Starting phenix.real_space_refine on Thu Sep 26 09:20:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/09_2024/6he4_0209.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/09_2024/6he4_0209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/09_2024/6he4_0209.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/09_2024/6he4_0209.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/09_2024/6he4_0209.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6he4_0209/09_2024/6he4_0209.cif" } resolution = 4.85 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= 0.002 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 14 5.49 5 Mg 5 5.21 5 S 42 5.16 5 C 8042 2.51 5 N 2161 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12684 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 247} Chain: "I" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 248} Chain: "K" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "L" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 249} Chain: "M" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 249} Chain: "J" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 245} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.04, per 1000 atoms: 0.71 Number of scatterers: 12684 At special positions: 0 Unit cell: (134, 128.64, 80.4, 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 42 16.00 P 14 15.00 Mg 5 11.99 O 2420 8.00 N 2161 7.00 C 8042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.5 seconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2964 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 7 sheets defined 53.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'H' and resid 124 through 129 Processing helix chain 'H' and resid 147 through 157 removed outlier: 3.984A pdb=" N GLU H 151 " --> pdb=" O ASP H 147 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 152 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 162 Processing helix chain 'H' and resid 163 through 171 removed outlier: 3.644A pdb=" N PHE H 167 " --> pdb=" O LYS H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 200 removed outlier: 3.539A pdb=" N LEU H 191 " --> pdb=" O GLY H 187 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG H 200 " --> pdb=" O ALA H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 233 removed outlier: 3.642A pdb=" N VAL H 223 " --> pdb=" O GLY H 219 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE H 227 " --> pdb=" O VAL H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 275 removed outlier: 4.190A pdb=" N GLU H 260 " --> pdb=" O SER H 256 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU H 269 " --> pdb=" O MET H 265 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H 271 " --> pdb=" O GLN H 267 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE H 275 " --> pdb=" O GLU H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 328 removed outlier: 3.809A pdb=" N ILE H 318 " --> pdb=" O PHE H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 343 removed outlier: 3.804A pdb=" N LEU H 339 " --> pdb=" O ASP H 335 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG H 341 " --> pdb=" O LYS H 337 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE H 342 " --> pdb=" O GLU H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 365 Processing helix chain 'H' and resid 371 through 385 removed outlier: 3.654A pdb=" N PHE H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 129 Processing helix chain 'I' and resid 147 through 163 removed outlier: 3.719A pdb=" N GLU I 151 " --> pdb=" O ASP I 147 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 164 through 171 removed outlier: 3.541A pdb=" N VAL I 170 " --> pdb=" O LEU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 200 removed outlier: 3.721A pdb=" N ASN I 197 " --> pdb=" O LYS I 193 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN I 198 " --> pdb=" O ALA I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 234 removed outlier: 3.690A pdb=" N LEU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS I 233 " --> pdb=" O LEU I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 246 removed outlier: 3.687A pdb=" N ILE I 246 " --> pdb=" O LEU I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 273 removed outlier: 3.574A pdb=" N VAL I 261 " --> pdb=" O GLY I 257 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN I 267 " --> pdb=" O ARG I 263 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA I 270 " --> pdb=" O MET I 266 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP I 273 " --> pdb=" O LEU I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 299 Processing helix chain 'I' and resid 313 through 328 removed outlier: 3.769A pdb=" N ILE I 318 " --> pdb=" O PHE I 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS I 327 " --> pdb=" O ILE I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 343 Processing helix chain 'I' and resid 347 through 365 Processing helix chain 'I' and resid 371 through 387 removed outlier: 3.652A pdb=" N LYS I 381 " --> pdb=" O LYS I 377 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL I 382 " --> pdb=" O ALA I 378 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS I 385 " --> pdb=" O LYS I 381 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR I 386 " --> pdb=" O VAL I 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 163 removed outlier: 3.660A pdb=" N GLU K 152 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL K 157 " --> pdb=" O ILE K 153 " (cutoff:3.500A) Proline residue: K 160 - end of helix Processing helix chain 'K' and resid 163 through 171 removed outlier: 4.254A pdb=" N PHE K 167 " --> pdb=" O LYS K 163 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA K 168 " --> pdb=" O PRO K 164 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 199 Processing helix chain 'K' and resid 209 through 211 No H-bonds generated for 'chain 'K' and resid 209 through 211' Processing helix chain 'K' and resid 217 through 233 Processing helix chain 'K' and resid 261 through 269 removed outlier: 3.962A pdb=" N GLN K 267 " --> pdb=" O ARG K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 299 removed outlier: 3.541A pdb=" N LEU K 298 " --> pdb=" O ASP K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 328 removed outlier: 3.532A pdb=" N HIS K 324 " --> pdb=" O ILE K 320 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS K 327 " --> pdb=" O ILE K 323 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 343 removed outlier: 3.675A pdb=" N LEU K 339 " --> pdb=" O ASP K 335 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE K 342 " --> pdb=" O GLU K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 365 Processing helix chain 'K' and resid 371 through 385 removed outlier: 3.534A pdb=" N PHE K 375 " --> pdb=" O THR K 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 146 through 157 removed outlier: 3.523A pdb=" N GLU L 152 " --> pdb=" O VAL L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 163 Processing helix chain 'L' and resid 164 through 169 removed outlier: 3.684A pdb=" N ALA L 168 " --> pdb=" O PRO L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 200 removed outlier: 3.956A pdb=" N ARG L 200 " --> pdb=" O ALA L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 233 removed outlier: 3.521A pdb=" N VAL L 223 " --> pdb=" O GLY L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 274 removed outlier: 4.097A pdb=" N ARG L 259 " --> pdb=" O THR L 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU L 260 " --> pdb=" O SER L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 299 removed outlier: 3.734A pdb=" N ARG L 299 " --> pdb=" O PRO L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 327 removed outlier: 3.841A pdb=" N ILE L 318 " --> pdb=" O PHE L 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS L 327 " --> pdb=" O ILE L 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 344 removed outlier: 4.379A pdb=" N LEU L 339 " --> pdb=" O ASP L 335 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE L 342 " --> pdb=" O GLU L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 347 through 365 removed outlier: 3.512A pdb=" N CYS L 355 " --> pdb=" O ILE L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 387 removed outlier: 4.417A pdb=" N LYS L 385 " --> pdb=" O LYS L 381 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR L 386 " --> pdb=" O VAL L 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 157 removed outlier: 3.847A pdb=" N GLU M 151 " --> pdb=" O ASP M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 163 Processing helix chain 'M' and resid 165 through 170 Processing helix chain 'M' and resid 187 through 200 Processing helix chain 'M' and resid 220 through 233 Processing helix chain 'M' and resid 255 through 275 removed outlier: 3.692A pdb=" N GLU M 260 " --> pdb=" O SER M 256 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL M 261 " --> pdb=" O GLY M 257 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN M 267 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU M 268 " --> pdb=" O THR M 264 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU M 271 " --> pdb=" O GLN M 267 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP M 273 " --> pdb=" O LEU M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 326 removed outlier: 3.833A pdb=" N ILE M 323 " --> pdb=" O GLN M 319 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS M 324 " --> pdb=" O ILE M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 343 removed outlier: 3.926A pdb=" N LEU M 339 " --> pdb=" O ASP M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 365 removed outlier: 3.644A pdb=" N GLY M 359 " --> pdb=" O CYS M 355 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET M 360 " --> pdb=" O THR M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 371 through 382 Processing helix chain 'J' and resid 126 through 131 removed outlier: 3.801A pdb=" N PHE J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 157 Processing helix chain 'J' and resid 157 through 163 Processing helix chain 'J' and resid 164 through 171 removed outlier: 3.670A pdb=" N ALA J 168 " --> pdb=" O PRO J 164 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 200 removed outlier: 3.883A pdb=" N GLN J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 233 Processing helix chain 'J' and resid 242 through 247 Processing helix chain 'J' and resid 261 through 273 removed outlier: 3.895A pdb=" N MET J 265 " --> pdb=" O VAL J 261 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET J 266 " --> pdb=" O GLN J 262 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN J 267 " --> pdb=" O ARG J 263 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU J 268 " --> pdb=" O THR J 264 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP J 273 " --> pdb=" O LEU J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 299 removed outlier: 3.553A pdb=" N ARG J 299 " --> pdb=" O PRO J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 328 removed outlier: 3.678A pdb=" N ILE J 318 " --> pdb=" O PHE J 314 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE J 323 " --> pdb=" O GLN J 319 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS J 324 " --> pdb=" O ILE J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 343 Processing helix chain 'J' and resid 347 through 365 Processing helix chain 'J' and resid 371 through 385 removed outlier: 3.525A pdb=" N LYS J 385 " --> pdb=" O LYS J 381 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 204 through 205 removed outlier: 3.514A pdb=" N ILE H 204 " --> pdb=" O ILE H 237 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE H 238 " --> pdb=" O ILE H 284 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU H 180 " --> pdb=" O GLY H 285 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY H 177 " --> pdb=" O ARG H 305 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE H 307 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU H 179 " --> pdb=" O ILE H 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 203 through 206 removed outlier: 6.333A pdb=" N ILE I 238 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA I 286 " --> pdb=" O ILE I 238 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE I 240 " --> pdb=" O ALA I 286 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL I 178 " --> pdb=" O GLY I 285 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ILE I 307 " --> pdb=" O GLY I 177 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU I 179 " --> pdb=" O ILE I 307 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 203 through 207 removed outlier: 6.470A pdb=" N ILE K 204 " --> pdb=" O PHE K 239 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASP K 241 " --> pdb=" O ILE K 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL K 206 " --> pdb=" O ASP K 241 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL K 178 " --> pdb=" O GLY K 285 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLY K 177 " --> pdb=" O ARG K 305 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE K 307 " --> pdb=" O GLY K 177 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU K 179 " --> pdb=" O ILE K 307 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 285 through 287 removed outlier: 3.632A pdb=" N GLY L 285 " --> pdb=" O VAL L 178 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU L 179 " --> pdb=" O ILE L 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 202 through 207 removed outlier: 3.506A pdb=" N ASP L 241 " --> pdb=" O VAL L 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 132 through 134 removed outlier: 6.166A pdb=" N THR M 202 " --> pdb=" O ILE M 237 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE M 239 " --> pdb=" O THR M 202 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE M 204 " --> pdb=" O PHE M 239 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER M 236 " --> pdb=" O LYS M 282 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE M 284 " --> pdb=" O SER M 236 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE M 238 " --> pdb=" O ILE M 284 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA M 286 " --> pdb=" O ILE M 238 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE M 240 " --> pdb=" O ALA M 286 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL M 178 " --> pdb=" O GLY M 285 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU M 179 " --> pdb=" O ARG M 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 202 through 206 removed outlier: 8.185A pdb=" N ILE J 284 " --> pdb=" O SER J 236 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE J 238 " --> pdb=" O ILE J 284 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA J 286 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE J 240 " --> pdb=" O ALA J 286 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR J 287 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY J 177 " --> pdb=" O ARG J 305 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE J 307 " --> pdb=" O GLY J 177 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU J 179 " --> pdb=" O ILE J 307 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.54 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 2235 1.30 - 1.45: 3773 1.45 - 1.60: 6582 1.60 - 1.75: 210 1.75 - 1.90: 81 Bond restraints: 12881 Sorted by residual: bond pdb=" O3A ATP J 401 " pdb=" PB ATP J 401 " ideal model delta sigma weight residual 1.592 1.786 -0.194 1.10e-02 8.26e+03 3.11e+02 bond pdb=" O3A ATP K 401 " pdb=" PB ATP K 401 " ideal model delta sigma weight residual 1.592 1.764 -0.172 1.10e-02 8.26e+03 2.45e+02 bond pdb=" CA VAL H 206 " pdb=" C VAL H 206 " ideal model delta sigma weight residual 1.523 1.381 0.141 1.17e-02 7.31e+03 1.46e+02 bond pdb=" N ALA L 353 " pdb=" CA ALA L 353 " ideal model delta sigma weight residual 1.459 1.314 0.145 1.23e-02 6.61e+03 1.40e+02 bond pdb=" O3A ATP I 401 " pdb=" PB ATP I 401 " ideal model delta sigma weight residual 1.592 1.716 -0.124 1.10e-02 8.26e+03 1.26e+02 ... (remaining 12876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.46: 15202 5.46 - 10.93: 2104 10.93 - 16.39: 91 16.39 - 21.85: 8 21.85 - 27.31: 2 Bond angle restraints: 17407 Sorted by residual: angle pdb=" PA ATP K 401 " pdb=" O3A ATP K 401 " pdb=" PB ATP K 401 " ideal model delta sigma weight residual 136.83 158.87 -22.04 1.00e+00 1.00e+00 4.86e+02 angle pdb=" PA ATP H 401 " pdb=" O3A ATP H 401 " pdb=" PB ATP H 401 " ideal model delta sigma weight residual 136.83 158.43 -21.60 1.00e+00 1.00e+00 4.66e+02 angle pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " pdb=" PG ATP I 401 " ideal model delta sigma weight residual 139.87 158.05 -18.18 1.00e+00 1.00e+00 3.30e+02 angle pdb=" PB ATP J 401 " pdb=" O3B ATP J 401 " pdb=" PG ATP J 401 " ideal model delta sigma weight residual 139.87 157.49 -17.62 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 156.19 -16.32 1.00e+00 1.00e+00 2.66e+02 ... (remaining 17402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.64: 7567 28.64 - 57.28: 358 57.28 - 85.92: 124 85.92 - 114.56: 15 114.56 - 143.20: 3 Dihedral angle restraints: 8067 sinusoidal: 3483 harmonic: 4584 Sorted by residual: dihedral pdb=" CA GLU H 218 " pdb=" C GLU H 218 " pdb=" N GLY H 219 " pdb=" CA GLY H 219 " ideal model delta harmonic sigma weight residual -180.00 -45.34 -134.66 0 5.00e+00 4.00e-02 7.25e+02 dihedral pdb=" CA ASP I 254 " pdb=" C ASP I 254 " pdb=" N THR I 255 " pdb=" CA THR I 255 " ideal model delta harmonic sigma weight residual 180.00 45.62 134.38 0 5.00e+00 4.00e-02 7.22e+02 dihedral pdb=" CA ILE H 240 " pdb=" C ILE H 240 " pdb=" N ASP H 241 " pdb=" CA ASP H 241 " ideal model delta harmonic sigma weight residual -180.00 -86.63 -93.37 0 5.00e+00 4.00e-02 3.49e+02 ... (remaining 8064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1148 0.161 - 0.323: 632 0.323 - 0.484: 164 0.484 - 0.645: 50 0.645 - 0.806: 6 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CA LYS K 282 " pdb=" N LYS K 282 " pdb=" C LYS K 282 " pdb=" CB LYS K 282 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CB VAL I 195 " pdb=" CA VAL I 195 " pdb=" CG1 VAL I 195 " pdb=" CG2 VAL I 195 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CA PHE I 361 " pdb=" N PHE I 361 " pdb=" C PHE I 361 " pdb=" CB PHE I 361 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 1997 not shown) Planarity restraints: 2243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP K 401 " 0.191 2.00e-02 2.50e+03 1.12e-01 3.43e+02 pdb=" C2 ATP K 401 " -0.047 2.00e-02 2.50e+03 pdb=" C4 ATP K 401 " -0.039 2.00e-02 2.50e+03 pdb=" C5 ATP K 401 " -0.130 2.00e-02 2.50e+03 pdb=" C6 ATP K 401 " -0.057 2.00e-02 2.50e+03 pdb=" C8 ATP K 401 " -0.026 2.00e-02 2.50e+03 pdb=" N1 ATP K 401 " 0.029 2.00e-02 2.50e+03 pdb=" N3 ATP K 401 " -0.039 2.00e-02 2.50e+03 pdb=" N6 ATP K 401 " 0.238 2.00e-02 2.50e+03 pdb=" N7 ATP K 401 " -0.131 2.00e-02 2.50e+03 pdb=" N9 ATP K 401 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 128 " 0.250 2.00e-02 2.50e+03 1.30e-01 3.39e+02 pdb=" CG TYR I 128 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR I 128 " -0.121 2.00e-02 2.50e+03 pdb=" CD2 TYR I 128 " -0.122 2.00e-02 2.50e+03 pdb=" CE1 TYR I 128 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR I 128 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR I 128 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR I 128 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 215 " 0.220 2.00e-02 2.50e+03 1.16e-01 2.70e+02 pdb=" CG TYR H 215 " -0.129 2.00e-02 2.50e+03 pdb=" CD1 TYR H 215 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR H 215 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR H 215 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR H 215 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR H 215 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR H 215 " 0.165 2.00e-02 2.50e+03 ... (remaining 2240 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 117 2.54 - 3.13: 8663 3.13 - 3.72: 19148 3.72 - 4.31: 28913 4.31 - 4.90: 45979 Nonbonded interactions: 102820 Sorted by model distance: nonbonded pdb=" O2G ATP I 401 " pdb="MG MG I 402 " model vdw 1.953 2.170 nonbonded pdb=" O2G ATP K 401 " pdb="MG MG K 402 " model vdw 1.998 2.170 nonbonded pdb=" O2G ATP H 401 " pdb="MG MG H 402 " model vdw 1.999 2.170 nonbonded pdb=" O2B ATP K 401 " pdb="MG MG K 402 " model vdw 2.103 2.170 nonbonded pdb=" O2B ATP I 401 " pdb="MG MG I 402 " model vdw 2.153 2.170 ... (remaining 102815 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 'H' and resid 123 through 389) selection = (chain 'I' and resid 123 through 389) selection = (chain 'J' and resid 123 through 389) selection = (chain 'K' and resid 123 through 389) selection = (chain 'L' and resid 123 through 389) selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.490 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 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 : 0.036 0.205 12881 Z= 2.314 Angle : 3.648 27.314 17407 Z= 2.465 Chirality : 0.208 0.806 2000 Planarity : 0.031 0.256 2243 Dihedral : 19.331 143.201 5103 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 4.09 % Allowed : 6.42 % Favored : 89.50 % Rotamer: Outliers : 3.66 % Allowed : 9.12 % Favored : 87.22 % Cbeta Deviations : 7.49 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 1.13 % Twisted Proline : 5.56 % Twisted General : 1.66 % 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: -2.84 (0.18), residues: 1590 helix: -1.19 (0.16), residues: 763 sheet: -1.00 (0.37), residues: 141 loop : -2.88 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.037 0.016 HIS L 324 PHE 0.167 0.040 PHE I 167 TYR 0.250 0.051 TYR I 128 ARG 0.079 0.011 ARG J 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 827 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 179 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8371 (mt) REVERT: H 229 LEU cc_start: 0.8759 (tp) cc_final: 0.8347 (tp) REVERT: H 268 LEU cc_start: 0.7203 (tp) cc_final: 0.6920 (tp) REVERT: H 269 LEU cc_start: 0.8934 (mt) cc_final: 0.8614 (mp) REVERT: H 336 PHE cc_start: 0.6879 (m-80) cc_final: 0.6645 (m-80) REVERT: H 337 LYS cc_start: 0.7673 (mtpp) cc_final: 0.7446 (mtmt) REVERT: H 354 ILE cc_start: 0.8837 (mt) cc_final: 0.8551 (mt) REVERT: H 361 PHE cc_start: 0.5084 (t80) cc_final: 0.4410 (t80) REVERT: H 363 ILE cc_start: 0.8560 (mt) cc_final: 0.8303 (mt) REVERT: H 373 LEU cc_start: 0.7768 (tp) cc_final: 0.7284 (tp) REVERT: H 379 ILE cc_start: 0.8435 (mt) cc_final: 0.8095 (mt) REVERT: I 127 VAL cc_start: 0.6647 (m) cc_final: 0.5630 (m) REVERT: I 150 ILE cc_start: 0.7193 (mt) cc_final: 0.6375 (mt) REVERT: I 159 LEU cc_start: 0.8150 (tp) cc_final: 0.7895 (tp) REVERT: I 184 PRO cc_start: 0.8121 (Cg_exo) cc_final: 0.7807 (Cg_endo) REVERT: I 186 THR cc_start: 0.7500 (p) cc_final: 0.7152 (p) REVERT: I 207 VAL cc_start: 0.8451 (t) cc_final: 0.7529 (t) REVERT: I 231 LYS cc_start: 0.8767 (mttm) cc_final: 0.8554 (mmmt) REVERT: I 294 ASP cc_start: 0.8610 (m-30) cc_final: 0.8316 (t0) REVERT: I 297 ILE cc_start: 0.8608 (mp) cc_final: 0.7972 (mp) REVERT: I 309 VAL cc_start: 0.9142 (t) cc_final: 0.8718 (p) REVERT: I 320 ILE cc_start: 0.8850 (mt) cc_final: 0.8584 (mm) REVERT: I 370 VAL cc_start: 0.4448 (t) cc_final: 0.3688 (p) REVERT: I 371 THR cc_start: 0.6843 (p) cc_final: 0.5431 (p) REVERT: K 149 GLN cc_start: 0.9100 (mp10) cc_final: 0.8880 (mp10) REVERT: K 150 ILE cc_start: 0.8253 (mt) cc_final: 0.7774 (mt) REVERT: K 165 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: K 173 GLU cc_start: 0.7513 (mp0) cc_final: 0.7019 (mp0) REVERT: K 186 THR cc_start: 0.5477 (p) cc_final: 0.5232 (p) REVERT: K 188 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7332 (ptpt) REVERT: K 189 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.6336 (m) REVERT: K 190 LEU cc_start: 0.7340 (mt) cc_final: 0.7053 (mt) REVERT: K 204 ILE cc_start: 0.7858 (mt) cc_final: 0.7607 (mt) REVERT: K 207 VAL cc_start: 0.8389 (t) cc_final: 0.7740 (m) REVERT: K 216 ILE cc_start: 0.6021 (OUTLIER) cc_final: 0.5634 (pt) REVERT: K 243 LEU cc_start: 0.8507 (mt) cc_final: 0.7974 (mt) REVERT: K 255 THR cc_start: 0.6484 (OUTLIER) cc_final: 0.6237 (p) REVERT: K 266 MET cc_start: 0.6619 (mtt) cc_final: 0.6417 (mtt) REVERT: K 269 LEU cc_start: 0.8562 (mt) cc_final: 0.8239 (mt) REVERT: K 287 THR cc_start: 0.8333 (t) cc_final: 0.8006 (m) REVERT: K 324 HIS cc_start: 0.7727 (m-70) cc_final: 0.7069 (m-70) REVERT: K 330 LEU cc_start: 0.7005 (pt) cc_final: 0.6417 (pt) REVERT: K 351 ILE cc_start: 0.8522 (mm) cc_final: 0.7718 (mm) REVERT: K 356 THR cc_start: 0.8994 (m) cc_final: 0.8700 (m) REVERT: K 365 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6023 (mt-10) REVERT: K 376 THR cc_start: 0.8236 (p) cc_final: 0.7956 (p) REVERT: L 132 VAL cc_start: 0.6721 (p) cc_final: 0.6469 (p) REVERT: L 140 TYR cc_start: 0.6359 (p90) cc_final: 0.6153 (p90) REVERT: L 161 LEU cc_start: 0.9127 (mt) cc_final: 0.8874 (mm) REVERT: L 202 THR cc_start: 0.7891 (m) cc_final: 0.7180 (p) REVERT: L 260 GLU cc_start: 0.5091 (tt0) cc_final: 0.4611 (tt0) REVERT: L 268 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7347 (pp) REVERT: L 292 ILE cc_start: 0.6423 (tt) cc_final: 0.6181 (tt) REVERT: L 297 ILE cc_start: 0.6505 (tt) cc_final: 0.6078 (tt) REVERT: L 318 ILE cc_start: 0.8065 (mt) cc_final: 0.7395 (tt) REVERT: L 320 ILE cc_start: 0.8108 (mt) cc_final: 0.7861 (mt) REVERT: L 336 PHE cc_start: 0.6836 (m-80) cc_final: 0.6156 (m-80) REVERT: L 364 ARG cc_start: 0.7134 (mtt90) cc_final: 0.6689 (mtt-85) REVERT: M 149 GLN cc_start: 0.8379 (mp10) cc_final: 0.7816 (mp10) REVERT: M 150 ILE cc_start: 0.7462 (mt) cc_final: 0.7108 (mt) REVERT: M 188 LYS cc_start: 0.5654 (mmtp) cc_final: 0.4907 (pttm) REVERT: M 199 THR cc_start: 0.8415 (p) cc_final: 0.7983 (t) REVERT: M 203 PHE cc_start: 0.7633 (t80) cc_final: 0.7023 (t80) REVERT: M 218 GLU cc_start: 0.4206 (OUTLIER) cc_final: 0.3959 (tm-30) REVERT: M 246 ILE cc_start: 0.5909 (tt) cc_final: 0.5206 (tt) REVERT: M 269 LEU cc_start: 0.7967 (mt) cc_final: 0.7732 (mt) REVERT: M 343 THR cc_start: 0.8801 (p) cc_final: 0.8441 (p) REVERT: M 354 ILE cc_start: 0.8507 (mt) cc_final: 0.8231 (tp) REVERT: M 363 ILE cc_start: 0.8518 (mt) cc_final: 0.8315 (mm) REVERT: J 158 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6764 (mt-10) REVERT: J 159 LEU cc_start: 0.7847 (tp) cc_final: 0.7284 (tp) REVERT: J 180 LEU cc_start: 0.7732 (mt) cc_final: 0.7285 (mt) REVERT: J 231 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8074 (mtmp) REVERT: J 272 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.4405 (tp) REVERT: J 321 PHE cc_start: 0.6740 (m-80) cc_final: 0.6228 (m-80) REVERT: J 324 HIS cc_start: 0.7010 (m170) cc_final: 0.6790 (m-70) REVERT: J 325 THR cc_start: 0.8140 (m) cc_final: 0.7278 (t) REVERT: J 327 LYS cc_start: 0.7672 (tttt) cc_final: 0.7227 (tptt) REVERT: J 339 LEU cc_start: 0.8699 (mt) cc_final: 0.8130 (mt) REVERT: J 364 ARG cc_start: 0.6975 (mtm-85) cc_final: 0.6711 (ptp-110) REVERT: J 374 ASP cc_start: 0.8187 (m-30) cc_final: 0.7355 (m-30) outliers start: 49 outliers final: 10 residues processed: 852 average time/residue: 0.3209 time to fit residues: 358.1108 Evaluate side-chains 646 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 627 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 GLN H 252 ASN ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 HIS I 228 GLN I 267 GLN K 149 GLN ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN J 198 GLN J 262 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6272 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 12881 Z= 0.340 Angle : 0.983 15.306 17407 Z= 0.528 Chirality : 0.052 0.273 2000 Planarity : 0.008 0.074 2243 Dihedral : 12.903 136.100 1881 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.29 % Favored : 92.89 % Rotamer: Outliers : 0.75 % Allowed : 4.63 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 1.11 % Twisted General : 0.40 % 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: -1.48 (0.20), residues: 1590 helix: -0.14 (0.17), residues: 794 sheet: -1.14 (0.39), residues: 145 loop : -1.96 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 324 PHE 0.040 0.003 PHE H 167 TYR 0.024 0.003 TYR M 215 ARG 0.015 0.001 ARG J 278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 757 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 141 GLU cc_start: 0.8631 (pm20) cc_final: 0.8037 (pm20) REVERT: H 186 THR cc_start: 0.7823 (p) cc_final: 0.7509 (p) REVERT: H 229 LEU cc_start: 0.8371 (tp) cc_final: 0.8140 (tp) REVERT: H 241 ASP cc_start: 0.7583 (p0) cc_final: 0.6541 (p0) REVERT: H 255 THR cc_start: 0.3971 (m) cc_final: 0.3277 (m) REVERT: H 268 LEU cc_start: 0.7742 (tp) cc_final: 0.7466 (tp) REVERT: H 269 LEU cc_start: 0.8811 (mt) cc_final: 0.8322 (mt) REVERT: H 320 ILE cc_start: 0.9111 (mt) cc_final: 0.8724 (mt) REVERT: H 324 HIS cc_start: 0.5858 (m90) cc_final: 0.5126 (m90) REVERT: H 363 ILE cc_start: 0.8472 (mt) cc_final: 0.8063 (mt) REVERT: I 186 THR cc_start: 0.7585 (p) cc_final: 0.7002 (p) REVERT: I 258 ASP cc_start: 0.6138 (m-30) cc_final: 0.5550 (t0) REVERT: I 264 THR cc_start: 0.8283 (p) cc_final: 0.8010 (p) REVERT: I 294 ASP cc_start: 0.8648 (m-30) cc_final: 0.8047 (t0) REVERT: I 318 ILE cc_start: 0.7979 (mt) cc_final: 0.7411 (mt) REVERT: I 319 GLN cc_start: 0.7879 (mm110) cc_final: 0.7604 (mm-40) REVERT: I 325 THR cc_start: 0.8084 (p) cc_final: 0.7489 (p) REVERT: I 326 ARG cc_start: 0.6890 (mtm110) cc_final: 0.6303 (mtm110) REVERT: K 148 VAL cc_start: 0.9045 (p) cc_final: 0.8790 (p) REVERT: K 150 ILE cc_start: 0.8838 (mt) cc_final: 0.8454 (mt) REVERT: K 154 ARG cc_start: 0.5890 (ttt-90) cc_final: 0.4077 (tmm160) REVERT: K 178 VAL cc_start: 0.8480 (t) cc_final: 0.8257 (t) REVERT: K 179 LEU cc_start: 0.7384 (tp) cc_final: 0.6366 (tp) REVERT: K 186 THR cc_start: 0.6239 (p) cc_final: 0.5517 (p) REVERT: K 243 LEU cc_start: 0.8716 (mt) cc_final: 0.8007 (mt) REVERT: K 303 PHE cc_start: 0.8031 (m-80) cc_final: 0.7607 (m-80) REVERT: K 325 THR cc_start: 0.8299 (m) cc_final: 0.7930 (m) REVERT: K 351 ILE cc_start: 0.8684 (mm) cc_final: 0.8065 (mm) REVERT: L 132 VAL cc_start: 0.6329 (p) cc_final: 0.5087 (p) REVERT: L 149 GLN cc_start: 0.8500 (mp10) cc_final: 0.8166 (mp10) REVERT: L 153 ILE cc_start: 0.7990 (mt) cc_final: 0.7709 (mt) REVERT: L 154 ARG cc_start: 0.6593 (mmt180) cc_final: 0.5985 (tpp-160) REVERT: L 193 LYS cc_start: 0.7403 (tptt) cc_final: 0.7100 (tptt) REVERT: L 221 ARG cc_start: 0.6889 (tpm170) cc_final: 0.5915 (tpp-160) REVERT: L 224 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.7232 (ttp-110) REVERT: L 225 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7380 (mt-10) REVERT: L 228 GLN cc_start: 0.8032 (tp40) cc_final: 0.7604 (tp40) REVERT: L 231 LYS cc_start: 0.9024 (mmmt) cc_final: 0.8644 (mmtt) REVERT: L 238 ILE cc_start: 0.9066 (mt) cc_final: 0.8784 (mp) REVERT: L 258 ASP cc_start: 0.6119 (p0) cc_final: 0.4616 (p0) REVERT: L 284 ILE cc_start: 0.8283 (mm) cc_final: 0.7645 (mm) REVERT: L 320 ILE cc_start: 0.8334 (mt) cc_final: 0.7928 (mm) REVERT: L 328 MET cc_start: 0.7387 (ppp) cc_final: 0.6809 (ppp) REVERT: L 343 THR cc_start: 0.8844 (p) cc_final: 0.8581 (p) REVERT: M 175 PRO cc_start: 0.7571 (Cg_exo) cc_final: 0.7298 (Cg_endo) REVERT: M 225 GLU cc_start: 0.7866 (pp20) cc_final: 0.7304 (pp20) REVERT: M 228 GLN cc_start: 0.6665 (tp40) cc_final: 0.5108 (tp40) REVERT: M 307 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6743 (mt) REVERT: M 310 PRO cc_start: 0.8375 (Cg_endo) cc_final: 0.8166 (Cg_exo) REVERT: M 357 GLU cc_start: 0.6608 (tm-30) cc_final: 0.5555 (tp30) REVERT: M 367 ARG cc_start: 0.4491 (ptt90) cc_final: 0.2861 (ptt-90) REVERT: M 374 ASP cc_start: 0.6771 (m-30) cc_final: 0.6084 (m-30) REVERT: J 149 GLN cc_start: 0.9349 (mp10) cc_final: 0.8262 (mp10) REVERT: J 159 LEU cc_start: 0.8035 (tp) cc_final: 0.7604 (tp) REVERT: J 214 LYS cc_start: 0.7674 (ptmm) cc_final: 0.6679 (ptmm) REVERT: J 216 ILE cc_start: 0.7298 (mp) cc_final: 0.6856 (mp) REVERT: J 242 GLU cc_start: 0.5458 (tm-30) cc_final: 0.4767 (tm-30) REVERT: J 262 GLN cc_start: 0.7416 (tt0) cc_final: 0.7010 (tt0) REVERT: J 267 GLN cc_start: 0.8468 (mm110) cc_final: 0.8194 (mm110) REVERT: J 308 GLU cc_start: 0.6117 (pp20) cc_final: 0.5644 (pp20) REVERT: J 321 PHE cc_start: 0.7287 (m-80) cc_final: 0.6976 (m-80) REVERT: J 324 HIS cc_start: 0.6935 (m170) cc_final: 0.6380 (m-70) REVERT: J 327 LYS cc_start: 0.8383 (tttt) cc_final: 0.7902 (tptt) REVERT: J 336 PHE cc_start: 0.6804 (m-80) cc_final: 0.6562 (m-80) REVERT: J 343 THR cc_start: 0.9324 (t) cc_final: 0.9070 (t) REVERT: J 350 ASP cc_start: 0.9065 (m-30) cc_final: 0.8768 (m-30) REVERT: J 351 ILE cc_start: 0.9239 (mt) cc_final: 0.8672 (mt) REVERT: J 366 GLU cc_start: 0.6615 (tp30) cc_final: 0.5372 (tp30) outliers start: 10 outliers final: 2 residues processed: 761 average time/residue: 0.3277 time to fit residues: 325.8378 Evaluate side-chains 609 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 606 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 117 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 GLN K 262 GLN M 262 GLN J 228 GLN J 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12881 Z= 0.342 Angle : 0.917 16.663 17407 Z= 0.497 Chirality : 0.051 0.300 2000 Planarity : 0.007 0.083 2243 Dihedral : 12.316 137.793 1881 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 24.24 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.42 % Favored : 92.70 % Rotamer: Outliers : 0.30 % Allowed : 4.93 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.28 (0.20), residues: 1590 helix: -0.22 (0.17), residues: 794 sheet: -0.86 (0.41), residues: 144 loop : -1.55 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS H 324 PHE 0.054 0.004 PHE K 321 TYR 0.016 0.003 TYR K 140 ARG 0.009 0.001 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 725 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 186 THR cc_start: 0.8346 (p) cc_final: 0.8002 (p) REVERT: H 221 ARG cc_start: 0.7681 (ppt170) cc_final: 0.7181 (ppt170) REVERT: H 223 VAL cc_start: 0.9004 (t) cc_final: 0.8653 (t) REVERT: H 239 PHE cc_start: 0.7742 (t80) cc_final: 0.7224 (t80) REVERT: H 267 GLN cc_start: 0.8566 (mt0) cc_final: 0.8044 (mt0) REVERT: H 269 LEU cc_start: 0.8622 (mt) cc_final: 0.8211 (mt) REVERT: H 290 ILE cc_start: 0.7424 (tp) cc_final: 0.7026 (tp) REVERT: H 325 THR cc_start: 0.7922 (t) cc_final: 0.7608 (t) REVERT: H 328 MET cc_start: 0.6081 (ptp) cc_final: 0.5218 (ptp) REVERT: H 356 THR cc_start: 0.8993 (p) cc_final: 0.8768 (p) REVERT: H 364 ARG cc_start: 0.7450 (mtm180) cc_final: 0.6468 (mtm180) REVERT: I 308 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6893 (tm-30) REVERT: I 309 VAL cc_start: 0.8561 (p) cc_final: 0.8215 (p) REVERT: I 318 ILE cc_start: 0.8228 (mt) cc_final: 0.7483 (mt) REVERT: I 319 GLN cc_start: 0.8050 (mm110) cc_final: 0.7818 (mm-40) REVERT: I 322 LYS cc_start: 0.9334 (mptt) cc_final: 0.8959 (mmtm) REVERT: I 363 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8972 (mp) REVERT: I 374 ASP cc_start: 0.8438 (m-30) cc_final: 0.8131 (m-30) REVERT: K 186 THR cc_start: 0.6475 (p) cc_final: 0.5856 (p) REVERT: K 211 PHE cc_start: 0.8252 (m-80) cc_final: 0.7630 (m-80) REVERT: K 238 ILE cc_start: 0.7835 (mt) cc_final: 0.7440 (mt) REVERT: K 267 GLN cc_start: 0.6950 (tp40) cc_final: 0.6358 (tp40) REVERT: K 310 PRO cc_start: 0.7680 (Cg_endo) cc_final: 0.7031 (Cg_exo) REVERT: K 351 ILE cc_start: 0.8709 (mm) cc_final: 0.8303 (mm) REVERT: L 149 GLN cc_start: 0.8385 (mp10) cc_final: 0.8013 (mp10) REVERT: L 193 LYS cc_start: 0.6919 (tptt) cc_final: 0.6601 (tptt) REVERT: L 202 THR cc_start: 0.7754 (m) cc_final: 0.7092 (m) REVERT: L 210 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6628 (mm-30) REVERT: L 224 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7523 (mtm-85) REVERT: L 225 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7168 (mt-10) REVERT: L 231 LYS cc_start: 0.9033 (mmmt) cc_final: 0.8821 (mmtt) REVERT: L 284 ILE cc_start: 0.8279 (mm) cc_final: 0.7748 (mm) REVERT: L 317 ARG cc_start: 0.8274 (mpt90) cc_final: 0.8057 (mpt90) REVERT: L 328 MET cc_start: 0.7528 (ppp) cc_final: 0.6911 (ppp) REVERT: L 341 ARG cc_start: 0.8242 (ptp-110) cc_final: 0.7509 (ptp-110) REVERT: M 175 PRO cc_start: 0.7531 (Cg_exo) cc_final: 0.7095 (Cg_endo) REVERT: M 199 THR cc_start: 0.8729 (p) cc_final: 0.8266 (t) REVERT: M 206 VAL cc_start: 0.7274 (t) cc_final: 0.7050 (t) REVERT: M 307 ILE cc_start: 0.7355 (mp) cc_final: 0.7132 (mt) REVERT: M 310 PRO cc_start: 0.8532 (Cg_endo) cc_final: 0.8198 (Cg_exo) REVERT: M 333 ASP cc_start: 0.7036 (p0) cc_final: 0.6474 (p0) REVERT: J 149 GLN cc_start: 0.9332 (mp10) cc_final: 0.8609 (mp10) REVERT: J 181 TYR cc_start: 0.7784 (p90) cc_final: 0.7381 (p90) REVERT: J 198 GLN cc_start: 0.7651 (mt0) cc_final: 0.7419 (mt0) REVERT: J 199 THR cc_start: 0.8559 (p) cc_final: 0.8237 (p) REVERT: J 214 LYS cc_start: 0.7131 (ptmm) cc_final: 0.6424 (ptmm) REVERT: J 327 LYS cc_start: 0.7933 (tttt) cc_final: 0.7600 (tptt) REVERT: J 343 THR cc_start: 0.9276 (t) cc_final: 0.9023 (t) REVERT: J 350 ASP cc_start: 0.9165 (m-30) cc_final: 0.8839 (m-30) REVERT: J 351 ILE cc_start: 0.9088 (mt) cc_final: 0.8725 (mt) REVERT: J 379 ILE cc_start: 0.9538 (mt) cc_final: 0.9249 (mt) outliers start: 4 outliers final: 0 residues processed: 726 average time/residue: 0.3491 time to fit residues: 336.1774 Evaluate side-chains 581 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 580 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 15 optimal weight: 0.0000 chunk 67 optimal weight: 0.2980 chunk 95 optimal weight: 0.3980 chunk 142 optimal weight: 0.9980 chunk 150 optimal weight: 0.0020 chunk 74 optimal weight: 0.1980 chunk 134 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 overall best weight: 0.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 ASN ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 GLN ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 GLN J 262 GLN ** J 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12881 Z= 0.256 Angle : 0.882 16.487 17407 Z= 0.468 Chirality : 0.052 0.290 2000 Planarity : 0.006 0.050 2243 Dihedral : 12.055 135.552 1881 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.04 % Favored : 93.14 % Rotamer: Outliers : 0.37 % Allowed : 3.89 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.14 (0.21), residues: 1590 helix: -0.16 (0.17), residues: 791 sheet: -1.07 (0.41), residues: 153 loop : -1.31 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.004 HIS J 324 PHE 0.041 0.003 PHE M 321 TYR 0.013 0.002 TYR L 215 ARG 0.011 0.001 ARG K 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 697 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 172 ILE cc_start: 0.6790 (pt) cc_final: 0.6398 (pt) REVERT: H 186 THR cc_start: 0.8078 (p) cc_final: 0.7799 (p) REVERT: H 223 VAL cc_start: 0.8758 (t) cc_final: 0.8333 (t) REVERT: H 265 MET cc_start: 0.6649 (tmm) cc_final: 0.6386 (tmm) REVERT: H 269 LEU cc_start: 0.8628 (mt) cc_final: 0.8373 (mt) REVERT: H 290 ILE cc_start: 0.7626 (tp) cc_final: 0.7147 (tp) REVERT: H 363 ILE cc_start: 0.8467 (mt) cc_final: 0.8256 (mt) REVERT: H 364 ARG cc_start: 0.7560 (mtt180) cc_final: 0.7260 (mtm-85) REVERT: I 153 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8165 (mp) REVERT: I 163 LYS cc_start: 0.7730 (ttmt) cc_final: 0.7452 (ttmm) REVERT: I 239 PHE cc_start: 0.7412 (t80) cc_final: 0.7126 (t80) REVERT: I 260 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6787 (mt-10) REVERT: I 284 ILE cc_start: 0.8605 (mt) cc_final: 0.8374 (mt) REVERT: I 309 VAL cc_start: 0.8684 (p) cc_final: 0.8443 (p) REVERT: I 314 PHE cc_start: 0.6525 (t80) cc_final: 0.6301 (t80) REVERT: I 318 ILE cc_start: 0.8304 (mt) cc_final: 0.7265 (mt) REVERT: I 351 ILE cc_start: 0.8507 (mt) cc_final: 0.8074 (mt) REVERT: K 127 VAL cc_start: 0.7095 (t) cc_final: 0.6846 (t) REVERT: K 151 GLU cc_start: 0.5628 (tp30) cc_final: 0.5170 (tp30) REVERT: K 186 THR cc_start: 0.6536 (p) cc_final: 0.6151 (p) REVERT: K 211 PHE cc_start: 0.8004 (m-80) cc_final: 0.7570 (m-80) REVERT: K 222 LEU cc_start: 0.8486 (tp) cc_final: 0.7990 (tp) REVERT: K 238 ILE cc_start: 0.7418 (mt) cc_final: 0.7086 (mt) REVERT: K 243 LEU cc_start: 0.8578 (mt) cc_final: 0.8087 (mt) REVERT: K 266 MET cc_start: 0.6569 (mtm) cc_final: 0.6277 (mtm) REVERT: K 267 GLN cc_start: 0.6838 (tp40) cc_final: 0.6502 (tp40) REVERT: K 318 ILE cc_start: 0.7613 (mm) cc_final: 0.7205 (mm) REVERT: K 323 ILE cc_start: 0.8481 (mm) cc_final: 0.7886 (tp) REVERT: K 337 LYS cc_start: 0.9192 (pptt) cc_final: 0.8851 (pptt) REVERT: K 351 ILE cc_start: 0.8689 (mm) cc_final: 0.8150 (mm) REVERT: L 132 VAL cc_start: 0.5904 (p) cc_final: 0.5337 (p) REVERT: L 153 ILE cc_start: 0.8354 (mm) cc_final: 0.8103 (mm) REVERT: L 206 VAL cc_start: 0.8628 (m) cc_final: 0.8305 (t) REVERT: L 210 GLU cc_start: 0.6489 (mm-30) cc_final: 0.6056 (mm-30) REVERT: L 224 ARG cc_start: 0.7904 (mtm-85) cc_final: 0.7212 (mtm-85) REVERT: L 225 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7500 (mt-10) REVERT: L 238 ILE cc_start: 0.9276 (mp) cc_final: 0.8981 (mp) REVERT: L 284 ILE cc_start: 0.8005 (mm) cc_final: 0.7763 (mm) REVERT: L 290 ILE cc_start: 0.7687 (tt) cc_final: 0.7460 (tt) REVERT: L 356 THR cc_start: 0.8286 (p) cc_final: 0.7929 (p) REVERT: L 365 GLU cc_start: 0.4595 (pt0) cc_final: 0.2743 (mt-10) REVERT: M 179 LEU cc_start: 0.7678 (tp) cc_final: 0.6797 (tp) REVERT: M 199 THR cc_start: 0.8499 (p) cc_final: 0.8260 (t) REVERT: M 283 VAL cc_start: 0.7975 (m) cc_final: 0.7763 (m) REVERT: M 307 ILE cc_start: 0.7185 (mp) cc_final: 0.4973 (mp) REVERT: M 310 PRO cc_start: 0.8676 (Cg_endo) cc_final: 0.8237 (Cg_exo) REVERT: M 333 ASP cc_start: 0.6538 (p0) cc_final: 0.6081 (p0) REVERT: M 372 MET cc_start: 0.3902 (mmt) cc_final: 0.3561 (mmt) REVERT: J 149 GLN cc_start: 0.9409 (mp10) cc_final: 0.8656 (mp10) REVERT: J 159 LEU cc_start: 0.7989 (tp) cc_final: 0.7593 (tp) REVERT: J 198 GLN cc_start: 0.7685 (mt0) cc_final: 0.7318 (tt0) REVERT: J 214 LYS cc_start: 0.7236 (ptmm) cc_final: 0.6512 (ptmm) REVERT: J 334 VAL cc_start: 0.8210 (m) cc_final: 0.7855 (m) REVERT: J 356 THR cc_start: 0.8561 (m) cc_final: 0.8091 (m) REVERT: J 363 ILE cc_start: 0.8884 (pt) cc_final: 0.8568 (pt) REVERT: J 364 ARG cc_start: 0.6737 (mmm160) cc_final: 0.6383 (tpp-160) REVERT: J 379 ILE cc_start: 0.9327 (mt) cc_final: 0.8965 (mt) outliers start: 5 outliers final: 0 residues processed: 697 average time/residue: 0.3118 time to fit residues: 287.6428 Evaluate side-chains 566 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 565 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 128 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 moved from start: 0.7869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 12881 Z= 0.359 Angle : 0.938 16.531 17407 Z= 0.501 Chirality : 0.051 0.306 2000 Planarity : 0.007 0.069 2243 Dihedral : 11.895 135.837 1881 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 26.77 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.23 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.26 (0.21), residues: 1590 helix: -0.43 (0.17), residues: 811 sheet: -0.96 (0.40), residues: 153 loop : -1.17 (0.27), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 324 PHE 0.069 0.004 PHE K 321 TYR 0.028 0.003 TYR K 140 ARG 0.033 0.001 ARG I 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 684 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 161 LEU cc_start: 0.8799 (tp) cc_final: 0.8327 (tp) REVERT: H 186 THR cc_start: 0.8710 (p) cc_final: 0.8293 (p) REVERT: H 264 THR cc_start: 0.8699 (p) cc_final: 0.8322 (p) REVERT: H 269 LEU cc_start: 0.8639 (mt) cc_final: 0.8163 (mt) REVERT: I 149 GLN cc_start: 0.6831 (tt0) cc_final: 0.6459 (tt0) REVERT: I 163 LYS cc_start: 0.7753 (ttmt) cc_final: 0.7500 (ttmm) REVERT: I 308 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6405 (tm-30) REVERT: I 309 VAL cc_start: 0.9077 (p) cc_final: 0.8824 (p) REVERT: I 310 PRO cc_start: 0.8589 (Cg_endo) cc_final: 0.8104 (Cg_exo) REVERT: I 318 ILE cc_start: 0.8070 (mt) cc_final: 0.7299 (mt) REVERT: I 322 LYS cc_start: 0.9269 (mptt) cc_final: 0.8716 (mmmm) REVERT: I 351 ILE cc_start: 0.8743 (mt) cc_final: 0.8472 (mt) REVERT: I 356 THR cc_start: 0.9450 (m) cc_final: 0.9178 (m) REVERT: K 186 THR cc_start: 0.6710 (p) cc_final: 0.6426 (p) REVERT: K 206 VAL cc_start: 0.8939 (t) cc_final: 0.8734 (t) REVERT: K 211 PHE cc_start: 0.8104 (m-80) cc_final: 0.7625 (m-80) REVERT: K 222 LEU cc_start: 0.8606 (tp) cc_final: 0.8132 (tp) REVERT: K 238 ILE cc_start: 0.7434 (mt) cc_final: 0.7061 (mt) REVERT: K 264 THR cc_start: 0.8832 (p) cc_final: 0.8613 (p) REVERT: K 267 GLN cc_start: 0.7144 (tp40) cc_final: 0.6506 (tp40) REVERT: K 269 LEU cc_start: 0.8844 (mt) cc_final: 0.8561 (mt) REVERT: K 337 LYS cc_start: 0.9393 (pptt) cc_final: 0.8842 (pptt) REVERT: K 351 ILE cc_start: 0.8692 (mm) cc_final: 0.8400 (mm) REVERT: K 357 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6250 (tm-30) REVERT: L 153 ILE cc_start: 0.8385 (mm) cc_final: 0.8106 (mm) REVERT: L 193 LYS cc_start: 0.6978 (tptt) cc_final: 0.6699 (tptt) REVERT: L 204 ILE cc_start: 0.7562 (mm) cc_final: 0.7198 (mm) REVERT: L 206 VAL cc_start: 0.8701 (m) cc_final: 0.8391 (t) REVERT: L 210 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6634 (mm-30) REVERT: L 225 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7581 (mt-10) REVERT: L 238 ILE cc_start: 0.9275 (mp) cc_final: 0.8914 (mp) REVERT: L 284 ILE cc_start: 0.8321 (mm) cc_final: 0.8098 (mm) REVERT: L 305 ARG cc_start: 0.5525 (ttm170) cc_final: 0.5295 (ttm170) REVERT: L 308 GLU cc_start: 0.6792 (tm-30) cc_final: 0.6494 (tm-30) REVERT: L 356 THR cc_start: 0.8327 (p) cc_final: 0.7537 (p) REVERT: L 375 PHE cc_start: 0.6330 (m-80) cc_final: 0.5952 (m-80) REVERT: M 132 VAL cc_start: 0.8628 (t) cc_final: 0.8366 (m) REVERT: M 179 LEU cc_start: 0.7871 (tp) cc_final: 0.7331 (tp) REVERT: M 180 LEU cc_start: 0.7720 (mp) cc_final: 0.7217 (mp) REVERT: M 210 GLU cc_start: 0.5792 (mt-10) cc_final: 0.5475 (mt-10) REVERT: M 225 GLU cc_start: 0.7917 (pp20) cc_final: 0.7343 (pp20) REVERT: M 269 LEU cc_start: 0.7923 (mt) cc_final: 0.7702 (mt) REVERT: M 283 VAL cc_start: 0.7942 (m) cc_final: 0.7598 (m) REVERT: M 306 ILE cc_start: 0.8520 (pt) cc_final: 0.8240 (pt) REVERT: M 307 ILE cc_start: 0.8220 (mp) cc_final: 0.6281 (tp) REVERT: M 310 PRO cc_start: 0.8612 (Cg_endo) cc_final: 0.8220 (Cg_exo) REVERT: M 333 ASP cc_start: 0.6578 (p0) cc_final: 0.6102 (p0) REVERT: J 149 GLN cc_start: 0.9358 (mp10) cc_final: 0.8630 (mp10) REVERT: J 167 PHE cc_start: 0.6303 (m-80) cc_final: 0.6064 (m-80) REVERT: J 327 LYS cc_start: 0.8144 (tmtt) cc_final: 0.7727 (tptt) REVERT: J 334 VAL cc_start: 0.8293 (m) cc_final: 0.7941 (m) REVERT: J 343 THR cc_start: 0.9147 (t) cc_final: 0.8876 (t) REVERT: J 354 ILE cc_start: 0.8939 (tt) cc_final: 0.8671 (tt) REVERT: J 360 MET cc_start: 0.6342 (tmm) cc_final: 0.6094 (tmm) REVERT: J 363 ILE cc_start: 0.8905 (pt) cc_final: 0.8314 (pt) REVERT: J 364 ARG cc_start: 0.6821 (mmm160) cc_final: 0.6558 (tpp-160) REVERT: J 379 ILE cc_start: 0.9427 (mt) cc_final: 0.9149 (mt) REVERT: J 383 LEU cc_start: 0.8891 (mm) cc_final: 0.8602 (mm) outliers start: 0 outliers final: 0 residues processed: 684 average time/residue: 0.3111 time to fit residues: 284.0716 Evaluate side-chains 570 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 570 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 88 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.0470 chunk 12 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 GLN J 197 ASN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.8182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12881 Z= 0.271 Angle : 0.912 16.162 17407 Z= 0.480 Chirality : 0.052 0.270 2000 Planarity : 0.007 0.091 2243 Dihedral : 11.706 137.748 1881 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.23 % Favored : 92.01 % Rotamer: Outliers : 0.07 % Allowed : 1.94 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.22 (0.21), residues: 1590 helix: -0.40 (0.17), residues: 803 sheet: -0.78 (0.42), residues: 144 loop : -1.20 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS H 324 PHE 0.064 0.003 PHE K 361 TYR 0.018 0.002 TYR K 181 ARG 0.016 0.001 ARG K 305 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 679 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 143 ILE cc_start: 0.7857 (pt) cc_final: 0.7530 (pt) REVERT: H 161 LEU cc_start: 0.8753 (tp) cc_final: 0.8236 (tp) REVERT: H 186 THR cc_start: 0.8624 (p) cc_final: 0.8186 (p) REVERT: H 264 THR cc_start: 0.8463 (p) cc_final: 0.8254 (p) REVERT: H 269 LEU cc_start: 0.8771 (mt) cc_final: 0.8245 (mt) REVERT: H 290 ILE cc_start: 0.7505 (tp) cc_final: 0.6974 (tp) REVERT: H 356 THR cc_start: 0.9086 (p) cc_final: 0.8711 (p) REVERT: H 372 MET cc_start: 0.6501 (mmm) cc_final: 0.5943 (mmm) REVERT: I 198 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7349 (mm-40) REVERT: I 260 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7301 (mt-10) REVERT: I 308 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6852 (tm-30) REVERT: I 318 ILE cc_start: 0.8434 (mt) cc_final: 0.7105 (mt) REVERT: I 319 GLN cc_start: 0.8390 (mm110) cc_final: 0.7990 (mm-40) REVERT: I 322 LYS cc_start: 0.9182 (mptt) cc_final: 0.8826 (mmtm) REVERT: I 323 ILE cc_start: 0.9167 (mm) cc_final: 0.8861 (mm) REVERT: I 351 ILE cc_start: 0.8533 (mt) cc_final: 0.8219 (mt) REVERT: I 356 THR cc_start: 0.9439 (m) cc_final: 0.9230 (p) REVERT: K 151 GLU cc_start: 0.6368 (tp30) cc_final: 0.5406 (tp30) REVERT: K 170 VAL cc_start: 0.5253 (m) cc_final: 0.5005 (m) REVERT: K 172 ILE cc_start: 0.4453 (tp) cc_final: 0.3991 (tp) REVERT: K 186 THR cc_start: 0.6894 (p) cc_final: 0.6410 (p) REVERT: K 206 VAL cc_start: 0.8911 (t) cc_final: 0.8693 (t) REVERT: K 211 PHE cc_start: 0.8117 (m-80) cc_final: 0.7581 (m-80) REVERT: K 222 LEU cc_start: 0.8510 (tp) cc_final: 0.8166 (tp) REVERT: K 224 ARG cc_start: 0.5159 (ttt180) cc_final: 0.4848 (ttt180) REVERT: K 238 ILE cc_start: 0.7404 (mt) cc_final: 0.7174 (mt) REVERT: K 291 ASP cc_start: 0.7421 (m-30) cc_final: 0.7167 (m-30) REVERT: K 318 ILE cc_start: 0.7634 (mm) cc_final: 0.7433 (mm) REVERT: K 337 LYS cc_start: 0.9449 (pptt) cc_final: 0.8929 (pptt) REVERT: K 351 ILE cc_start: 0.8664 (mm) cc_final: 0.8316 (mm) REVERT: K 357 GLU cc_start: 0.6964 (tm-30) cc_final: 0.6648 (tm-30) REVERT: K 372 MET cc_start: 0.5247 (mmm) cc_final: 0.5037 (mmm) REVERT: L 123 LYS cc_start: 0.3645 (mptt) cc_final: 0.2880 (mttp) REVERT: L 153 ILE cc_start: 0.8512 (mm) cc_final: 0.8131 (mm) REVERT: L 204 ILE cc_start: 0.7635 (mm) cc_final: 0.7208 (mm) REVERT: L 210 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6384 (mm-30) REVERT: L 225 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7492 (mt-10) REVERT: L 238 ILE cc_start: 0.9224 (mp) cc_final: 0.8898 (mp) REVERT: L 240 ILE cc_start: 0.8734 (tp) cc_final: 0.8354 (tp) REVERT: L 308 GLU cc_start: 0.6522 (tm-30) cc_final: 0.6228 (tm-30) REVERT: L 365 GLU cc_start: 0.4627 (pt0) cc_final: 0.2762 (mt-10) REVERT: L 372 MET cc_start: 0.5799 (mmm) cc_final: 0.5296 (mmm) REVERT: M 179 LEU cc_start: 0.8101 (tp) cc_final: 0.7781 (tp) REVERT: M 180 LEU cc_start: 0.7467 (mp) cc_final: 0.7239 (mp) REVERT: M 199 THR cc_start: 0.8296 (p) cc_final: 0.8087 (t) REVERT: M 225 GLU cc_start: 0.7871 (pp20) cc_final: 0.7282 (pp20) REVERT: M 307 ILE cc_start: 0.7974 (mp) cc_final: 0.7467 (tp) REVERT: M 310 PRO cc_start: 0.8521 (Cg_endo) cc_final: 0.8188 (Cg_exo) REVERT: M 333 ASP cc_start: 0.6687 (p0) cc_final: 0.6129 (p0) REVERT: J 167 PHE cc_start: 0.6272 (m-80) cc_final: 0.5951 (m-80) REVERT: J 186 THR cc_start: 0.8550 (p) cc_final: 0.8091 (p) REVERT: J 202 THR cc_start: 0.7295 (p) cc_final: 0.7074 (p) REVERT: J 214 LYS cc_start: 0.6942 (ptmm) cc_final: 0.6649 (ptmm) REVERT: J 327 LYS cc_start: 0.8079 (tmtt) cc_final: 0.7440 (tptt) REVERT: J 334 VAL cc_start: 0.7989 (m) cc_final: 0.7627 (t) REVERT: J 347 SER cc_start: 0.8956 (m) cc_final: 0.8694 (p) REVERT: J 356 THR cc_start: 0.9068 (m) cc_final: 0.8737 (m) REVERT: J 363 ILE cc_start: 0.8594 (pt) cc_final: 0.8227 (pt) REVERT: J 364 ARG cc_start: 0.6808 (mmm160) cc_final: 0.6330 (tpp-160) REVERT: J 373 LEU cc_start: 0.8377 (tp) cc_final: 0.8122 (tp) REVERT: J 379 ILE cc_start: 0.9229 (mt) cc_final: 0.8997 (mt) REVERT: J 383 LEU cc_start: 0.8752 (mm) cc_final: 0.8327 (mm) outliers start: 1 outliers final: 0 residues processed: 679 average time/residue: 0.3070 time to fit residues: 276.2812 Evaluate side-chains 584 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 584 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 0.0370 chunk 17 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN L 198 GLN ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.8493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 12881 Z= 0.294 Angle : 0.892 15.762 17407 Z= 0.475 Chirality : 0.050 0.266 2000 Planarity : 0.007 0.099 2243 Dihedral : 11.536 134.401 1881 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 24.98 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.36 % Favored : 91.89 % Rotamer: Outliers : 0.07 % Allowed : 2.47 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.27 (0.21), residues: 1590 helix: -0.49 (0.17), residues: 805 sheet: -0.79 (0.42), residues: 144 loop : -1.15 (0.27), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.004 HIS J 324 PHE 0.064 0.003 PHE K 321 TYR 0.019 0.002 TYR M 181 ARG 0.018 0.001 ARG K 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 673 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 161 LEU cc_start: 0.8439 (tp) cc_final: 0.8104 (tp) REVERT: H 172 ILE cc_start: 0.7780 (pt) cc_final: 0.7265 (pt) REVERT: H 186 THR cc_start: 0.8956 (p) cc_final: 0.8633 (p) REVERT: H 204 ILE cc_start: 0.6959 (mt) cc_final: 0.6753 (mt) REVERT: H 269 LEU cc_start: 0.8704 (mt) cc_final: 0.8175 (mt) REVERT: H 276 ASP cc_start: 0.7602 (m-30) cc_final: 0.7185 (m-30) REVERT: H 290 ILE cc_start: 0.7602 (tp) cc_final: 0.6947 (tp) REVERT: H 326 ARG cc_start: 0.7573 (ppt170) cc_final: 0.6932 (ppt170) REVERT: H 356 THR cc_start: 0.9159 (p) cc_final: 0.8612 (p) REVERT: H 372 MET cc_start: 0.6245 (mmm) cc_final: 0.5445 (mmm) REVERT: H 386 THR cc_start: 0.5752 (p) cc_final: 0.5456 (p) REVERT: I 205 ARG cc_start: 0.7212 (ptt-90) cc_final: 0.6797 (ptt-90) REVERT: I 229 LEU cc_start: 0.8984 (tp) cc_final: 0.8752 (tp) REVERT: I 260 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7389 (mt-10) REVERT: I 284 ILE cc_start: 0.8711 (mt) cc_final: 0.8491 (mt) REVERT: I 308 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6777 (tm-30) REVERT: I 309 VAL cc_start: 0.8999 (p) cc_final: 0.8590 (p) REVERT: I 310 PRO cc_start: 0.8160 (Cg_endo) cc_final: 0.7613 (Cg_exo) REVERT: I 314 PHE cc_start: 0.6790 (t80) cc_final: 0.6574 (t80) REVERT: I 318 ILE cc_start: 0.8188 (mt) cc_final: 0.7375 (mt) REVERT: I 322 LYS cc_start: 0.9165 (mptt) cc_final: 0.8664 (mmmm) REVERT: I 325 THR cc_start: 0.7867 (p) cc_final: 0.7643 (p) REVERT: I 356 THR cc_start: 0.9476 (m) cc_final: 0.9070 (p) REVERT: K 151 GLU cc_start: 0.6273 (tp30) cc_final: 0.5385 (tp30) REVERT: K 170 VAL cc_start: 0.5629 (m) cc_final: 0.5339 (m) REVERT: K 172 ILE cc_start: 0.4611 (tp) cc_final: 0.4279 (tp) REVERT: K 186 THR cc_start: 0.7245 (p) cc_final: 0.6633 (p) REVERT: K 211 PHE cc_start: 0.8267 (m-80) cc_final: 0.7893 (m-80) REVERT: K 222 LEU cc_start: 0.8612 (tp) cc_final: 0.8224 (tp) REVERT: K 238 ILE cc_start: 0.7430 (mt) cc_final: 0.7205 (mt) REVERT: K 260 GLU cc_start: 0.6652 (tp30) cc_final: 0.6254 (tp30) REVERT: K 337 LYS cc_start: 0.9428 (pptt) cc_final: 0.8875 (pptt) REVERT: K 341 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7682 (ttp80) REVERT: K 351 ILE cc_start: 0.8746 (mm) cc_final: 0.8356 (mm) REVERT: L 153 ILE cc_start: 0.8512 (mm) cc_final: 0.8280 (mm) REVERT: L 202 THR cc_start: 0.6958 (t) cc_final: 0.6732 (t) REVERT: L 204 ILE cc_start: 0.7578 (mm) cc_final: 0.7283 (mm) REVERT: L 225 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7650 (mt-10) REVERT: L 238 ILE cc_start: 0.8999 (mp) cc_final: 0.8640 (mp) REVERT: L 284 ILE cc_start: 0.8166 (mm) cc_final: 0.7717 (mm) REVERT: L 320 ILE cc_start: 0.8474 (tp) cc_final: 0.8184 (mm) REVERT: L 372 MET cc_start: 0.5722 (mmm) cc_final: 0.4539 (mmm) REVERT: M 179 LEU cc_start: 0.7890 (tp) cc_final: 0.7605 (tp) REVERT: M 199 THR cc_start: 0.8442 (p) cc_final: 0.8169 (t) REVERT: M 225 GLU cc_start: 0.7937 (pp20) cc_final: 0.7197 (pp20) REVERT: M 307 ILE cc_start: 0.7995 (mp) cc_final: 0.7710 (tp) REVERT: M 310 PRO cc_start: 0.8441 (Cg_endo) cc_final: 0.8105 (Cg_exo) REVERT: M 318 ILE cc_start: 0.7044 (mm) cc_final: 0.6727 (mm) REVERT: M 327 LYS cc_start: 0.8025 (tmmt) cc_final: 0.7773 (tmmt) REVERT: M 333 ASP cc_start: 0.6464 (p0) cc_final: 0.5896 (p0) REVERT: M 338 GLU cc_start: 0.4418 (tp30) cc_final: 0.3894 (tp30) REVERT: M 354 ILE cc_start: 0.8761 (mt) cc_final: 0.8413 (mt) REVERT: M 370 VAL cc_start: 0.6701 (t) cc_final: 0.6223 (t) REVERT: M 371 THR cc_start: 0.5909 (p) cc_final: 0.5059 (t) REVERT: J 149 GLN cc_start: 0.9379 (mp10) cc_final: 0.9150 (mp10) REVERT: J 198 GLN cc_start: 0.7527 (pt0) cc_final: 0.7069 (pt0) REVERT: J 327 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7492 (tptt) REVERT: J 334 VAL cc_start: 0.8038 (m) cc_final: 0.7834 (m) REVERT: J 347 SER cc_start: 0.8999 (m) cc_final: 0.8566 (p) REVERT: J 351 ILE cc_start: 0.9297 (mt) cc_final: 0.8978 (mt) REVERT: J 352 LYS cc_start: 0.8988 (mptt) cc_final: 0.8543 (mmtt) REVERT: J 356 THR cc_start: 0.9060 (m) cc_final: 0.8818 (m) REVERT: J 357 GLU cc_start: 0.6770 (pt0) cc_final: 0.6016 (pt0) REVERT: J 364 ARG cc_start: 0.6860 (mmm160) cc_final: 0.6572 (tpp-160) REVERT: J 373 LEU cc_start: 0.8029 (tp) cc_final: 0.7636 (tt) REVERT: J 379 ILE cc_start: 0.9331 (mt) cc_final: 0.8936 (mt) REVERT: J 383 LEU cc_start: 0.8931 (mm) cc_final: 0.8498 (mm) outliers start: 1 outliers final: 0 residues processed: 674 average time/residue: 0.3100 time to fit residues: 278.2627 Evaluate side-chains 567 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 567 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 118 optimal weight: 0.0670 chunk 136 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 GLN ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN J 198 GLN ** J 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.8706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 12881 Z= 0.291 Angle : 0.921 15.543 17407 Z= 0.484 Chirality : 0.053 0.348 2000 Planarity : 0.007 0.160 2243 Dihedral : 11.306 134.057 1881 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.61 % Favored : 91.70 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.27 (0.21), residues: 1590 helix: -0.50 (0.17), residues: 810 sheet: -0.67 (0.44), residues: 145 loop : -1.16 (0.27), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.004 HIS J 324 PHE 0.048 0.003 PHE K 361 TYR 0.017 0.002 TYR H 140 ARG 0.016 0.001 ARG K 154 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 676 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 127 VAL cc_start: 0.9200 (m) cc_final: 0.8874 (m) REVERT: H 128 TYR cc_start: 0.6701 (m-10) cc_final: 0.6287 (m-10) REVERT: H 143 ILE cc_start: 0.7627 (pt) cc_final: 0.6469 (tp) REVERT: H 161 LEU cc_start: 0.8425 (tp) cc_final: 0.8014 (tp) REVERT: H 172 ILE cc_start: 0.7881 (pt) cc_final: 0.7571 (pt) REVERT: H 186 THR cc_start: 0.8884 (p) cc_final: 0.8518 (p) REVERT: H 269 LEU cc_start: 0.8655 (mt) cc_final: 0.8146 (mt) REVERT: H 276 ASP cc_start: 0.7651 (m-30) cc_final: 0.7205 (m-30) REVERT: H 290 ILE cc_start: 0.7592 (tp) cc_final: 0.7037 (tp) REVERT: H 326 ARG cc_start: 0.7710 (ppt170) cc_final: 0.6438 (ppt170) REVERT: H 337 LYS cc_start: 0.7885 (mtmt) cc_final: 0.7550 (mtmm) REVERT: H 356 THR cc_start: 0.9078 (p) cc_final: 0.8600 (p) REVERT: H 372 MET cc_start: 0.6341 (mmm) cc_final: 0.5818 (mmm) REVERT: H 386 THR cc_start: 0.5772 (p) cc_final: 0.5479 (p) REVERT: I 198 GLN cc_start: 0.7557 (mm-40) cc_final: 0.7155 (mm-40) REVERT: I 205 ARG cc_start: 0.7043 (ptt-90) cc_final: 0.6819 (ptt-90) REVERT: I 229 LEU cc_start: 0.9031 (tp) cc_final: 0.8804 (tp) REVERT: I 231 LYS cc_start: 0.8641 (mmmt) cc_final: 0.8275 (mmmt) REVERT: I 260 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7224 (mt-10) REVERT: I 284 ILE cc_start: 0.8777 (mt) cc_final: 0.8426 (mt) REVERT: I 308 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6289 (tm-30) REVERT: I 309 VAL cc_start: 0.8984 (p) cc_final: 0.8588 (p) REVERT: I 310 PRO cc_start: 0.8180 (Cg_endo) cc_final: 0.7411 (Cg_exo) REVERT: I 318 ILE cc_start: 0.8377 (mt) cc_final: 0.7317 (mt) REVERT: I 319 GLN cc_start: 0.8367 (mm110) cc_final: 0.8148 (mm-40) REVERT: I 322 LYS cc_start: 0.9359 (mptt) cc_final: 0.8457 (mmmm) REVERT: I 356 THR cc_start: 0.9523 (m) cc_final: 0.9211 (p) REVERT: I 363 ILE cc_start: 0.8973 (mp) cc_final: 0.8748 (mp) REVERT: K 151 GLU cc_start: 0.6015 (tp30) cc_final: 0.5293 (tp30) REVERT: K 155 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7337 (mt-10) REVERT: K 170 VAL cc_start: 0.5356 (m) cc_final: 0.5140 (m) REVERT: K 172 ILE cc_start: 0.4455 (tp) cc_final: 0.4114 (tp) REVERT: K 186 THR cc_start: 0.7285 (p) cc_final: 0.6726 (p) REVERT: K 211 PHE cc_start: 0.8109 (m-80) cc_final: 0.7779 (m-80) REVERT: K 222 LEU cc_start: 0.8537 (tp) cc_final: 0.8281 (tp) REVERT: K 263 ARG cc_start: 0.6764 (mtm-85) cc_final: 0.6164 (mtm-85) REVERT: K 291 ASP cc_start: 0.7214 (m-30) cc_final: 0.6982 (m-30) REVERT: K 318 ILE cc_start: 0.7790 (mm) cc_final: 0.7504 (mm) REVERT: K 337 LYS cc_start: 0.9410 (pptt) cc_final: 0.8876 (pptt) REVERT: K 351 ILE cc_start: 0.8760 (mm) cc_final: 0.8385 (mm) REVERT: K 357 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6915 (tm-30) REVERT: K 372 MET cc_start: 0.6034 (mmm) cc_final: 0.5299 (mmm) REVERT: L 153 ILE cc_start: 0.8562 (mm) cc_final: 0.8285 (mm) REVERT: L 204 ILE cc_start: 0.7397 (mm) cc_final: 0.6903 (mm) REVERT: L 225 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7499 (mt-10) REVERT: L 238 ILE cc_start: 0.8875 (mp) cc_final: 0.8656 (mp) REVERT: L 284 ILE cc_start: 0.8172 (mm) cc_final: 0.7923 (mm) REVERT: L 308 GLU cc_start: 0.6777 (tm-30) cc_final: 0.6549 (tm-30) REVERT: L 361 PHE cc_start: 0.6188 (t80) cc_final: 0.5965 (t80) REVERT: L 365 GLU cc_start: 0.4607 (pt0) cc_final: 0.2747 (mt-10) REVERT: L 372 MET cc_start: 0.5496 (mmm) cc_final: 0.5148 (mmm) REVERT: M 180 LEU cc_start: 0.7635 (mp) cc_final: 0.7380 (mp) REVERT: M 225 GLU cc_start: 0.7992 (pp20) cc_final: 0.7461 (pp20) REVERT: M 246 ILE cc_start: 0.6708 (tt) cc_final: 0.6461 (tt) REVERT: M 265 MET cc_start: 0.7471 (mtm) cc_final: 0.7207 (mtp) REVERT: M 283 VAL cc_start: 0.8128 (m) cc_final: 0.7876 (m) REVERT: M 307 ILE cc_start: 0.8001 (mp) cc_final: 0.7404 (tp) REVERT: M 310 PRO cc_start: 0.8433 (Cg_endo) cc_final: 0.8056 (Cg_exo) REVERT: M 333 ASP cc_start: 0.6242 (p0) cc_final: 0.5742 (p0) REVERT: J 149 GLN cc_start: 0.9486 (mp10) cc_final: 0.9023 (mp10) REVERT: J 152 GLU cc_start: 0.7503 (pm20) cc_final: 0.7251 (pm20) REVERT: J 262 GLN cc_start: 0.7836 (tt0) cc_final: 0.7633 (tt0) REVERT: J 307 ILE cc_start: 0.8314 (mp) cc_final: 0.8103 (mp) REVERT: J 327 LYS cc_start: 0.8156 (tmtt) cc_final: 0.7469 (tptt) REVERT: J 334 VAL cc_start: 0.7948 (m) cc_final: 0.7735 (m) REVERT: J 335 ASP cc_start: 0.6209 (t0) cc_final: 0.5910 (t0) REVERT: J 347 SER cc_start: 0.8940 (m) cc_final: 0.8590 (p) REVERT: J 351 ILE cc_start: 0.9187 (mt) cc_final: 0.8884 (mt) REVERT: J 356 THR cc_start: 0.9028 (m) cc_final: 0.8780 (m) REVERT: J 373 LEU cc_start: 0.8514 (tp) cc_final: 0.8041 (tt) REVERT: J 379 ILE cc_start: 0.9318 (mt) cc_final: 0.9096 (mt) outliers start: 0 outliers final: 0 residues processed: 676 average time/residue: 0.3101 time to fit residues: 278.8818 Evaluate side-chains 575 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 575 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.1980 chunk 140 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 84 optimal weight: 0.0270 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 chunk 132 optimal weight: 0.9980 chunk 139 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.8882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12881 Z= 0.287 Angle : 0.945 15.068 17407 Z= 0.500 Chirality : 0.053 0.243 2000 Planarity : 0.007 0.140 2243 Dihedral : 10.969 132.062 1881 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 26.62 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.74 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.35 (0.21), residues: 1590 helix: -0.56 (0.17), residues: 810 sheet: -0.63 (0.46), residues: 127 loop : -1.22 (0.27), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS J 324 PHE 0.034 0.003 PHE K 361 TYR 0.031 0.002 TYR H 140 ARG 0.015 0.001 ARG K 341 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 670 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 161 LEU cc_start: 0.8368 (tp) cc_final: 0.8011 (tp) REVERT: H 269 LEU cc_start: 0.8681 (mt) cc_final: 0.8147 (mt) REVERT: H 276 ASP cc_start: 0.7629 (m-30) cc_final: 0.7204 (m-30) REVERT: H 290 ILE cc_start: 0.7621 (tp) cc_final: 0.7018 (tp) REVERT: H 326 ARG cc_start: 0.7688 (ppt170) cc_final: 0.6972 (ppt170) REVERT: H 360 MET cc_start: 0.5474 (ptp) cc_final: 0.5017 (ptp) REVERT: H 372 MET cc_start: 0.6106 (mmm) cc_final: 0.5620 (mmm) REVERT: I 198 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7232 (mm-40) REVERT: I 221 ARG cc_start: 0.7722 (ttp80) cc_final: 0.7363 (ttp80) REVERT: I 284 ILE cc_start: 0.8578 (mt) cc_final: 0.8263 (mt) REVERT: I 308 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6792 (tm-30) REVERT: I 309 VAL cc_start: 0.8948 (p) cc_final: 0.8678 (p) REVERT: I 318 ILE cc_start: 0.8415 (mt) cc_final: 0.7428 (mt) REVERT: I 319 GLN cc_start: 0.8221 (mm110) cc_final: 0.7991 (mm-40) REVERT: I 322 LYS cc_start: 0.9354 (mptt) cc_final: 0.8522 (mmmm) REVERT: I 356 THR cc_start: 0.9494 (m) cc_final: 0.9036 (p) REVERT: I 363 ILE cc_start: 0.8949 (mp) cc_final: 0.8674 (mp) REVERT: K 151 GLU cc_start: 0.5879 (tp30) cc_final: 0.5581 (tp30) REVERT: K 170 VAL cc_start: 0.5306 (m) cc_final: 0.5083 (m) REVERT: K 172 ILE cc_start: 0.4333 (tp) cc_final: 0.4065 (tp) REVERT: K 186 THR cc_start: 0.7160 (p) cc_final: 0.6323 (p) REVERT: K 222 LEU cc_start: 0.8630 (tp) cc_final: 0.8386 (tp) REVERT: K 260 GLU cc_start: 0.6383 (tp30) cc_final: 0.5900 (tp30) REVERT: K 310 PRO cc_start: 0.8786 (Cg_exo) cc_final: 0.8483 (Cg_endo) REVERT: K 315 GLU cc_start: 0.8558 (pm20) cc_final: 0.8279 (pm20) REVERT: K 318 ILE cc_start: 0.7736 (mm) cc_final: 0.7422 (mm) REVERT: K 337 LYS cc_start: 0.9397 (pptt) cc_final: 0.8804 (pptt) REVERT: K 338 GLU cc_start: 0.6455 (tp30) cc_final: 0.6213 (tp30) REVERT: K 351 ILE cc_start: 0.8687 (mm) cc_final: 0.8393 (mm) REVERT: K 357 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7125 (tm-30) REVERT: K 372 MET cc_start: 0.6173 (mmm) cc_final: 0.5561 (mmm) REVERT: L 123 LYS cc_start: 0.3878 (mptt) cc_final: 0.3301 (mttp) REVERT: L 153 ILE cc_start: 0.8535 (mm) cc_final: 0.8286 (mm) REVERT: L 193 LYS cc_start: 0.6580 (tptt) cc_final: 0.6055 (mmmt) REVERT: L 202 THR cc_start: 0.7939 (t) cc_final: 0.7706 (t) REVERT: L 221 ARG cc_start: 0.6699 (tpp-160) cc_final: 0.6151 (tpp-160) REVERT: L 225 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7612 (mt-10) REVERT: L 233 LYS cc_start: 0.7970 (tppt) cc_final: 0.7698 (tppt) REVERT: L 284 ILE cc_start: 0.8333 (mm) cc_final: 0.7870 (mm) REVERT: L 365 GLU cc_start: 0.4929 (pt0) cc_final: 0.2902 (mt-10) REVERT: L 372 MET cc_start: 0.5518 (mmm) cc_final: 0.5248 (mmm) REVERT: M 153 ILE cc_start: 0.8030 (tt) cc_final: 0.7817 (tt) REVERT: M 179 LEU cc_start: 0.8152 (tp) cc_final: 0.7791 (tp) REVERT: M 180 LEU cc_start: 0.7616 (mp) cc_final: 0.7370 (mp) REVERT: M 199 THR cc_start: 0.8387 (p) cc_final: 0.8120 (t) REVERT: M 225 GLU cc_start: 0.8006 (pp20) cc_final: 0.7297 (pp20) REVERT: M 307 ILE cc_start: 0.7692 (mp) cc_final: 0.7278 (tp) REVERT: M 310 PRO cc_start: 0.8413 (Cg_endo) cc_final: 0.8017 (Cg_exo) REVERT: M 328 MET cc_start: 0.7683 (tmm) cc_final: 0.7345 (tmm) REVERT: M 333 ASP cc_start: 0.5886 (p0) cc_final: 0.5282 (p0) REVERT: J 149 GLN cc_start: 0.9466 (mp10) cc_final: 0.8837 (mp10) REVERT: J 159 LEU cc_start: 0.8242 (tp) cc_final: 0.8024 (tp) REVERT: J 202 THR cc_start: 0.7063 (p) cc_final: 0.6841 (p) REVERT: J 327 LYS cc_start: 0.7959 (tmtt) cc_final: 0.7453 (tptt) REVERT: J 347 SER cc_start: 0.8968 (m) cc_final: 0.8689 (p) REVERT: J 356 THR cc_start: 0.9011 (m) cc_final: 0.8761 (m) REVERT: J 373 LEU cc_start: 0.8393 (tp) cc_final: 0.7916 (tt) REVERT: J 379 ILE cc_start: 0.9254 (mt) cc_final: 0.8944 (mt) outliers start: 0 outliers final: 0 residues processed: 670 average time/residue: 0.3236 time to fit residues: 292.9470 Evaluate side-chains 568 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 568 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.0980 chunk 90 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 155 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 123 optimal weight: 0.1980 chunk 12 optimal weight: 0.3980 chunk 95 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN J 198 GLN ** J 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.9075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12881 Z= 0.298 Angle : 0.962 17.733 17407 Z= 0.506 Chirality : 0.053 0.260 2000 Planarity : 0.007 0.138 2243 Dihedral : 10.820 130.575 1881 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.18 % Favored : 91.13 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.36 (0.21), residues: 1590 helix: -0.51 (0.18), residues: 807 sheet: -0.73 (0.48), residues: 118 loop : -1.31 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS J 324 PHE 0.057 0.003 PHE K 361 TYR 0.013 0.001 TYR M 181 ARG 0.017 0.001 ARG K 154 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 667 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 161 LEU cc_start: 0.8420 (tp) cc_final: 0.7962 (tp) REVERT: H 269 LEU cc_start: 0.8597 (mt) cc_final: 0.7814 (mt) REVERT: H 276 ASP cc_start: 0.7673 (m-30) cc_final: 0.7278 (m-30) REVERT: H 290 ILE cc_start: 0.7261 (tp) cc_final: 0.6913 (tp) REVERT: H 326 ARG cc_start: 0.7902 (ppt170) cc_final: 0.7488 (ppt170) REVERT: H 386 THR cc_start: 0.6009 (p) cc_final: 0.5786 (p) REVERT: I 140 TYR cc_start: 0.5991 (m-10) cc_final: 0.5697 (m-10) REVERT: I 143 ILE cc_start: 0.7163 (tt) cc_final: 0.6895 (tt) REVERT: I 198 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7230 (mm-40) REVERT: I 229 LEU cc_start: 0.9028 (tp) cc_final: 0.8770 (tt) REVERT: I 284 ILE cc_start: 0.8768 (mt) cc_final: 0.8374 (mt) REVERT: I 314 PHE cc_start: 0.6738 (t80) cc_final: 0.6440 (t80) REVERT: I 318 ILE cc_start: 0.8599 (mt) cc_final: 0.7700 (mt) REVERT: I 322 LYS cc_start: 0.9338 (mptt) cc_final: 0.8799 (mmmm) REVERT: I 342 ILE cc_start: 0.8927 (mt) cc_final: 0.8567 (mt) REVERT: I 354 ILE cc_start: 0.8755 (mt) cc_final: 0.8532 (mt) REVERT: I 356 THR cc_start: 0.9404 (m) cc_final: 0.9004 (p) REVERT: K 151 GLU cc_start: 0.6519 (tp30) cc_final: 0.6187 (tp30) REVERT: K 170 VAL cc_start: 0.5251 (m) cc_final: 0.4927 (m) REVERT: K 178 VAL cc_start: 0.8487 (t) cc_final: 0.8043 (t) REVERT: K 186 THR cc_start: 0.7136 (p) cc_final: 0.6444 (p) REVERT: K 222 LEU cc_start: 0.8492 (tp) cc_final: 0.8095 (tp) REVERT: K 238 ILE cc_start: 0.7656 (mt) cc_final: 0.7402 (mt) REVERT: K 307 ILE cc_start: 0.5813 (tt) cc_final: 0.5400 (tt) REVERT: K 310 PRO cc_start: 0.8805 (Cg_exo) cc_final: 0.8590 (Cg_endo) REVERT: K 326 ARG cc_start: 0.7894 (ttp80) cc_final: 0.7452 (ttp80) REVERT: K 337 LYS cc_start: 0.9367 (pptt) cc_final: 0.8779 (pptt) REVERT: K 338 GLU cc_start: 0.6525 (tp30) cc_final: 0.6313 (tp30) REVERT: K 351 ILE cc_start: 0.8703 (mm) cc_final: 0.8439 (mm) REVERT: K 372 MET cc_start: 0.6945 (mmm) cc_final: 0.6349 (mmm) REVERT: K 374 ASP cc_start: 0.7379 (m-30) cc_final: 0.6906 (m-30) REVERT: L 153 ILE cc_start: 0.8570 (mm) cc_final: 0.8315 (mm) REVERT: L 193 LYS cc_start: 0.6388 (tptt) cc_final: 0.5883 (mmmt) REVERT: L 202 THR cc_start: 0.7365 (t) cc_final: 0.7092 (t) REVERT: L 221 ARG cc_start: 0.6460 (tpp-160) cc_final: 0.5902 (tpp-160) REVERT: L 225 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7622 (mt-10) REVERT: L 238 ILE cc_start: 0.8860 (mp) cc_final: 0.8651 (mp) REVERT: L 365 GLU cc_start: 0.5050 (pt0) cc_final: 0.2897 (mt-10) REVERT: M 154 ARG cc_start: 0.6790 (ptt180) cc_final: 0.6517 (ptt180) REVERT: M 157 VAL cc_start: 0.6973 (t) cc_final: 0.6709 (p) REVERT: M 179 LEU cc_start: 0.8068 (tp) cc_final: 0.7712 (tp) REVERT: M 180 LEU cc_start: 0.7649 (mp) cc_final: 0.7311 (mp) REVERT: M 199 THR cc_start: 0.8301 (p) cc_final: 0.7955 (t) REVERT: M 225 GLU cc_start: 0.7963 (pp20) cc_final: 0.7523 (pp20) REVERT: M 237 ILE cc_start: 0.6381 (mp) cc_final: 0.6170 (mp) REVERT: M 238 ILE cc_start: 0.8420 (mt) cc_final: 0.8137 (mt) REVERT: M 283 VAL cc_start: 0.8191 (m) cc_final: 0.7801 (m) REVERT: M 307 ILE cc_start: 0.7648 (mp) cc_final: 0.6910 (tp) REVERT: M 333 ASP cc_start: 0.5423 (p0) cc_final: 0.4972 (p0) REVERT: M 338 GLU cc_start: 0.8236 (mp0) cc_final: 0.8001 (mp0) REVERT: M 361 PHE cc_start: 0.6773 (m-80) cc_final: 0.6552 (m-80) REVERT: M 370 VAL cc_start: 0.6462 (t) cc_final: 0.5976 (t) REVERT: M 376 THR cc_start: 0.8079 (p) cc_final: 0.7755 (p) REVERT: J 149 GLN cc_start: 0.9459 (mp10) cc_final: 0.8874 (mp10) REVERT: J 159 LEU cc_start: 0.8584 (tp) cc_final: 0.8295 (tp) REVERT: J 327 LYS cc_start: 0.7897 (tmtt) cc_final: 0.7378 (tptt) REVERT: J 354 ILE cc_start: 0.8589 (tt) cc_final: 0.8305 (tt) REVERT: J 356 THR cc_start: 0.9063 (m) cc_final: 0.8743 (m) REVERT: J 373 LEU cc_start: 0.8629 (tp) cc_final: 0.8407 (tt) outliers start: 0 outliers final: 0 residues processed: 667 average time/residue: 0.3137 time to fit residues: 278.2132 Evaluate side-chains 564 residues out of total 1338 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 564 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 127 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.135057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.109331 restraints weight = 34532.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112884 restraints weight = 25114.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.115680 restraints weight = 19368.096| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.9322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12881 Z= 0.328 Angle : 0.998 14.638 17407 Z= 0.527 Chirality : 0.054 0.258 2000 Planarity : 0.009 0.171 2243 Dihedral : 10.914 130.361 1881 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 29.15 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.99 % Favored : 91.32 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.45 (0.21), residues: 1590 helix: -0.59 (0.17), residues: 809 sheet: -0.40 (0.46), residues: 129 loop : -1.42 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS J 324 PHE 0.054 0.003 PHE K 361 TYR 0.014 0.002 TYR K 140 ARG 0.016 0.001 ARG J 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4916.32 seconds wall clock time: 86 minutes 53.57 seconds (5213.57 seconds total)