Starting phenix.real_space_refine on Thu Jun 4 16:37:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xus_67276/06_2026/9xus_67276.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xus_67276/06_2026/9xus_67276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xus_67276/06_2026/9xus_67276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xus_67276/06_2026/9xus_67276.map" model { file = "/net/cci-nas-00/data/ceres_data/9xus_67276/06_2026/9xus_67276.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xus_67276/06_2026/9xus_67276.cif" } resolution = 2.81 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 50 5.16 5 C 8678 2.51 5 N 2342 2.21 5 O 2674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13768 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3367 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3429 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 422} Chain: "C" Number of atoms: 3367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3367 Classifications: {'peptide': 435} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3429 Classifications: {'peptide': 439} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 422} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' MG': 2, '3PG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' MG': 2, '3PG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' MG': 2, '3PG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 44 Unusual residues: {' MG': 2, '3PG': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.32, per 1000 atoms: 0.24 Number of scatterers: 13768 At special positions: 0 Unit cell: (107.61, 120.27, 113.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 50 16.00 P 16 15.00 Mg 8 11.99 O 2674 8.00 N 2342 7.00 C 8678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS C 81 " distance=2.03 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: 1.11 Conformation dependent library (CDL) restraints added in 665.3 milliseconds 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 24 sheets defined 30.9% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 111 through 114 Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 147 through 158 removed outlier: 3.585A pdb=" N ARG A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 196 through 201 Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.538A pdb=" N PHE A 224 " --> pdb=" O ASP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.809A pdb=" N THR A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 286 through 293 removed outlier: 3.577A pdb=" N GLU A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 443 through 448 removed outlier: 3.565A pdb=" N SER A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 removed outlier: 3.638A pdb=" N ASP A 497 " --> pdb=" O ARG A 494 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 147 through 158 Processing helix chain 'B' and resid 159 through 164 Processing helix chain 'B' and resid 189 through 196 removed outlier: 3.525A pdb=" N VAL B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 203 through 207 removed outlier: 3.739A pdb=" N SER B 206 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS B 207 " --> pdb=" O ALA B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 207' Processing helix chain 'B' and resid 224 through 233 removed outlier: 3.641A pdb=" N PHE B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 232 " --> pdb=" O PHE B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 253 removed outlier: 4.307A pdb=" N SER B 252 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP B 253 " --> pdb=" O ARG B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 removed outlier: 3.661A pdb=" N LYS B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 288 removed outlier: 3.557A pdb=" N ILE B 286 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 309 through 319 Processing helix chain 'B' and resid 326 through 331 Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 355 through 365 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 445 through 456 removed outlier: 3.703A pdb=" N GLU B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 111 through 114 Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.800A pdb=" N ARG C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 195 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.709A pdb=" N PHE C 224 " --> pdb=" O ASP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 276 Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 327 through 333 removed outlier: 3.675A pdb=" N SER C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 443 through 448 removed outlier: 3.560A pdb=" N SER C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 497 Processing helix chain 'D' and resid 86 through 90 Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 111 through 114 Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 147 through 158 Processing helix chain 'D' and resid 159 through 164 Processing helix chain 'D' and resid 180 through 184 removed outlier: 4.149A pdb=" N LYS D 184 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 197 removed outlier: 3.530A pdb=" N VAL D 194 " --> pdb=" O THR D 190 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 224 through 233 removed outlier: 3.933A pdb=" N PHE D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'D' and resid 283 through 288 removed outlier: 3.678A pdb=" N ILE D 286 " --> pdb=" O ASP D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 309 through 319 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 355 through 365 Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 445 through 456 removed outlier: 3.911A pdb=" N GLU D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 95 removed outlier: 4.901A pdb=" N LYS A 138 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 139 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU A 174 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 141 " --> pdb=" O LEU A 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 170 through 175 current: chain 'A' and resid 261 through 264 Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 395 removed outlier: 6.156A pdb=" N LYS A 391 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL A 407 " --> pdb=" O ILE A 424 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 423 through 424 current: chain 'B' and resid 414 through 416 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 414 through 416 current: chain 'B' and resid 431 through 437 removed outlier: 6.239A pdb=" N GLN B 431 " --> pdb=" O ILE B 468 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N GLU B 470 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N LYS B 433 " --> pdb=" O GLU B 470 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE B 472 " --> pdb=" O LYS B 433 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N THR B 435 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS B 467 " --> pdb=" O ILE B 485 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 484 through 485 current: chain 'B' and resid 501 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 491 through 492 removed outlier: 5.870A pdb=" N VAL A 417 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL A 401 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS B 393 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE B 409 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 412 through 414 removed outlier: 6.315A pdb=" N LYS A 482 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 476 through 477 removed outlier: 6.655A pdb=" N ARG A 476 " --> pdb=" O ILE A 514 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 174 removed outlier: 6.519A pdb=" N VAL B 139 " --> pdb=" O GLU B 171 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU B 173 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 141 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 93 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B 216 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N GLY B 304 " --> pdb=" O SER B 216 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA B 301 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE B 246 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N MET B 303 " --> pdb=" O ILE B 244 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 244 " --> pdb=" O MET B 303 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL B 305 " --> pdb=" O SER B 242 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ILE B 239 " --> pdb=" O ASN B 342 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N TYR B 344 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE B 241 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'B' and resid 219 through 221 Processing sheet with id=AB2, first strand: chain 'B' and resid 255 through 258 removed outlier: 3.501A pdb=" N SER B 269 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 258 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER B 267 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 461 through 462 removed outlier: 5.608A pdb=" N GLY B 461 " --> pdb=" O VAL B 479 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG B 478 " --> pdb=" O ILE B 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 170 through 175 removed outlier: 6.553A pdb=" N ILE C 139 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N LEU C 174 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL C 141 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LYS C 138 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU C 91 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU C 211 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 93 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ALA C 212 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N GLY C 300 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ALA C 238 " --> pdb=" O MET C 299 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE C 301 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C 236 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE C 235 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TYR C 341 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL C 237 " --> pdb=" O TYR C 341 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 116 through 117 Processing sheet with id=AB6, first strand: chain 'C' and resid 215 through 217 Processing sheet with id=AB7, first strand: chain 'C' and resid 253 through 255 removed outlier: 6.953A pdb=" N LYS C 254 " --> pdb=" O ILE C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 390 through 395 removed outlier: 6.069A pdb=" N LYS C 391 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL C 407 " --> pdb=" O ILE C 424 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 423 through 424 current: chain 'D' and resid 414 through 416 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 414 through 416 current: chain 'D' and resid 431 through 437 removed outlier: 6.296A pdb=" N GLN D 431 " --> pdb=" O ILE D 468 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLU D 470 " --> pdb=" O GLN D 431 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LYS D 433 " --> pdb=" O GLU D 470 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE D 472 " --> pdb=" O LYS D 433 " (cutoff:3.500A) removed outlier: 9.303A pdb=" N THR D 435 " --> pdb=" O ILE D 472 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 484 through 485 current: chain 'D' and resid 501 through 503 Processing sheet with id=AB9, first strand: chain 'C' and resid 491 through 492 removed outlier: 6.000A pdb=" N VAL C 417 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY C 437 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY C 419 " --> pdb=" O GLY C 437 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL C 401 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU C 420 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS D 393 " --> pdb=" O LEU D 410 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 412 through 414 removed outlier: 6.542A pdb=" N LYS C 412 " --> pdb=" O ILE C 430 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS C 482 " --> pdb=" O ILE C 520 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 169 through 174 removed outlier: 6.508A pdb=" N VAL D 139 " --> pdb=" O GLU D 171 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU D 173 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 141 " --> pdb=" O LEU D 173 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE D 93 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER D 216 " --> pdb=" O GLY D 304 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N GLY D 304 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA D 301 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE D 246 " --> pdb=" O ALA D 301 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET D 303 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE D 244 " --> pdb=" O MET D 303 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL D 305 " --> pdb=" O SER D 242 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE D 239 " --> pdb=" O ASN D 342 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR D 344 " --> pdb=" O ILE D 239 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE D 241 " --> pdb=" O TYR D 344 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 116 through 117 Processing sheet with id=AC4, first strand: chain 'D' and resid 219 through 221 Processing sheet with id=AC5, first strand: chain 'D' and resid 255 through 258 removed outlier: 3.998A pdb=" N SER D 267 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 461 through 462 removed outlier: 5.555A pdb=" N GLY D 461 " --> pdb=" O VAL D 479 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG D 478 " --> pdb=" O ILE D 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 350 hydrogen bonds defined for protein. 891 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: 2.24 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4524 1.34 - 1.46: 2538 1.46 - 1.58: 6860 1.58 - 1.70: 24 1.70 - 1.81: 82 Bond restraints: 14028 Sorted by residual: bond pdb=" CA THR C 80 " pdb=" C THR C 80 " ideal model delta sigma weight residual 1.523 1.486 0.037 1.34e-02 5.57e+03 7.63e+00 bond pdb=" O2B ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 1.529 1.475 0.054 2.20e-02 2.07e+03 5.96e+00 bond pdb=" O2B ATP D 602 " pdb=" PB ATP D 602 " ideal model delta sigma weight residual 1.529 1.476 0.053 2.20e-02 2.07e+03 5.72e+00 bond pdb=" O2B ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 1.529 1.478 0.051 2.20e-02 2.07e+03 5.43e+00 bond pdb=" O2B ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 1.529 1.478 0.051 2.20e-02 2.07e+03 5.33e+00 ... (remaining 14023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 18755 2.59 - 5.19: 217 5.19 - 7.78: 43 7.78 - 10.38: 6 10.38 - 12.97: 1 Bond angle restraints: 19022 Sorted by residual: angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 129.71 10.16 1.00e+00 1.00e+00 1.03e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 130.56 9.31 1.00e+00 1.00e+00 8.66e+01 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 131.65 8.22 1.00e+00 1.00e+00 6.76e+01 angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 133.03 6.84 1.00e+00 1.00e+00 4.68e+01 angle pdb=" PA ATP C 602 " pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 136.83 130.00 6.83 1.00e+00 1.00e+00 4.67e+01 ... (remaining 19017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 7390 17.76 - 35.52: 816 35.52 - 53.28: 249 53.28 - 71.05: 56 71.05 - 88.81: 18 Dihedral angle restraints: 8529 sinusoidal: 3495 harmonic: 5034 Sorted by residual: dihedral pdb=" CA GLY C 498 " pdb=" C GLY C 498 " pdb=" N TYR C 499 " pdb=" CA TYR C 499 " ideal model delta harmonic sigma weight residual -180.00 -152.22 -27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLY A 498 " pdb=" C GLY A 498 " pdb=" N TYR A 499 " pdb=" CA TYR A 499 " ideal model delta harmonic sigma weight residual -180.00 -155.57 -24.43 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA GLN D 230 " pdb=" C GLN D 230 " pdb=" N ASP D 231 " pdb=" CA ASP D 231 " ideal model delta harmonic sigma weight residual 180.00 156.35 23.65 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 8526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1428 0.049 - 0.099: 527 0.099 - 0.148: 158 0.148 - 0.197: 6 0.197 - 0.246: 1 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CG LEU B 410 " pdb=" CB LEU B 410 " pdb=" CD1 LEU B 410 " pdb=" CD2 LEU B 410 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ASN D 388 " pdb=" N ASN D 388 " pdb=" C ASN D 388 " pdb=" CB ASN D 388 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.01e-01 ... (remaining 2117 not shown) Planarity restraints: 2446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 287 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C ASP C 287 " -0.036 2.00e-02 2.50e+03 pdb=" O ASP C 287 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN C 288 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 257 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.46e+00 pdb=" CD GLU A 257 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU A 257 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 257 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 320 " -0.112 9.50e-02 1.11e+02 5.06e-02 2.18e+00 pdb=" NE ARG D 320 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG D 320 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG D 320 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG D 320 " 0.000 2.00e-02 2.50e+03 ... (remaining 2443 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 25 2.50 - 3.10: 10049 3.10 - 3.70: 20236 3.70 - 4.30: 31722 4.30 - 4.90: 53951 Nonbonded interactions: 115983 Sorted by model distance: nonbonded pdb=" OD2 ASP A 214 " pdb="MG MG A 603 " model vdw 1.900 2.170 nonbonded pdb=" O1A ATP C 602 " pdb="MG MG C 604 " model vdw 1.990 2.170 nonbonded pdb=" OD2 ASP D 218 " pdb="MG MG D 603 " model vdw 1.994 2.170 nonbonded pdb=" OD2 ASP C 214 " pdb="MG MG C 603 " model vdw 2.025 2.170 nonbonded pdb=" O1A ATP A 602 " pdb="MG MG A 604 " model vdw 2.046 2.170 ... (remaining 115978 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.960 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:6.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 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 : 0.009 0.062 14029 Z= 0.368 Angle : 0.759 12.971 19024 Z= 0.407 Chirality : 0.053 0.246 2120 Planarity : 0.004 0.051 2446 Dihedral : 16.933 88.807 5306 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 1.85 % Allowed : 22.19 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -1.13 (0.20), residues: 1736 helix: -0.50 (0.27), residues: 378 sheet: -0.50 (0.25), residues: 456 loop : -0.90 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 320 TYR 0.023 0.002 TYR A 343 PHE 0.018 0.002 PHE A 356 TRP 0.010 0.002 TRP D 350 HIS 0.007 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00862 / 0.37 (14028) covalent geometry : angle 0.75905 / 0.41 (19022) SS BOND : bond 0.00071 / 0.04 ( 1) SS BOND : angle 0.36245 / 0.21 ( 2) hydrogen bonds : bond 0.20025 / 12.97 ( 350) hydrogen bonds : angle 8.53624 / 5.87 ( 891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 151 ASN cc_start: 0.6979 (p0) cc_final: 0.6608 (OUTLIER) REVERT: A 156 ARG cc_start: 0.6776 (mtp85) cc_final: 0.5602 (mtt90) REVERT: A 223 LYS cc_start: 0.6281 (mtpt) cc_final: 0.5879 (mtpp) REVERT: A 226 GLN cc_start: 0.6151 (tp-100) cc_final: 0.5929 (tp40) REVERT: A 232 ASP cc_start: 0.7570 (t0) cc_final: 0.6971 (t0) REVERT: A 242 MET cc_start: 0.7130 (mtp) cc_final: 0.6783 (mtt) REVERT: A 250 PHE cc_start: 0.7409 (m-80) cc_final: 0.7013 (m-80) REVERT: A 337 ARG cc_start: 0.6460 (ttm-80) cc_final: 0.5770 (mtp-110) REVERT: A 344 ASP cc_start: 0.6283 (p0) cc_final: 0.6071 (t70) REVERT: A 354 GLU cc_start: 0.6866 (tt0) cc_final: 0.6294 (tt0) REVERT: A 375 ASP cc_start: 0.7024 (t0) cc_final: 0.6750 (m-30) REVERT: A 453 LYS cc_start: 0.6509 (OUTLIER) cc_final: 0.6253 (ptpt) REVERT: A 482 LYS cc_start: 0.7151 (mttt) cc_final: 0.6329 (mmtm) REVERT: A 496 THR cc_start: 0.7168 (OUTLIER) cc_final: 0.6907 (p) REVERT: A 502 LYS cc_start: 0.6599 (mttm) cc_final: 0.6387 (mtmt) REVERT: B 88 ARG cc_start: 0.7507 (mmm-85) cc_final: 0.6263 (ttp-110) REVERT: B 156 ARG cc_start: 0.7148 (mtp85) cc_final: 0.6521 (mtt-85) REVERT: B 205 ARG cc_start: 0.7935 (ptp90) cc_final: 0.7704 (ptp90) REVERT: B 315 ASN cc_start: 0.6780 (t0) cc_final: 0.6487 (t0) REVERT: B 334 PHE cc_start: 0.7170 (m-10) cc_final: 0.6954 (m-10) REVERT: B 338 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7625 (mp0) REVERT: B 348 ASP cc_start: 0.7983 (m-30) cc_final: 0.7583 (m-30) REVERT: B 351 GLU cc_start: 0.7465 (tp30) cc_final: 0.7213 (tp30) REVERT: B 361 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6882 (mt-10) REVERT: C 79 GLN cc_start: 0.4294 (OUTLIER) cc_final: 0.3020 (tp40) REVERT: C 135 ASN cc_start: 0.7553 (m-40) cc_final: 0.7334 (m-40) REVERT: C 156 ARG cc_start: 0.6902 (mtp85) cc_final: 0.6133 (mtt-85) REVERT: C 202 GLU cc_start: 0.6434 (tt0) cc_final: 0.5699 (mt-10) REVERT: C 254 LYS cc_start: 0.6395 (tttt) cc_final: 0.5749 (tttp) REVERT: C 266 GLU cc_start: 0.7008 (tp30) cc_final: 0.6771 (tm-30) REVERT: C 276 MET cc_start: 0.7281 (tpp) cc_final: 0.6963 (tpp) REVERT: C 295 PHE cc_start: 0.6712 (m-80) cc_final: 0.6475 (m-80) REVERT: C 334 LEU cc_start: 0.7052 (mt) cc_final: 0.6799 (mt) REVERT: C 385 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.5997 (ptp-110) REVERT: C 467 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7100 (tttm) REVERT: C 482 LYS cc_start: 0.7084 (mtmt) cc_final: 0.5950 (mmtm) REVERT: C 487 ASP cc_start: 0.7848 (t70) cc_final: 0.7239 (t0) REVERT: D 88 ARG cc_start: 0.7371 (mtm110) cc_final: 0.6300 (ptt90) REVERT: D 109 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7644 (ttp-170) REVERT: D 156 ARG cc_start: 0.7350 (mtp85) cc_final: 0.6865 (mtt180) REVERT: D 203 ASP cc_start: 0.6613 (t0) cc_final: 0.5909 (m-30) REVERT: D 247 ASP cc_start: 0.6540 (t0) cc_final: 0.5735 (p0) REVERT: D 280 MET cc_start: 0.5481 (OUTLIER) cc_final: 0.5131 (mtp) REVERT: D 315 ASN cc_start: 0.7287 (t0) cc_final: 0.7058 (t0) REVERT: D 337 LYS cc_start: 0.7548 (mmmm) cc_final: 0.7254 (tmmt) REVERT: D 340 TYR cc_start: 0.7650 (t80) cc_final: 0.7401 (t80) REVERT: D 348 ASP cc_start: 0.7875 (m-30) cc_final: 0.7641 (m-30) REVERT: D 361 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7049 (mm-30) REVERT: D 386 ARG cc_start: 0.7985 (mtt90) cc_final: 0.7688 (mmt-90) REVERT: D 398 LYS cc_start: 0.7729 (tttm) cc_final: 0.7394 (tttt) REVERT: D 429 ASN cc_start: 0.7299 (m-40) cc_final: 0.6636 (t160) REVERT: D 446 GLU cc_start: 0.6648 (mp0) cc_final: 0.6362 (mm-30) REVERT: D 464 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6894 (mt-10) REVERT: D 467 LYS cc_start: 0.6635 (mttt) cc_final: 0.6261 (mtpp) REVERT: D 489 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6205 (mp0) REVERT: D 517 LYS cc_start: 0.7561 (mttt) cc_final: 0.7179 (mmtm) outliers start: 27 outliers final: 9 residues processed: 257 average time/residue: 0.6619 time to fit residues: 184.7599 Evaluate side-chains 188 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 453 LYS Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 280 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN D 347 ASN D 396 ASN D 406 HIS D 412 ASN D 487 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.139673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.109890 restraints weight = 15370.286| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.86 r_work: 0.3190 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14029 Z= 0.129 Angle : 0.528 6.958 19024 Z= 0.280 Chirality : 0.048 0.160 2120 Planarity : 0.004 0.034 2446 Dihedral : 10.497 87.843 2111 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.90 % Allowed : 20.00 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -0.99 (0.20), residues: 1736 helix: -0.17 (0.27), residues: 384 sheet: -0.51 (0.24), residues: 466 loop : -0.87 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 385 TYR 0.015 0.001 TYR C 386 PHE 0.014 0.001 PHE D 360 TRP 0.007 0.001 TRP C 185 HIS 0.004 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14028) covalent geometry : angle 0.52832 / 0.28 (19022) SS BOND : bond 0.00235 / 0.12 ( 1) SS BOND : angle 0.94718 / 0.50 ( 2) hydrogen bonds : bond 0.03622 / 2.42 ( 350) hydrogen bonds : angle 6.48855 / 4.49 ( 891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 0.520 Fit side-chains REVERT: A 156 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7107 (mtt90) REVERT: A 226 GLN cc_start: 0.7404 (tp-100) cc_final: 0.7041 (tp40) REVERT: A 232 ASP cc_start: 0.8073 (t0) cc_final: 0.7662 (t0) REVERT: A 242 MET cc_start: 0.8018 (mtp) cc_final: 0.7692 (mtt) REVERT: A 263 GLU cc_start: 0.7502 (tt0) cc_final: 0.6834 (tm-30) REVERT: A 337 ARG cc_start: 0.7393 (ttm-80) cc_final: 0.6867 (ttt-90) REVERT: A 366 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.6724 (mmtt) REVERT: A 372 SER cc_start: 0.8709 (p) cc_final: 0.8502 (m) REVERT: A 375 ASP cc_start: 0.7921 (t0) cc_final: 0.7665 (t0) REVERT: A 398 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8121 (p) REVERT: A 482 LYS cc_start: 0.8099 (mttt) cc_final: 0.7501 (mmtm) REVERT: A 487 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7470 (p0) REVERT: A 496 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7454 (p) REVERT: B 88 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7364 (ttp-110) REVERT: B 156 ARG cc_start: 0.7970 (mtp85) cc_final: 0.7744 (mtt-85) REVERT: B 215 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8568 (mt) REVERT: B 262 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7486 (pttm) REVERT: B 315 ASN cc_start: 0.7897 (t0) cc_final: 0.7657 (t0) REVERT: B 348 ASP cc_start: 0.8354 (m-30) cc_final: 0.8009 (m-30) REVERT: B 361 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7891 (mt-10) REVERT: C 79 GLN cc_start: 0.4278 (OUTLIER) cc_final: 0.3083 (tp40) REVERT: C 151 ASN cc_start: 0.7287 (p0) cc_final: 0.7021 (p0) REVERT: C 156 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7412 (mtt-85) REVERT: C 202 GLU cc_start: 0.7463 (tt0) cc_final: 0.6790 (mt-10) REVERT: C 254 LYS cc_start: 0.7177 (tttt) cc_final: 0.6677 (tttp) REVERT: C 276 MET cc_start: 0.7852 (tpp) cc_final: 0.7612 (tpp) REVERT: C 295 PHE cc_start: 0.7666 (m-80) cc_final: 0.7401 (m-80) REVERT: C 334 LEU cc_start: 0.8259 (mt) cc_final: 0.7935 (mt) REVERT: C 467 LYS cc_start: 0.8414 (ttmt) cc_final: 0.8055 (tttm) REVERT: C 482 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7360 (mmtm) REVERT: C 487 ASP cc_start: 0.7986 (t70) cc_final: 0.7408 (t0) REVERT: D 88 ARG cc_start: 0.8295 (mtm110) cc_final: 0.7456 (ptt90) REVERT: D 203 ASP cc_start: 0.7024 (t0) cc_final: 0.6634 (m-30) REVERT: D 247 ASP cc_start: 0.6781 (t0) cc_final: 0.6237 (p0) REVERT: D 315 ASN cc_start: 0.8291 (t0) cc_final: 0.7783 (t0) REVERT: D 347 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7753 (m110) REVERT: D 429 ASN cc_start: 0.8007 (m-40) cc_final: 0.7611 (t160) REVERT: D 464 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7679 (mt-10) REVERT: D 489 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6808 (mp0) outliers start: 57 outliers final: 19 residues processed: 233 average time/residue: 0.5997 time to fit residues: 152.9784 Evaluate side-chains 195 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 353 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 120 optimal weight: 0.1980 chunk 47 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 20 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN D 196 GLN D 347 ASN D 406 HIS D 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.135664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104914 restraints weight = 15492.924| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.12 r_work: 0.3104 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14029 Z= 0.121 Angle : 0.502 7.736 19024 Z= 0.267 Chirality : 0.048 0.149 2120 Planarity : 0.003 0.029 2446 Dihedral : 9.544 89.112 2092 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.22 % Allowed : 21.92 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -0.88 (0.20), residues: 1736 helix: 0.04 (0.27), residues: 386 sheet: -0.62 (0.24), residues: 458 loop : -0.75 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 385 TYR 0.017 0.001 TYR C 386 PHE 0.013 0.001 PHE D 359 TRP 0.007 0.001 TRP C 185 HIS 0.004 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14028) covalent geometry : angle 0.50189 / 0.27 (19022) SS BOND : bond 0.00026 / 0.01 ( 1) SS BOND : angle 0.32820 / 0.17 ( 2) hydrogen bonds : bond 0.03256 / 2.19 ( 350) hydrogen bonds : angle 6.04735 / 4.19 ( 891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 174 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 156 ARG cc_start: 0.7532 (mtp85) cc_final: 0.6766 (mtt-85) REVERT: A 181 GLU cc_start: 0.5786 (OUTLIER) cc_final: 0.5455 (mp0) REVERT: A 232 ASP cc_start: 0.7886 (t0) cc_final: 0.7443 (t0) REVERT: A 242 MET cc_start: 0.7909 (mtp) cc_final: 0.7369 (mtm) REVERT: A 337 ARG cc_start: 0.7111 (ttm-80) cc_final: 0.6481 (ttt-90) REVERT: A 366 LYS cc_start: 0.7544 (OUTLIER) cc_final: 0.6561 (mmtt) REVERT: A 372 SER cc_start: 0.8573 (p) cc_final: 0.8360 (m) REVERT: A 398 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.7867 (p) REVERT: A 433 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8938 (m) REVERT: A 482 LYS cc_start: 0.7890 (mttt) cc_final: 0.7148 (mmtt) REVERT: A 487 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7365 (p0) REVERT: A 496 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7324 (p) REVERT: B 88 ARG cc_start: 0.8136 (mmm-85) cc_final: 0.7226 (ttp-110) REVERT: B 156 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7381 (mtt-85) REVERT: B 262 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7397 (pttm) REVERT: B 315 ASN cc_start: 0.7467 (t0) cc_final: 0.7255 (t0) REVERT: B 348 ASP cc_start: 0.8120 (m-30) cc_final: 0.7671 (m-30) REVERT: B 361 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7514 (mt-10) REVERT: B 401 ASP cc_start: 0.7905 (m-30) cc_final: 0.7502 (t70) REVERT: C 79 GLN cc_start: 0.3991 (OUTLIER) cc_final: 0.2998 (tp40) REVERT: C 156 ARG cc_start: 0.7714 (mtp85) cc_final: 0.7010 (mtt-85) REVERT: C 202 GLU cc_start: 0.7160 (tt0) cc_final: 0.6438 (mt-10) REVERT: C 254 LYS cc_start: 0.6702 (tttt) cc_final: 0.6424 (mtpp) REVERT: C 276 MET cc_start: 0.7745 (tpp) cc_final: 0.7404 (tpp) REVERT: C 295 PHE cc_start: 0.7466 (m-80) cc_final: 0.7177 (m-80) REVERT: C 322 ASP cc_start: 0.6673 (t70) cc_final: 0.6250 (t70) REVERT: C 467 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7769 (tttm) REVERT: C 482 LYS cc_start: 0.8123 (mtmt) cc_final: 0.6931 (mmtm) REVERT: C 487 ASP cc_start: 0.7925 (t70) cc_final: 0.7296 (t0) REVERT: D 88 ARG cc_start: 0.8162 (mtm110) cc_final: 0.7261 (ptt90) REVERT: D 109 ARG cc_start: 0.8319 (ttp-170) cc_final: 0.8023 (ttp-170) REVERT: D 203 ASP cc_start: 0.6944 (t0) cc_final: 0.6460 (m-30) REVERT: D 247 ASP cc_start: 0.6694 (t0) cc_final: 0.6026 (p0) REVERT: D 315 ASN cc_start: 0.7892 (t0) cc_final: 0.7355 (t0) REVERT: D 393 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7668 (mmmt) REVERT: D 429 ASN cc_start: 0.7930 (m-40) cc_final: 0.7374 (t160) REVERT: D 464 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7471 (mt-10) REVERT: D 489 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6686 (mp0) outliers start: 47 outliers final: 20 residues processed: 211 average time/residue: 0.5773 time to fit residues: 133.8400 Evaluate side-chains 192 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 393 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 170 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 79 optimal weight: 0.0470 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 68 optimal weight: 0.0170 chunk 157 optimal weight: 0.8980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN D 196 GLN D 347 ASN D 406 HIS D 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.108759 restraints weight = 15388.054| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.98 r_work: 0.3176 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14029 Z= 0.099 Angle : 0.476 8.349 19024 Z= 0.253 Chirality : 0.047 0.144 2120 Planarity : 0.003 0.030 2446 Dihedral : 9.035 89.812 2092 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.63 % Allowed : 21.92 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -0.74 (0.20), residues: 1736 helix: 0.15 (0.27), residues: 388 sheet: -0.54 (0.25), residues: 442 loop : -0.66 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 205 TYR 0.015 0.001 TYR C 386 PHE 0.015 0.001 PHE D 228 TRP 0.007 0.001 TRP C 185 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (14028) covalent geometry : angle 0.47568 / 0.25 (19022) SS BOND : bond 0.00055 / 0.03 ( 1) SS BOND : angle 0.26688 / 0.14 ( 2) hydrogen bonds : bond 0.02967 / 1.97 ( 350) hydrogen bonds : angle 5.80671 / 4.03 ( 891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 0.348 Fit side-chains REVERT: A 156 ARG cc_start: 0.7557 (mtp85) cc_final: 0.6850 (mtt-85) REVERT: A 181 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5606 (mp0) REVERT: A 232 ASP cc_start: 0.7941 (t0) cc_final: 0.7514 (t0) REVERT: A 242 MET cc_start: 0.7883 (mtp) cc_final: 0.7421 (mtm) REVERT: A 263 GLU cc_start: 0.7502 (tt0) cc_final: 0.6623 (tm-30) REVERT: A 366 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.6625 (mmtt) REVERT: A 372 SER cc_start: 0.8663 (p) cc_final: 0.8375 (m) REVERT: A 375 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7312 (t70) REVERT: A 398 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8054 (p) REVERT: A 482 LYS cc_start: 0.7890 (mttt) cc_final: 0.7183 (mmtt) REVERT: A 496 THR cc_start: 0.7665 (OUTLIER) cc_final: 0.7358 (p) REVERT: B 88 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7323 (ttp-110) REVERT: B 156 ARG cc_start: 0.7754 (mtp85) cc_final: 0.7377 (mtt-85) REVERT: B 262 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7452 (pttm) REVERT: B 348 ASP cc_start: 0.8080 (m-30) cc_final: 0.7642 (m-30) REVERT: B 361 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7640 (mt-10) REVERT: B 401 ASP cc_start: 0.7891 (m-30) cc_final: 0.7504 (t70) REVERT: C 151 ASN cc_start: 0.7581 (p0) cc_final: 0.7226 (OUTLIER) REVERT: C 156 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7056 (mtt-85) REVERT: C 202 GLU cc_start: 0.7224 (tt0) cc_final: 0.6519 (mt-10) REVERT: C 254 LYS cc_start: 0.6834 (tttt) cc_final: 0.6548 (mtpp) REVERT: C 258 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7252 (mm-30) REVERT: C 266 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: C 276 MET cc_start: 0.7695 (tpp) cc_final: 0.7447 (tpp) REVERT: C 295 PHE cc_start: 0.7568 (m-80) cc_final: 0.7283 (m-80) REVERT: C 322 ASP cc_start: 0.6593 (t70) cc_final: 0.6192 (t70) REVERT: C 348 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: C 385 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6590 (mtt90) REVERT: C 467 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7817 (tttm) REVERT: C 482 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7007 (mmtm) REVERT: C 487 ASP cc_start: 0.7873 (t70) cc_final: 0.7245 (t0) REVERT: D 88 ARG cc_start: 0.8208 (mtm110) cc_final: 0.7308 (ppt170) REVERT: D 109 ARG cc_start: 0.8321 (ttp-170) cc_final: 0.7969 (ttp-170) REVERT: D 203 ASP cc_start: 0.6997 (t0) cc_final: 0.6571 (m-30) REVERT: D 231 ASP cc_start: 0.8095 (t70) cc_final: 0.7870 (t0) REVERT: D 247 ASP cc_start: 0.6701 (t0) cc_final: 0.6078 (p0) REVERT: D 315 ASN cc_start: 0.7862 (t0) cc_final: 0.7337 (t0) REVERT: D 393 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7737 (mmmt) REVERT: D 398 LYS cc_start: 0.8293 (tptt) cc_final: 0.7999 (ttmm) REVERT: D 429 ASN cc_start: 0.7919 (m-40) cc_final: 0.7395 (t160) REVERT: D 464 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7422 (mt-10) REVERT: D 470 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7956 (tp30) REVERT: D 489 GLU cc_start: 0.7201 (mm-30) cc_final: 0.6761 (mp0) REVERT: D 520 VAL cc_start: 0.8484 (t) cc_final: 0.8250 (m) outliers start: 53 outliers final: 26 residues processed: 217 average time/residue: 0.5790 time to fit residues: 137.7106 Evaluate side-chains 205 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 470 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN B 315 ASN D 196 GLN D 406 HIS D 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107937 restraints weight = 15476.412| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.02 r_work: 0.3156 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14029 Z= 0.114 Angle : 0.483 8.578 19024 Z= 0.257 Chirality : 0.047 0.146 2120 Planarity : 0.003 0.029 2446 Dihedral : 8.769 89.876 2089 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.18 % Allowed : 21.71 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -0.75 (0.20), residues: 1736 helix: 0.20 (0.27), residues: 388 sheet: -0.68 (0.25), residues: 454 loop : -0.61 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 494 TYR 0.015 0.001 TYR C 386 PHE 0.013 0.001 PHE D 359 TRP 0.007 0.001 TRP C 185 HIS 0.004 0.001 HIS D 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (14028) covalent geometry : angle 0.48352 / 0.26 (19022) SS BOND : bond 0.00013 / 0.01 ( 1) SS BOND : angle 0.22940 / 0.12 ( 2) hydrogen bonds : bond 0.02968 / 1.98 ( 350) hydrogen bonds : angle 5.64825 / 3.91 ( 891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 170 time to evaluate : 0.509 Fit side-chains REVERT: A 156 ARG cc_start: 0.7678 (mtp85) cc_final: 0.6987 (mtt-85) REVERT: A 232 ASP cc_start: 0.8011 (t0) cc_final: 0.7552 (t0) REVERT: A 242 MET cc_start: 0.7949 (mtp) cc_final: 0.7536 (mtp) REVERT: A 263 GLU cc_start: 0.7434 (tt0) cc_final: 0.6532 (tm-30) REVERT: A 366 LYS cc_start: 0.7608 (pttp) cc_final: 0.6643 (mmtt) REVERT: A 372 SER cc_start: 0.8682 (p) cc_final: 0.8411 (m) REVERT: A 398 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8087 (p) REVERT: A 482 LYS cc_start: 0.7916 (mttt) cc_final: 0.7208 (mmtt) REVERT: A 496 THR cc_start: 0.7694 (OUTLIER) cc_final: 0.7397 (p) REVERT: B 88 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7447 (ttp-110) REVERT: B 156 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7431 (mtt-85) REVERT: B 262 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7459 (tmmt) REVERT: B 348 ASP cc_start: 0.8129 (m-30) cc_final: 0.7694 (m-30) REVERT: B 361 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7729 (mt-10) REVERT: B 401 ASP cc_start: 0.7934 (m-30) cc_final: 0.7543 (t70) REVERT: C 151 ASN cc_start: 0.7065 (p0) cc_final: 0.6676 (OUTLIER) REVERT: C 156 ARG cc_start: 0.7767 (mtp85) cc_final: 0.7136 (mtt-85) REVERT: C 202 GLU cc_start: 0.7268 (tt0) cc_final: 0.6571 (mt-10) REVERT: C 254 LYS cc_start: 0.6905 (tttt) cc_final: 0.6627 (mtpp) REVERT: C 258 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7223 (mm-30) REVERT: C 266 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: C 276 MET cc_start: 0.7705 (tpp) cc_final: 0.7467 (tpp) REVERT: C 293 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6710 (ptt) REVERT: C 295 PHE cc_start: 0.7552 (m-80) cc_final: 0.7284 (m-80) REVERT: C 301 ILE cc_start: 0.8361 (mt) cc_final: 0.8139 (mm) REVERT: C 322 ASP cc_start: 0.6751 (t70) cc_final: 0.6375 (t70) REVERT: C 348 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: C 385 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6555 (mtt90) REVERT: C 467 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7846 (tttm) REVERT: C 482 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7031 (mmtm) REVERT: C 487 ASP cc_start: 0.7922 (t70) cc_final: 0.7318 (t0) REVERT: D 88 ARG cc_start: 0.8186 (mtm110) cc_final: 0.7303 (ptt90) REVERT: D 109 ARG cc_start: 0.8339 (ttp-170) cc_final: 0.7944 (ttp-170) REVERT: D 203 ASP cc_start: 0.7026 (t0) cc_final: 0.6613 (m-30) REVERT: D 247 ASP cc_start: 0.6712 (t0) cc_final: 0.6093 (p0) REVERT: D 315 ASN cc_start: 0.7930 (t0) cc_final: 0.7459 (t0) REVERT: D 393 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.7733 (mmmt) REVERT: D 398 LYS cc_start: 0.8332 (tttt) cc_final: 0.8033 (ttmm) REVERT: D 429 ASN cc_start: 0.7944 (m-40) cc_final: 0.7426 (t160) REVERT: D 464 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7227 (pt0) REVERT: D 489 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6808 (mp0) REVERT: D 493 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7733 (mm-30) outliers start: 61 outliers final: 24 residues processed: 216 average time/residue: 0.5817 time to fit residues: 137.3358 Evaluate side-chains 196 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 429 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 307 ASP Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 393 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 9 optimal weight: 0.0980 chunk 100 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN B 315 ASN D 196 GLN D 406 HIS D 412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.138998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109262 restraints weight = 15431.191| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.04 r_work: 0.3173 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14029 Z= 0.095 Angle : 0.462 9.341 19024 Z= 0.246 Chirality : 0.047 0.143 2120 Planarity : 0.003 0.040 2446 Dihedral : 8.503 89.846 2089 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.22 % Allowed : 23.01 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -0.64 (0.21), residues: 1736 helix: 0.35 (0.27), residues: 384 sheet: -0.64 (0.24), residues: 450 loop : -0.55 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 496 TYR 0.014 0.001 TYR C 386 PHE 0.013 0.001 PHE D 359 TRP 0.007 0.001 TRP C 185 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (14028) covalent geometry : angle 0.46237 / 0.25 (19022) SS BOND : bond 0.00046 / 0.02 ( 1) SS BOND : angle 0.21379 / 0.11 ( 2) hydrogen bonds : bond 0.02759 / 1.84 ( 350) hydrogen bonds : angle 5.51771 / 3.82 ( 891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 175 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 156 ARG cc_start: 0.7597 (mtp85) cc_final: 0.6925 (mtt90) REVERT: A 232 ASP cc_start: 0.7932 (t0) cc_final: 0.7490 (t0) REVERT: A 242 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7433 (mtp) REVERT: A 366 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6598 (mmtt) REVERT: A 372 SER cc_start: 0.8603 (p) cc_final: 0.8335 (m) REVERT: A 398 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8071 (p) REVERT: A 482 LYS cc_start: 0.7818 (mttt) cc_final: 0.7068 (mmtt) REVERT: A 496 THR cc_start: 0.7595 (OUTLIER) cc_final: 0.7298 (p) REVERT: B 88 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7342 (ttp-110) REVERT: B 156 ARG cc_start: 0.7702 (mtp85) cc_final: 0.7329 (mtt-85) REVERT: B 262 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7434 (tmmt) REVERT: B 348 ASP cc_start: 0.8022 (m-30) cc_final: 0.7579 (m-30) REVERT: B 361 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7605 (mt-10) REVERT: B 401 ASP cc_start: 0.7854 (m-30) cc_final: 0.7464 (t70) REVERT: C 151 ASN cc_start: 0.6790 (p0) cc_final: 0.6460 (OUTLIER) REVERT: C 156 ARG cc_start: 0.7654 (mtp85) cc_final: 0.6736 (mmt-90) REVERT: C 202 GLU cc_start: 0.7153 (tt0) cc_final: 0.6437 (mt-10) REVERT: C 254 LYS cc_start: 0.6597 (tttt) cc_final: 0.6338 (mtpp) REVERT: C 258 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7200 (mm-30) REVERT: C 266 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: C 276 MET cc_start: 0.7734 (tpp) cc_final: 0.7440 (tpp) REVERT: C 293 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6525 (ptt) REVERT: C 295 PHE cc_start: 0.7386 (m-80) cc_final: 0.7110 (m-80) REVERT: C 301 ILE cc_start: 0.8265 (mt) cc_final: 0.8023 (mm) REVERT: C 322 ASP cc_start: 0.6578 (t70) cc_final: 0.6200 (t70) REVERT: C 348 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7929 (tp30) REVERT: C 385 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.6458 (mtt90) REVERT: C 467 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7737 (tttm) REVERT: C 482 LYS cc_start: 0.8062 (mtmt) cc_final: 0.6878 (mmtm) REVERT: C 487 ASP cc_start: 0.7910 (t70) cc_final: 0.7325 (t0) REVERT: D 88 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7316 (ptt90) REVERT: D 109 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7909 (ttp-170) REVERT: D 203 ASP cc_start: 0.6974 (t0) cc_final: 0.6479 (m-30) REVERT: D 207 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7544 (ptmm) REVERT: D 231 ASP cc_start: 0.8077 (t70) cc_final: 0.7860 (t0) REVERT: D 247 ASP cc_start: 0.6683 (t0) cc_final: 0.6033 (p0) REVERT: D 315 ASN cc_start: 0.7751 (t0) cc_final: 0.7271 (t0) REVERT: D 393 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7603 (mmmt) REVERT: D 398 LYS cc_start: 0.8201 (tttt) cc_final: 0.7864 (ttmm) REVERT: D 429 ASN cc_start: 0.7888 (m-40) cc_final: 0.7316 (t160) REVERT: D 464 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7026 (pt0) REVERT: D 470 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: D 489 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6740 (mp0) REVERT: D 493 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7705 (mm-30) REVERT: D 520 VAL cc_start: 0.8473 (t) cc_final: 0.8211 (m) outliers start: 47 outliers final: 25 residues processed: 210 average time/residue: 0.5952 time to fit residues: 137.4107 Evaluate side-chains 201 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 164 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 151 ASN Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 366 LYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 207 LYS Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 470 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 170 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 138 optimal weight: 0.0050 chunk 40 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 130 optimal weight: 0.0970 chunk 101 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 overall best weight: 0.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN B 315 ASN D 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.137851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.107113 restraints weight = 15495.416| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.06 r_work: 0.3146 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14029 Z= 0.095 Angle : 0.465 10.032 19024 Z= 0.247 Chirality : 0.047 0.143 2120 Planarity : 0.003 0.043 2446 Dihedral : 8.390 88.987 2089 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.15 % Allowed : 23.22 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -0.60 (0.21), residues: 1736 helix: 0.31 (0.27), residues: 384 sheet: -0.64 (0.24), residues: 456 loop : -0.46 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 494 TYR 0.011 0.001 TYR C 386 PHE 0.014 0.001 PHE B 334 TRP 0.007 0.001 TRP C 185 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (14028) covalent geometry : angle 0.46506 / 0.25 (19022) SS BOND : bond 0.00025 / 0.01 ( 1) SS BOND : angle 0.24216 / 0.13 ( 2) hydrogen bonds : bond 0.02741 / 1.82 ( 350) hydrogen bonds : angle 5.46219 / 3.78 ( 891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 156 ARG cc_start: 0.7453 (mtp85) cc_final: 0.6746 (mtt90) REVERT: A 232 ASP cc_start: 0.7807 (t0) cc_final: 0.7361 (t0) REVERT: A 242 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7321 (mtp) REVERT: A 366 LYS cc_start: 0.7469 (pttp) cc_final: 0.6531 (mmtt) REVERT: A 372 SER cc_start: 0.8495 (p) cc_final: 0.8239 (m) REVERT: A 398 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.7987 (p) REVERT: A 482 LYS cc_start: 0.7644 (mttt) cc_final: 0.6845 (mmtt) REVERT: A 496 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7187 (p) REVERT: B 88 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7261 (ttp-110) REVERT: B 156 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7243 (mtt-85) REVERT: B 262 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7476 (pttm) REVERT: B 348 ASP cc_start: 0.7939 (m-30) cc_final: 0.7486 (m-30) REVERT: B 361 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7438 (mt-10) REVERT: B 401 ASP cc_start: 0.7830 (m-30) cc_final: 0.7406 (t70) REVERT: C 151 ASN cc_start: 0.6454 (p0) cc_final: 0.6175 (OUTLIER) REVERT: C 156 ARG cc_start: 0.7589 (mtp85) cc_final: 0.6621 (mmt-90) REVERT: C 202 GLU cc_start: 0.7027 (tt0) cc_final: 0.6326 (mt-10) REVERT: C 254 LYS cc_start: 0.6473 (tttt) cc_final: 0.6229 (mtpp) REVERT: C 258 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7175 (mm-30) REVERT: C 266 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: C 276 MET cc_start: 0.7693 (tpp) cc_final: 0.7378 (tpp) REVERT: C 295 PHE cc_start: 0.7265 (m-80) cc_final: 0.6928 (m-80) REVERT: C 301 ILE cc_start: 0.8159 (mt) cc_final: 0.7900 (mm) REVERT: C 322 ASP cc_start: 0.6488 (t70) cc_final: 0.6079 (t70) REVERT: C 337 ARG cc_start: 0.7403 (ttm-80) cc_final: 0.6934 (ttm-80) REVERT: C 348 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: C 385 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6337 (mtt90) REVERT: C 467 LYS cc_start: 0.8110 (ttmt) cc_final: 0.7619 (tttm) REVERT: C 482 LYS cc_start: 0.7945 (mtmt) cc_final: 0.6725 (mmtm) REVERT: C 487 ASP cc_start: 0.7805 (t70) cc_final: 0.7233 (t0) REVERT: D 88 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7235 (ptt90) REVERT: D 109 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7833 (ttp-170) REVERT: D 203 ASP cc_start: 0.6915 (t0) cc_final: 0.6361 (m-30) REVERT: D 247 ASP cc_start: 0.6648 (t0) cc_final: 0.5976 (p0) REVERT: D 315 ASN cc_start: 0.7539 (t0) cc_final: 0.7010 (t0) REVERT: D 393 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7439 (mmmt) REVERT: D 398 LYS cc_start: 0.8114 (tttt) cc_final: 0.7759 (ttmm) REVERT: D 429 ASN cc_start: 0.7838 (m-40) cc_final: 0.7197 (t160) REVERT: D 464 GLU cc_start: 0.7472 (mt-10) cc_final: 0.6907 (pt0) REVERT: D 470 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: D 489 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6660 (mp0) REVERT: D 493 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7623 (mm-30) REVERT: D 520 VAL cc_start: 0.8333 (t) cc_final: 0.8039 (m) outliers start: 46 outliers final: 25 residues processed: 205 average time/residue: 0.5945 time to fit residues: 133.6116 Evaluate side-chains 196 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 406 HIS Chi-restraints excluded: chain D residue 470 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 4 optimal weight: 0.6980 chunk 163 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 151 ASN B 196 GLN B 315 ASN D 196 GLN D 412 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.137508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106840 restraints weight = 15275.453| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.04 r_work: 0.3135 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14029 Z= 0.102 Angle : 0.477 11.801 19024 Z= 0.252 Chirality : 0.047 0.143 2120 Planarity : 0.003 0.042 2446 Dihedral : 8.377 88.798 2089 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.88 % Allowed : 23.49 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -0.63 (0.21), residues: 1736 helix: 0.23 (0.27), residues: 400 sheet: -0.70 (0.24), residues: 456 loop : -0.43 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.012 0.001 TYR C 386 PHE 0.017 0.001 PHE B 334 TRP 0.006 0.001 TRP C 185 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (14028) covalent geometry : angle 0.47681 / 0.25 (19022) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 0.25413 / 0.13 ( 2) hydrogen bonds : bond 0.02751 / 1.82 ( 350) hydrogen bonds : angle 5.44451 / 3.76 ( 891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 156 ARG cc_start: 0.7468 (mtp85) cc_final: 0.6761 (mtt90) REVERT: A 172 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: A 181 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5428 (mp0) REVERT: A 232 ASP cc_start: 0.7743 (t0) cc_final: 0.7262 (t0) REVERT: A 242 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7285 (mtm) REVERT: A 366 LYS cc_start: 0.7481 (pttp) cc_final: 0.6542 (mmtt) REVERT: A 372 SER cc_start: 0.8481 (p) cc_final: 0.8234 (m) REVERT: A 398 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8016 (p) REVERT: A 482 LYS cc_start: 0.7610 (mttt) cc_final: 0.6826 (mmtt) REVERT: A 496 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7191 (p) REVERT: B 88 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7315 (ttp-110) REVERT: B 156 ARG cc_start: 0.7663 (mtp85) cc_final: 0.7255 (mtt-85) REVERT: B 262 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7502 (pttm) REVERT: B 348 ASP cc_start: 0.7948 (m-30) cc_final: 0.7487 (m-30) REVERT: B 361 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7428 (mt-10) REVERT: B 401 ASP cc_start: 0.7812 (m-30) cc_final: 0.7374 (t70) REVERT: C 151 ASN cc_start: 0.6526 (p0) cc_final: 0.6217 (OUTLIER) REVERT: C 156 ARG cc_start: 0.7590 (mtp85) cc_final: 0.6632 (mmt-90) REVERT: C 202 GLU cc_start: 0.7032 (tt0) cc_final: 0.6330 (mt-10) REVERT: C 254 LYS cc_start: 0.6506 (tttt) cc_final: 0.6276 (mtpp) REVERT: C 258 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7180 (mm-30) REVERT: C 266 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: C 276 MET cc_start: 0.7662 (tpp) cc_final: 0.7440 (tpp) REVERT: C 295 PHE cc_start: 0.7207 (m-80) cc_final: 0.6909 (m-80) REVERT: C 301 ILE cc_start: 0.8155 (mt) cc_final: 0.7894 (mm) REVERT: C 322 ASP cc_start: 0.6485 (t70) cc_final: 0.6055 (t70) REVERT: C 348 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7826 (tp30) REVERT: C 385 ARG cc_start: 0.6590 (OUTLIER) cc_final: 0.6311 (mtt90) REVERT: C 467 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7632 (tttm) REVERT: C 482 LYS cc_start: 0.7960 (mtmt) cc_final: 0.6739 (mmtm) REVERT: C 487 ASP cc_start: 0.7806 (t70) cc_final: 0.7259 (t0) REVERT: D 88 ARG cc_start: 0.8120 (mtm110) cc_final: 0.7234 (ptt90) REVERT: D 203 ASP cc_start: 0.6917 (t0) cc_final: 0.6368 (m-30) REVERT: D 247 ASP cc_start: 0.6673 (t0) cc_final: 0.5915 (p0) REVERT: D 296 LYS cc_start: 0.7172 (tptt) cc_final: 0.6909 (tptm) REVERT: D 315 ASN cc_start: 0.7576 (t0) cc_final: 0.7081 (t0) REVERT: D 393 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7421 (mmmt) REVERT: D 398 LYS cc_start: 0.8065 (tttt) cc_final: 0.7699 (ttmm) REVERT: D 429 ASN cc_start: 0.7813 (m-40) cc_final: 0.7177 (t160) REVERT: D 464 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6942 (pt0) REVERT: D 470 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7809 (tp30) REVERT: D 489 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6685 (mp0) REVERT: D 493 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7634 (mm-30) REVERT: D 520 VAL cc_start: 0.8391 (t) cc_final: 0.8069 (m) outliers start: 42 outliers final: 24 residues processed: 200 average time/residue: 0.6247 time to fit residues: 136.8381 Evaluate side-chains 197 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 162 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 470 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 4 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN B 315 ASN D 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.134980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.104300 restraints weight = 15457.113| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.03 r_work: 0.3097 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14029 Z= 0.137 Angle : 0.507 10.562 19024 Z= 0.268 Chirality : 0.048 0.145 2120 Planarity : 0.004 0.046 2446 Dihedral : 8.516 89.912 2089 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.88 % Allowed : 23.56 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -0.66 (0.20), residues: 1736 helix: 0.30 (0.27), residues: 400 sheet: -0.59 (0.24), residues: 452 loop : -0.60 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.015 0.001 TYR C 386 PHE 0.018 0.001 PHE B 334 TRP 0.005 0.001 TRP A 185 HIS 0.005 0.001 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (14028) covalent geometry : angle 0.50751 / 0.27 (19022) SS BOND : bond 0.00000 / 0.00 ( 1) SS BOND : angle 0.30618 / 0.16 ( 2) hydrogen bonds : bond 0.03013 / 2.01 ( 350) hydrogen bonds : angle 5.57951 / 3.85 ( 891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 156 ARG cc_start: 0.7472 (mtp85) cc_final: 0.6745 (mtt90) REVERT: A 181 GLU cc_start: 0.5681 (OUTLIER) cc_final: 0.5301 (mp0) REVERT: A 232 ASP cc_start: 0.7719 (t0) cc_final: 0.7252 (t0) REVERT: A 242 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7345 (mtp) REVERT: A 366 LYS cc_start: 0.7464 (pttp) cc_final: 0.6513 (mmtt) REVERT: A 372 SER cc_start: 0.8493 (p) cc_final: 0.8237 (m) REVERT: A 398 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7909 (p) REVERT: A 482 LYS cc_start: 0.7667 (mttt) cc_final: 0.6857 (mmtt) REVERT: B 88 ARG cc_start: 0.8351 (mmm-85) cc_final: 0.7324 (ttp-110) REVERT: B 156 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7239 (mtt-85) REVERT: B 205 ARG cc_start: 0.8334 (ptp-170) cc_final: 0.8055 (ptp-170) REVERT: B 262 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7547 (pttm) REVERT: B 348 ASP cc_start: 0.8019 (m-30) cc_final: 0.7531 (m-30) REVERT: B 361 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7525 (mt-10) REVERT: B 401 ASP cc_start: 0.7812 (m-30) cc_final: 0.7357 (t70) REVERT: B 481 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7803 (mtmm) REVERT: C 151 ASN cc_start: 0.6818 (p0) cc_final: 0.6440 (p0) REVERT: C 156 ARG cc_start: 0.7605 (mtp85) cc_final: 0.6896 (mtt-85) REVERT: C 202 GLU cc_start: 0.7023 (tt0) cc_final: 0.6281 (mt-10) REVERT: C 254 LYS cc_start: 0.6518 (tttt) cc_final: 0.6272 (mtpp) REVERT: C 258 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7301 (mm-30) REVERT: C 266 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: C 276 MET cc_start: 0.7597 (tpp) cc_final: 0.7377 (tpp) REVERT: C 295 PHE cc_start: 0.7174 (m-80) cc_final: 0.6911 (m-80) REVERT: C 301 ILE cc_start: 0.8196 (mt) cc_final: 0.7942 (mm) REVERT: C 322 ASP cc_start: 0.6632 (t70) cc_final: 0.6192 (t70) REVERT: C 348 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7825 (tp30) REVERT: C 385 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6423 (mtt90) REVERT: C 467 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7613 (tttm) REVERT: C 487 ASP cc_start: 0.7794 (t70) cc_final: 0.7235 (t0) REVERT: D 88 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7225 (ptt180) REVERT: D 203 ASP cc_start: 0.6943 (t0) cc_final: 0.6411 (m-30) REVERT: D 247 ASP cc_start: 0.6639 (t0) cc_final: 0.5935 (p0) REVERT: D 296 LYS cc_start: 0.6990 (tptt) cc_final: 0.6747 (tmtp) REVERT: D 315 ASN cc_start: 0.7680 (t0) cc_final: 0.7163 (t0) REVERT: D 393 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7464 (mmmt) REVERT: D 398 LYS cc_start: 0.8105 (tttt) cc_final: 0.7736 (ttmm) REVERT: D 429 ASN cc_start: 0.7890 (m-40) cc_final: 0.7255 (t160) REVERT: D 464 GLU cc_start: 0.7564 (mt-10) cc_final: 0.6993 (pt0) REVERT: D 470 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: D 489 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6720 (mp0) outliers start: 42 outliers final: 22 residues processed: 200 average time/residue: 0.6054 time to fit residues: 132.9969 Evaluate side-chains 192 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 326 ASP Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 393 LYS Chi-restraints excluded: chain D residue 470 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 93 optimal weight: 0.0870 chunk 167 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 86 optimal weight: 0.0570 chunk 71 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN B 315 ASN D 196 GLN D 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.137416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107117 restraints weight = 15375.095| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.98 r_work: 0.3146 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14029 Z= 0.097 Angle : 0.482 10.886 19024 Z= 0.254 Chirality : 0.047 0.142 2120 Planarity : 0.003 0.051 2446 Dihedral : 8.226 88.070 2089 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.47 % Allowed : 24.04 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -0.66 (0.21), residues: 1736 helix: 0.26 (0.27), residues: 400 sheet: -0.69 (0.24), residues: 456 loop : -0.51 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.012 0.001 TYR C 386 PHE 0.018 0.001 PHE B 334 TRP 0.007 0.001 TRP C 185 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (14028) covalent geometry : angle 0.48227 / 0.25 (19022) SS BOND : bond 0.00043 / 0.02 ( 1) SS BOND : angle 0.22727 / 0.12 ( 2) hydrogen bonds : bond 0.02750 / 1.82 ( 350) hydrogen bonds : angle 5.46313 / 3.78 ( 891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 156 ARG cc_start: 0.7478 (mtp85) cc_final: 0.6764 (mtt90) REVERT: A 172 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7592 (tt0) REVERT: A 232 ASP cc_start: 0.7729 (t0) cc_final: 0.7103 (t0) REVERT: A 242 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7398 (mtp) REVERT: A 337 ARG cc_start: 0.7260 (ttm-80) cc_final: 0.6406 (ttm-80) REVERT: A 366 LYS cc_start: 0.7500 (pttp) cc_final: 0.6573 (mmtt) REVERT: A 372 SER cc_start: 0.8486 (p) cc_final: 0.8245 (m) REVERT: A 398 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8073 (p) REVERT: A 482 LYS cc_start: 0.7615 (mttt) cc_final: 0.6868 (mmtt) REVERT: A 496 THR cc_start: 0.7481 (OUTLIER) cc_final: 0.7200 (p) REVERT: B 88 ARG cc_start: 0.8356 (mmm-85) cc_final: 0.7318 (ttp-110) REVERT: B 156 ARG cc_start: 0.7663 (mtp85) cc_final: 0.7112 (mtt-85) REVERT: B 262 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7407 (pttm) REVERT: B 348 ASP cc_start: 0.7946 (m-30) cc_final: 0.7469 (m-30) REVERT: B 361 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7460 (mt-10) REVERT: B 401 ASP cc_start: 0.7803 (m-30) cc_final: 0.7356 (t70) REVERT: B 481 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7835 (mtmm) REVERT: C 151 ASN cc_start: 0.6526 (p0) cc_final: 0.6219 (OUTLIER) REVERT: C 156 ARG cc_start: 0.7586 (mtp85) cc_final: 0.6649 (mmt-90) REVERT: C 202 GLU cc_start: 0.7074 (tt0) cc_final: 0.6368 (mt-10) REVERT: C 254 LYS cc_start: 0.6548 (tttt) cc_final: 0.6313 (mtpp) REVERT: C 258 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7344 (mm-30) REVERT: C 266 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6973 (tm-30) REVERT: C 276 MET cc_start: 0.7657 (tpp) cc_final: 0.7443 (tpp) REVERT: C 295 PHE cc_start: 0.7213 (m-80) cc_final: 0.6925 (m-80) REVERT: C 301 ILE cc_start: 0.8155 (mt) cc_final: 0.7907 (mm) REVERT: C 322 ASP cc_start: 0.6552 (t70) cc_final: 0.6132 (t70) REVERT: C 348 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: C 385 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6369 (mtt90) REVERT: C 467 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7663 (tttm) REVERT: C 487 ASP cc_start: 0.7809 (t70) cc_final: 0.7257 (t0) REVERT: D 88 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7242 (ptt90) REVERT: D 203 ASP cc_start: 0.6942 (t0) cc_final: 0.6413 (m-30) REVERT: D 207 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7492 (ptmm) REVERT: D 247 ASP cc_start: 0.6676 (t0) cc_final: 0.5958 (p0) REVERT: D 296 LYS cc_start: 0.7010 (tptt) cc_final: 0.6766 (tmtp) REVERT: D 315 ASN cc_start: 0.7621 (t0) cc_final: 0.7072 (t0) REVERT: D 393 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7506 (mmmt) REVERT: D 398 LYS cc_start: 0.8117 (tttt) cc_final: 0.7765 (ttmm) REVERT: D 429 ASN cc_start: 0.7864 (m-40) cc_final: 0.7239 (t160) REVERT: D 464 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6970 (pt0) REVERT: D 489 GLU cc_start: 0.7338 (mm-30) cc_final: 0.6726 (mp0) REVERT: D 493 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7563 (mm-30) REVERT: D 520 VAL cc_start: 0.8396 (t) cc_final: 0.8075 (m) outliers start: 36 outliers final: 20 residues processed: 197 average time/residue: 0.6125 time to fit residues: 132.5962 Evaluate side-chains 191 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain B residue 353 ILE Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain B residue 397 SER Chi-restraints excluded: chain B residue 406 HIS Chi-restraints excluded: chain B residue 497 SER Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 266 GLU Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 456 VAL Chi-restraints excluded: chain D residue 207 LYS Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 337 LYS Chi-restraints excluded: chain D residue 393 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 19 optimal weight: 0.0020 chunk 111 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN B 315 ASN D 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105869 restraints weight = 15533.548| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.05 r_work: 0.3122 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14029 Z= 0.111 Angle : 0.489 10.554 19024 Z= 0.259 Chirality : 0.047 0.143 2120 Planarity : 0.003 0.052 2446 Dihedral : 8.208 88.275 2089 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.19 % Allowed : 24.52 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.89 % Cis-general : 0.00 % 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: -0.73 (0.20), residues: 1736 helix: 0.13 (0.27), residues: 412 sheet: -0.64 (0.24), residues: 454 loop : -0.59 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 337 TYR 0.013 0.001 TYR C 386 PHE 0.016 0.001 PHE B 334 TRP 0.006 0.001 TRP C 185 HIS 0.003 0.001 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (14028) covalent geometry : angle 0.48893 / 0.26 (19022) SS BOND : bond 0.00019 / 0.01 ( 1) SS BOND : angle 0.27300 / 0.14 ( 2) hydrogen bonds : bond 0.02839 / 1.88 ( 350) hydrogen bonds : angle 5.43921 / 3.75 ( 891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4803.90 seconds wall clock time: 82 minutes 39.18 seconds (4959.18 seconds total)