Starting phenix.real_space_refine on Sat Sep 12 20:17:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5xmk_6734/09_2026/5xmk_6734.cif Found real_map, /net/cci-nas-00/data/ceres_data/5xmk_6734/09_2026/5xmk_6734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5xmk_6734/09_2026/5xmk_6734.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5xmk_6734/09_2026/5xmk_6734.map" model { file = "/net/cci-nas-00/data/ceres_data/5xmk_6734/09_2026/5xmk_6734.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5xmk_6734/09_2026/5xmk_6734.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5xmk_6734/09_2026/5xmk_6734.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5xmk_6734/09_2026/5xmk_6734.cif" } 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-2.2.1-6174/lib/python3.11/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: 3.21, per 1000 atoms: 0.18 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: 1.58 Conformation dependent library (CDL) restraints added in 636.1 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: 0.37 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: 2.48 Time building geometry restraints manager: 2.01 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 - 16.31: 10092 16.31 - 32.62: 911 32.62 - 48.93: 194 48.93 - 65.24: 47 65.24 - 81.55: 17 Dihedral angle restraints: 11261 sinusoidal: 4607 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 11258 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: 0.410 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.100 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 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 : 13.657 81.547 6941 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/Z covalent geometry : bond 0.01032 / 0.75 (18299) covalent geometry : angle 1.54731 / 1.07 (24758) hydrogen bonds : bond 0.13817 / 8.80 ( 977) hydrogen bonds : angle 6.17715 / 4.35 ( 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 : 0.624 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: 0.7624 (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: 0.7861 (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: 0.1625 time to fit residues: 206.9973 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 : 0.468 ------------------------------------------------------------------------------- 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... 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 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 297 GLN N 297 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.132060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.108868 restraints weight = 67507.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.110923 restraints weight = 48429.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.112378 restraints weight = 37879.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.113176 restraints weight = 31590.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.113993 restraints weight = 28075.380| |-----------------------------------------------------------------------------| r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18299 Z= 0.160 Angle : 0.763 15.014 24758 Z= 0.386 Chirality : 0.045 0.282 2846 Planarity : 0.006 0.073 3173 Dihedral : 6.408 74.449 2461 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.58 % Favored : 94.93 % Rotamer: Outliers : 0.15 % Allowed : 3.61 % Favored : 96.24 % 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: 0.31 (0.30), residues: 260 loop : -0.74 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 289 TYR 0.015 0.002 TYR B 324 PHE 0.026 0.002 PHE B 308 TRP 0.018 0.002 TRP E 206 HIS 0.002 0.000 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (18299) covalent geometry : angle 0.76307 / 0.39 (24758) hydrogen bonds : bond 0.03645 / 2.41 ( 977) hydrogen bonds : angle 4.38086 / 3.14 ( 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 576 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 573 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 PHE cc_start: 0.7170 (m-80) cc_final: 0.6922 (m-80) REVERT: A 212 LYS cc_start: 0.8287 (tttm) cc_final: 0.7967 (ttpp) REVERT: A 217 LEU cc_start: 0.8971 (tp) cc_final: 0.8707 (tp) REVERT: A 305 THR cc_start: 0.8601 (m) cc_final: 0.8372 (p) REVERT: A 308 PHE cc_start: 0.6555 (m-10) cc_final: 0.5977 (m-10) REVERT: A 349 GLN cc_start: 0.8736 (tp-100) cc_final: 0.8217 (tt0) REVERT: A 361 LYS cc_start: 0.9186 (tttt) cc_final: 0.8877 (tptt) REVERT: A 405 ASP cc_start: 0.8120 (m-30) cc_final: 0.7642 (m-30) REVERT: A 422 LEU cc_start: 0.7961 (tt) cc_final: 0.7460 (tt) REVERT: A 428 PHE cc_start: 0.7510 (t80) cc_final: 0.7259 (t80) REVERT: B 268 GLN cc_start: 0.7270 (tp-100) cc_final: 0.6138 (tp40) REVERT: B 326 THR cc_start: 0.8265 (m) cc_final: 0.8048 (p) REVERT: B 330 MET cc_start: 0.7648 (ppp) cc_final: 0.7396 (ppp) REVERT: B 405 ASP cc_start: 0.7278 (m-30) cc_final: 0.6834 (m-30) REVERT: C 181 TYR cc_start: 0.7598 (t80) cc_final: 0.7252 (t80) REVERT: C 232 ASP cc_start: 0.6515 (t70) cc_final: 0.5461 (t70) REVERT: C 278 ILE cc_start: 0.8234 (mt) cc_final: 0.8008 (mt) REVERT: C 349 GLN cc_start: 0.9178 (mm110) cc_final: 0.8837 (mm110) REVERT: C 353 LYS cc_start: 0.9262 (mmtt) cc_final: 0.9019 (mmmt) REVERT: D 211 GLU cc_start: 0.8144 (pp20) cc_final: 0.7864 (pp20) REVERT: D 230 PHE cc_start: 0.7682 (t80) cc_final: 0.7482 (t80) REVERT: E 133 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6981 (tt0) REVERT: E 177 THR cc_start: 0.8541 (p) cc_final: 0.8250 (p) REVERT: E 207 MET cc_start: 0.0663 (mtt) cc_final: 0.0415 (mtp) REVERT: E 211 GLU cc_start: 0.7669 (mp0) cc_final: 0.7407 (mp0) REVERT: E 324 TYR cc_start: 0.7743 (m-10) cc_final: 0.7458 (m-80) REVERT: E 405 ASP cc_start: 0.7502 (m-30) cc_final: 0.5853 (m-30) REVERT: E 424 LYS cc_start: 0.8468 (mttp) cc_final: 0.8205 (mtmm) REVERT: F 251 ARG cc_start: 0.7784 (ptm160) cc_final: 0.7536 (mtm-85) REVERT: G 284 THR cc_start: 0.8502 (p) cc_final: 0.7187 (p) REVERT: G 288 ASP cc_start: 0.8584 (m-30) cc_final: 0.8069 (m-30) REVERT: G 319 LEU cc_start: 0.8223 (mt) cc_final: 0.7993 (mt) REVERT: H 318 GLU cc_start: 0.6016 (mp0) cc_final: 0.5697 (mp0) REVERT: I 325 LEU cc_start: 0.8021 (tp) cc_final: 0.7603 (tp) REVERT: K 288 ASP cc_start: 0.7432 (m-30) cc_final: 0.6881 (m-30) REVERT: K 295 GLN cc_start: 0.7647 (tm-30) cc_final: 0.7347 (tm-30) REVERT: L 326 LEU cc_start: 0.6437 (mt) cc_final: 0.5765 (tp) REVERT: M 323 LEU cc_start: 0.7699 (tp) cc_final: 0.7445 (mt) REVERT: N 298 LYS cc_start: 0.7585 (tptt) cc_final: 0.7318 (ttpp) outliers start: 3 outliers final: 1 residues processed: 574 average time/residue: 0.1428 time to fit residues: 119.0296 Evaluate side-chains 405 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 404 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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: 9.9990 chunk 104 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 209 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 205 optimal weight: 30.0000 chunk 191 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 216 GLN B 259 GLN B 261 ASN C 233 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 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 ** M 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.126115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.101818 restraints weight = 68069.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.103805 restraints weight = 48102.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.105164 restraints weight = 37360.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.105988 restraints weight = 31311.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.106718 restraints weight = 27810.719| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18299 Z= 0.208 Angle : 0.767 15.787 24758 Z= 0.393 Chirality : 0.046 0.232 2846 Planarity : 0.006 0.079 3173 Dihedral : 5.997 62.421 2461 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.81 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % 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: 0.65 (0.18), residues: 2270 helix: 1.20 (0.15), residues: 1204 sheet: 0.49 (0.31), residues: 258 loop : -0.69 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 352 TYR 0.035 0.002 TYR N 302 PHE 0.026 0.003 PHE B 308 TRP 0.020 0.002 TRP A 132 HIS 0.003 0.001 HIS E 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (18299) covalent geometry : angle 0.76698 / 0.39 (24758) hydrogen bonds : bond 0.03633 / 2.32 ( 977) hydrogen bonds : angle 4.48943 / 3.24 ( 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 514 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 514 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.7744 (mmp) cc_final: 0.7364 (mmm) REVERT: A 305 THR cc_start: 0.8400 (m) cc_final: 0.8098 (p) REVERT: A 308 PHE cc_start: 0.6425 (m-80) cc_final: 0.6195 (m-10) REVERT: A 349 GLN cc_start: 0.8838 (tp40) cc_final: 0.8480 (tt0) REVERT: A 361 LYS cc_start: 0.9019 (tttt) cc_final: 0.8703 (tptt) REVERT: A 405 ASP cc_start: 0.8221 (m-30) cc_final: 0.7698 (m-30) REVERT: B 150 ILE cc_start: 0.8052 (mp) cc_final: 0.7787 (mm) REVERT: B 215 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8571 (mmmm) REVERT: B 295 TYR cc_start: 0.8970 (t80) cc_final: 0.8252 (t80) REVERT: B 327 LEU cc_start: 0.9000 (mm) cc_final: 0.8697 (mm) REVERT: C 181 TYR cc_start: 0.7807 (t80) cc_final: 0.7369 (t80) REVERT: C 260 MET cc_start: 0.5331 (ttp) cc_final: 0.4673 (ttp) REVERT: C 278 ILE cc_start: 0.8434 (mt) cc_final: 0.8080 (mt) REVERT: D 211 GLU cc_start: 0.7995 (pp20) cc_final: 0.7750 (pp20) REVERT: D 220 MET cc_start: 0.6968 (mmt) cc_final: 0.6346 (mmt) REVERT: D 224 ASN cc_start: 0.7294 (p0) cc_final: 0.7036 (p0) REVERT: D 259 GLN cc_start: 0.8614 (mm-40) cc_final: 0.7794 (mm-40) REVERT: D 292 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7597 (mmp80) REVERT: D 321 LYS cc_start: 0.8392 (mmtm) cc_final: 0.7943 (mmtp) REVERT: E 181 TYR cc_start: 0.6946 (t80) cc_final: 0.6586 (t80) REVERT: E 207 MET cc_start: 0.0637 (mtt) cc_final: 0.0229 (mtp) REVERT: E 233 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8231 (mm110) REVERT: E 251 ARG cc_start: 0.8169 (ptp-170) cc_final: 0.7613 (ptp-170) REVERT: E 254 THR cc_start: 0.8179 (p) cc_final: 0.7490 (p) REVERT: E 292 ARG cc_start: 0.8439 (mmm160) cc_final: 0.8197 (mmm160) REVERT: E 386 MET cc_start: 0.8076 (pmm) cc_final: 0.7608 (pmm) REVERT: E 425 GLN cc_start: 0.8469 (mt0) cc_final: 0.8267 (mt0) REVERT: F 251 ARG cc_start: 0.7859 (ptm160) cc_final: 0.7580 (mtm-85) REVERT: G 308 ASN cc_start: 0.4983 (m-40) cc_final: 0.4771 (m-40) REVERT: G 319 LEU cc_start: 0.8360 (mt) cc_final: 0.8148 (mt) REVERT: H 295 GLN cc_start: 0.5938 (tt0) cc_final: 0.5105 (tp40) REVERT: H 318 GLU cc_start: 0.5949 (mp0) cc_final: 0.5638 (mp0) REVERT: I 298 LYS cc_start: 0.8858 (tptt) cc_final: 0.7982 (tptt) REVERT: I 302 TYR cc_start: 0.7663 (m-80) cc_final: 0.6998 (m-80) REVERT: L 317 ASP cc_start: 0.6446 (m-30) cc_final: 0.6080 (m-30) REVERT: L 326 LEU cc_start: 0.5717 (mt) cc_final: 0.5073 (tp) REVERT: M 323 LEU cc_start: 0.7916 (tp) cc_final: 0.7604 (mt) outliers start: 0 outliers final: 0 residues processed: 514 average time/residue: 0.1602 time to fit residues: 119.2576 Evaluate side-chains 377 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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: 20.0000 chunk 118 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 177 optimal weight: 0.9980 chunk 155 optimal weight: 30.0000 chunk 20 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 GLN E 191 ASN ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN F 355 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.124849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.100805 restraints weight = 68387.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.102847 restraints weight = 47705.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.104231 restraints weight = 36469.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.105174 restraints weight = 30328.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.105664 restraints weight = 26682.723| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.7104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18299 Z= 0.179 Angle : 0.746 16.247 24758 Z= 0.381 Chirality : 0.046 0.293 2846 Planarity : 0.006 0.079 3173 Dihedral : 5.897 57.547 2461 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.55 % Favored : 94.01 % Rotamer: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.44 % 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: 0.56 (0.18), residues: 2270 helix: 1.16 (0.15), residues: 1198 sheet: 0.44 (0.31), residues: 260 loop : -0.78 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 289 TYR 0.027 0.002 TYR N 302 PHE 0.027 0.002 PHE D 290 TRP 0.014 0.002 TRP A 132 HIS 0.003 0.001 HIS E 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (18299) covalent geometry : angle 0.74647 / 0.38 (24758) hydrogen bonds : bond 0.03337 / 2.17 ( 977) hydrogen bonds : angle 4.39983 / 3.15 ( 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 489 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 487 time to evaluate : 0.691 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: A 172 TYR cc_start: 0.6189 (p90) cc_final: 0.5930 (p90) REVERT: A 215 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8222 (mmmt) REVERT: A 220 MET cc_start: 0.7572 (mmp) cc_final: 0.7273 (mmm) REVERT: A 305 THR cc_start: 0.8489 (m) cc_final: 0.8180 (p) REVERT: A 349 GLN cc_start: 0.8765 (tp40) cc_final: 0.8361 (tt0) REVERT: A 374 THR cc_start: 0.7952 (t) cc_final: 0.7316 (t) REVERT: A 405 ASP cc_start: 0.8226 (m-30) cc_final: 0.7823 (m-30) REVERT: A 415 PRO cc_start: 0.6940 (Cg_exo) cc_final: 0.6663 (Cg_endo) REVERT: A 422 LEU cc_start: 0.8189 (tt) cc_final: 0.7839 (tt) REVERT: A 425 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7351 (mt0) REVERT: A 428 PHE cc_start: 0.7595 (t80) cc_final: 0.7390 (t80) REVERT: B 230 PHE cc_start: 0.7681 (t80) cc_final: 0.7436 (t80) REVERT: B 281 GLN cc_start: 0.7704 (tp40) cc_final: 0.7439 (tt0) REVERT: B 295 TYR cc_start: 0.8945 (t80) cc_final: 0.8292 (t80) REVERT: B 327 LEU cc_start: 0.9057 (mm) cc_final: 0.8687 (mm) REVERT: C 181 TYR cc_start: 0.7835 (t80) cc_final: 0.7441 (t80) REVERT: C 278 ILE cc_start: 0.8671 (mt) cc_final: 0.8265 (mt) REVERT: C 337 SER cc_start: 0.6962 (m) cc_final: 0.5964 (p) REVERT: D 211 GLU cc_start: 0.8049 (pp20) cc_final: 0.7589 (pp20) REVERT: D 259 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8617 (mm-40) REVERT: D 348 MET cc_start: 0.8498 (tpp) cc_final: 0.8203 (tpp) REVERT: D 380 ASP cc_start: 0.6500 (t0) cc_final: 0.6127 (t0) REVERT: E 207 MET cc_start: 0.1098 (mtt) cc_final: 0.0683 (mtp) REVERT: E 233 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8376 (mm-40) REVERT: E 255 GLU cc_start: 0.7056 (mp0) cc_final: 0.6694 (mp0) REVERT: E 386 MET cc_start: 0.8238 (pmm) cc_final: 0.7826 (pmm) REVERT: E 422 LEU cc_start: 0.9022 (mp) cc_final: 0.8739 (mt) REVERT: E 425 GLN cc_start: 0.8467 (mt0) cc_final: 0.8243 (mt0) REVERT: F 348 MET cc_start: 0.7061 (mmp) cc_final: 0.6814 (tpp) REVERT: G 319 LEU cc_start: 0.8124 (mt) cc_final: 0.7921 (mt) REVERT: L 317 ASP cc_start: 0.6504 (m-30) cc_final: 0.6219 (m-30) REVERT: L 326 LEU cc_start: 0.6268 (mt) cc_final: 0.5595 (tp) REVERT: M 323 LEU cc_start: 0.7964 (tp) cc_final: 0.7690 (mt) outliers start: 2 outliers final: 0 residues processed: 488 average time/residue: 0.1525 time to fit residues: 110.1085 Evaluate side-chains 350 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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: 4.9990 chunk 116 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 186 optimal weight: 0.2980 chunk 164 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 HIS E 216 GLN ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 295 GLN ** M 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 = 0.4159 r_free = 0.4159 target = 0.123016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.098831 restraints weight = 68754.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.100809 restraints weight = 48176.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.102190 restraints weight = 37241.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.103139 restraints weight = 30958.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.103709 restraints weight = 27246.701| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.7836 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= 0.197 Angle : 0.759 17.390 24758 Z= 0.390 Chirality : 0.046 0.271 2846 Planarity : 0.005 0.081 3173 Dihedral : 5.957 62.387 2461 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.08 % Favored : 93.57 % Rotamer: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % 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: 0.31 (0.18), residues: 2270 helix: 0.85 (0.15), residues: 1212 sheet: 0.33 (0.31), residues: 258 loop : -0.72 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 293 TYR 0.028 0.002 TYR M 302 PHE 0.039 0.003 PHE D 290 TRP 0.012 0.002 TRP E 132 HIS 0.003 0.001 HIS E 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (18299) covalent geometry : angle 0.75939 / 0.39 (24758) hydrogen bonds : bond 0.03430 / 2.25 ( 977) hydrogen bonds : angle 4.53875 / 3.24 ( 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 467 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 466 time to evaluate : 0.702 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 172 TYR cc_start: 0.5929 (p90) cc_final: 0.4306 (p90) REVERT: A 305 THR cc_start: 0.8559 (m) cc_final: 0.8221 (p) REVERT: A 307 MET cc_start: 0.7363 (ppp) cc_final: 0.7060 (ppp) REVERT: A 311 ASN cc_start: 0.7941 (m-40) cc_final: 0.7675 (m-40) REVERT: A 349 GLN cc_start: 0.9032 (tp40) cc_final: 0.8667 (tt0) REVERT: A 405 ASP cc_start: 0.8102 (m-30) cc_final: 0.7649 (m-30) REVERT: A 422 LEU cc_start: 0.8260 (tt) cc_final: 0.7937 (tt) REVERT: A 428 PHE cc_start: 0.7646 (t80) cc_final: 0.7412 (t80) REVERT: B 169 ILE cc_start: 0.8642 (mm) cc_final: 0.8417 (mm) REVERT: B 230 PHE cc_start: 0.7702 (t80) cc_final: 0.7430 (t80) REVERT: B 268 GLN cc_start: 0.7254 (tp-100) cc_final: 0.6470 (tp-100) REVERT: B 281 GLN cc_start: 0.7967 (tp40) cc_final: 0.7523 (tt0) REVERT: C 181 TYR cc_start: 0.7995 (t80) cc_final: 0.7650 (t80) REVERT: C 337 SER cc_start: 0.7028 (m) cc_final: 0.6112 (p) REVERT: C 413 THR cc_start: 0.7512 (m) cc_final: 0.7239 (m) REVERT: D 211 GLU cc_start: 0.8092 (pp20) cc_final: 0.7665 (pp20) REVERT: D 259 GLN cc_start: 0.8967 (tp40) cc_final: 0.8579 (tp40) REVERT: D 307 MET cc_start: 0.7841 (tpp) cc_final: 0.7513 (tpp) REVERT: E 207 MET cc_start: 0.1224 (mtt) cc_final: 0.0248 (mtm) REVERT: E 233 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8430 (mm110) REVERT: E 292 ARG cc_start: 0.8811 (mmm-85) cc_final: 0.8603 (mmm160) REVERT: E 307 MET cc_start: 0.8113 (tpp) cc_final: 0.7877 (mmt) REVERT: E 386 MET cc_start: 0.8475 (pmm) cc_final: 0.8061 (pmm) REVERT: E 405 ASP cc_start: 0.7960 (m-30) cc_final: 0.7087 (m-30) REVERT: E 422 LEU cc_start: 0.8913 (mp) cc_final: 0.8615 (mt) REVERT: E 425 GLN cc_start: 0.8444 (mt0) cc_final: 0.8119 (mt0) REVERT: F 216 GLN cc_start: 0.8247 (mm-40) cc_final: 0.8001 (mm-40) REVERT: F 220 MET cc_start: 0.8033 (ptm) cc_final: 0.7768 (ttm) REVERT: F 330 MET cc_start: 0.8169 (mmp) cc_final: 0.7969 (mmm) REVERT: F 348 MET cc_start: 0.7227 (mmp) cc_final: 0.6908 (tpp) REVERT: G 319 LEU cc_start: 0.8065 (mt) cc_final: 0.7858 (mt) REVERT: H 318 GLU cc_start: 0.5787 (mp0) cc_final: 0.5422 (mp0) REVERT: L 326 LEU cc_start: 0.5834 (mt) cc_final: 0.5027 (tp) REVERT: M 287 MET cc_start: 0.7129 (ptt) cc_final: 0.6925 (ptt) REVERT: M 323 LEU cc_start: 0.8079 (tp) cc_final: 0.7873 (mt) outliers start: 1 outliers final: 0 residues processed: 467 average time/residue: 0.1449 time to fit residues: 100.3095 Evaluate side-chains 338 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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: 1.9990 chunk 99 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 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 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.123611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.099216 restraints weight = 67799.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.101238 restraints weight = 47142.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.102522 restraints weight = 36289.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.103599 restraints weight = 30349.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104115 restraints weight = 26633.954| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.8165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18299 Z= 0.165 Angle : 0.725 16.475 24758 Z= 0.368 Chirality : 0.045 0.266 2846 Planarity : 0.005 0.076 3173 Dihedral : 5.792 63.255 2461 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.59 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 0.33 (0.18), residues: 2270 helix: 0.92 (0.15), residues: 1211 sheet: 0.02 (0.32), residues: 245 loop : -0.67 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 251 TYR 0.028 0.002 TYR N 302 PHE 0.023 0.002 PHE D 290 TRP 0.013 0.002 TRP E 206 HIS 0.004 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (18299) covalent geometry : angle 0.72542 / 0.37 (24758) hydrogen bonds : bond 0.03175 / 2.05 ( 977) hydrogen bonds : angle 4.41447 / 3.17 ( 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 466 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 0.647 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: A 172 TYR cc_start: 0.5724 (p90) cc_final: 0.5184 (p90) REVERT: A 230 PHE cc_start: 0.8639 (t80) cc_final: 0.8434 (t80) REVERT: A 249 SER cc_start: 0.6396 (m) cc_final: 0.6187 (m) REVERT: A 305 THR cc_start: 0.8530 (m) cc_final: 0.8198 (p) REVERT: A 307 MET cc_start: 0.7005 (ppp) cc_final: 0.6658 (ppp) REVERT: A 349 GLN cc_start: 0.9010 (tp40) cc_final: 0.8416 (tt0) REVERT: A 428 PHE cc_start: 0.7621 (t80) cc_final: 0.7378 (t80) REVERT: A 435 GLU cc_start: 0.5287 (mp0) cc_final: 0.4816 (mt-10) REVERT: B 230 PHE cc_start: 0.7731 (t80) cc_final: 0.7402 (t80) REVERT: B 281 GLN cc_start: 0.7861 (tp40) cc_final: 0.7532 (tt0) REVERT: C 181 TYR cc_start: 0.7911 (t80) cc_final: 0.7664 (t80) REVERT: C 202 LEU cc_start: 0.7213 (mp) cc_final: 0.6978 (mp) REVERT: C 230 PHE cc_start: 0.7659 (t80) cc_final: 0.7273 (t80) REVERT: C 277 ASN cc_start: 0.7553 (t0) cc_final: 0.7295 (t0) REVERT: C 324 TYR cc_start: 0.7695 (m-10) cc_final: 0.7295 (m-10) REVERT: C 337 SER cc_start: 0.6927 (m) cc_final: 0.6107 (p) REVERT: C 413 THR cc_start: 0.7473 (m) cc_final: 0.7142 (m) REVERT: D 259 GLN cc_start: 0.8853 (tp40) cc_final: 0.8496 (tp40) REVERT: E 207 MET cc_start: 0.1134 (mtt) cc_final: 0.0118 (mtm) REVERT: E 233 GLN cc_start: 0.8708 (mm-40) cc_final: 0.8338 (mm-40) REVERT: E 292 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.8265 (mmm160) REVERT: E 307 MET cc_start: 0.8225 (tpp) cc_final: 0.7996 (mmt) REVERT: E 386 MET cc_start: 0.8406 (pmm) cc_final: 0.7996 (pmm) REVERT: E 422 LEU cc_start: 0.8961 (mp) cc_final: 0.8697 (mt) REVERT: E 425 GLN cc_start: 0.8461 (mt0) cc_final: 0.8154 (mt0) REVERT: F 216 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8065 (mm-40) REVERT: F 220 MET cc_start: 0.8042 (ptm) cc_final: 0.7810 (ttm) REVERT: F 330 MET cc_start: 0.8226 (mmp) cc_final: 0.8011 (mmm) REVERT: G 319 LEU cc_start: 0.8128 (mt) cc_final: 0.7899 (mt) REVERT: L 326 LEU cc_start: 0.6484 (mt) cc_final: 0.5722 (tp) REVERT: M 287 MET cc_start: 0.7059 (ptt) cc_final: 0.6685 (ptt) outliers start: 0 outliers final: 0 residues processed: 466 average time/residue: 0.1438 time to fit residues: 99.4581 Evaluate side-chains 344 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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: 4.9990 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 211 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 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 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 = 0.4165 r_free = 0.4165 target = 0.123765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.099705 restraints weight = 69310.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.101794 restraints weight = 47789.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.103000 restraints weight = 36461.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.104103 restraints weight = 30595.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.104603 restraints weight = 26859.159| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.8507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18299 Z= 0.167 Angle : 0.745 16.637 24758 Z= 0.378 Chirality : 0.045 0.282 2846 Planarity : 0.005 0.067 3173 Dihedral : 5.779 63.875 2461 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.81 % Favored : 93.83 % Rotamer: Outliers : 0.05 % Allowed : 1.73 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.18), residues: 2270 helix: 0.86 (0.15), residues: 1206 sheet: -0.19 (0.33), residues: 238 loop : -0.65 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 251 TYR 0.019 0.002 TYR M 302 PHE 0.026 0.002 PHE B 218 TRP 0.011 0.002 TRP D 206 HIS 0.005 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (18299) covalent geometry : angle 0.74542 / 0.38 (24758) hydrogen bonds : bond 0.03246 / 2.14 ( 977) hydrogen bonds : angle 4.45575 / 3.19 ( 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 462 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 461 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6103 (p90) cc_final: 0.4316 (p90) REVERT: A 207 MET cc_start: 0.1522 (mpp) cc_final: 0.0986 (mpt) REVERT: A 305 THR cc_start: 0.8526 (m) cc_final: 0.8178 (p) REVERT: A 307 MET cc_start: 0.7103 (ppp) cc_final: 0.6771 (ppp) REVERT: A 311 ASN cc_start: 0.8150 (m-40) cc_final: 0.7859 (m-40) REVERT: A 405 ASP cc_start: 0.7346 (t0) cc_final: 0.6541 (t70) REVERT: A 435 GLU cc_start: 0.5092 (mp0) cc_final: 0.4697 (mt-10) REVERT: B 146 LYS cc_start: 0.8630 (ptpt) cc_final: 0.8418 (ptpp) REVERT: B 230 PHE cc_start: 0.7713 (t80) cc_final: 0.7414 (t80) REVERT: B 281 GLN cc_start: 0.7726 (tp40) cc_final: 0.7519 (tt0) REVERT: C 260 MET cc_start: 0.5927 (ttp) cc_final: 0.5549 (ttp) REVERT: C 337 SER cc_start: 0.6832 (m) cc_final: 0.5956 (p) REVERT: C 413 THR cc_start: 0.7463 (m) cc_final: 0.7241 (m) REVERT: D 211 GLU cc_start: 0.8032 (pp20) cc_final: 0.7722 (pp20) REVERT: D 259 GLN cc_start: 0.8867 (tp40) cc_final: 0.8604 (tp40) REVERT: D 307 MET cc_start: 0.7631 (tpp) cc_final: 0.7329 (tpp) REVERT: E 207 MET cc_start: 0.0964 (mtt) cc_final: -0.0037 (mtm) REVERT: E 233 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8354 (mm-40) REVERT: E 292 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.8217 (mmm160) REVERT: E 386 MET cc_start: 0.8527 (pmm) cc_final: 0.8018 (pmm) REVERT: E 405 ASP cc_start: 0.8016 (m-30) cc_final: 0.7632 (m-30) REVERT: E 422 LEU cc_start: 0.8824 (mp) cc_final: 0.8618 (mt) REVERT: E 425 GLN cc_start: 0.8394 (mt0) cc_final: 0.8110 (mt0) REVERT: F 207 MET cc_start: 0.2022 (mmp) cc_final: 0.1474 (ttp) REVERT: F 216 GLN cc_start: 0.8316 (mm-40) cc_final: 0.8071 (mm-40) REVERT: F 330 MET cc_start: 0.8307 (mmp) cc_final: 0.8054 (mmm) REVERT: F 345 ASP cc_start: 0.7180 (t70) cc_final: 0.6943 (t70) REVERT: G 319 LEU cc_start: 0.8042 (mt) cc_final: 0.7806 (mt) REVERT: H 302 TYR cc_start: 0.4959 (m-10) cc_final: 0.4602 (t80) REVERT: L 326 LEU cc_start: 0.6640 (mt) cc_final: 0.5923 (tp) REVERT: M 287 MET cc_start: 0.7065 (ptt) cc_final: 0.6687 (ptt) outliers start: 1 outliers final: 0 residues processed: 462 average time/residue: 0.1451 time to fit residues: 99.5420 Evaluate side-chains 346 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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: 1.9990 chunk 214 optimal weight: 20.0000 chunk 98 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 146 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 46 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 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 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 ASN ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 261 ASN F 277 ASN G 295 GLN J 297 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.122991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.099235 restraints weight = 69353.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.101220 restraints weight = 47813.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.102462 restraints weight = 36761.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.103446 restraints weight = 30648.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.103924 restraints weight = 27124.910| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.8771 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= 0.180 Angle : 0.749 16.589 24758 Z= 0.381 Chirality : 0.046 0.285 2846 Planarity : 0.005 0.073 3173 Dihedral : 5.944 67.075 2461 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.86 % Favored : 93.83 % 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: 0.15 (0.18), residues: 2270 helix: 0.78 (0.15), residues: 1203 sheet: -0.28 (0.33), residues: 237 loop : -0.67 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 289 TYR 0.012 0.002 TYR E 295 PHE 0.030 0.002 PHE D 290 TRP 0.012 0.002 TRP B 206 HIS 0.004 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (18299) covalent geometry : angle 0.74894 / 0.38 (24758) hydrogen bonds : bond 0.03316 / 2.22 ( 977) hydrogen bonds : angle 4.55044 / 3.26 ( 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 437 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 436 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 MET cc_start: 0.1595 (mpp) cc_final: 0.1014 (mpp) REVERT: A 230 PHE cc_start: 0.8659 (t80) cc_final: 0.7864 (t80) REVERT: A 273 LEU cc_start: 0.9005 (mt) cc_final: 0.8474 (tp) REVERT: A 391 ILE cc_start: 0.7780 (tp) cc_final: 0.7526 (mm) REVERT: A 435 GLU cc_start: 0.4745 (mp0) cc_final: 0.4443 (mt-10) REVERT: B 230 PHE cc_start: 0.7649 (t80) cc_final: 0.7317 (t80) REVERT: C 232 ASP cc_start: 0.7366 (t0) cc_final: 0.7152 (t0) REVERT: C 233 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7204 (mm-40) REVERT: C 324 TYR cc_start: 0.7726 (m-10) cc_final: 0.7377 (m-10) REVERT: C 337 SER cc_start: 0.6820 (m) cc_final: 0.6113 (p) REVERT: D 211 GLU cc_start: 0.7988 (pp20) cc_final: 0.7724 (pp20) REVERT: D 259 GLN cc_start: 0.8888 (tp40) cc_final: 0.8643 (tp40) REVERT: D 307 MET cc_start: 0.7911 (tpp) cc_final: 0.7625 (tpp) REVERT: D 325 ARG cc_start: 0.8140 (ptp-170) cc_final: 0.7860 (mtm180) REVERT: E 207 MET cc_start: 0.1035 (mtt) cc_final: 0.0003 (mtm) REVERT: E 233 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8330 (mm-40) REVERT: E 292 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.8366 (mmm160) REVERT: F 207 MET cc_start: 0.1815 (mmp) cc_final: 0.1465 (ttp) REVERT: F 215 LYS cc_start: 0.8649 (pttm) cc_final: 0.8425 (pttm) REVERT: F 256 LEU cc_start: 0.8447 (tt) cc_final: 0.8124 (pp) REVERT: F 330 MET cc_start: 0.8346 (mmp) cc_final: 0.8066 (mmm) REVERT: G 319 LEU cc_start: 0.8035 (mt) cc_final: 0.7784 (mt) REVERT: H 302 TYR cc_start: 0.4985 (m-10) cc_final: 0.4612 (t80) REVERT: L 326 LEU cc_start: 0.6870 (mt) cc_final: 0.6092 (tp) REVERT: M 287 MET cc_start: 0.6944 (ptt) cc_final: 0.6662 (ptt) outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.1394 time to fit residues: 91.9185 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 : 0.744 ------------------------------------------------------------------------------- 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: 6.9990 chunk 194 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 143 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 349 GLN ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 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 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN F 216 GLN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4173 r_free = 0.4173 target = 0.124643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.101128 restraints weight = 67587.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.103080 restraints weight = 46309.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104340 restraints weight = 35495.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.105384 restraints weight = 29526.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.105815 restraints weight = 25856.099| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.8888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18299 Z= 0.148 Angle : 0.731 16.682 24758 Z= 0.371 Chirality : 0.046 0.279 2846 Planarity : 0.005 0.068 3173 Dihedral : 5.713 65.628 2461 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.64 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.18), residues: 2270 helix: 0.81 (0.15), residues: 1205 sheet: -0.24 (0.34), residues: 236 loop : -0.55 (0.23), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 289 TYR 0.015 0.001 TYR A 172 PHE 0.021 0.002 PHE B 218 TRP 0.014 0.002 TRP F 280 HIS 0.004 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (18299) covalent geometry : angle 0.73122 / 0.37 (24758) hydrogen bonds : bond 0.03268 / 2.18 ( 977) hydrogen bonds : angle 4.42656 / 3.17 ( 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 432 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 TYR cc_start: 0.6271 (p90) cc_final: 0.5223 (p90) REVERT: A 207 MET cc_start: 0.1562 (mpp) cc_final: 0.0980 (mpp) REVERT: A 216 GLN cc_start: 0.8297 (mt0) cc_final: 0.7872 (mp10) REVERT: A 230 PHE cc_start: 0.8799 (t80) cc_final: 0.8057 (t80) REVERT: A 273 LEU cc_start: 0.8971 (mt) cc_final: 0.8407 (tp) REVERT: A 435 GLU cc_start: 0.4919 (mp0) cc_final: 0.4702 (mt-10) REVERT: B 222 ARG cc_start: 0.8230 (mpt-90) cc_final: 0.7987 (mpt180) REVERT: B 230 PHE cc_start: 0.7736 (t80) cc_final: 0.7452 (t80) REVERT: B 281 GLN cc_start: 0.7720 (tp40) cc_final: 0.7440 (tt0) REVERT: B 321 LYS cc_start: 0.8710 (mmtm) cc_final: 0.8244 (tppt) REVERT: C 233 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7313 (mm-40) REVERT: C 324 TYR cc_start: 0.7570 (m-10) cc_final: 0.7259 (m-10) REVERT: C 337 SER cc_start: 0.6913 (m) cc_final: 0.6185 (p) REVERT: C 413 THR cc_start: 0.7555 (m) cc_final: 0.7187 (m) REVERT: D 209 GLU cc_start: 0.8517 (pt0) cc_final: 0.8258 (pt0) REVERT: D 211 GLU cc_start: 0.8073 (pp20) cc_final: 0.7790 (pp20) REVERT: D 259 GLN cc_start: 0.8856 (tp40) cc_final: 0.8642 (tp40) REVERT: D 307 MET cc_start: 0.7910 (tpp) cc_final: 0.7588 (tpp) REVERT: D 325 ARG cc_start: 0.8004 (ptp-170) cc_final: 0.7710 (mtm180) REVERT: E 207 MET cc_start: 0.1014 (mtt) cc_final: 0.0033 (mtm) REVERT: E 233 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8309 (mm-40) REVERT: E 292 ARG cc_start: 0.8722 (mmm-85) cc_final: 0.8327 (mmm160) REVERT: E 386 MET cc_start: 0.8344 (pmm) cc_final: 0.7625 (pmm) REVERT: F 207 MET cc_start: 0.1632 (mmp) cc_final: 0.1405 (ttp) REVERT: F 330 MET cc_start: 0.8370 (mmp) cc_final: 0.8073 (mmm) REVERT: F 345 ASP cc_start: 0.7434 (t70) cc_final: 0.7184 (t70) REVERT: G 319 LEU cc_start: 0.7955 (mt) cc_final: 0.7700 (mt) REVERT: H 302 TYR cc_start: 0.5037 (m-10) cc_final: 0.4720 (t80) REVERT: I 294 GLU cc_start: 0.8034 (pt0) cc_final: 0.6490 (mm-30) REVERT: L 326 LEU cc_start: 0.6790 (mt) cc_final: 0.6067 (tp) REVERT: M 287 MET cc_start: 0.7064 (ptt) cc_final: 0.6726 (ptt) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.1442 time to fit residues: 92.7145 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 : 0.701 ------------------------------------------------------------------------------- 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: 10.0000 chunk 102 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 143 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN ** 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 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN ** M 297 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 = 0.4109 r_free = 0.4109 target = 0.120204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.098327 restraints weight = 68370.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.098286 restraints weight = 52118.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.099134 restraints weight = 41156.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.099449 restraints weight = 37544.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099515 restraints weight = 32881.922| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.9318 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= 0.221 Angle : 0.814 16.927 24758 Z= 0.417 Chirality : 0.048 0.294 2846 Planarity : 0.006 0.074 3173 Dihedral : 6.146 72.414 2461 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.65 % Favored : 93.00 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.18), residues: 2270 helix: 0.50 (0.15), residues: 1202 sheet: -0.28 (0.34), residues: 228 loop : -0.71 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 289 TYR 0.017 0.002 TYR A 172 PHE 0.039 0.003 PHE D 290 TRP 0.015 0.002 TRP B 206 HIS 0.005 0.001 HIS E 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (18299) covalent geometry : angle 0.81372 / 0.42 (24758) hydrogen bonds : bond 0.03705 / 2.43 ( 977) hydrogen bonds : angle 4.79987 / 3.43 ( 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 392 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.731 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: A 207 MET cc_start: 0.1750 (mpp) cc_final: 0.1315 (mpp) REVERT: A 230 PHE cc_start: 0.8703 (t80) cc_final: 0.8493 (t80) REVERT: A 339 ILE cc_start: 0.8522 (pt) cc_final: 0.8196 (pt) REVERT: A 435 GLU cc_start: 0.4804 (mp0) cc_final: 0.4504 (mt-10) REVERT: B 207 MET cc_start: 0.4082 (ppp) cc_final: 0.3806 (ppp) REVERT: B 222 ARG cc_start: 0.8333 (mpt-90) cc_final: 0.8062 (mpt180) REVERT: B 230 PHE cc_start: 0.7677 (t80) cc_final: 0.7218 (t80) REVERT: B 281 GLN cc_start: 0.7722 (tp40) cc_final: 0.7328 (tt0) REVERT: C 295 TYR cc_start: 0.8879 (t80) cc_final: 0.8636 (t80) REVERT: C 324 TYR cc_start: 0.7630 (m-10) cc_final: 0.7163 (m-10) REVERT: C 413 THR cc_start: 0.7588 (m) cc_final: 0.7274 (m) REVERT: D 230 PHE cc_start: 0.8062 (t80) cc_final: 0.7860 (t80) REVERT: D 259 GLN cc_start: 0.9009 (tp40) cc_final: 0.8771 (tp40) REVERT: D 307 MET cc_start: 0.8191 (tpp) cc_final: 0.7842 (tpp) REVERT: E 207 MET cc_start: 0.1003 (mtt) cc_final: -0.0023 (mtm) REVERT: E 233 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8347 (mm-40) REVERT: E 292 ARG cc_start: 0.8731 (mmm-85) cc_final: 0.8418 (mmm160) REVERT: E 386 MET cc_start: 0.8507 (pmm) cc_final: 0.7850 (pmm) REVERT: F 126 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7336 (tm-30) REVERT: F 207 MET cc_start: 0.1963 (mmp) cc_final: 0.1653 (ttp) REVERT: F 265 ASN cc_start: 0.7593 (m-40) cc_final: 0.7239 (m110) REVERT: F 330 MET cc_start: 0.8687 (mmp) cc_final: 0.8320 (mmm) REVERT: F 348 MET cc_start: 0.7286 (mmp) cc_final: 0.6722 (tpp) REVERT: F 351 ILE cc_start: 0.8766 (mp) cc_final: 0.8460 (mp) REVERT: G 319 LEU cc_start: 0.8012 (mt) cc_final: 0.7742 (mt) REVERT: H 302 TYR cc_start: 0.4730 (m-10) cc_final: 0.4433 (t80) REVERT: J 317 ASP cc_start: 0.8556 (t0) cc_final: 0.8247 (m-30) REVERT: M 283 LEU cc_start: 0.7021 (mp) cc_final: 0.6742 (mp) REVERT: M 287 MET cc_start: 0.7039 (ptt) cc_final: 0.6773 (ptt) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.1424 time to fit residues: 84.3902 Evaluate side-chains 301 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 8.9990 chunk 32 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 209 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 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 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.119422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.096886 restraints weight = 68400.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.097305 restraints weight = 50611.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.098088 restraints weight = 38123.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.098257 restraints weight = 38281.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.098357 restraints weight = 33204.548| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.9686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18299 Z= 0.245 Angle : 0.844 17.065 24758 Z= 0.433 Chirality : 0.048 0.301 2846 Planarity : 0.006 0.072 3173 Dihedral : 6.396 79.749 2461 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.09 % Favored : 92.64 % 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: -0.37 (0.18), residues: 2270 helix: 0.32 (0.15), residues: 1183 sheet: -0.48 (0.34), residues: 230 loop : -0.83 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 325 TYR 0.018 0.002 TYR D 324 PHE 0.040 0.003 PHE D 290 TRP 0.019 0.003 TRP B 206 HIS 0.005 0.001 HIS E 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 (18299) covalent geometry : angle 0.84410 / 0.43 (24758) hydrogen bonds : bond 0.03909 / 2.61 ( 977) hydrogen bonds : angle 5.00718 / 3.58 ( 2748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3601.71 seconds wall clock time: 63 minutes 12.14 seconds (3792.14 seconds total)