Starting phenix.real_space_refine on Sat Feb 17 07:56:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmk_6734/02_2024/5xmk_6734_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmk_6734/02_2024/5xmk_6734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmk_6734/02_2024/5xmk_6734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmk_6734/02_2024/5xmk_6734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmk_6734/02_2024/5xmk_6734_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmk_6734/02_2024/5xmk_6734_updated.pdb" } resolution = 4.18 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= 0.007 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 58 5.16 5 C 11290 2.51 5 N 3031 2.21 5 O 3623 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18017 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 299} Chain: "B" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 300} Chain: "C" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 301} Chain: "D" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Chain: "E" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 302} Chain: "F" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 301} Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "H" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "I" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "J" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "K" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "L" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "M" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "N" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 331 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.24, per 1000 atoms: 0.51 Number of scatterers: 18017 At special positions: 0 Unit cell: (165.931, 164.624, 92.7643, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 15 15.00 O 3623 8.00 N 3031 7.00 C 11290 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 - 3.50 Amino acid : False - 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: 7.59 Conformation dependent library (CDL) restraints added in 3.5 seconds 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 113 helices and 12 sheets defined 51.6% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 139 through 148 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 179 through 190 Processing helix chain 'A' and resid 208 through 222 removed outlier: 4.013A pdb=" N PHE A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 244 through 262 removed outlier: 3.846A pdb=" N SER A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ARG A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 336 through 356 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 388 through 390 No H-bonds generated for 'chain 'A' and resid 388 through 390' Processing helix chain 'A' and resid 393 through 395 No H-bonds generated for 'chain 'A' and resid 393 through 395' Processing helix chain 'A' and resid 403 through 412 Processing helix chain 'A' and resid 419 through 431 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 139 through 148 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 156 through 159 Processing helix chain 'B' and resid 179 through 190 Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 249 through 261 removed outlier: 3.585A pdb=" N ASN B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 284 through 287 No H-bonds generated for 'chain 'B' and resid 284 through 287' Processing helix chain 'B' and resid 301 through 310 Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 336 through 356 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 388 through 390 No H-bonds generated for 'chain 'B' and resid 388 through 390' Processing helix chain 'B' and resid 403 through 412 Processing helix chain 'B' and resid 419 through 431 Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 140 through 154 removed outlier: 4.382A pdb=" N LEU C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 156 through 159 Processing helix chain 'C' and resid 179 through 190 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 243 through 246 No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'C' and resid 249 through 259 Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 284 through 289 removed outlier: 3.876A pdb=" N ARG C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 289' Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 321 through 330 removed outlier: 4.084A pdb=" N ARG C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 326 " --> pdb=" O GLU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 349 through 356 Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 393 through 395 No H-bonds generated for 'chain 'C' and resid 393 through 395' Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 419 through 431 removed outlier: 3.551A pdb=" N LYS C 424 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 139 through 154 removed outlier: 4.373A pdb=" N LEU D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Proline residue: D 152 - end of helix Processing helix chain 'D' and resid 156 through 159 Processing helix chain 'D' and resid 179 through 190 Processing helix chain 'D' and resid 209 through 223 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 244 through 247 No H-bonds generated for 'chain 'D' and resid 244 through 247' Processing helix chain 'D' and resid 249 through 264 removed outlier: 4.013A pdb=" N VAL D 263 " --> pdb=" O GLN D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 301 through 310 Processing helix chain 'D' and resid 322 through 330 Processing helix chain 'D' and resid 336 through 355 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 403 through 412 Processing helix chain 'D' and resid 423 through 431 Processing helix chain 'E' and resid 132 through 134 No H-bonds generated for 'chain 'E' and resid 132 through 134' Processing helix chain 'E' and resid 139 through 154 removed outlier: 4.828A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 156 through 159 Processing helix chain 'E' and resid 179 through 190 Processing helix chain 'E' and resid 210 through 223 removed outlier: 3.662A pdb=" N LEU E 213 " --> pdb=" O SER E 210 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN E 216 " --> pdb=" O LEU E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 248 through 264 removed outlier: 3.552A pdb=" N VAL E 263 " --> pdb=" O GLN E 259 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLY E 264 " --> pdb=" O MET E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 322 through 330 Processing helix chain 'E' and resid 336 through 356 removed outlier: 3.586A pdb=" N GLN E 349 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Proline residue: E 350 - end of helix Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 403 through 412 Processing helix chain 'E' and resid 419 through 431 removed outlier: 3.656A pdb=" N LEU E 423 " --> pdb=" O GLU E 419 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS E 424 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 139 through 154 removed outlier: 4.634A pdb=" N LEU F 151 " --> pdb=" O GLU F 147 " (cutoff:3.500A) Proline residue: F 152 - end of helix Processing helix chain 'F' and resid 156 through 159 Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 212 through 224 Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 248 through 264 removed outlier: 3.625A pdb=" N ILE F 252 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY F 264 " --> pdb=" O MET F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 284 through 289 Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 322 through 330 Processing helix chain 'F' and resid 336 through 355 Proline residue: F 350 - end of helix Processing helix chain 'F' and resid 388 through 390 No H-bonds generated for 'chain 'F' and resid 388 through 390' Processing helix chain 'F' and resid 403 through 411 Processing helix chain 'F' and resid 419 through 431 Processing helix chain 'G' and resid 282 through 308 Processing helix chain 'G' and resid 312 through 328 Processing helix chain 'H' and resid 291 through 308 Processing helix chain 'H' and resid 312 through 328 Processing helix chain 'I' and resid 280 through 309 removed outlier: 4.047A pdb=" N LYS I 285 " --> pdb=" O ASP I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 312 through 327 Processing helix chain 'J' and resid 291 through 308 Processing helix chain 'J' and resid 312 through 328 Processing helix chain 'K' and resid 282 through 308 Processing helix chain 'K' and resid 312 through 328 Processing helix chain 'L' and resid 291 through 308 Processing helix chain 'L' and resid 312 through 328 Processing helix chain 'M' and resid 281 through 309 Processing helix chain 'M' and resid 312 through 328 Processing helix chain 'N' and resid 291 through 308 Processing helix chain 'N' and resid 312 through 328 Processing sheet with id= A, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.776A pdb=" N ARG A 292 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N TYR A 172 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 294 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 360 through 362 Processing sheet with id= C, first strand: chain 'B' and resid 293 through 295 removed outlier: 7.963A pdb=" N ILE B 294 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 170 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ILE B 169 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL B 272 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU B 171 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLY B 274 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N SER B 227 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU B 273 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 229 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ALA B 275 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE B 231 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N PHE B 230 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE B 195 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP B 232 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL B 197 " --> pdb=" O ASP B 232 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 360 through 362 Processing sheet with id= E, first strand: chain 'C' and resid 292 through 295 removed outlier: 8.426A pdb=" N ILE C 169 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 272 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N LEU C 171 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY C 274 " --> pdb=" O LEU C 171 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER C 227 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU C 273 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA C 275 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 231 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR C 193 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N PHE C 230 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE C 195 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ASP C 232 " --> pdb=" O PHE C 195 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL C 197 " --> pdb=" O ASP C 232 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 360 through 362 Processing sheet with id= G, first strand: chain 'D' and resid 293 through 295 removed outlier: 7.812A pdb=" N ILE D 294 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 170 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ILE D 169 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL D 272 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU D 171 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY D 274 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER D 227 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU D 273 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE D 229 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ALA D 275 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE D 231 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N THR D 193 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE D 230 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N PHE D 195 " --> pdb=" O PHE D 230 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 360 through 364 removed outlier: 6.205A pdb=" N LYS D 372 " --> pdb=" O VAL D 363 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 293 through 296 removed outlier: 7.668A pdb=" N ILE E 294 " --> pdb=" O GLY E 168 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU E 170 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE E 296 " --> pdb=" O LEU E 170 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR E 172 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ILE E 169 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL E 272 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU E 171 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLY E 274 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 8.628A pdb=" N GLY E 173 " --> pdb=" O GLY E 274 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR E 276 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N SER E 227 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU E 273 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE E 229 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA E 275 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ILE E 231 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 360 through 362 Processing sheet with id= K, first strand: chain 'F' and resid 292 through 295 removed outlier: 6.851A pdb=" N SER F 227 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU F 273 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE F 229 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ALA F 275 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE F 231 " --> pdb=" O ALA F 275 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR F 193 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N PHE F 230 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE F 195 " --> pdb=" O PHE F 230 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ASP F 232 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL F 197 " --> pdb=" O ASP F 232 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 360 through 362 759 hydrogen bonds defined for protein. 2217 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: 5.37 Time building geometry restraints manager: 8.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3179 1.31 - 1.43: 4221 1.43 - 1.56: 10710 1.56 - 1.69: 85 1.69 - 1.81: 104 Bond restraints: 18299 Sorted by residual: bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.474 -0.086 1.00e-02 1.00e+04 7.36e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.31e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.12e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.12e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.87e+01 ... (remaining 18294 not shown) Histogram of bond angle deviations from ideal: 97.96 - 105.68: 415 105.68 - 113.39: 9672 113.39 - 121.11: 8782 121.11 - 128.83: 5770 128.83 - 136.55: 119 Bond angle restraints: 24758 Sorted by residual: angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 117.52 19.31 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.04 18.83 1.00e+00 1.00e+00 3.54e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 121.72 18.15 1.00e+00 1.00e+00 3.29e+02 angle pdb=" PA ATP F 501 " pdb=" O3A ATP F 501 " pdb=" PB ATP F 501 " ideal model delta sigma weight residual 136.83 118.90 17.93 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 119.17 17.66 1.00e+00 1.00e+00 3.12e+02 ... (remaining 24753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10380 17.94 - 35.88: 803 35.88 - 53.82: 158 53.82 - 71.76: 44 71.76 - 89.70: 31 Dihedral angle restraints: 11416 sinusoidal: 4762 harmonic: 6654 Sorted by residual: dihedral pdb=" C THR B 238 " pdb=" N THR B 238 " pdb=" CA THR B 238 " pdb=" CB THR B 238 " ideal model delta harmonic sigma weight residual -122.00 -141.26 19.26 0 2.50e+00 1.60e-01 5.94e+01 dihedral pdb=" N THR B 238 " pdb=" C THR B 238 " pdb=" CA THR B 238 " pdb=" CB THR B 238 " ideal model delta harmonic sigma weight residual 123.40 141.17 -17.77 0 2.50e+00 1.60e-01 5.05e+01 dihedral pdb=" CA LEU B 237 " pdb=" C LEU B 237 " pdb=" N THR B 238 " pdb=" CA THR B 238 " ideal model delta harmonic sigma weight residual 0.00 30.98 -30.98 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 11413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2554 0.146 - 0.291: 272 0.291 - 0.437: 18 0.437 - 0.583: 1 0.583 - 0.728: 1 Chirality restraints: 2846 Sorted by residual: chirality pdb=" CA THR B 238 " pdb=" N THR B 238 " pdb=" C THR B 238 " pdb=" CB THR B 238 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.73 2.00e-01 2.50e+01 1.33e+01 chirality pdb=" CA LEU B 237 " pdb=" N LEU B 237 " pdb=" C LEU B 237 " pdb=" CB LEU B 237 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.88e+00 chirality pdb=" CA THR B 320 " pdb=" N THR B 320 " pdb=" C THR B 320 " pdb=" CB THR B 320 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.32e+00 ... (remaining 2843 not shown) Planarity restraints: 3173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 151 " 0.058 5.00e-02 4.00e+02 8.73e-02 1.22e+01 pdb=" N PRO A 152 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 152 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 152 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 151 " 0.054 5.00e-02 4.00e+02 8.19e-02 1.07e+01 pdb=" N PRO B 152 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 152 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 152 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 304 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C ARG D 304 " 0.051 2.00e-02 2.50e+03 pdb=" O ARG D 304 " -0.019 2.00e-02 2.50e+03 pdb=" N THR D 305 " -0.017 2.00e-02 2.50e+03 ... (remaining 3170 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1461 2.76 - 3.30: 19661 3.30 - 3.83: 30089 3.83 - 4.37: 36437 4.37 - 4.90: 57371 Nonbonded interactions: 145019 Sorted by model distance: nonbonded pdb=" O ASN C 277 " pdb=" NE2 GLN C 425 " model vdw 2.230 2.520 nonbonded pdb=" OD2 ASP A 338 " pdb=" OG1 THR A 416 " model vdw 2.273 2.440 nonbonded pdb=" OG SER B 192 " pdb=" O PRO B 226 " model vdw 2.292 2.440 nonbonded pdb=" O ASN A 277 " pdb=" NE2 GLN A 425 " model vdw 2.317 2.520 nonbonded pdb=" N SER F 167 " pdb=" OE1 GLU F 291 " model vdw 2.331 2.520 ... (remaining 145014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 119 through 437) selection = (chain 'C' and resid 119 through 437) selection = (chain 'D' and resid 119 through 437) selection = (chain 'E' and resid 119 through 437) selection = (chain 'F' and resid 119 through 437) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.640 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 48.870 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 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 : 0.010 0.086 18299 Z= 0.674 Angle : 1.547 19.310 24758 Z= 1.074 Chirality : 0.092 0.728 2846 Planarity : 0.008 0.087 3173 Dihedral : 14.776 89.700 7096 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 1.67 % Allowed : 4.98 % Favored : 93.35 % Rotamer: Outliers : 1.17 % Allowed : 5.18 % Favored : 93.65 % Cbeta Deviations : 0.56 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.16), residues: 2270 helix: 0.01 (0.14), residues: 1182 sheet: -0.29 (0.30), residues: 252 loop : -1.48 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.006 TRP D 132 HIS 0.022 0.005 HIS A 359 PHE 0.026 0.005 PHE A 230 TYR 0.024 0.004 TYR H 302 ARG 0.027 0.001 ARG F 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 894 time to evaluate : 1.942 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: A 155 PHE cc_start: 0.8029 (m-80) cc_final: 0.7623 (m-80) REVERT: A 157 HIS cc_start: 0.6398 (p90) cc_final: 0.5637 (p-80) REVERT: A 200 SER cc_start: 0.4699 (OUTLIER) cc_final: 0.4460 (p) REVERT: A 212 LYS cc_start: 0.8014 (tttm) cc_final: 0.7686 (ttpp) REVERT: A 253 LYS cc_start: 0.7028 (tttm) cc_final: 0.6286 (ttpt) REVERT: A 263 VAL cc_start: 0.6329 (p) cc_final: 0.5245 (t) REVERT: A 408 LYS cc_start: 0.7046 (mttm) cc_final: 0.6653 (mmmt) REVERT: A 421 ASP cc_start: 0.5327 (t70) cc_final: 0.4558 (t70) REVERT: B 146 LYS cc_start: 0.8710 (mttm) cc_final: 0.8482 (mttm) REVERT: B 181 TYR cc_start: 0.7130 (t80) cc_final: 0.6488 (t80) REVERT: B 205 LYS cc_start: 0.8770 (tttp) cc_final: 0.8402 (tppt) REVERT: B 259 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8418 (tt0) REVERT: B 260 MET cc_start: 0.6836 (ptm) cc_final: 0.6122 (ptt) REVERT: B 278 ILE cc_start: 0.9167 (mt) cc_final: 0.8803 (tt) REVERT: B 321 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8143 (tptt) REVERT: B 327 LEU cc_start: 0.9216 (mt) cc_final: 0.8987 (mm) REVERT: B 420 ASP cc_start: 0.9091 (m-30) cc_final: 0.8809 (t70) REVERT: B 425 GLN cc_start: 0.7427 (mm-40) cc_final: 0.6560 (mt0) REVERT: C 120 SER cc_start: 0.9055 (m) cc_final: 0.8604 (p) REVERT: C 123 ILE cc_start: 0.7621 (mt) cc_final: 0.7100 (mp) REVERT: C 154 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8762 (ptpp) REVERT: C 162 ASN cc_start: 0.8488 (m-40) cc_final: 0.7616 (p0) REVERT: C 164 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8435 (mtpt) REVERT: C 181 TYR cc_start: 0.7998 (t80) cc_final: 0.7388 (t80) REVERT: C 233 GLN cc_start: 0.9050 (mm110) cc_final: 0.8653 (mm-40) REVERT: C 278 ILE cc_start: 0.8751 (mt) cc_final: 0.8533 (mt) REVERT: C 293 ARG cc_start: 0.9451 (ttm-80) cc_final: 0.9233 (ttm-80) REVERT: C 311 ASN cc_start: 0.8173 (m-40) cc_final: 0.7909 (m110) REVERT: C 312 VAL cc_start: 0.8699 (t) cc_final: 0.8482 (m) REVERT: C 341 VAL cc_start: 0.9023 (t) cc_final: 0.8726 (t) REVERT: D 166 THR cc_start: 0.8659 (m) cc_final: 0.8110 (m) REVERT: D 202 LEU cc_start: 0.6644 (mp) cc_final: 0.6304 (mp) REVERT: D 270 VAL cc_start: 0.5973 (OUTLIER) cc_final: 0.5668 (t) REVERT: D 278 ILE cc_start: 0.8912 (mt) cc_final: 0.8649 (pt) REVERT: D 291 GLU cc_start: 0.9091 (tt0) cc_final: 0.8483 (tt0) REVERT: D 345 ASP cc_start: 0.9052 (t0) cc_final: 0.7722 (t0) REVERT: D 419 GLU cc_start: 0.8290 (tt0) cc_final: 0.8047 (tp30) REVERT: D 426 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8788 (mt-10) REVERT: E 133 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7469 (tt0) REVERT: E 134 ASP cc_start: 0.8613 (m-30) cc_final: 0.8026 (t0) REVERT: E 196 SER cc_start: 0.7742 (p) cc_final: 0.7227 (p) REVERT: E 205 LYS cc_start: 0.8405 (tttt) cc_final: 0.8152 (tppt) REVERT: E 211 GLU cc_start: 0.8771 (mp0) cc_final: 0.8494 (mp0) REVERT: E 215 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8487 (pptt) REVERT: E 222 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8555 (mtt-85) REVERT: E 254 THR cc_start: 0.9593 (m) cc_final: 0.9227 (p) REVERT: E 255 GLU cc_start: 0.8807 (tp30) cc_final: 0.8490 (tp30) REVERT: E 277 ASN cc_start: 0.6864 (m-40) cc_final: 0.6644 (m-40) REVERT: E 290 PHE cc_start: 0.6583 (t80) cc_final: 0.6168 (t80) REVERT: E 334 TYR cc_start: 0.7862 (m-10) cc_final: 0.7257 (m-80) REVERT: E 349 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8425 (mt0) REVERT: E 373 LEU cc_start: 0.8835 (mt) cc_final: 0.8613 (tp) REVERT: E 405 ASP cc_start: 0.9348 (m-30) cc_final: 0.8692 (m-30) REVERT: E 406 PHE cc_start: 0.9216 (m-80) cc_final: 0.8783 (m-80) REVERT: E 419 GLU cc_start: 0.8437 (tt0) cc_final: 0.7978 (tm-30) REVERT: E 423 LEU cc_start: 0.8368 (mt) cc_final: 0.8068 (mt) REVERT: E 425 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8723 (mt0) REVERT: F 172 TYR cc_start: 0.8797 (p90) cc_final: 0.8364 (p90) REVERT: F 181 TYR cc_start: 0.7160 (t80) cc_final: 0.6932 (t80) REVERT: F 191 ASN cc_start: 0.7667 (t0) cc_final: 0.7460 (m-40) REVERT: F 195 PHE cc_start: 0.8400 (m-80) cc_final: 0.7903 (m-80) REVERT: F 216 GLN cc_start: 0.8610 (mt0) cc_final: 0.8353 (mm-40) REVERT: F 222 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7919 (mmm-85) REVERT: F 229 ILE cc_start: 0.8220 (mt) cc_final: 0.8012 (pt) REVERT: F 256 LEU cc_start: 0.9511 (tp) cc_final: 0.9179 (mp) REVERT: F 271 LEU cc_start: 0.7999 (tp) cc_final: 0.7750 (mp) REVERT: F 294 ILE cc_start: 0.9276 (mt) cc_final: 0.8931 (tt) REVERT: F 309 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8385 (mm-30) REVERT: F 325 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7183 (mmm160) REVERT: F 345 ASP cc_start: 0.8588 (t0) cc_final: 0.8251 (t0) REVERT: F 348 MET cc_start: 0.8709 (mmp) cc_final: 0.8507 (ttt) REVERT: F 371 ARG cc_start: 0.7843 (ptm-80) cc_final: 0.7480 (mmp80) REVERT: F 405 ASP cc_start: 0.9007 (m-30) cc_final: 0.8798 (m-30) REVERT: F 406 PHE cc_start: 0.9335 (m-80) cc_final: 0.9051 (m-80) REVERT: F 408 LYS cc_start: 0.9124 (mttp) cc_final: 0.8884 (tptt) REVERT: F 418 ASN cc_start: 0.6456 (p0) cc_final: 0.5799 (t0) REVERT: F 425 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8453 (mm-40) REVERT: G 280 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8272 (mmtt) REVERT: G 281 ASP cc_start: 0.8544 (m-30) cc_final: 0.8254 (t70) REVERT: G 284 THR cc_start: 0.8460 (p) cc_final: 0.8110 (p) REVERT: G 319 LEU cc_start: 0.8187 (mt) cc_final: 0.7982 (mt) REVERT: H 312 LEU cc_start: 0.8034 (pp) cc_final: 0.7816 (mm) REVERT: I 283 LEU cc_start: 0.8413 (mp) cc_final: 0.8138 (mt) REVERT: I 288 ASP cc_start: 0.9032 (m-30) cc_final: 0.8677 (m-30) REVERT: I 294 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7823 (mm-30) REVERT: K 325 LEU cc_start: 0.5077 (OUTLIER) cc_final: 0.4527 (tt) REVERT: M 279 THR cc_start: 0.5748 (OUTLIER) cc_final: 0.5051 (m) REVERT: M 293 ILE cc_start: 0.6223 (mt) cc_final: 0.5839 (mt) REVERT: M 299 LEU cc_start: 0.7273 (mt) cc_final: 0.6961 (mt) REVERT: M 323 LEU cc_start: 0.7520 (tp) cc_final: 0.7081 (mt) REVERT: N 292 LYS cc_start: 0.6500 (mptt) cc_final: 0.6207 (mtpp) REVERT: N 298 LYS cc_start: 0.8107 (tptt) cc_final: 0.7334 (ttpp) REVERT: N 302 TYR cc_start: 0.6001 (m-10) cc_final: 0.5634 (m-10) REVERT: N 305 SER cc_start: 0.7031 (t) cc_final: 0.5891 (p) outliers start: 23 outliers final: 2 residues processed: 908 average time/residue: 0.3846 time to fit residues: 480.1910 Evaluate side-chains 461 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 455 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 201 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 261 ASN B 265 ASN C 355 GLN ** D 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN E 265 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18299 Z= 0.214 Angle : 0.730 14.488 24758 Z= 0.369 Chirality : 0.044 0.294 2846 Planarity : 0.005 0.061 3173 Dihedral : 10.471 84.259 2616 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.71 % Favored : 94.85 % Rotamer: Outliers : 0.05 % Allowed : 3.40 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2270 helix: 1.42 (0.15), residues: 1183 sheet: 0.36 (0.29), residues: 266 loop : -0.78 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 206 HIS 0.002 0.001 HIS C 359 PHE 0.025 0.002 PHE B 308 TYR 0.016 0.002 TYR D 181 ARG 0.005 0.001 ARG B 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 575 time to evaluate : 2.238 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: A 155 PHE cc_start: 0.7853 (m-80) cc_final: 0.7474 (m-80) REVERT: A 157 HIS cc_start: 0.5739 (p90) cc_final: 0.5444 (p-80) REVERT: A 212 LYS cc_start: 0.7838 (tttm) cc_final: 0.7557 (ttpp) REVERT: A 259 GLN cc_start: 0.7619 (mm-40) cc_final: 0.7417 (mm-40) REVERT: A 305 THR cc_start: 0.8862 (m) cc_final: 0.8580 (p) REVERT: A 308 PHE cc_start: 0.6605 (m-10) cc_final: 0.6335 (m-10) REVERT: A 327 LEU cc_start: 0.7218 (mt) cc_final: 0.6899 (tp) REVERT: A 349 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7998 (tt0) REVERT: A 374 THR cc_start: 0.7667 (t) cc_final: 0.7330 (t) REVERT: A 405 ASP cc_start: 0.8727 (m-30) cc_final: 0.8273 (m-30) REVERT: A 425 GLN cc_start: 0.7996 (mt0) cc_final: 0.7748 (mm-40) REVERT: B 133 GLU cc_start: 0.8487 (mp0) cc_final: 0.8179 (tp30) REVERT: B 223 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8337 (tm-30) REVERT: B 245 GLU cc_start: 0.7352 (tp30) cc_final: 0.6600 (tp30) REVERT: B 295 TYR cc_start: 0.8339 (t80) cc_final: 0.8065 (t80) REVERT: B 308 PHE cc_start: 0.8567 (m-80) cc_final: 0.8342 (m-80) REVERT: C 120 SER cc_start: 0.9009 (m) cc_final: 0.8557 (p) REVERT: C 146 LYS cc_start: 0.8916 (mmmt) cc_final: 0.8585 (mmmt) REVERT: C 162 ASN cc_start: 0.8500 (m-40) cc_final: 0.7982 (p0) REVERT: C 163 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.7730 (ttm-80) REVERT: C 166 THR cc_start: 0.7760 (m) cc_final: 0.7352 (m) REVERT: C 181 TYR cc_start: 0.8318 (t80) cc_final: 0.7598 (t80) REVERT: C 193 THR cc_start: 0.7991 (p) cc_final: 0.7776 (p) REVERT: C 232 ASP cc_start: 0.8587 (t70) cc_final: 0.7775 (t70) REVERT: C 233 GLN cc_start: 0.9156 (mm110) cc_final: 0.8663 (mm-40) REVERT: C 291 GLU cc_start: 0.8742 (mt-10) cc_final: 0.7495 (mp0) REVERT: C 311 ASN cc_start: 0.8254 (m-40) cc_final: 0.7949 (m110) REVERT: C 353 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8962 (mmpt) REVERT: C 405 ASP cc_start: 0.8622 (m-30) cc_final: 0.8373 (m-30) REVERT: C 408 LYS cc_start: 0.8926 (mttp) cc_final: 0.8639 (mmmt) REVERT: C 414 ARG cc_start: 0.8192 (mmp80) cc_final: 0.7892 (mmm160) REVERT: D 135 VAL cc_start: 0.8760 (t) cc_final: 0.8416 (m) REVERT: D 166 THR cc_start: 0.8663 (m) cc_final: 0.7903 (m) REVERT: D 181 TYR cc_start: 0.7831 (t80) cc_final: 0.7336 (t80) REVERT: D 188 THR cc_start: 0.8176 (m) cc_final: 0.7955 (p) REVERT: D 205 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6811 (tppt) REVERT: D 211 GLU cc_start: 0.7971 (pp20) cc_final: 0.7728 (pp20) REVERT: D 247 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6565 (mt-10) REVERT: D 259 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8242 (mm-40) REVERT: D 271 LEU cc_start: 0.8658 (tp) cc_final: 0.8441 (tp) REVERT: D 291 GLU cc_start: 0.8931 (tt0) cc_final: 0.8729 (tt0) REVERT: D 414 ARG cc_start: 0.7174 (mmm-85) cc_final: 0.6819 (mmm-85) REVERT: D 419 GLU cc_start: 0.8414 (tt0) cc_final: 0.8068 (tp30) REVERT: E 133 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7234 (tt0) REVERT: E 134 ASP cc_start: 0.8587 (m-30) cc_final: 0.7659 (t0) REVERT: E 172 TYR cc_start: 0.8095 (p90) cc_final: 0.7823 (p90) REVERT: E 177 THR cc_start: 0.8097 (p) cc_final: 0.7827 (p) REVERT: E 196 SER cc_start: 0.8230 (p) cc_final: 0.7710 (t) REVERT: E 211 GLU cc_start: 0.8679 (mp0) cc_final: 0.8262 (mp0) REVERT: E 215 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8762 (pptt) REVERT: E 255 GLU cc_start: 0.8968 (tp30) cc_final: 0.8424 (tp30) REVERT: E 261 ASN cc_start: 0.6784 (t0) cc_final: 0.6530 (p0) REVERT: E 277 ASN cc_start: 0.7644 (m-40) cc_final: 0.7388 (m110) REVERT: E 330 MET cc_start: 0.8964 (mmt) cc_final: 0.8742 (mmm) REVERT: E 349 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8383 (mt0) REVERT: E 355 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8351 (mm110) REVERT: E 386 MET cc_start: 0.8764 (pmm) cc_final: 0.8415 (pmm) REVERT: E 405 ASP cc_start: 0.9367 (m-30) cc_final: 0.8675 (m-30) REVERT: E 406 PHE cc_start: 0.9293 (m-80) cc_final: 0.8933 (m-80) REVERT: E 420 ASP cc_start: 0.8884 (m-30) cc_final: 0.8601 (t0) REVERT: E 423 LEU cc_start: 0.8295 (mt) cc_final: 0.7949 (mt) REVERT: E 424 LYS cc_start: 0.8700 (mttp) cc_final: 0.8326 (tppt) REVERT: E 425 GLN cc_start: 0.9285 (mm-40) cc_final: 0.8827 (mt0) REVERT: E 427 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8686 (tm-30) REVERT: E 430 ARG cc_start: 0.8937 (mtm-85) cc_final: 0.8730 (mtm110) REVERT: F 191 ASN cc_start: 0.7827 (t0) cc_final: 0.7580 (m-40) REVERT: F 216 GLN cc_start: 0.8619 (mt0) cc_final: 0.8405 (mm-40) REVERT: F 217 LEU cc_start: 0.9380 (tt) cc_final: 0.9154 (tp) REVERT: F 222 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7753 (mmm160) REVERT: F 233 GLN cc_start: 0.7677 (mm-40) cc_final: 0.7451 (mm-40) REVERT: F 251 ARG cc_start: 0.7837 (ptm160) cc_final: 0.7492 (mtm180) REVERT: F 255 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8411 (tt0) REVERT: F 256 LEU cc_start: 0.9484 (tp) cc_final: 0.9108 (mp) REVERT: F 330 MET cc_start: 0.9391 (tpt) cc_final: 0.9137 (mmm) REVERT: F 345 ASP cc_start: 0.8123 (t0) cc_final: 0.7596 (t70) REVERT: F 401 LEU cc_start: 0.7767 (mt) cc_final: 0.7546 (mm) REVERT: F 405 ASP cc_start: 0.9048 (m-30) cc_final: 0.8387 (t0) REVERT: F 406 PHE cc_start: 0.9347 (m-80) cc_final: 0.9074 (m-80) REVERT: F 408 LYS cc_start: 0.9080 (mttp) cc_final: 0.8674 (tppt) REVERT: F 421 ASP cc_start: 0.8450 (m-30) cc_final: 0.7872 (t70) REVERT: G 284 THR cc_start: 0.7965 (p) cc_final: 0.7585 (p) REVERT: G 288 ASP cc_start: 0.8821 (m-30) cc_final: 0.8505 (m-30) REVERT: H 295 GLN cc_start: 0.4982 (tt0) cc_final: 0.4493 (tp40) REVERT: J 307 LEU cc_start: 0.7491 (tp) cc_final: 0.7195 (mt) REVERT: K 288 ASP cc_start: 0.8153 (m-30) cc_final: 0.7825 (m-30) REVERT: K 295 GLN cc_start: 0.7260 (tm-30) cc_final: 0.7007 (tm-30) REVERT: M 323 LEU cc_start: 0.7479 (tp) cc_final: 0.7101 (mt) outliers start: 1 outliers final: 0 residues processed: 576 average time/residue: 0.3513 time to fit residues: 287.7818 Evaluate side-chains 429 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 428 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 167 optimal weight: 0.0980 chunk 137 optimal weight: 9.9990 chunk 55 optimal weight: 30.0000 chunk 201 optimal weight: 20.0000 chunk 218 optimal weight: 6.9990 chunk 179 optimal weight: 30.0000 chunk 200 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 overall best weight: 5.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN B 259 GLN B 261 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 HIS G 295 GLN K 327 ASN N 295 GLN N 297 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 18299 Z= 0.380 Angle : 0.843 17.029 24758 Z= 0.431 Chirality : 0.047 0.300 2846 Planarity : 0.006 0.094 3173 Dihedral : 10.655 88.971 2616 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.99 % Favored : 93.61 % Rotamer: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.18), residues: 2270 helix: 0.78 (0.15), residues: 1180 sheet: 0.61 (0.32), residues: 259 loop : -0.83 (0.23), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP B 206 HIS 0.004 0.001 HIS E 359 PHE 0.031 0.003 PHE A 230 TYR 0.037 0.003 TYR N 302 ARG 0.008 0.001 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 495 time to evaluate : 2.582 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: A 132 TRP cc_start: 0.7987 (m100) cc_final: 0.7709 (m100) REVERT: A 172 TYR cc_start: 0.6341 (p90) cc_final: 0.5590 (p90) REVERT: A 215 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7957 (mmmt) REVERT: A 288 ARG cc_start: 0.7742 (mmt90) cc_final: 0.7498 (mmp-170) REVERT: A 308 PHE cc_start: 0.7261 (m-80) cc_final: 0.6964 (m-10) REVERT: A 327 LEU cc_start: 0.7320 (mt) cc_final: 0.7057 (tp) REVERT: A 405 ASP cc_start: 0.8737 (m-30) cc_final: 0.8371 (t0) REVERT: B 133 GLU cc_start: 0.8732 (mp0) cc_final: 0.8386 (tp30) REVERT: B 215 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8817 (pttm) REVERT: B 268 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7635 (tp40) REVERT: B 278 ILE cc_start: 0.8636 (mt) cc_final: 0.8376 (tt) REVERT: B 327 LEU cc_start: 0.9068 (mm) cc_final: 0.8842 (mm) REVERT: C 162 ASN cc_start: 0.8450 (m-40) cc_final: 0.7743 (p0) REVERT: C 181 TYR cc_start: 0.8758 (t80) cc_final: 0.8419 (t80) REVERT: C 201 ASP cc_start: 0.8311 (t70) cc_final: 0.7991 (t0) REVERT: C 207 MET cc_start: 0.8491 (ppp) cc_final: 0.8259 (ppp) REVERT: C 254 THR cc_start: 0.8599 (m) cc_final: 0.8392 (p) REVERT: C 293 ARG cc_start: 0.9499 (ttm-80) cc_final: 0.8561 (ttm-80) REVERT: C 408 LYS cc_start: 0.8823 (mttp) cc_final: 0.8593 (mmmt) REVERT: D 135 VAL cc_start: 0.8854 (t) cc_final: 0.8431 (m) REVERT: D 181 TYR cc_start: 0.8453 (t80) cc_final: 0.7696 (t80) REVERT: D 207 MET cc_start: 0.9098 (tpt) cc_final: 0.8501 (mtt) REVERT: D 259 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8144 (mm-40) REVERT: D 273 LEU cc_start: 0.9445 (mt) cc_final: 0.9180 (mt) REVERT: D 291 GLU cc_start: 0.9035 (tt0) cc_final: 0.8805 (tt0) REVERT: D 345 ASP cc_start: 0.9112 (t0) cc_final: 0.8814 (t0) REVERT: D 349 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8431 (mp10) REVERT: E 211 GLU cc_start: 0.8867 (mp0) cc_final: 0.8613 (mp0) REVERT: E 261 ASN cc_start: 0.7073 (t0) cc_final: 0.6513 (p0) REVERT: E 290 PHE cc_start: 0.6335 (t80) cc_final: 0.5987 (t80) REVERT: E 292 ARG cc_start: 0.8485 (mmm-85) cc_final: 0.7975 (mmm160) REVERT: E 330 MET cc_start: 0.9126 (mmt) cc_final: 0.8599 (mmp) REVERT: E 414 ARG cc_start: 0.8430 (mmp-170) cc_final: 0.7983 (mmp80) REVERT: E 425 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8644 (mt0) REVERT: F 216 GLN cc_start: 0.8464 (mt0) cc_final: 0.8228 (mm-40) REVERT: F 222 ARG cc_start: 0.8440 (mtt180) cc_final: 0.8021 (mmt180) REVERT: F 251 ARG cc_start: 0.7898 (ptm160) cc_final: 0.7657 (mtm-85) REVERT: F 256 LEU cc_start: 0.9389 (tp) cc_final: 0.9173 (mt) REVERT: F 325 ARG cc_start: 0.7582 (mtt180) cc_final: 0.7138 (mmm-85) REVERT: F 330 MET cc_start: 0.9323 (tpt) cc_final: 0.9069 (mmm) REVERT: F 345 ASP cc_start: 0.7812 (t0) cc_final: 0.7364 (t0) REVERT: F 405 ASP cc_start: 0.8908 (m-30) cc_final: 0.8352 (t0) REVERT: F 406 PHE cc_start: 0.9273 (m-80) cc_final: 0.8975 (m-80) REVERT: F 408 LYS cc_start: 0.9120 (mttp) cc_final: 0.8879 (tppt) REVERT: F 421 ASP cc_start: 0.8652 (m-30) cc_final: 0.8101 (t70) REVERT: G 287 MET cc_start: 0.9263 (ppp) cc_final: 0.8821 (mtm) REVERT: G 308 ASN cc_start: 0.4847 (m-40) cc_final: 0.4540 (m-40) REVERT: H 302 TYR cc_start: 0.4757 (m-80) cc_final: 0.4448 (m-80) REVERT: H 318 GLU cc_start: 0.5741 (mp0) cc_final: 0.5534 (mp0) REVERT: I 302 TYR cc_start: 0.8029 (m-80) cc_final: 0.7745 (m-80) REVERT: I 321 LYS cc_start: 0.6397 (mtmt) cc_final: 0.6087 (mtmt) REVERT: I 325 LEU cc_start: 0.7371 (tp) cc_final: 0.6914 (tp) REVERT: M 309 TYR cc_start: 0.7062 (m-80) cc_final: 0.6787 (m-80) outliers start: 2 outliers final: 1 residues processed: 495 average time/residue: 0.3661 time to fit residues: 261.5368 Evaluate side-chains 365 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 364 time to evaluate : 2.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 199 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 214 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 192 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN A 434 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN ** F 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.7270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18299 Z= 0.242 Angle : 0.700 16.634 24758 Z= 0.358 Chirality : 0.044 0.288 2846 Planarity : 0.005 0.059 3173 Dihedral : 10.254 89.747 2616 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.98 % Favored : 94.67 % Rotamer: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2270 helix: 1.05 (0.15), residues: 1182 sheet: 0.80 (0.32), residues: 253 loop : -0.71 (0.23), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 206 HIS 0.003 0.001 HIS E 157 PHE 0.027 0.002 PHE A 230 TYR 0.028 0.002 TYR N 302 ARG 0.005 0.001 ARG C 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 495 time to evaluate : 2.180 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: A 172 TYR cc_start: 0.6057 (p90) cc_final: 0.4740 (p90) REVERT: A 293 ARG cc_start: 0.3592 (ptp-170) cc_final: 0.2621 (ptp-170) REVERT: A 308 PHE cc_start: 0.7242 (m-80) cc_final: 0.6852 (m-10) REVERT: A 327 LEU cc_start: 0.7701 (mt) cc_final: 0.7303 (tp) REVERT: A 405 ASP cc_start: 0.8678 (m-30) cc_final: 0.8350 (t0) REVERT: A 422 LEU cc_start: 0.7872 (tt) cc_final: 0.7654 (tt) REVERT: B 133 GLU cc_start: 0.8871 (mp0) cc_final: 0.8497 (tp30) REVERT: B 215 LYS cc_start: 0.9229 (mmmm) cc_final: 0.8913 (pttm) REVERT: B 259 GLN cc_start: 0.9138 (tp-100) cc_final: 0.8546 (pt0) REVERT: B 268 GLN cc_start: 0.7654 (tp-100) cc_final: 0.7256 (tp40) REVERT: B 278 ILE cc_start: 0.8678 (mt) cc_final: 0.8419 (tt) REVERT: B 290 PHE cc_start: 0.7439 (t80) cc_final: 0.7170 (t80) REVERT: C 162 ASN cc_start: 0.8521 (m-40) cc_final: 0.7944 (p0) REVERT: C 181 TYR cc_start: 0.8683 (t80) cc_final: 0.8268 (t80) REVERT: C 201 ASP cc_start: 0.8465 (t70) cc_final: 0.8143 (t0) REVERT: C 232 ASP cc_start: 0.8699 (t70) cc_final: 0.7992 (t70) REVERT: C 233 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8418 (mm-40) REVERT: C 293 ARG cc_start: 0.9524 (ttm-80) cc_final: 0.8553 (ttm-80) REVERT: C 311 ASN cc_start: 0.8541 (m-40) cc_final: 0.8322 (m-40) REVERT: C 408 LYS cc_start: 0.8860 (mttp) cc_final: 0.8588 (mmmt) REVERT: C 413 THR cc_start: 0.7916 (m) cc_final: 0.7571 (m) REVERT: D 135 VAL cc_start: 0.8821 (t) cc_final: 0.8382 (m) REVERT: D 181 TYR cc_start: 0.8551 (t80) cc_final: 0.7740 (t80) REVERT: D 207 MET cc_start: 0.9190 (tpt) cc_final: 0.8590 (mtt) REVERT: D 211 GLU cc_start: 0.7867 (pp20) cc_final: 0.7639 (pp20) REVERT: D 273 LEU cc_start: 0.9371 (mt) cc_final: 0.9138 (mt) REVERT: D 291 GLU cc_start: 0.9193 (tt0) cc_final: 0.8959 (tt0) REVERT: D 345 ASP cc_start: 0.9097 (t0) cc_final: 0.8838 (t0) REVERT: D 349 GLN cc_start: 0.8906 (tp-100) cc_final: 0.8699 (mt0) REVERT: D 380 ASP cc_start: 0.5642 (t0) cc_final: 0.5349 (t0) REVERT: E 179 LYS cc_start: 0.9298 (mtmt) cc_final: 0.9073 (mttp) REVERT: E 195 PHE cc_start: 0.7607 (m-80) cc_final: 0.7374 (m-80) REVERT: E 251 ARG cc_start: 0.7387 (ptp-170) cc_final: 0.6973 (ptp90) REVERT: E 254 THR cc_start: 0.8828 (p) cc_final: 0.8250 (p) REVERT: E 255 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8728 (mm-30) REVERT: E 259 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8357 (mm-40) REVERT: E 260 MET cc_start: 0.7023 (tmm) cc_final: 0.6796 (tmm) REVERT: E 292 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.7887 (mmm160) REVERT: E 330 MET cc_start: 0.9253 (mmt) cc_final: 0.8803 (mmp) REVERT: E 349 GLN cc_start: 0.9290 (mm110) cc_final: 0.9046 (tt0) REVERT: E 386 MET cc_start: 0.8308 (pmm) cc_final: 0.7908 (pmm) REVERT: E 406 PHE cc_start: 0.9306 (m-80) cc_final: 0.9063 (m-80) REVERT: E 414 ARG cc_start: 0.8213 (mmp-170) cc_final: 0.7962 (mmp80) REVERT: E 420 ASP cc_start: 0.8761 (m-30) cc_final: 0.8401 (t0) REVERT: E 424 LYS cc_start: 0.8742 (mttp) cc_final: 0.8435 (mtmm) REVERT: E 425 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8581 (mt0) REVERT: F 143 GLU cc_start: 0.8349 (tt0) cc_final: 0.8011 (mm-30) REVERT: F 215 LYS cc_start: 0.8543 (ptpt) cc_final: 0.8294 (pttt) REVERT: F 216 GLN cc_start: 0.8354 (mt0) cc_final: 0.8152 (mm-40) REVERT: F 222 ARG cc_start: 0.8458 (mtt180) cc_final: 0.7979 (mmt180) REVERT: F 330 MET cc_start: 0.9384 (tpt) cc_final: 0.9156 (mmm) REVERT: F 345 ASP cc_start: 0.7926 (t0) cc_final: 0.7558 (t70) REVERT: F 348 MET cc_start: 0.8459 (mmp) cc_final: 0.7870 (tpp) REVERT: F 405 ASP cc_start: 0.8825 (m-30) cc_final: 0.8389 (t0) REVERT: F 406 PHE cc_start: 0.9234 (m-80) cc_final: 0.8996 (m-80) REVERT: F 408 LYS cc_start: 0.9078 (mttp) cc_final: 0.8803 (tptt) REVERT: F 421 ASP cc_start: 0.8610 (m-30) cc_final: 0.8056 (t70) REVERT: G 287 MET cc_start: 0.9242 (ppp) cc_final: 0.8797 (mtm) REVERT: I 294 GLU cc_start: 0.8027 (pt0) cc_final: 0.6924 (mm-30) outliers start: 2 outliers final: 0 residues processed: 495 average time/residue: 0.3266 time to fit residues: 234.9861 Evaluate side-chains 375 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 375 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 178 optimal weight: 0.7980 chunk 121 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 159 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 109 optimal weight: 0.9990 chunk 192 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN B 233 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN C 311 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.7671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18299 Z= 0.215 Angle : 0.680 16.823 24758 Z= 0.347 Chirality : 0.043 0.280 2846 Planarity : 0.005 0.055 3173 Dihedral : 10.035 89.993 2616 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.55 % Favored : 94.10 % Rotamer: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2270 helix: 1.11 (0.15), residues: 1172 sheet: 0.90 (0.31), residues: 246 loop : -0.65 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 132 HIS 0.003 0.001 HIS E 157 PHE 0.023 0.002 PHE A 230 TYR 0.027 0.002 TYR N 302 ARG 0.004 0.001 ARG C 325 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 474 time to evaluate : 2.162 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: A 172 TYR cc_start: 0.6447 (p90) cc_final: 0.5748 (p90) REVERT: A 308 PHE cc_start: 0.7434 (m-80) cc_final: 0.7007 (m-10) REVERT: A 327 LEU cc_start: 0.7946 (mt) cc_final: 0.7611 (tp) REVERT: A 405 ASP cc_start: 0.8692 (m-30) cc_final: 0.8302 (t70) REVERT: A 425 GLN cc_start: 0.7603 (mp10) cc_final: 0.7397 (mm110) REVERT: A 435 GLU cc_start: 0.5242 (mp0) cc_final: 0.4930 (tt0) REVERT: B 215 LYS cc_start: 0.9222 (mmmm) cc_final: 0.8867 (pttm) REVERT: B 220 MET cc_start: 0.9299 (ttm) cc_final: 0.8994 (tpp) REVERT: B 268 GLN cc_start: 0.7763 (tp-100) cc_final: 0.7303 (tp40) REVERT: B 271 LEU cc_start: 0.9216 (tp) cc_final: 0.8919 (tp) REVERT: B 278 ILE cc_start: 0.8653 (mt) cc_final: 0.8392 (tt) REVERT: B 290 PHE cc_start: 0.7205 (t80) cc_final: 0.6918 (t80) REVERT: C 151 LEU cc_start: 0.8695 (tp) cc_final: 0.8479 (tp) REVERT: C 162 ASN cc_start: 0.8456 (m-40) cc_final: 0.8109 (p0) REVERT: C 181 TYR cc_start: 0.8695 (t80) cc_final: 0.8300 (t80) REVERT: C 196 SER cc_start: 0.9201 (p) cc_final: 0.8861 (m) REVERT: C 293 ARG cc_start: 0.9470 (ttm-80) cc_final: 0.8598 (ttm-80) REVERT: C 324 TYR cc_start: 0.7446 (m-10) cc_final: 0.7153 (m-80) REVERT: C 408 LYS cc_start: 0.8814 (mttp) cc_final: 0.8567 (mmmt) REVERT: D 135 VAL cc_start: 0.8771 (t) cc_final: 0.8322 (m) REVERT: D 181 TYR cc_start: 0.8594 (t80) cc_final: 0.7717 (t80) REVERT: D 207 MET cc_start: 0.9179 (tpt) cc_final: 0.8411 (mtt) REVERT: D 211 GLU cc_start: 0.7969 (pp20) cc_final: 0.7713 (pp20) REVERT: E 179 LYS cc_start: 0.9297 (mtmt) cc_final: 0.9049 (mttp) REVERT: E 181 TYR cc_start: 0.7169 (t80) cc_final: 0.6926 (t80) REVERT: E 195 PHE cc_start: 0.7718 (m-80) cc_final: 0.7434 (m-80) REVERT: E 233 GLN cc_start: 0.8508 (mm110) cc_final: 0.8159 (mm-40) REVERT: E 254 THR cc_start: 0.8893 (p) cc_final: 0.8375 (p) REVERT: E 255 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8657 (mm-30) REVERT: E 259 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8190 (mm-40) REVERT: E 292 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.7914 (mmm160) REVERT: E 321 LYS cc_start: 0.8637 (mmpt) cc_final: 0.8393 (mmmt) REVERT: E 330 MET cc_start: 0.9204 (mmt) cc_final: 0.8779 (mmp) REVERT: E 349 GLN cc_start: 0.9265 (mm110) cc_final: 0.9010 (tt0) REVERT: E 386 MET cc_start: 0.8327 (pmm) cc_final: 0.7952 (pmm) REVERT: E 406 PHE cc_start: 0.9267 (m-80) cc_final: 0.9001 (m-80) REVERT: E 414 ARG cc_start: 0.8143 (mmp-170) cc_final: 0.7886 (mmp80) REVERT: E 420 ASP cc_start: 0.8526 (m-30) cc_final: 0.8122 (t0) REVERT: E 425 GLN cc_start: 0.9208 (mm-40) cc_final: 0.8576 (mt0) REVERT: F 195 PHE cc_start: 0.7615 (m-80) cc_final: 0.7114 (m-80) REVERT: F 222 ARG cc_start: 0.8360 (mtt180) cc_final: 0.7870 (mmt180) REVERT: F 330 MET cc_start: 0.9426 (tpt) cc_final: 0.9192 (mmm) REVERT: F 345 ASP cc_start: 0.7807 (t0) cc_final: 0.7479 (t70) REVERT: F 348 MET cc_start: 0.8517 (mmp) cc_final: 0.7914 (tpp) REVERT: F 405 ASP cc_start: 0.8821 (m-30) cc_final: 0.8418 (t0) REVERT: F 406 PHE cc_start: 0.9221 (m-80) cc_final: 0.8995 (m-80) REVERT: F 408 LYS cc_start: 0.9097 (mttp) cc_final: 0.8890 (mmtt) REVERT: F 421 ASP cc_start: 0.8641 (m-30) cc_final: 0.8087 (t70) REVERT: G 287 MET cc_start: 0.9242 (ppp) cc_final: 0.8845 (mtm) REVERT: G 288 ASP cc_start: 0.8771 (m-30) cc_final: 0.8570 (m-30) REVERT: H 302 TYR cc_start: 0.5090 (m-10) cc_final: 0.4830 (t80) REVERT: I 294 GLU cc_start: 0.8073 (pt0) cc_final: 0.7127 (mm-30) outliers start: 2 outliers final: 0 residues processed: 475 average time/residue: 0.3152 time to fit residues: 219.6237 Evaluate side-chains 374 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 374 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN B 233 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN C 359 HIS ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN E 265 ASN E 311 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.8515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 18299 Z= 0.316 Angle : 0.775 16.948 24758 Z= 0.398 Chirality : 0.046 0.297 2846 Planarity : 0.005 0.051 3173 Dihedral : 10.231 89.508 2616 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 26.19 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.70 % Favored : 93.00 % Rotamer: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.18), residues: 2270 helix: 0.64 (0.15), residues: 1177 sheet: 0.47 (0.31), residues: 251 loop : -0.79 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 206 HIS 0.005 0.001 HIS D 359 PHE 0.028 0.003 PHE B 290 TYR 0.027 0.002 TYR N 302 ARG 0.008 0.001 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 457 time to evaluate : 2.219 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: A 172 TYR cc_start: 0.6607 (p90) cc_final: 0.5640 (p90) REVERT: A 230 PHE cc_start: 0.8804 (t80) cc_final: 0.8323 (t80) REVERT: A 273 LEU cc_start: 0.9060 (mt) cc_final: 0.8399 (tp) REVERT: A 405 ASP cc_start: 0.8625 (m-30) cc_final: 0.8228 (t0) REVERT: A 425 GLN cc_start: 0.7688 (mp10) cc_final: 0.7472 (mm110) REVERT: A 435 GLU cc_start: 0.5529 (mp0) cc_final: 0.5000 (tt0) REVERT: B 215 LYS cc_start: 0.9252 (mmmm) cc_final: 0.8873 (pttm) REVERT: B 268 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7485 (tp40) REVERT: B 271 LEU cc_start: 0.9258 (tp) cc_final: 0.9019 (tp) REVERT: B 278 ILE cc_start: 0.8549 (mt) cc_final: 0.7960 (tt) REVERT: B 281 GLN cc_start: 0.8452 (tp40) cc_final: 0.7234 (tt0) REVERT: B 307 MET cc_start: 0.8926 (mmp) cc_final: 0.8713 (mmt) REVERT: B 431 ASP cc_start: 0.9239 (t70) cc_final: 0.9036 (t0) REVERT: C 146 LYS cc_start: 0.9194 (mmtt) cc_final: 0.8882 (mmmm) REVERT: C 162 ASN cc_start: 0.8648 (m-40) cc_final: 0.8345 (p0) REVERT: C 181 TYR cc_start: 0.8797 (t80) cc_final: 0.8486 (t80) REVERT: C 196 SER cc_start: 0.9190 (p) cc_final: 0.8986 (t) REVERT: C 201 ASP cc_start: 0.8393 (t70) cc_final: 0.8100 (t0) REVERT: C 220 MET cc_start: 0.8959 (mmp) cc_final: 0.8714 (mmm) REVERT: C 254 THR cc_start: 0.8631 (m) cc_final: 0.8428 (p) REVERT: C 293 ARG cc_start: 0.9468 (ttm-80) cc_final: 0.8635 (ttm-80) REVERT: C 408 LYS cc_start: 0.9000 (mttp) cc_final: 0.8747 (mmmt) REVERT: D 135 VAL cc_start: 0.8787 (t) cc_final: 0.8495 (m) REVERT: D 181 TYR cc_start: 0.8669 (t80) cc_final: 0.7752 (t80) REVERT: D 207 MET cc_start: 0.9087 (tpt) cc_final: 0.8328 (mtt) REVERT: D 209 GLU cc_start: 0.8099 (tt0) cc_final: 0.7811 (pt0) REVERT: D 211 GLU cc_start: 0.7961 (pp20) cc_final: 0.7717 (pp20) REVERT: D 290 PHE cc_start: 0.8394 (t80) cc_final: 0.7999 (t80) REVERT: D 307 MET cc_start: 0.8511 (tpp) cc_final: 0.8309 (tpp) REVERT: D 348 MET cc_start: 0.8750 (tpp) cc_final: 0.8482 (tpp) REVERT: E 151 LEU cc_start: 0.8832 (tp) cc_final: 0.8585 (tp) REVERT: E 216 GLN cc_start: 0.8244 (mt0) cc_final: 0.7763 (pt0) REVERT: E 233 GLN cc_start: 0.8577 (mm110) cc_final: 0.8369 (mm110) REVERT: E 281 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8779 (tm-30) REVERT: E 290 PHE cc_start: 0.7317 (t80) cc_final: 0.7089 (t80) REVERT: E 292 ARG cc_start: 0.8585 (mmm-85) cc_final: 0.7966 (mmm160) REVERT: E 330 MET cc_start: 0.9213 (mmt) cc_final: 0.8812 (mmp) REVERT: E 349 GLN cc_start: 0.9257 (mm110) cc_final: 0.8880 (mt0) REVERT: E 406 PHE cc_start: 0.9267 (m-80) cc_final: 0.9015 (m-80) REVERT: E 420 ASP cc_start: 0.8559 (m-30) cc_final: 0.8328 (t0) REVERT: E 424 LYS cc_start: 0.8713 (mttp) cc_final: 0.8301 (pttm) REVERT: E 425 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8653 (mt0) REVERT: F 126 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6850 (tm-30) REVERT: F 195 PHE cc_start: 0.7765 (m-80) cc_final: 0.7411 (m-80) REVERT: F 222 ARG cc_start: 0.8441 (mtt180) cc_final: 0.7852 (mmm160) REVERT: F 345 ASP cc_start: 0.7860 (t0) cc_final: 0.7494 (t70) REVERT: F 348 MET cc_start: 0.8470 (mmp) cc_final: 0.7784 (tpp) REVERT: F 405 ASP cc_start: 0.8779 (m-30) cc_final: 0.8415 (t0) REVERT: F 406 PHE cc_start: 0.9166 (m-80) cc_final: 0.8926 (m-80) REVERT: F 408 LYS cc_start: 0.9104 (mttp) cc_final: 0.8816 (mmtt) REVERT: F 421 ASP cc_start: 0.8708 (m-30) cc_final: 0.8222 (t70) REVERT: G 287 MET cc_start: 0.9214 (ppp) cc_final: 0.8776 (mtm) REVERT: H 302 TYR cc_start: 0.5050 (m-10) cc_final: 0.4743 (t80) REVERT: H 318 GLU cc_start: 0.5565 (mp0) cc_final: 0.5354 (mp0) REVERT: I 329 ILE cc_start: 0.6355 (pt) cc_final: 0.6128 (pt) REVERT: N 318 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6653 (mt-10) outliers start: 2 outliers final: 1 residues processed: 458 average time/residue: 0.3206 time to fit residues: 216.0583 Evaluate side-chains 349 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 348 time to evaluate : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 207 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 122 optimal weight: 0.5980 chunk 156 optimal weight: 20.0000 chunk 121 optimal weight: 0.9990 chunk 180 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 213 optimal weight: 0.0030 chunk 133 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN E 265 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 ASN ** F 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.8509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 18299 Z= 0.185 Angle : 0.676 16.413 24758 Z= 0.341 Chirality : 0.044 0.274 2846 Planarity : 0.005 0.055 3173 Dihedral : 9.921 88.507 2616 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.89 % Favored : 94.76 % Rotamer: Outliers : 0.10 % Allowed : 1.68 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2270 helix: 1.06 (0.15), residues: 1168 sheet: 0.51 (0.32), residues: 241 loop : -0.65 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 206 HIS 0.005 0.001 HIS A 359 PHE 0.020 0.002 PHE A 230 TYR 0.022 0.001 TYR N 302 ARG 0.008 0.001 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 477 time to evaluate : 2.158 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: A 172 TYR cc_start: 0.6893 (p90) cc_final: 0.5752 (p90) REVERT: A 334 TYR cc_start: 0.5806 (m-80) cc_final: 0.5489 (m-80) REVERT: A 405 ASP cc_start: 0.8455 (m-30) cc_final: 0.8100 (t0) REVERT: A 428 PHE cc_start: 0.7735 (t80) cc_final: 0.7370 (t80) REVERT: B 181 TYR cc_start: 0.7257 (t80) cc_final: 0.6973 (t80) REVERT: B 195 PHE cc_start: 0.8689 (m-10) cc_final: 0.8261 (m-10) REVERT: B 215 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8939 (pttm) REVERT: B 233 GLN cc_start: 0.8623 (mp10) cc_final: 0.8344 (mp10) REVERT: B 250 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7570 (tpt90) REVERT: B 259 GLN cc_start: 0.8895 (tp40) cc_final: 0.8276 (tt0) REVERT: B 268 GLN cc_start: 0.7631 (tp-100) cc_final: 0.7373 (tp40) REVERT: B 271 LEU cc_start: 0.9137 (tp) cc_final: 0.8833 (tp) REVERT: B 278 ILE cc_start: 0.8578 (mt) cc_final: 0.7940 (tt) REVERT: B 281 GLN cc_start: 0.8355 (tp40) cc_final: 0.7228 (tt0) REVERT: B 290 PHE cc_start: 0.7463 (t80) cc_final: 0.7253 (t80) REVERT: C 146 LYS cc_start: 0.9237 (mmtt) cc_final: 0.8912 (mmmm) REVERT: C 162 ASN cc_start: 0.8668 (m-40) cc_final: 0.8324 (p0) REVERT: C 181 TYR cc_start: 0.8628 (t80) cc_final: 0.8214 (t80) REVERT: C 196 SER cc_start: 0.9230 (p) cc_final: 0.8957 (m) REVERT: C 201 ASP cc_start: 0.8324 (t70) cc_final: 0.8096 (t0) REVERT: C 220 MET cc_start: 0.8911 (mmp) cc_final: 0.8662 (mmm) REVERT: C 233 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8588 (mm-40) REVERT: C 256 LEU cc_start: 0.8723 (tp) cc_final: 0.8289 (mm) REVERT: C 293 ARG cc_start: 0.9428 (ttm-80) cc_final: 0.8620 (ttm-80) REVERT: C 311 ASN cc_start: 0.8961 (m-40) cc_final: 0.8745 (m-40) REVERT: C 324 TYR cc_start: 0.7796 (m-10) cc_final: 0.7373 (m-10) REVERT: C 337 SER cc_start: 0.7201 (m) cc_final: 0.6606 (p) REVERT: C 405 ASP cc_start: 0.8543 (m-30) cc_final: 0.8312 (m-30) REVERT: C 408 LYS cc_start: 0.8982 (mttp) cc_final: 0.8731 (mmmt) REVERT: D 135 VAL cc_start: 0.8838 (t) cc_final: 0.8338 (m) REVERT: D 181 TYR cc_start: 0.8550 (t80) cc_final: 0.7644 (t80) REVERT: D 211 GLU cc_start: 0.7916 (pp20) cc_final: 0.7514 (pp20) REVERT: D 259 GLN cc_start: 0.8311 (mm-40) cc_final: 0.7608 (mt0) REVERT: D 307 MET cc_start: 0.8455 (tpp) cc_final: 0.8247 (tpp) REVERT: E 151 LEU cc_start: 0.8878 (tp) cc_final: 0.8648 (tp) REVERT: E 179 LYS cc_start: 0.9380 (mtmt) cc_final: 0.9135 (mttp) REVERT: E 181 TYR cc_start: 0.7423 (t80) cc_final: 0.7132 (t80) REVERT: E 195 PHE cc_start: 0.8041 (m-80) cc_final: 0.7833 (m-80) REVERT: E 216 GLN cc_start: 0.8091 (mt0) cc_final: 0.7557 (pt0) REVERT: E 220 MET cc_start: 0.9109 (mmp) cc_final: 0.8883 (mmm) REVERT: E 281 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8727 (tm-30) REVERT: E 292 ARG cc_start: 0.8526 (mmm-85) cc_final: 0.7868 (mmm160) REVERT: E 330 MET cc_start: 0.9268 (mmt) cc_final: 0.8858 (mmp) REVERT: E 349 GLN cc_start: 0.9177 (mm110) cc_final: 0.8888 (mt0) REVERT: E 386 MET cc_start: 0.8254 (pmm) cc_final: 0.7879 (pmm) REVERT: E 406 PHE cc_start: 0.9281 (m-80) cc_final: 0.8999 (m-80) REVERT: E 414 ARG cc_start: 0.8358 (mmp-170) cc_final: 0.8156 (mmp80) REVERT: E 424 LYS cc_start: 0.8908 (mttp) cc_final: 0.8636 (pttm) REVERT: E 425 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8599 (mt0) REVERT: F 126 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7174 (tm-30) REVERT: F 195 PHE cc_start: 0.7963 (m-80) cc_final: 0.7477 (m-80) REVERT: F 207 MET cc_start: 0.1275 (mmp) cc_final: 0.0496 (ttp) REVERT: F 222 ARG cc_start: 0.8367 (mtt180) cc_final: 0.7877 (mmm160) REVERT: F 345 ASP cc_start: 0.8009 (t0) cc_final: 0.7643 (t70) REVERT: F 348 MET cc_start: 0.8482 (mmp) cc_final: 0.7690 (tpp) REVERT: F 405 ASP cc_start: 0.8865 (m-30) cc_final: 0.8478 (t0) REVERT: F 406 PHE cc_start: 0.9188 (m-80) cc_final: 0.8971 (m-80) REVERT: F 408 LYS cc_start: 0.9067 (mttp) cc_final: 0.8835 (mmtt) REVERT: F 421 ASP cc_start: 0.8679 (m-30) cc_final: 0.8186 (t70) REVERT: G 287 MET cc_start: 0.9214 (ppp) cc_final: 0.8826 (mtm) REVERT: H 302 TYR cc_start: 0.5074 (m-10) cc_final: 0.4783 (t80) REVERT: H 318 GLU cc_start: 0.5646 (mp0) cc_final: 0.5446 (mp0) REVERT: M 298 LYS cc_start: 0.6940 (mtmm) cc_final: 0.6735 (tppt) REVERT: N 309 TYR cc_start: 0.7269 (m-80) cc_final: 0.6905 (m-80) REVERT: N 318 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7166 (mt-10) outliers start: 2 outliers final: 1 residues processed: 478 average time/residue: 0.3085 time to fit residues: 217.8811 Evaluate side-chains 395 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 394 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 132 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 105 optimal weight: 0.7980 chunk 19 optimal weight: 0.0570 chunk 168 optimal weight: 6.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 ASN B 224 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 437 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 259 GLN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 ASN G 295 GLN ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 327 ASN ** M 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.8636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18299 Z= 0.185 Angle : 0.671 16.311 24758 Z= 0.338 Chirality : 0.044 0.320 2846 Planarity : 0.004 0.074 3173 Dihedral : 9.560 88.299 2616 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.85 % Favored : 94.80 % Rotamer: Outliers : 0.05 % Allowed : 1.17 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2270 helix: 1.22 (0.15), residues: 1156 sheet: 0.60 (0.32), residues: 241 loop : -0.57 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 206 HIS 0.002 0.001 HIS D 359 PHE 0.024 0.002 PHE A 230 TYR 0.012 0.001 TYR D 295 ARG 0.007 0.000 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 477 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 TYR cc_start: 0.5693 (m-80) cc_final: 0.5296 (m-80) REVERT: A 339 ILE cc_start: 0.7572 (mt) cc_final: 0.7369 (mt) REVERT: A 349 GLN cc_start: 0.8852 (tp40) cc_final: 0.8533 (tt0) REVERT: A 405 ASP cc_start: 0.8453 (m-30) cc_final: 0.7740 (t0) REVERT: B 181 TYR cc_start: 0.7228 (t80) cc_final: 0.6924 (t80) REVERT: B 195 PHE cc_start: 0.8795 (m-10) cc_final: 0.8386 (m-10) REVERT: B 215 LYS cc_start: 0.9201 (mmmm) cc_final: 0.8950 (pttm) REVERT: B 233 GLN cc_start: 0.8609 (mp10) cc_final: 0.8362 (mp10) REVERT: B 259 GLN cc_start: 0.8915 (tp40) cc_final: 0.8291 (tt0) REVERT: B 268 GLN cc_start: 0.7591 (tp-100) cc_final: 0.7372 (tp40) REVERT: B 278 ILE cc_start: 0.8545 (mt) cc_final: 0.8248 (tt) REVERT: B 290 PHE cc_start: 0.7528 (t80) cc_final: 0.7142 (t80) REVERT: B 308 PHE cc_start: 0.8664 (m-80) cc_final: 0.8133 (m-80) REVERT: B 321 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8517 (tptm) REVERT: B 327 LEU cc_start: 0.9243 (mm) cc_final: 0.9008 (tt) REVERT: C 146 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8895 (mmmm) REVERT: C 162 ASN cc_start: 0.8770 (m-40) cc_final: 0.8384 (p0) REVERT: C 170 LEU cc_start: 0.8712 (tp) cc_final: 0.8475 (tp) REVERT: C 181 TYR cc_start: 0.8660 (t80) cc_final: 0.8211 (t80) REVERT: C 196 SER cc_start: 0.9242 (p) cc_final: 0.9016 (t) REVERT: C 220 MET cc_start: 0.8904 (mmp) cc_final: 0.8663 (mmm) REVERT: C 233 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8480 (mm-40) REVERT: C 256 LEU cc_start: 0.8750 (tp) cc_final: 0.8317 (mm) REVERT: C 291 GLU cc_start: 0.9066 (pt0) cc_final: 0.8309 (pp20) REVERT: C 293 ARG cc_start: 0.9439 (ttm-80) cc_final: 0.8646 (ttm-80) REVERT: C 324 TYR cc_start: 0.7728 (m-10) cc_final: 0.7149 (m-10) REVERT: C 337 SER cc_start: 0.6837 (m) cc_final: 0.6247 (p) REVERT: C 405 ASP cc_start: 0.8563 (m-30) cc_final: 0.8283 (m-30) REVERT: C 408 LYS cc_start: 0.8990 (mttp) cc_final: 0.8717 (mmmt) REVERT: D 135 VAL cc_start: 0.8827 (t) cc_final: 0.8327 (m) REVERT: D 181 TYR cc_start: 0.8588 (t80) cc_final: 0.7677 (t80) REVERT: D 211 GLU cc_start: 0.8037 (pp20) cc_final: 0.7608 (pp20) REVERT: D 259 GLN cc_start: 0.8272 (tp40) cc_final: 0.7748 (tt0) REVERT: D 291 GLU cc_start: 0.9247 (tt0) cc_final: 0.8961 (tt0) REVERT: E 151 LEU cc_start: 0.8804 (tp) cc_final: 0.8568 (tp) REVERT: E 181 TYR cc_start: 0.7550 (t80) cc_final: 0.7273 (t80) REVERT: E 195 PHE cc_start: 0.7881 (m-80) cc_final: 0.7630 (m-80) REVERT: E 216 GLN cc_start: 0.8130 (mt0) cc_final: 0.7486 (pt0) REVERT: E 220 MET cc_start: 0.9067 (mmp) cc_final: 0.8839 (mmm) REVERT: E 265 ASN cc_start: 0.5150 (m-40) cc_final: 0.4637 (p0) REVERT: E 281 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8617 (tm-30) REVERT: E 290 PHE cc_start: 0.7424 (t80) cc_final: 0.7145 (t80) REVERT: E 292 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8029 (mmm160) REVERT: E 330 MET cc_start: 0.9263 (mmt) cc_final: 0.8871 (mmp) REVERT: E 349 GLN cc_start: 0.9218 (mm110) cc_final: 0.8503 (mt0) REVERT: E 386 MET cc_start: 0.8236 (pmm) cc_final: 0.7799 (pmm) REVERT: E 405 ASP cc_start: 0.9438 (m-30) cc_final: 0.9124 (m-30) REVERT: E 406 PHE cc_start: 0.9176 (m-80) cc_final: 0.8965 (m-80) REVERT: E 425 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8566 (mt0) REVERT: F 126 GLU cc_start: 0.7499 (tm-30) cc_final: 0.7143 (tm-30) REVERT: F 195 PHE cc_start: 0.8089 (m-80) cc_final: 0.7816 (m-80) REVERT: F 207 MET cc_start: 0.1427 (mmp) cc_final: 0.0682 (ttp) REVERT: F 222 ARG cc_start: 0.8383 (mtt180) cc_final: 0.7806 (mmm160) REVERT: F 345 ASP cc_start: 0.8032 (t0) cc_final: 0.7679 (t70) REVERT: F 348 MET cc_start: 0.8432 (mmp) cc_final: 0.7625 (tpp) REVERT: F 351 ILE cc_start: 0.8809 (mp) cc_final: 0.7997 (mp) REVERT: F 386 MET cc_start: 0.7085 (pmm) cc_final: 0.6761 (pmm) REVERT: F 405 ASP cc_start: 0.8863 (m-30) cc_final: 0.8481 (t0) REVERT: F 406 PHE cc_start: 0.9186 (m-80) cc_final: 0.8966 (m-80) REVERT: F 408 LYS cc_start: 0.9070 (mttp) cc_final: 0.8854 (mmtt) REVERT: F 421 ASP cc_start: 0.8663 (m-30) cc_final: 0.8204 (t70) REVERT: G 287 MET cc_start: 0.9192 (ppp) cc_final: 0.8820 (mtm) REVERT: H 302 TYR cc_start: 0.5064 (m-10) cc_final: 0.4801 (t80) REVERT: H 318 GLU cc_start: 0.5436 (mp0) cc_final: 0.5228 (mp0) REVERT: I 289 ARG cc_start: 0.7528 (mtp85) cc_final: 0.7165 (mmm160) REVERT: I 292 LYS cc_start: 0.6460 (ptmt) cc_final: 0.6197 (ttpt) REVERT: K 310 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8401 (tm-30) REVERT: N 301 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7587 (mtmm) REVERT: N 302 TYR cc_start: 0.5803 (m-10) cc_final: 0.5530 (m-80) REVERT: N 308 ASN cc_start: 0.7485 (t0) cc_final: 0.7205 (t0) REVERT: N 309 TYR cc_start: 0.7376 (m-80) cc_final: 0.7090 (m-80) REVERT: N 318 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7170 (mt-10) outliers start: 1 outliers final: 1 residues processed: 478 average time/residue: 0.3184 time to fit residues: 226.0352 Evaluate side-chains 377 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 376 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 194 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 198 optimal weight: 0.8980 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN E 233 GLN E 265 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.9080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 18299 Z= 0.295 Angle : 0.744 17.160 24758 Z= 0.380 Chirality : 0.046 0.319 2846 Planarity : 0.005 0.073 3173 Dihedral : 9.980 87.998 2616 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 24.17 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.26 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.18), residues: 2270 helix: 0.91 (0.15), residues: 1165 sheet: 0.37 (0.31), residues: 255 loop : -0.64 (0.23), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 206 HIS 0.004 0.001 HIS D 359 PHE 0.022 0.002 PHE A 230 TYR 0.014 0.002 TYR B 324 ARG 0.009 0.001 ARG D 251 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 405 ASP cc_start: 0.8601 (m-30) cc_final: 0.8193 (t0) REVERT: B 195 PHE cc_start: 0.8811 (m-10) cc_final: 0.8323 (m-10) REVERT: B 215 LYS cc_start: 0.9191 (mmmm) cc_final: 0.8915 (pttm) REVERT: B 243 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6414 (tp30) REVERT: B 278 ILE cc_start: 0.8514 (mt) cc_final: 0.8219 (tt) REVERT: B 307 MET cc_start: 0.8859 (mmp) cc_final: 0.8634 (mmt) REVERT: B 321 LYS cc_start: 0.8852 (mmtm) cc_final: 0.8390 (tptm) REVERT: C 146 LYS cc_start: 0.9264 (mmtt) cc_final: 0.8960 (mmmm) REVERT: C 162 ASN cc_start: 0.8744 (m-40) cc_final: 0.8346 (p0) REVERT: C 170 LEU cc_start: 0.8780 (tp) cc_final: 0.8546 (tp) REVERT: C 181 TYR cc_start: 0.8788 (t80) cc_final: 0.8420 (t80) REVERT: C 196 SER cc_start: 0.9179 (p) cc_final: 0.8819 (t) REVERT: C 291 GLU cc_start: 0.9122 (pt0) cc_final: 0.8242 (pp20) REVERT: C 293 ARG cc_start: 0.9456 (ttm-80) cc_final: 0.8700 (ttm-80) REVERT: C 324 TYR cc_start: 0.7586 (m-10) cc_final: 0.7225 (m-10) REVERT: C 337 SER cc_start: 0.7198 (m) cc_final: 0.6652 (p) REVERT: C 405 ASP cc_start: 0.8674 (m-30) cc_final: 0.8432 (m-30) REVERT: C 408 LYS cc_start: 0.8978 (mttp) cc_final: 0.8726 (mmmt) REVERT: C 426 GLU cc_start: 0.7854 (mp0) cc_final: 0.7643 (mp0) REVERT: D 135 VAL cc_start: 0.8709 (t) cc_final: 0.8248 (m) REVERT: D 181 TYR cc_start: 0.8626 (t80) cc_final: 0.7706 (t80) REVERT: D 211 GLU cc_start: 0.8141 (pp20) cc_final: 0.7847 (pp20) REVERT: D 259 GLN cc_start: 0.8350 (tp40) cc_final: 0.7744 (tp40) REVERT: D 290 PHE cc_start: 0.7322 (t80) cc_final: 0.7076 (t80) REVERT: D 348 MET cc_start: 0.8733 (tpp) cc_final: 0.8467 (tpp) REVERT: E 151 LEU cc_start: 0.8900 (tp) cc_final: 0.8671 (tp) REVERT: E 216 GLN cc_start: 0.8207 (mt0) cc_final: 0.7581 (pt0) REVERT: E 261 ASN cc_start: 0.6549 (t0) cc_final: 0.5694 (p0) REVERT: E 281 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8732 (tm-30) REVERT: E 292 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8007 (mmm160) REVERT: E 330 MET cc_start: 0.9300 (mmt) cc_final: 0.8887 (mmp) REVERT: E 349 GLN cc_start: 0.9223 (mm110) cc_final: 0.8957 (mt0) REVERT: E 386 MET cc_start: 0.8111 (pmm) cc_final: 0.7669 (pmm) REVERT: E 406 PHE cc_start: 0.9314 (m-80) cc_final: 0.9024 (m-80) REVERT: E 425 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8577 (mt0) REVERT: F 126 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7107 (tm-30) REVERT: F 195 PHE cc_start: 0.7996 (m-80) cc_final: 0.7599 (m-80) REVERT: F 207 MET cc_start: 0.1406 (mmp) cc_final: 0.0745 (ttp) REVERT: F 345 ASP cc_start: 0.7963 (t0) cc_final: 0.6800 (t70) REVERT: F 348 MET cc_start: 0.8428 (mmp) cc_final: 0.7662 (tpp) REVERT: F 349 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8755 (mm-40) REVERT: F 405 ASP cc_start: 0.8808 (m-30) cc_final: 0.8342 (t0) REVERT: F 406 PHE cc_start: 0.9181 (m-80) cc_final: 0.8953 (m-80) REVERT: F 408 LYS cc_start: 0.9077 (mttp) cc_final: 0.8874 (mmtt) REVERT: F 421 ASP cc_start: 0.8724 (m-30) cc_final: 0.8225 (t70) REVERT: G 287 MET cc_start: 0.9200 (ppp) cc_final: 0.8817 (mtm) REVERT: H 302 TYR cc_start: 0.4797 (m-10) cc_final: 0.4563 (m-10) REVERT: I 289 ARG cc_start: 0.7573 (mtp85) cc_final: 0.7184 (mmm160) REVERT: M 298 LYS cc_start: 0.7036 (mtmm) cc_final: 0.6809 (tppt) REVERT: M 326 LEU cc_start: 0.7933 (mp) cc_final: 0.7719 (mp) REVERT: N 318 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7266 (mt-10) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.3353 time to fit residues: 218.9700 Evaluate side-chains 348 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 128 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 203 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 136 optimal weight: 0.0570 chunk 107 optimal weight: 3.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 ASN D 265 ASN E 265 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.9143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18299 Z= 0.201 Angle : 0.705 17.305 24758 Z= 0.356 Chirality : 0.045 0.305 2846 Planarity : 0.005 0.065 3173 Dihedral : 9.972 87.810 2616 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.07 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2270 helix: 1.03 (0.15), residues: 1170 sheet: 0.33 (0.33), residues: 233 loop : -0.53 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 206 HIS 0.003 0.001 HIS D 359 PHE 0.022 0.002 PHE A 230 TYR 0.017 0.001 TYR A 172 ARG 0.015 0.001 ARG B 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4540 Ramachandran restraints generated. 2270 Oldfield, 0 Emsley, 2270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6902 (p90) cc_final: 0.6011 (p90) REVERT: A 339 ILE cc_start: 0.8137 (pt) cc_final: 0.7630 (pt) REVERT: A 405 ASP cc_start: 0.8434 (m-30) cc_final: 0.8033 (t0) REVERT: B 195 PHE cc_start: 0.8841 (m-10) cc_final: 0.8431 (m-10) REVERT: B 207 MET cc_start: 0.2555 (ptm) cc_final: 0.2175 (ptm) REVERT: B 259 GLN cc_start: 0.8747 (tp40) cc_final: 0.8131 (tt0) REVERT: B 278 ILE cc_start: 0.8515 (mt) cc_final: 0.8202 (tt) REVERT: B 307 MET cc_start: 0.8852 (mmp) cc_final: 0.8646 (mmt) REVERT: B 308 PHE cc_start: 0.8566 (m-80) cc_final: 0.7978 (m-80) REVERT: B 327 LEU cc_start: 0.9249 (mm) cc_final: 0.9003 (tt) REVERT: B 426 GLU cc_start: 0.8932 (tm-30) cc_final: 0.8710 (tm-30) REVERT: C 146 LYS cc_start: 0.9259 (mmtt) cc_final: 0.8921 (mmmm) REVERT: C 162 ASN cc_start: 0.8780 (m-40) cc_final: 0.8380 (p0) REVERT: C 170 LEU cc_start: 0.8629 (tp) cc_final: 0.8383 (tp) REVERT: C 181 TYR cc_start: 0.8726 (t80) cc_final: 0.8333 (t80) REVERT: C 196 SER cc_start: 0.9058 (p) cc_final: 0.8764 (t) REVERT: C 233 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8578 (mm-40) REVERT: C 293 ARG cc_start: 0.9481 (ttm-80) cc_final: 0.8678 (ttm-80) REVERT: C 324 TYR cc_start: 0.7469 (m-10) cc_final: 0.7068 (m-10) REVERT: C 405 ASP cc_start: 0.8525 (m-30) cc_final: 0.8262 (m-30) REVERT: C 408 LYS cc_start: 0.8953 (mttp) cc_final: 0.8713 (mmmt) REVERT: D 135 VAL cc_start: 0.8686 (t) cc_final: 0.8182 (m) REVERT: D 181 TYR cc_start: 0.8631 (t80) cc_final: 0.7660 (t80) REVERT: D 211 GLU cc_start: 0.8150 (pp20) cc_final: 0.7845 (pp20) REVERT: D 259 GLN cc_start: 0.8286 (tp40) cc_final: 0.7614 (tp40) REVERT: E 181 TYR cc_start: 0.7596 (t80) cc_final: 0.7179 (t80) REVERT: E 216 GLN cc_start: 0.8138 (mt0) cc_final: 0.7463 (pt0) REVERT: E 220 MET cc_start: 0.9077 (mmp) cc_final: 0.8851 (mmm) REVERT: E 261 ASN cc_start: 0.6821 (t0) cc_final: 0.6041 (p0) REVERT: E 281 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8708 (tm-30) REVERT: E 290 PHE cc_start: 0.7547 (t80) cc_final: 0.7290 (t80) REVERT: E 292 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.7987 (mmm160) REVERT: E 321 LYS cc_start: 0.8650 (mmpt) cc_final: 0.8314 (mttp) REVERT: E 324 TYR cc_start: 0.8580 (m-10) cc_final: 0.8335 (m-80) REVERT: E 349 GLN cc_start: 0.9212 (mm110) cc_final: 0.8529 (mt0) REVERT: E 386 MET cc_start: 0.8231 (pmm) cc_final: 0.7837 (pmm) REVERT: E 405 ASP cc_start: 0.9451 (m-30) cc_final: 0.9251 (m-30) REVERT: E 406 PHE cc_start: 0.9304 (m-80) cc_final: 0.9052 (m-80) REVERT: E 425 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8570 (mt0) REVERT: F 126 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7240 (tm-30) REVERT: F 195 PHE cc_start: 0.8281 (m-80) cc_final: 0.8021 (m-80) REVERT: F 207 MET cc_start: 0.1303 (mmp) cc_final: 0.0698 (ttp) REVERT: F 222 ARG cc_start: 0.8469 (mtt180) cc_final: 0.7855 (mmm160) REVERT: F 345 ASP cc_start: 0.7964 (t0) cc_final: 0.7600 (t70) REVERT: F 348 MET cc_start: 0.8364 (mmp) cc_final: 0.7525 (tpp) REVERT: F 351 ILE cc_start: 0.8835 (mp) cc_final: 0.8141 (mp) REVERT: F 386 MET cc_start: 0.6551 (pmm) cc_final: 0.6243 (pmm) REVERT: F 405 ASP cc_start: 0.8843 (m-30) cc_final: 0.8514 (t0) REVERT: F 406 PHE cc_start: 0.9225 (m-80) cc_final: 0.9006 (m-80) REVERT: F 408 LYS cc_start: 0.9077 (mttp) cc_final: 0.8826 (mmtt) REVERT: F 421 ASP cc_start: 0.8707 (m-30) cc_final: 0.8199 (t70) REVERT: G 287 MET cc_start: 0.9208 (ppp) cc_final: 0.8901 (mtm) REVERT: G 294 GLU cc_start: 0.7042 (pp20) cc_final: 0.6804 (pp20) REVERT: H 302 TYR cc_start: 0.4754 (m-10) cc_final: 0.4543 (m-10) REVERT: M 298 LYS cc_start: 0.6981 (mtmm) cc_final: 0.6759 (tppt) REVERT: N 301 LYS cc_start: 0.7929 (mmmt) cc_final: 0.7611 (mtmm) REVERT: N 318 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6983 (mt-10) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.3162 time to fit residues: 205.8979 Evaluate side-chains 361 residues out of total 1968 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 361 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 139 optimal weight: 9.9990 chunk 187 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 224 ASN ** B 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 ASN ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.118173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.096808 restraints weight = 67513.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.097121 restraints weight = 53084.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.097079 restraints weight = 40822.730| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.9729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 18299 Z= 0.379 Angle : 0.846 17.603 24758 Z= 0.432 Chirality : 0.048 0.328 2846 Planarity : 0.006 0.081 3173 Dihedral : 10.590 87.160 2616 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 29.81 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.18 % Favored : 92.51 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2270 helix: 0.38 (0.15), residues: 1167 sheet: -0.01 (0.32), residues: 250 loop : -0.91 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 206 HIS 0.005 0.001 HIS D 359 PHE 0.033 0.003 PHE C 290 TYR 0.026 0.002 TYR B 324 ARG 0.014 0.001 ARG B 250 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4641.36 seconds wall clock time: 84 minutes 58.94 seconds (5098.94 seconds total)