: A 1498 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: A 1758 PHE cc_start: 0.8490 (p90) cc_final: 0.8285 (p90) REVERT: A 1830 ASP cc_start: 0.5889 (OUTLIER) cc_final: 0.5566 (p0) REVERT: B 91 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.8161 (ttm110) REVERT: B 146 MET cc_start: 0.9228 (tpp) cc_final: 0.9011 (mmm) REVERT: C 76 GLN cc_start: 0.7435 (pt0) cc_final: 0.7183 (pt0) REVERT: D 36 LYS cc_start: 0.5668 (OUTLIER) cc_final: 0.5402 (tptm) REVERT: D 102 ARG cc_start: 0.8264 (mmt180) cc_final: 0.7598 (tmm160) REVERT: E 51 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.7220 (mtt90) REVERT: E 99 ASP cc_start: 0.7813 (m-30) cc_final: 0.7481 (m-30) REVERT: E 338 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8766 (mmtt) REVERT: F 199 MET cc_start: 0.5338 (tmm) cc_final: 0.4660 (tmm) REVERT: F 238 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7179 (mm-30) REVERT: F 248 LYS cc_start: 0.7260 (mtpt) cc_final: 0.7024 (mtpt) REVERT: G 5 ARG cc_start: 0.7868 (tpt90) cc_final: 0.7603 (tpt90) REVERT: G 72 LEU cc_start: 0.7765 (pt) cc_final: 0.7284 (mt) REVERT: G 154 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7417 (mt) outliers start: 72 outliers final: 52 residues processed: 375 average time/residue: 0.4246 time to fit residues: 240.4445 Evaluate side-chains 360 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 301 time to evaluate : 2.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 955 ASN 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 1498 GLU Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1709 LYS 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 214 THR Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 48 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 36 LYS 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 178 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 51 ARG 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 338 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 49 GLN 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 121 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE 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 196 THR Chi-restraints excluded: chain G residue 206 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 173 optimal weight: 0.4980 chunk 71 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 239 optimal weight: 5.9990 chunk 242 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 157 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.165700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.125124 restraints weight = 30498.099| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.73 r_work: 0.3216 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20147 Z= 0.129 Angle : 0.572 12.600 27235 Z= 0.287 Chirality : 0.041 0.212 3156 Planarity : 0.004 0.071 3459 Dihedral : 7.095 165.560 2755 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.22 % Allowed : 23.89 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2475 helix: 1.38 (0.15), residues: 1246 sheet: -0.25 (0.26), residues: 374 loop : -0.47 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.042 0.001 PHE F 214 TYR 0.029 0.001 TYR F 249 ARG 0.008 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 1044) hydrogen bonds : angle 4.21926 ( 3003) covalent geometry : bond 0.00302 (20147) covalent geometry : angle 0.57210 (27235) *********************** 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 382 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 311 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8866 (pt) cc_final: 0.8613 (mm) REVERT: A 1498 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: A 1758 PHE cc_start: 0.8494 (p90) cc_final: 0.8290 (p90) REVERT: A 1830 ASP cc_start: 0.5869 (OUTLIER) cc_final: 0.5576 (p0) REVERT: B 91 ARG cc_start: 0.8458 (ttm-80) cc_final: 0.8182 (ttm110) REVERT: B 146 MET cc_start: 0.9240 (tpp) cc_final: 0.9026 (mmm) REVERT: C 76 GLN cc_start: 0.7442 (pt0) cc_final: 0.7202 (pt0) REVERT: D 36 LYS cc_start: 0.5692 (OUTLIER) cc_final: 0.5434 (tptm) REVERT: E 51 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.7259 (mtt90) REVERT: E 99 ASP cc_start: 0.7798 (m-30) cc_final: 0.7472 (m-30) REVERT: E 338 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8778 (mmtt) REVERT: F 139 MET cc_start: 0.7281 (ttm) cc_final: 0.7053 (ttm) REVERT: F 199 MET cc_start: 0.5385 (tmm) cc_final: 0.4696 (tmm) REVERT: F 238 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7217 (mm-30) REVERT: F 248 LYS cc_start: 0.7258 (mtpt) cc_final: 0.7007 (mtpt) REVERT: G 5 ARG cc_start: 0.7940 (tpt90) cc_final: 0.7671 (tpt90) REVERT: G 72 LEU cc_start: 0.7772 (pt) cc_final: 0.7285 (mt) REVERT: G 154 ILE cc_start: 0.7971 (OUTLIER) cc_final: 0.7437 (mt) outliers start: 71 outliers final: 56 residues processed: 363 average time/residue: 0.4510 time to fit residues: 246.0177 Evaluate side-chains 361 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 298 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1522 ILE 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 1709 LYS Chi-restraints excluded: chain A residue 1772 ILE 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 1827 ILE 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 249 GLU 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 48 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 36 LYS 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 173 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 62 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 E residue 338 LYS 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 121 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 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 196 THR 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 17 optimal weight: 0.5980 chunk 194 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 207 optimal weight: 0.0270 chunk 169 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- 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 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.165296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120560 restraints weight = 30358.914| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.74 r_work: 0.3213 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20147 Z= 0.143 Angle : 0.588 12.746 27235 Z= 0.295 Chirality : 0.042 0.195 3156 Planarity : 0.004 0.072 3459 Dihedral : 7.080 164.393 2755 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.58 % Allowed : 23.66 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.17), residues: 2475 helix: 1.37 (0.15), residues: 1247 sheet: -0.22 (0.26), residues: 374 loop : -0.45 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 28 HIS 0.005 0.001 HIS A1490 PHE 0.015 0.001 PHE D 101 TYR 0.031 0.002 TYR F 249 ARG 0.009 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 1044) hydrogen bonds : angle 4.21398 ( 3003) covalent geometry : bond 0.00340 (20147) covalent geometry : angle 0.58760 (27235) *********************** 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 383 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 304 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8824 (pt) cc_final: 0.8581 (mm) REVERT: A 1498 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6677 (tm-30) REVERT: A 1758 PHE cc_start: 0.8507 (p90) cc_final: 0.8280 (p90) REVERT: A 1786 TYR cc_start: 0.8049 (m-10) cc_final: 0.7811 (m-10) REVERT: A 1830 ASP cc_start: 0.5908 (OUTLIER) cc_final: 0.5590 (p0) REVERT: B 91 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8213 (ttm110) REVERT: B 146 MET cc_start: 0.9260 (tpp) cc_final: 0.9032 (mmm) REVERT: C 76 GLN cc_start: 0.7454 (pt0) cc_final: 0.7229 (pt0) REVERT: C 177 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (pp) REVERT: D 102 ARG cc_start: 0.8331 (mmt180) cc_final: 0.7652 (tmm160) REVERT: E 51 ARG cc_start: 0.9363 (OUTLIER) cc_final: 0.7290 (mtt90) REVERT: E 99 ASP cc_start: 0.7814 (m-30) cc_final: 0.7506 (m-30) REVERT: F 49 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7343 (tm130) REVERT: F 199 MET cc_start: 0.5416 (tmm) cc_final: 0.4732 (tmm) REVERT: F 238 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7155 (mm-30) REVERT: F 248 LYS cc_start: 0.7273 (mtpt) cc_final: 0.6955 (mtpt) REVERT: G 5 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7659 (tpt90) REVERT: G 72 LEU cc_start: 0.7855 (pt) cc_final: 0.7345 (mt) REVERT: G 154 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7396 (mt) outliers start: 79 outliers final: 63 residues processed: 364 average time/residue: 0.4020 time to fit residues: 225.6984 Evaluate side-chains 375 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 304 time to evaluate : 3.266 ------------------------------------------------------------------------------- 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 1134 THR 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 1522 ILE 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 1709 LYS Chi-restraints excluded: chain A residue 1772 ILE 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 1827 ILE 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 218 LEU Chi-restraints excluded: chain B residue 249 GLU 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 48 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 177 LEU 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 42 GLU 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 173 THR 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 E residue 50 THR 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 118 SER 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 49 GLN 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 121 LEU Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE 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 196 THR 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 16 optimal weight: 0.0670 chunk 180 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 101 optimal weight: 0.0040 chunk 189 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 200 optimal weight: 0.0470 chunk 206 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 217 optimal weight: 9.9990 overall best weight: 0.4228 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.167810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.120797 restraints weight = 30289.874| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.52 r_work: 0.3265 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 20147 Z= 0.108 Angle : 0.581 13.040 27235 Z= 0.289 Chirality : 0.040 0.193 3156 Planarity : 0.004 0.072 3459 Dihedral : 6.911 163.645 2755 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.77 % Allowed : 24.34 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2475 helix: 1.48 (0.15), residues: 1247 sheet: -0.21 (0.26), residues: 374 loop : -0.45 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 28 HIS 0.006 0.001 HIS A1490 PHE 0.044 0.001 PHE F 214 TYR 0.034 0.001 TYR F 249 ARG 0.009 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 1044) hydrogen bonds : angle 4.13738 ( 3003) covalent geometry : bond 0.00244 (20147) covalent geometry : angle 0.58069 (27235) ********************** 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 387 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 326 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1073 ILE cc_start: 0.8753 (pt) cc_final: 0.8547 (mm) REVERT: A 1498 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6694 (tm-30) REVERT: A 1786 TYR cc_start: 0.7961 (m-10) cc_final: 0.7740 (m-10) REVERT: A 1830 ASP cc_start: 0.5783 (OUTLIER) cc_final: 0.5462 (p0) REVERT: B 91 ARG cc_start: 0.8403 (ttm-80) cc_final: 0.8136 (ttm110) REVERT: B 296 ILE cc_start: 0.9372 (tp) cc_final: 0.9130 (tp) REVERT: C 177 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8335 (pp) REVERT: D 102 ARG cc_start: 0.8366 (mmt180) cc_final: 0.7651 (tmm160) REVERT: E 51 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.7175 (mtt90) REVERT: E 99 ASP cc_start: 0.7776 (m-30) cc_final: 0.7463 (m-30) REVERT: F 49 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7313 (tm130) REVERT: F 199 MET cc_start: 0.5240 (tmm) cc_final: 0.4531 (tmm) REVERT: F 238 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: F 248 LYS cc_start: 0.7229 (mtpt) cc_final: 0.6907 (mtpt) REVERT: G 5 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7713 (tpt90) REVERT: G 72 LEU cc_start: 0.7844 (pt) cc_final: 0.7347 (mt) outliers start: 61 outliers final: 49 residues processed: 367 average time/residue: 0.4059 time to fit residues: 224.8193 Evaluate side-chains 362 residues out of total 2206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 306 time to evaluate : 2.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 923 LEU 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 1498 GLU Chi-restraints excluded: chain A residue 1522 ILE Chi-restraints excluded: chain A residue 1676 ASP Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1772 ILE 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 1827 ILE 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 218 LEU Chi-restraints excluded: chain B residue 249 GLU 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 177 LEU 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 42 GLU 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 212 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 51 ARG Chi-restraints excluded: chain E residue 62 VAL Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 27 CYS Chi-restraints excluded: chain F residue 49 GLN 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 121 LEU Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE 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 128 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 196 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 59 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 146 optimal weight: 0.0570 chunk 245 optimal weight: 0.0980 chunk 73 optimal weight: 0.0980 chunk 168 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- 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** C 76 GLN E 194 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.168529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121489 restraints weight = 30436.567| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.55 r_work: 0.3273 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20147 Z= 0.104 Angle : 0.570 12.403 27235 Z= 0.284 Chirality : 0.041 0.183 3156 Planarity : 0.004 0.074 3459 Dihedral : 6.809 164.687 2755 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.63 % Allowed : 24.52 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.17), residues: 2475 helix: 1.54 (0.15), residues: 1249 sheet: -0.20 (0.26), residues: 376 loop : -0.42 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 28 HIS 0.005 0.001 HIS E 194 PHE 0.036 0.001 PHE F 214 TYR 0.028 0.001 TYR F 249 ARG 0.008 0.000 ARG G 146 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 1044) hydrogen bonds : angle 4.07473 ( 3003) covalent geometry : bond 0.00235 (20147) covalent geometry : angle 0.57038 (27235) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11273.72 seconds wall clock time: 198 minutes 31.45 seconds (11911.45 seconds total)