Starting phenix.real_space_refine on Tue Nov 18 22:46:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5xmk_6734/11_2025/5xmk_6734.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xmk_6734/11_2025/5xmk_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 { model { file = "/net/cci-nas-00/data/ceres_data/5xmk_6734/11_2025/5xmk_6734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xmk_6734/11_2025/5xmk_6734.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5xmk_6734/11_2025/5xmk_6734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xmk_6734/11_2025/5xmk_6734.map" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 4.71, per 1000 atoms: 0.26 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 782.1 milliseconds 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... Secondary structure from input PDB file: 117 helices and 12 sheets defined 60.8% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 138 through 149 Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 156 through 159 Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 207 through 223 removed outlier: 3.971A pdb=" N GLU A 211 " --> pdb=" O MET A 207 " (cutoff:3.500A) 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 233 through 238 Processing helix chain 'A' and resid 243 through 263 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) removed outlier: 4.103A pdb=" N VAL A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 283 through 289 Processing helix chain 'A' and resid 300 through 311 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 335 through 357 Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.660A pdb=" N PHE A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 432 removed outlier: 3.573A pdb=" N LEU A 422 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 135 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 156 through 160 removed outlier: 4.009A pdb=" N LYS B 160 " --> pdb=" O HIS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 4.381A pdb=" N ASN B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 223 removed outlier: 4.062A pdb=" N VAL B 214 " --> pdb=" O SER B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.515A pdb=" N SER B 246 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU B 247 " --> pdb=" O GLY B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 247' Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 283 through 288 Processing helix chain 'B' and resid 300 through 311 Processing helix chain 'B' and resid 321 through 331 Processing helix chain 'B' and resid 335 through 357 Proline residue: B 350 - end of helix Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 402 through 413 removed outlier: 3.718A pdb=" N PHE B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 432 removed outlier: 3.596A pdb=" N LEU B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 135 Processing helix chain 'C' and resid 139 through 155 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 160 removed outlier: 3.984A pdb=" N LYS C 160 " --> pdb=" O HIS C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 removed outlier: 4.501A pdb=" N ASN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 224 removed outlier: 4.177A pdb=" N LYS C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 248 through 260 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.584A pdb=" N GLN C 281 " --> pdb=" O ILE C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 removed outlier: 3.870A pdb=" N ARG C 287 " --> pdb=" O ASP C 283 " (cutoff:3.500A) 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) Processing helix chain 'C' and resid 300 through 313 removed outlier: 3.847A pdb=" N GLY C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 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 335 through 348 Processing helix chain 'C' and resid 348 through 357 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 402 through 413 removed outlier: 3.659A pdb=" N PHE C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 432 removed outlier: 4.039A pdb=" N LEU C 422 " --> pdb=" O ASN C 418 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS C 424 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 135 Processing helix chain 'D' and resid 138 through 149 Processing helix chain 'D' and resid 149 through 155 Processing helix chain 'D' and resid 156 through 160 removed outlier: 4.064A pdb=" N LYS D 160 " --> pdb=" O HIS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.561A pdb=" N LYS D 212 " --> pdb=" O GLY D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 243 through 248 removed outlier: 3.674A pdb=" N GLU D 247 " --> pdb=" O GLU D 243 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 248' Processing helix chain 'D' and resid 248 through 265 removed outlier: 4.013A pdb=" N VAL D 263 " --> pdb=" O GLN D 259 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 265 " --> pdb=" O ASN D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.818A pdb=" N GLN D 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'D' and resid 300 through 311 removed outlier: 3.603A pdb=" N ASN D 311 " --> pdb=" O MET D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 331 Processing helix chain 'D' and resid 335 through 357 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 402 through 413 removed outlier: 3.669A pdb=" N PHE D 406 " --> pdb=" O THR D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 149 through 155 Processing helix chain 'E' and resid 156 through 160 removed outlier: 3.657A pdb=" N LYS E 160 " --> pdb=" O HIS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 191 removed outlier: 3.880A pdb=" N ASN E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 224 removed outlier: 4.036A pdb=" N VAL E 214 " --> pdb=" O SER E 210 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN E 224 " --> pdb=" O MET E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 247 through 265 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) removed outlier: 3.503A pdb=" N ASN E 265 " --> pdb=" O ASN E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 300 through 311 Processing helix chain 'E' and resid 321 through 331 Processing helix chain 'E' and resid 335 through 348 Processing helix chain 'E' and resid 348 through 357 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 402 through 413 removed outlier: 3.876A pdb=" N PHE E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 432 removed outlier: 4.581A pdb=" N LEU E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) 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 131 through 135 Processing helix chain 'F' and resid 138 through 149 Processing helix chain 'F' and resid 149 through 155 Processing helix chain 'F' and resid 156 through 160 removed outlier: 3.538A pdb=" N LYS F 160 " --> pdb=" O HIS F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 191 removed outlier: 4.227A pdb=" N ASN F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 224 Processing helix chain 'F' and resid 234 through 237 Processing helix chain 'F' and resid 247 through 265 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 278 through 282 Processing helix chain 'F' and resid 283 through 290 Processing helix chain 'F' and resid 300 through 313 Processing helix chain 'F' and resid 321 through 331 Processing helix chain 'F' and resid 335 through 356 Proline residue: F 350 - end of helix Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 402 through 412 removed outlier: 3.696A pdb=" N PHE F 406 " --> pdb=" O THR F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 432 removed outlier: 3.803A pdb=" N LEU F 422 " --> pdb=" O ASN F 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 309 removed outlier: 4.430A pdb=" N LYS G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 329 removed outlier: 4.252A pdb=" N ILE G 329 " --> pdb=" O LEU G 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 290 through 309 Processing helix chain 'H' and resid 311 through 329 Processing helix chain 'I' and resid 279 through 308 removed outlier: 4.047A pdb=" N LYS I 285 " --> pdb=" O ASP I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 328 Processing helix chain 'J' and resid 290 through 309 Processing helix chain 'J' and resid 311 through 329 Processing helix chain 'K' and resid 281 through 309 removed outlier: 3.982A pdb=" N LYS K 285 " --> pdb=" O ASP K 281 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR K 309 " --> pdb=" O SER K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 329 Processing helix chain 'L' and resid 290 through 309 Processing helix chain 'L' and resid 311 through 329 Processing helix chain 'M' and resid 280 through 309 Processing helix chain 'M' and resid 311 through 329 Processing helix chain 'N' and resid 290 through 309 Processing helix chain 'N' and resid 311 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.510A pdb=" N THR A 193 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N PHE A 230 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE A 195 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP A 232 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 197 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 375 Processing sheet with id=AA3, first strand: chain 'B' and resid 193 through 198 Processing sheet with id=AA4, first strand: chain 'B' and resid 360 through 362 Processing sheet with id=AA5, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.636A pdb=" N ASP C 232 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 169 " --> pdb=" O GLY C 274 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N THR C 276 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU C 171 " --> pdb=" O THR C 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AA7, first strand: chain 'D' and resid 193 through 197 removed outlier: 6.470A pdb=" N ILE D 169 " --> pdb=" O GLY D 274 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR D 276 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU D 171 " --> pdb=" O THR D 276 " (cutoff:3.500A) 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) Processing sheet with id=AA8, first strand: chain 'D' and resid 360 through 362 Processing sheet with id=AA9, first strand: chain 'E' and resid 194 through 198 removed outlier: 6.591A pdb=" N ILE E 169 " --> pdb=" O GLY E 274 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N THR E 276 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU E 171 " --> pdb=" O THR E 276 " (cutoff:3.500A) 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) Processing sheet with id=AB1, first strand: chain 'E' and resid 360 through 362 Processing sheet with id=AB2, first strand: chain 'F' and resid 193 through 198 removed outlier: 6.508A pdb=" N ILE F 169 " --> pdb=" O GLY F 274 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N THR F 276 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU F 171 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU F 170 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 373 through 375 977 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.05 Time building geometry restraints manager: 2.17 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: 0.00 - 3.86: 24208 3.86 - 7.72: 502 7.72 - 11.59: 33 11.59 - 15.45: 5 15.45 - 19.31: 10 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: 1419 2.76 - 3.30: 19501 3.30 - 3.83: 29779 3.83 - 4.37: 36105 4.37 - 4.90: 57343 Nonbonded interactions: 144147 Sorted by model distance: nonbonded pdb=" O ASN C 277 " pdb=" NE2 GLN C 425 " model vdw 2.230 3.120 nonbonded pdb=" OD2 ASP A 338 " pdb=" OG1 THR A 416 " model vdw 2.273 3.040 nonbonded pdb=" OG SER B 192 " pdb=" O PRO B 226 " model vdw 2.292 3.040 nonbonded pdb=" O ASN A 277 " pdb=" NE2 GLN A 425 " model vdw 2.317 3.120 nonbonded pdb=" N SER F 167 " pdb=" OE1 GLU F 291 " model vdw 2.331 3.120 ... (remaining 144142 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.880 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.610 ------------------------------------------------------------------------------- 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= 0.755 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.027 0.001 ARG F 304 TYR 0.024 0.004 TYR H 302 PHE 0.026 0.005 PHE A 230 TRP 0.025 0.006 TRP D 132 HIS 0.022 0.005 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.01032 (18299) covalent geometry : angle 1.54731 (24758) hydrogen bonds : bond 0.13817 ( 977) hydrogen bonds : angle 6.17715 ( 2748) *********************** 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 to be fit. rotamer outliers: 23 poor density : 894 time to evaluate : 0.782 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: 0.1877 time to fit residues: 236.5233 Evaluate side-chains 461 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 455 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.0030 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 7.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN ** C 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN D 355 GLN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN E 265 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN N 297 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.132115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.108731 restraints weight = 67764.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.110890 restraints weight = 48174.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.112273 restraints weight = 37372.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.113362 restraints weight = 31123.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.113907 restraints weight = 27380.308| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 18299 Z= 0.163 Angle : 0.766 15.189 24758 Z= 0.388 Chirality : 0.045 0.270 2846 Planarity : 0.006 0.075 3173 Dihedral : 10.752 87.416 2616 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.67 % Favored : 94.85 % Rotamer: Outliers : 0.15 % Allowed : 3.76 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2270 helix: 1.33 (0.15), residues: 1211 sheet: 0.30 (0.29), residues: 260 loop : -0.74 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 289 TYR 0.015 0.002 TYR D 181 PHE 0.025 0.002 PHE B 308 TRP 0.018 0.002 TRP E 206 HIS 0.002 0.001 HIS E 359 Details of bonding type rmsd covalent geometry : bond 0.00354 (18299) covalent geometry : angle 0.76589 (24758) hydrogen bonds : bond 0.03659 ( 977) hydrogen bonds : angle 4.38697 ( 2748) *********************** 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 575 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 572 time to evaluate : 0.739 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: A 155 PHE cc_start: 0.7199 (m-80) cc_final: 0.6942 (m-80) REVERT: A 212 LYS cc_start: 0.8280 (tttm) cc_final: 0.8011 (ttpp) REVERT: A 217 LEU cc_start: 0.8964 (tp) cc_final: 0.8706 (tp) REVERT: A 305 THR cc_start: 0.8632 (m) cc_final: 0.8398 (p) REVERT: A 308 PHE cc_start: 0.6561 (m-10) cc_final: 0.5634 (m-10) REVERT: A 349 GLN cc_start: 0.8742 (tp-100) cc_final: 0.8217 (tt0) REVERT: A 361 LYS cc_start: 0.9193 (tttt) cc_final: 0.8887 (tptt) REVERT: A 405 ASP cc_start: 0.8160 (m-30) cc_final: 0.7684 (m-30) REVERT: A 422 LEU cc_start: 0.7964 (tt) cc_final: 0.7443 (tt) REVERT: A 428 PHE cc_start: 0.7536 (t80) cc_final: 0.7277 (t80) REVERT: B 268 GLN cc_start: 0.7217 (tp-100) cc_final: 0.6045 (tp40) REVERT: B 326 THR cc_start: 0.8281 (m) cc_final: 0.8060 (p) REVERT: B 330 MET cc_start: 0.7663 (ppp) cc_final: 0.7403 (ppp) REVERT: C 181 TYR cc_start: 0.7689 (t80) cc_final: 0.7302 (t80) REVERT: C 232 ASP cc_start: 0.6540 (t70) cc_final: 0.5472 (t70) REVERT: C 278 ILE cc_start: 0.8270 (mt) cc_final: 0.8038 (mt) REVERT: C 349 GLN cc_start: 0.9200 (mm110) cc_final: 0.8869 (mm110) REVERT: C 353 LYS cc_start: 0.9254 (mmtt) cc_final: 0.8999 (mmmt) REVERT: D 211 GLU cc_start: 0.8140 (pp20) cc_final: 0.7847 (pp20) REVERT: E 133 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6989 (tt0) REVERT: E 177 THR cc_start: 0.8585 (p) cc_final: 0.8292 (p) REVERT: E 207 MET cc_start: 0.0629 (mtt) cc_final: 0.0379 (mtp) REVERT: E 211 GLU cc_start: 0.7719 (mp0) cc_final: 0.7446 (mp0) REVERT: E 324 TYR cc_start: 0.7795 (m-10) cc_final: 0.7499 (m-80) REVERT: E 405 ASP cc_start: 0.7557 (m-30) cc_final: 0.5921 (m-30) REVERT: E 424 LYS cc_start: 0.8495 (mttp) cc_final: 0.8199 (mtmm) REVERT: F 251 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7466 (mtm180) REVERT: G 319 LEU cc_start: 0.8214 (mt) cc_final: 0.7991 (mt) REVERT: H 318 GLU cc_start: 0.6004 (mp0) cc_final: 0.5697 (mp0) REVERT: I 325 LEU cc_start: 0.8013 (tp) cc_final: 0.7597 (tp) REVERT: J 298 LYS cc_start: 0.7498 (mmtt) cc_final: 0.7250 (mmmm) REVERT: K 288 ASP cc_start: 0.7479 (m-30) cc_final: 0.6924 (m-30) REVERT: K 295 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7323 (tm-30) REVERT: M 323 LEU cc_start: 0.7709 (tp) cc_final: 0.7448 (mt) REVERT: N 298 LYS cc_start: 0.7594 (tptt) cc_final: 0.7306 (ttpp) outliers start: 3 outliers final: 1 residues processed: 573 average time/residue: 0.1679 time to fit residues: 137.4074 Evaluate side-chains 404 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 403 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 81 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 209 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 205 optimal weight: 30.0000 chunk 191 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 174 optimal weight: 1.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 216 GLN B 259 GLN B 261 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN E 355 GLN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN F 281 GLN F 359 HIS G 295 GLN K 297 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.126233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.102275 restraints weight = 68609.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.104206 restraints weight = 48144.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.105609 restraints weight = 37386.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.106357 restraints weight = 31116.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.107099 restraints weight = 27771.300| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 18299 Z= 0.204 Angle : 0.774 15.767 24758 Z= 0.394 Chirality : 0.045 0.240 2846 Planarity : 0.005 0.079 3173 Dihedral : 10.474 85.782 2616 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.73 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.18), residues: 2270 helix: 1.16 (0.15), residues: 1210 sheet: 0.47 (0.31), residues: 258 loop : -0.70 (0.23), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 289 TYR 0.036 0.002 TYR I 302 PHE 0.030 0.003 PHE A 230 TRP 0.017 0.002 TRP A 132 HIS 0.003 0.001 HIS C 359 Details of bonding type rmsd covalent geometry : bond 0.00456 (18299) covalent geometry : angle 0.77365 (24758) hydrogen bonds : bond 0.03595 ( 977) hydrogen bonds : angle 4.52121 ( 2748) *********************** 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 509 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.741 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: A 220 MET cc_start: 0.7772 (mmp) cc_final: 0.7416 (mmm) REVERT: A 305 THR cc_start: 0.8415 (m) cc_final: 0.8077 (p) REVERT: A 349 GLN cc_start: 0.8829 (tp-100) cc_final: 0.8150 (tt0) REVERT: A 374 THR cc_start: 0.8470 (t) cc_final: 0.8045 (t) REVERT: B 146 LYS cc_start: 0.8171 (mtmm) cc_final: 0.7952 (ptpt) REVERT: B 150 ILE cc_start: 0.8093 (mp) cc_final: 0.7783 (mm) REVERT: B 215 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8511 (mmmm) REVERT: B 268 GLN cc_start: 0.7318 (tp-100) cc_final: 0.6488 (tp40) REVERT: B 295 TYR cc_start: 0.8934 (t80) cc_final: 0.8650 (t80) REVERT: B 327 LEU cc_start: 0.9073 (mm) cc_final: 0.8742 (mm) REVERT: C 181 TYR cc_start: 0.7950 (t80) cc_final: 0.7417 (t80) REVERT: C 278 ILE cc_start: 0.8420 (mt) cc_final: 0.8081 (mt) REVERT: D 211 GLU cc_start: 0.7960 (pp20) cc_final: 0.7449 (pp20) REVERT: D 292 ARG cc_start: 0.7904 (mmm160) cc_final: 0.7438 (mmp80) REVERT: D 321 LYS cc_start: 0.8350 (mmtm) cc_final: 0.7927 (mmtp) REVERT: E 181 TYR cc_start: 0.6795 (t80) cc_final: 0.6356 (t80) REVERT: E 207 MET cc_start: 0.0663 (mtt) cc_final: 0.0236 (mtp) REVERT: E 233 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8245 (mm110) REVERT: E 251 ARG cc_start: 0.8174 (ptp-170) cc_final: 0.7682 (ptp-170) REVERT: E 254 THR cc_start: 0.8147 (p) cc_final: 0.7439 (p) REVERT: E 292 ARG cc_start: 0.8474 (mmm160) cc_final: 0.8231 (mmm160) REVERT: E 324 TYR cc_start: 0.7935 (m-10) cc_final: 0.7673 (m-80) REVERT: E 386 MET cc_start: 0.8174 (pmm) cc_final: 0.7686 (pmm) REVERT: F 143 GLU cc_start: 0.6674 (tp30) cc_final: 0.6183 (tp30) REVERT: F 251 ARG cc_start: 0.7862 (ptm160) cc_final: 0.7532 (mtm-85) REVERT: G 319 LEU cc_start: 0.8362 (mt) cc_final: 0.8156 (mt) REVERT: H 295 GLN cc_start: 0.5883 (tt0) cc_final: 0.5139 (tp40) REVERT: I 298 LYS cc_start: 0.8818 (tptt) cc_final: 0.7953 (tptt) REVERT: I 302 TYR cc_start: 0.7742 (m-80) cc_final: 0.7154 (m-80) REVERT: I 325 LEU cc_start: 0.7997 (tp) cc_final: 0.7518 (tt) REVERT: J 317 ASP cc_start: 0.8199 (t0) cc_final: 0.7977 (t0) REVERT: L 317 ASP cc_start: 0.6452 (m-30) cc_final: 0.6091 (m-30) REVERT: M 323 LEU cc_start: 0.7930 (tp) cc_final: 0.7710 (mt) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.1620 time to fit residues: 119.1551 Evaluate side-chains 365 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 365 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 219 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 155 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 221 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 355 GLN B 259 GLN B 261 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 355 GLN ** C 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 GLN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN F 355 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.120108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.095785 restraints weight = 70583.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.097741 restraints weight = 49216.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.099081 restraints weight = 38027.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.099862 restraints weight = 31758.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.100501 restraints weight = 28254.938| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.7575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 18299 Z= 0.296 Angle : 0.880 16.872 24758 Z= 0.449 Chirality : 0.049 0.324 2846 Planarity : 0.006 0.101 3173 Dihedral : 10.776 89.326 2616 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.56 % Favored : 93.00 % Rotamer: Outliers : 0.10 % Allowed : 4.57 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.17), residues: 2270 helix: 0.38 (0.14), residues: 1219 sheet: 0.01 (0.31), residues: 267 loop : -0.91 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 293 TYR 0.024 0.003 TYR N 302 PHE 0.033 0.003 PHE D 290 TRP 0.018 0.003 TRP F 206 HIS 0.006 0.002 HIS E 157 Details of bonding type rmsd covalent geometry : bond 0.00650 (18299) covalent geometry : angle 0.87983 (24758) hydrogen bonds : bond 0.04134 ( 977) hydrogen bonds : angle 5.02435 ( 2748) *********************** 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 471 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 469 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6185 (p90) cc_final: 0.5456 (p90) REVERT: A 220 MET cc_start: 0.7781 (mmp) cc_final: 0.7571 (mmp) REVERT: A 250 ARG cc_start: 0.5969 (mmt180) cc_final: 0.5756 (mmt90) REVERT: A 305 THR cc_start: 0.8586 (m) cc_final: 0.8189 (p) REVERT: A 308 PHE cc_start: 0.6669 (m-10) cc_final: 0.6242 (m-10) REVERT: A 405 ASP cc_start: 0.7417 (t0) cc_final: 0.6416 (t70) REVERT: A 422 LEU cc_start: 0.8202 (tt) cc_final: 0.7606 (tt) REVERT: B 150 ILE cc_start: 0.8445 (mp) cc_final: 0.8204 (mm) REVERT: B 230 PHE cc_start: 0.7611 (t80) cc_final: 0.7365 (t80) REVERT: B 268 GLN cc_start: 0.7426 (tp-100) cc_final: 0.6527 (tp40) REVERT: B 295 TYR cc_start: 0.9067 (t80) cc_final: 0.8849 (t80) REVERT: B 327 LEU cc_start: 0.9175 (mm) cc_final: 0.8703 (mm) REVERT: C 181 TYR cc_start: 0.8240 (t80) cc_final: 0.7919 (t80) REVERT: C 278 ILE cc_start: 0.8633 (mt) cc_final: 0.8103 (mt) REVERT: D 211 GLU cc_start: 0.8200 (pp20) cc_final: 0.7780 (pp20) REVERT: D 380 ASP cc_start: 0.6733 (t0) cc_final: 0.6517 (m-30) REVERT: E 207 MET cc_start: 0.1041 (mtt) cc_final: 0.0776 (mtp) REVERT: E 386 MET cc_start: 0.8134 (pmm) cc_final: 0.7611 (pmm) REVERT: F 143 GLU cc_start: 0.7109 (tp30) cc_final: 0.6674 (tp30) REVERT: F 220 MET cc_start: 0.8130 (ptm) cc_final: 0.7905 (ttm) REVERT: F 222 ARG cc_start: 0.8134 (mmt180) cc_final: 0.7933 (mmt-90) REVERT: F 255 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7845 (tm-30) REVERT: G 319 LEU cc_start: 0.8286 (mt) cc_final: 0.8078 (mt) REVERT: H 318 GLU cc_start: 0.6332 (mp0) cc_final: 0.6067 (mp0) REVERT: I 325 LEU cc_start: 0.8277 (tp) cc_final: 0.7850 (tt) REVERT: L 317 ASP cc_start: 0.6556 (m-30) cc_final: 0.6355 (m-30) REVERT: L 326 LEU cc_start: 0.6367 (mt) cc_final: 0.5732 (tp) REVERT: M 323 LEU cc_start: 0.7903 (tp) cc_final: 0.7673 (mt) outliers start: 2 outliers final: 1 residues processed: 469 average time/residue: 0.1516 time to fit residues: 104.7427 Evaluate side-chains 322 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 321 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 14 optimal weight: 2.9990 chunk 116 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 186 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 122 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN B 261 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN F 277 ASN G 295 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.125319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.101411 restraints weight = 67682.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.103452 restraints weight = 47435.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.104879 restraints weight = 36696.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.105811 restraints weight = 30487.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.106337 restraints weight = 26901.798| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.7756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18299 Z= 0.148 Angle : 0.733 17.069 24758 Z= 0.375 Chirality : 0.046 0.282 2846 Planarity : 0.005 0.075 3173 Dihedral : 10.274 87.481 2616 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.46 % Favored : 94.23 % Rotamer: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.18), residues: 2270 helix: 0.82 (0.15), residues: 1213 sheet: 0.18 (0.32), residues: 256 loop : -0.71 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 289 TYR 0.012 0.002 TYR D 324 PHE 0.026 0.002 PHE A 230 TRP 0.015 0.001 TRP E 206 HIS 0.003 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00328 (18299) covalent geometry : angle 0.73308 (24758) hydrogen bonds : bond 0.03316 ( 977) hydrogen bonds : angle 4.49092 ( 2748) *********************** 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 498 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 497 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.7713 (mmp) cc_final: 0.7497 (mmp) REVERT: A 271 LEU cc_start: 0.8440 (mm) cc_final: 0.8124 (mm) REVERT: A 305 THR cc_start: 0.8530 (m) cc_final: 0.8095 (p) REVERT: A 307 MET cc_start: 0.7581 (ppp) cc_final: 0.7190 (ppp) REVERT: A 391 ILE cc_start: 0.7632 (tp) cc_final: 0.7377 (mm) REVERT: A 435 GLU cc_start: 0.4853 (mp0) cc_final: 0.4436 (mt-10) REVERT: B 150 ILE cc_start: 0.8341 (mp) cc_final: 0.8045 (mm) REVERT: B 281 GLN cc_start: 0.7887 (tp40) cc_final: 0.7479 (tt0) REVERT: B 295 TYR cc_start: 0.8985 (t80) cc_final: 0.8762 (t80) REVERT: C 181 TYR cc_start: 0.7863 (t80) cc_final: 0.7563 (t80) REVERT: C 271 LEU cc_start: 0.7884 (tp) cc_final: 0.7055 (tt) REVERT: C 307 MET cc_start: 0.8335 (ptt) cc_final: 0.7990 (ptm) REVERT: C 337 SER cc_start: 0.6155 (m) cc_final: 0.5417 (p) REVERT: D 211 GLU cc_start: 0.7960 (pp20) cc_final: 0.7503 (pp20) REVERT: D 325 ARG cc_start: 0.8206 (ptp90) cc_final: 0.7907 (mtm180) REVERT: E 170 LEU cc_start: 0.8149 (tp) cc_final: 0.7933 (tp) REVERT: E 207 MET cc_start: 0.1168 (mtt) cc_final: 0.0050 (mtm) REVERT: E 233 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8350 (mm110) REVERT: E 255 GLU cc_start: 0.7183 (mp0) cc_final: 0.6776 (mp0) REVERT: E 306 THR cc_start: 0.8677 (t) cc_final: 0.6906 (t) REVERT: E 386 MET cc_start: 0.8357 (pmm) cc_final: 0.7807 (pmm) REVERT: E 405 ASP cc_start: 0.8250 (m-30) cc_final: 0.7351 (m-30) REVERT: F 220 MET cc_start: 0.8049 (ptm) cc_final: 0.7641 (ttm) REVERT: F 330 MET cc_start: 0.8279 (mmp) cc_final: 0.8074 (mmm) REVERT: G 319 LEU cc_start: 0.8155 (mt) cc_final: 0.7943 (mt) REVERT: K 311 ASP cc_start: 0.8201 (m-30) cc_final: 0.7953 (t0) REVERT: L 302 TYR cc_start: 0.8190 (m-10) cc_final: 0.7892 (m-10) REVERT: L 326 LEU cc_start: 0.6508 (mt) cc_final: 0.5866 (tp) REVERT: M 323 LEU cc_start: 0.8068 (tp) cc_final: 0.7791 (mt) outliers start: 1 outliers final: 0 residues processed: 498 average time/residue: 0.1515 time to fit residues: 110.9193 Evaluate side-chains 349 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 55 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 164 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 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 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN D 359 HIS ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN F 277 ASN G 295 GLN ** I 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.119665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096952 restraints weight = 67670.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.097098 restraints weight = 53530.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.097952 restraints weight = 41405.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.098499 restraints weight = 36693.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.098617 restraints weight = 32354.257| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.8588 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= 0.263 Angle : 0.853 17.271 24758 Z= 0.438 Chirality : 0.048 0.315 2846 Planarity : 0.006 0.086 3173 Dihedral : 10.787 85.936 2616 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 23.25 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.43 % Favored : 93.22 % Rotamer: Outliers : 0.05 % Allowed : 2.90 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2270 helix: 0.35 (0.15), residues: 1209 sheet: -0.14 (0.31), residues: 261 loop : -0.90 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 293 TYR 0.027 0.003 TYR A 172 PHE 0.047 0.003 PHE D 290 TRP 0.016 0.002 TRP F 206 HIS 0.008 0.002 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00585 (18299) covalent geometry : angle 0.85310 (24758) hydrogen bonds : bond 0.03983 ( 977) hydrogen bonds : angle 4.99590 ( 2748) *********************** 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 429 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 428 time to evaluate : 0.776 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: A 220 MET cc_start: 0.7673 (mmp) cc_final: 0.7410 (mmp) REVERT: A 247 GLU cc_start: 0.7068 (pt0) cc_final: 0.6443 (pt0) REVERT: A 250 ARG cc_start: 0.6204 (mmt180) cc_final: 0.5879 (mmt90) REVERT: A 305 THR cc_start: 0.8544 (m) cc_final: 0.8199 (p) REVERT: A 307 MET cc_start: 0.7669 (ppp) cc_final: 0.7320 (ppp) REVERT: A 422 LEU cc_start: 0.8260 (tt) cc_final: 0.7717 (tt) REVERT: A 425 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7549 (mp10) REVERT: A 435 GLU cc_start: 0.5068 (mp0) cc_final: 0.4579 (mt-10) REVERT: B 233 GLN cc_start: 0.7692 (mp-120) cc_final: 0.7479 (mp10) REVERT: B 295 TYR cc_start: 0.9035 (t80) cc_final: 0.8786 (t80) REVERT: C 181 TYR cc_start: 0.8774 (t80) cc_final: 0.8428 (t80) REVERT: C 201 ASP cc_start: 0.7202 (t0) cc_final: 0.6997 (t0) REVERT: D 202 LEU cc_start: 0.8795 (mp) cc_final: 0.8530 (tt) REVERT: D 211 GLU cc_start: 0.8226 (pp20) cc_final: 0.7840 (pp20) REVERT: D 343 VAL cc_start: 0.9139 (t) cc_final: 0.8803 (p) REVERT: E 207 MET cc_start: 0.0816 (mtt) cc_final: -0.0231 (mtm) REVERT: E 233 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8311 (mm-40) REVERT: E 306 THR cc_start: 0.8591 (t) cc_final: 0.7996 (t) REVERT: E 307 MET cc_start: 0.8304 (tpp) cc_final: 0.7905 (mmt) REVERT: E 386 MET cc_start: 0.8196 (pmm) cc_final: 0.7951 (pmm) REVERT: F 215 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8544 (pttm) REVERT: F 216 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8130 (mm-40) REVERT: F 220 MET cc_start: 0.8210 (ptm) cc_final: 0.7976 (ttm) REVERT: F 307 MET cc_start: 0.8950 (ptm) cc_final: 0.8572 (ppp) REVERT: F 330 MET cc_start: 0.8550 (mmp) cc_final: 0.8234 (mmm) REVERT: F 348 MET cc_start: 0.7378 (mmp) cc_final: 0.6928 (tpp) REVERT: G 319 LEU cc_start: 0.8243 (mt) cc_final: 0.8012 (mt) REVERT: H 302 TYR cc_start: 0.4917 (m-10) cc_final: 0.4685 (t80) REVERT: L 326 LEU cc_start: 0.6431 (mt) cc_final: 0.5630 (tp) REVERT: N 299 LEU cc_start: 0.8551 (mt) cc_final: 0.8121 (mt) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.1492 time to fit residues: 93.8933 Evaluate side-chains 313 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 313 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 156 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN ** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** M 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.123250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.100090 restraints weight = 66966.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.101986 restraints weight = 46488.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.103298 restraints weight = 35842.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.104250 restraints weight = 29754.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.104848 restraints weight = 26190.157| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.8679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18299 Z= 0.164 Angle : 0.744 17.242 24758 Z= 0.381 Chirality : 0.046 0.294 2846 Planarity : 0.005 0.075 3173 Dihedral : 10.408 89.038 2616 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.33 % Favored : 94.36 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.18), residues: 2270 helix: 0.56 (0.15), residues: 1218 sheet: -0.11 (0.32), residues: 260 loop : -0.76 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 288 TYR 0.022 0.002 TYR A 172 PHE 0.028 0.002 PHE B 308 TRP 0.015 0.002 TRP E 206 HIS 0.005 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00371 (18299) covalent geometry : angle 0.74410 (24758) hydrogen bonds : bond 0.03470 ( 977) hydrogen bonds : angle 4.66044 ( 2748) *********************** 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 451 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 PHE cc_start: 0.8589 (t80) cc_final: 0.8285 (t80) REVERT: A 273 LEU cc_start: 0.8968 (mt) cc_final: 0.8694 (tp) REVERT: A 305 THR cc_start: 0.8491 (m) cc_final: 0.8206 (p) REVERT: A 425 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7281 (mt0) REVERT: A 428 PHE cc_start: 0.7108 (t80) cc_final: 0.6859 (t80) REVERT: A 435 GLU cc_start: 0.5138 (mp0) cc_final: 0.4714 (mt-10) REVERT: B 233 GLN cc_start: 0.7581 (mp-120) cc_final: 0.7368 (mp10) REVERT: B 268 GLN cc_start: 0.7302 (tp-100) cc_final: 0.6695 (tp40) REVERT: B 281 GLN cc_start: 0.7838 (tp40) cc_final: 0.7546 (tt0) REVERT: B 295 TYR cc_start: 0.8976 (t80) cc_final: 0.8745 (t80) REVERT: C 181 TYR cc_start: 0.8025 (t80) cc_final: 0.7747 (t80) REVERT: C 230 PHE cc_start: 0.6868 (t80) cc_final: 0.6549 (t80) REVERT: C 273 LEU cc_start: 0.7345 (tt) cc_final: 0.6999 (tt) REVERT: C 337 SER cc_start: 0.6425 (m) cc_final: 0.5668 (p) REVERT: D 211 GLU cc_start: 0.8232 (pp20) cc_final: 0.7846 (pp20) REVERT: D 307 MET cc_start: 0.7867 (tpp) cc_final: 0.7603 (tpp) REVERT: D 343 VAL cc_start: 0.8919 (t) cc_final: 0.8671 (p) REVERT: D 347 LEU cc_start: 0.8845 (mp) cc_final: 0.8634 (mp) REVERT: E 207 MET cc_start: 0.1093 (mtt) cc_final: 0.0126 (mtm) REVERT: E 233 GLN cc_start: 0.8650 (mm-40) cc_final: 0.8263 (mm-40) REVERT: E 306 THR cc_start: 0.8438 (t) cc_final: 0.7900 (t) REVERT: F 215 LYS cc_start: 0.8692 (mtmt) cc_final: 0.8341 (pttm) REVERT: F 216 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8136 (mm-40) REVERT: F 220 MET cc_start: 0.7971 (ptm) cc_final: 0.7584 (ttm) REVERT: F 330 MET cc_start: 0.8324 (mmp) cc_final: 0.8050 (mmm) REVERT: G 319 LEU cc_start: 0.8183 (mt) cc_final: 0.7952 (mt) REVERT: H 302 TYR cc_start: 0.4851 (m-10) cc_final: 0.4627 (t80) REVERT: I 294 GLU cc_start: 0.7847 (pt0) cc_final: 0.6696 (mm-30) REVERT: L 326 LEU cc_start: 0.6637 (mt) cc_final: 0.5876 (tp) REVERT: M 287 MET cc_start: 0.6960 (ptt) cc_final: 0.6611 (ptt) REVERT: N 294 GLU cc_start: 0.7569 (mp0) cc_final: 0.7127 (mp0) REVERT: N 301 LYS cc_start: 0.7957 (mmmt) cc_final: 0.7342 (mtmm) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.1489 time to fit residues: 99.5777 Evaluate side-chains 340 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 196 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 214 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 217 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 150 optimal weight: 20.0000 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 GLN ** A 434 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** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 191 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN ** M 295 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 = 0.4163 r_free = 0.4163 target = 0.124039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.100862 restraints weight = 66686.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.102825 restraints weight = 46793.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104177 restraints weight = 36125.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.105118 restraints weight = 30106.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.105608 restraints weight = 26473.083| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.8813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18299 Z= 0.152 Angle : 0.742 16.852 24758 Z= 0.378 Chirality : 0.046 0.294 2846 Planarity : 0.005 0.057 3173 Dihedral : 10.305 89.983 2616 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.68 % Favored : 94.01 % Rotamer: Outliers : 0.05 % Allowed : 1.32 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.18), residues: 2270 helix: 0.72 (0.15), residues: 1208 sheet: -0.10 (0.33), residues: 246 loop : -0.67 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 251 TYR 0.016 0.002 TYR E 181 PHE 0.028 0.002 PHE B 308 TRP 0.011 0.001 TRP E 206 HIS 0.004 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00343 (18299) covalent geometry : angle 0.74199 (24758) hydrogen bonds : bond 0.03315 ( 977) hydrogen bonds : angle 4.58876 ( 2748) *********************** 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 442 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 441 time to evaluate : 0.767 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 230 PHE cc_start: 0.8793 (t80) cc_final: 0.8503 (t80) REVERT: A 273 LEU cc_start: 0.8971 (mt) cc_final: 0.8712 (tp) REVERT: A 305 THR cc_start: 0.8510 (m) cc_final: 0.8223 (p) REVERT: A 425 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7341 (mt0) REVERT: A 428 PHE cc_start: 0.7214 (t80) cc_final: 0.6924 (t80) REVERT: B 233 GLN cc_start: 0.7659 (mp-120) cc_final: 0.7423 (mp10) REVERT: B 281 GLN cc_start: 0.7770 (tp40) cc_final: 0.7491 (tt0) REVERT: B 295 TYR cc_start: 0.9026 (t80) cc_final: 0.8786 (t80) REVERT: B 321 LYS cc_start: 0.8761 (mmtm) cc_final: 0.8228 (tppt) REVERT: C 181 TYR cc_start: 0.8158 (t80) cc_final: 0.7899 (t80) REVERT: C 230 PHE cc_start: 0.7227 (t80) cc_final: 0.6776 (t80) REVERT: C 233 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7239 (mm-40) REVERT: C 273 LEU cc_start: 0.7605 (tt) cc_final: 0.7393 (tt) REVERT: C 307 MET cc_start: 0.8289 (ptt) cc_final: 0.8005 (ptm) REVERT: C 337 SER cc_start: 0.6650 (m) cc_final: 0.5961 (p) REVERT: D 211 GLU cc_start: 0.8335 (pp20) cc_final: 0.8090 (pp20) REVERT: D 259 GLN cc_start: 0.8402 (tt0) cc_final: 0.8165 (mt0) REVERT: D 260 MET cc_start: 0.7933 (ppp) cc_final: 0.7556 (ttp) REVERT: D 343 VAL cc_start: 0.8975 (t) cc_final: 0.8662 (p) REVERT: E 207 MET cc_start: 0.0987 (mtt) cc_final: 0.0000 (mtm) REVERT: E 233 GLN cc_start: 0.8676 (mm-40) cc_final: 0.8329 (mm-40) REVERT: E 306 THR cc_start: 0.8561 (t) cc_final: 0.8172 (t) REVERT: E 386 MET cc_start: 0.8015 (pmm) cc_final: 0.7358 (pmm) REVERT: F 215 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8275 (pttm) REVERT: F 216 GLN cc_start: 0.8400 (mm-40) cc_final: 0.8163 (mm-40) REVERT: F 220 MET cc_start: 0.7992 (ptm) cc_final: 0.7590 (ttm) REVERT: F 330 MET cc_start: 0.8661 (mmp) cc_final: 0.8272 (mmm) REVERT: G 319 LEU cc_start: 0.7961 (mt) cc_final: 0.7675 (mt) REVERT: H 302 TYR cc_start: 0.5064 (m-10) cc_final: 0.4729 (t80) REVERT: I 294 GLU cc_start: 0.7891 (pt0) cc_final: 0.6720 (mm-30) REVERT: M 287 MET cc_start: 0.6789 (ptt) cc_final: 0.6538 (ptt) REVERT: N 301 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7365 (mtmm) outliers start: 1 outliers final: 0 residues processed: 442 average time/residue: 0.1516 time to fit residues: 99.8851 Evaluate side-chains 332 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 221 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 434 GLN B 224 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** H 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.120368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.097336 restraints weight = 67649.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.099063 restraints weight = 49294.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.099946 restraints weight = 37502.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.100975 restraints weight = 31231.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.100858 restraints weight = 28230.542| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.9225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18299 Z= 0.214 Angle : 0.804 17.368 24758 Z= 0.410 Chirality : 0.047 0.303 2846 Planarity : 0.005 0.068 3173 Dihedral : 10.393 89.546 2616 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.17 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2270 helix: 0.53 (0.15), residues: 1206 sheet: -0.25 (0.32), residues: 261 loop : -0.75 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 251 TYR 0.019 0.002 TYR A 172 PHE 0.038 0.003 PHE D 290 TRP 0.019 0.002 TRP A 132 HIS 0.005 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00479 (18299) covalent geometry : angle 0.80381 (24758) hydrogen bonds : bond 0.03657 ( 977) hydrogen bonds : angle 4.86723 ( 2748) *********************** 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 410 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6136 (p90) cc_final: 0.5076 (p90) REVERT: A 230 PHE cc_start: 0.8816 (t80) cc_final: 0.8587 (t80) REVERT: A 305 THR cc_start: 0.8310 (m) cc_final: 0.8018 (p) REVERT: A 348 MET cc_start: 0.8973 (ttp) cc_final: 0.8556 (tpp) REVERT: A 414 ARG cc_start: 0.8041 (mpt90) cc_final: 0.7643 (tmt-80) REVERT: B 195 PHE cc_start: 0.6626 (m-10) cc_final: 0.6422 (m-10) REVERT: B 281 GLN cc_start: 0.7816 (tp40) cc_final: 0.7440 (tt0) REVERT: B 295 TYR cc_start: 0.8971 (t80) cc_final: 0.8737 (t80) REVERT: C 167 SER cc_start: 0.7508 (p) cc_final: 0.7253 (t) REVERT: C 181 TYR cc_start: 0.8418 (t80) cc_final: 0.8213 (t80) REVERT: C 337 SER cc_start: 0.6851 (m) cc_final: 0.6205 (p) REVERT: C 406 PHE cc_start: 0.8241 (m-80) cc_final: 0.7829 (m-10) REVERT: D 211 GLU cc_start: 0.8250 (pp20) cc_final: 0.7837 (pp20) REVERT: E 207 MET cc_start: 0.0997 (mtt) cc_final: 0.0009 (mtm) REVERT: E 233 GLN cc_start: 0.8756 (mm-40) cc_final: 0.8341 (mm-40) REVERT: E 307 MET cc_start: 0.8459 (tpp) cc_final: 0.7973 (mmt) REVERT: E 386 MET cc_start: 0.8129 (pmm) cc_final: 0.7392 (pmm) REVERT: F 215 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8416 (pttm) REVERT: F 216 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8303 (mm-40) REVERT: F 330 MET cc_start: 0.8640 (mmp) cc_final: 0.8208 (mmm) REVERT: F 348 MET cc_start: 0.7400 (mmp) cc_final: 0.6803 (tpp) REVERT: F 351 ILE cc_start: 0.8803 (mp) cc_final: 0.7641 (mp) REVERT: F 386 MET cc_start: 0.6861 (pmm) cc_final: 0.6536 (pmm) REVERT: G 319 LEU cc_start: 0.7983 (mt) cc_final: 0.7710 (mt) REVERT: H 302 TYR cc_start: 0.5006 (m-10) cc_final: 0.4629 (t80) REVERT: M 283 LEU cc_start: 0.6962 (mp) cc_final: 0.6742 (mp) REVERT: M 287 MET cc_start: 0.6843 (ptt) cc_final: 0.6570 (ptt) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.1562 time to fit residues: 94.3670 Evaluate side-chains 309 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 71 optimal weight: 7.9990 chunk 189 optimal weight: 0.0050 chunk 159 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN A 425 GLN B 224 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** F 425 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 = 0.4150 r_free = 0.4150 target = 0.123109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.100076 restraints weight = 65804.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.101965 restraints weight = 46183.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.103283 restraints weight = 35689.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.104185 restraints weight = 29752.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.104654 restraints weight = 26191.408| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.9363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18299 Z= 0.173 Angle : 0.781 16.964 24758 Z= 0.399 Chirality : 0.047 0.305 2846 Planarity : 0.005 0.066 3173 Dihedral : 10.265 89.434 2616 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.08 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.18), residues: 2270 helix: 0.55 (0.15), residues: 1207 sheet: -0.39 (0.33), residues: 241 loop : -0.72 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 250 TYR 0.022 0.002 TYR N 302 PHE 0.031 0.002 PHE B 308 TRP 0.019 0.002 TRP F 280 HIS 0.003 0.001 HIS A 359 Details of bonding type rmsd covalent geometry : bond 0.00391 (18299) covalent geometry : angle 0.78140 (24758) hydrogen bonds : bond 0.03515 ( 977) hydrogen bonds : angle 4.74472 ( 2748) ********************** 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 428 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 TRP cc_start: 0.7333 (m100) cc_final: 0.7133 (m100) REVERT: A 172 TYR cc_start: 0.6247 (p90) cc_final: 0.5976 (p90) REVERT: A 218 PHE cc_start: 0.8419 (m-80) cc_final: 0.8209 (m-80) REVERT: A 230 PHE cc_start: 0.8743 (t80) cc_final: 0.8514 (t80) REVERT: A 305 THR cc_start: 0.8204 (m) cc_final: 0.7928 (p) REVERT: A 339 ILE cc_start: 0.8380 (pt) cc_final: 0.8133 (pt) REVERT: A 348 MET cc_start: 0.8824 (ttp) cc_final: 0.8520 (tpp) REVERT: B 207 MET cc_start: 0.2683 (ptt) cc_final: 0.2437 (ppp) REVERT: B 295 TYR cc_start: 0.8983 (t80) cc_final: 0.8769 (t80) REVERT: C 181 TYR cc_start: 0.7934 (t80) cc_final: 0.7653 (t80) REVERT: C 233 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7244 (mm-40) REVERT: C 337 SER cc_start: 0.6144 (m) cc_final: 0.5687 (p) REVERT: C 413 THR cc_start: 0.7721 (m) cc_final: 0.7412 (m) REVERT: D 211 GLU cc_start: 0.8276 (pp20) cc_final: 0.7879 (pp20) REVERT: D 260 MET cc_start: 0.8532 (tmm) cc_final: 0.8180 (ttp) REVERT: D 345 ASP cc_start: 0.8291 (t70) cc_final: 0.8069 (t70) REVERT: E 128 PRO cc_start: 0.7432 (Cg_endo) cc_final: 0.7081 (Cg_exo) REVERT: E 207 MET cc_start: 0.1061 (mtt) cc_final: 0.0098 (mtm) REVERT: E 233 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8286 (mm-40) REVERT: E 307 MET cc_start: 0.8420 (tpp) cc_final: 0.7947 (mmt) REVERT: E 386 MET cc_start: 0.8064 (pmm) cc_final: 0.7441 (pmm) REVERT: F 207 MET cc_start: 0.1900 (mmp) cc_final: 0.1472 (ttp) REVERT: F 215 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8372 (pttm) REVERT: F 330 MET cc_start: 0.8411 (mmp) cc_final: 0.8065 (mmm) REVERT: F 343 VAL cc_start: 0.9147 (t) cc_final: 0.8938 (t) REVERT: G 319 LEU cc_start: 0.8043 (mt) cc_final: 0.7769 (mt) REVERT: H 302 TYR cc_start: 0.4981 (m-10) cc_final: 0.4677 (t80) REVERT: H 318 GLU cc_start: 0.7413 (mm-30) cc_final: 0.6974 (mp0) REVERT: M 287 MET cc_start: 0.6869 (ptt) cc_final: 0.6596 (ptt) REVERT: N 301 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7381 (mtmm) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.1519 time to fit residues: 96.6462 Evaluate side-chains 321 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 29 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 155 optimal weight: 20.0000 chunk 64 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 160 optimal weight: 0.9990 chunk 209 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 GLN B 224 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.121620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.098921 restraints weight = 67204.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.100706 restraints weight = 47370.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.102001 restraints weight = 36780.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.102777 restraints weight = 30819.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.103402 restraints weight = 27375.321| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.9609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18299 Z= 0.202 Angle : 0.812 17.225 24758 Z= 0.416 Chirality : 0.048 0.305 2846 Planarity : 0.006 0.068 3173 Dihedral : 10.436 89.627 2616 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 21.45 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.43 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.18), residues: 2270 helix: 0.46 (0.15), residues: 1202 sheet: -0.51 (0.34), residues: 228 loop : -0.76 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 250 TYR 0.018 0.002 TYR A 172 PHE 0.035 0.003 PHE D 290 TRP 0.016 0.002 TRP B 206 HIS 0.004 0.001 HIS D 359 Details of bonding type rmsd covalent geometry : bond 0.00455 (18299) covalent geometry : angle 0.81204 (24758) hydrogen bonds : bond 0.03763 ( 977) hydrogen bonds : angle 4.90113 ( 2748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3830.62 seconds wall clock time: 66 minutes 59.00 seconds (4019.00 seconds total)