Starting phenix.real_space_refine on Thu Mar 5 17:47:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l1r_23116/03_2026/7l1r_23116.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l1r_23116/03_2026/7l1r_23116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l1r_23116/03_2026/7l1r_23116.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l1r_23116/03_2026/7l1r_23116.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l1r_23116/03_2026/7l1r_23116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l1r_23116/03_2026/7l1r_23116.map" } resolution = 3.1 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= 0.005 sd= 0.050 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 17 5.49 5 Mg 6 5.21 5 S 78 5.16 5 C 15235 2.51 5 N 4214 2.21 5 O 4649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 244 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24199 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "B" Number of atoms: 3643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3643 Classifications: {'peptide': 475} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "C" Number of atoms: 3649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3649 Classifications: {'peptide': 476} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "D" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3621 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "E" Number of atoms: 3622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3622 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3629 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "G" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2211 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 271} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.72, per 1000 atoms: 0.24 Number of scatterers: 24199 At special positions: 0 Unit cell: (152.88, 123.48, 126, 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 78 16.00 P 17 15.00 Mg 6 11.99 O 4649 8.00 N 4214 7.00 C 15235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5690 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 19 sheets defined 47.5% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 175 through 186 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 216 through 219 removed outlier: 3.844A pdb=" N ASP A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 216 through 219' Processing helix chain 'A' and resid 231 through 253 removed outlier: 3.746A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.845A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.630A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.671A pdb=" N SER A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.608A pdb=" N PHE A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 397 removed outlier: 3.931A pdb=" N LYS A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 429 through 442 removed outlier: 3.506A pdb=" N GLN A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 467 removed outlier: 4.041A pdb=" N LYS A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 removed outlier: 3.880A pdb=" N LEU A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS A 474 " --> pdb=" O HIS A 470 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 498 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.516A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.556A pdb=" N VAL B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 219 removed outlier: 3.844A pdb=" N ASP B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 253 removed outlier: 4.033A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.845A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.510A pdb=" N ILE B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 338 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 372 through 380 removed outlier: 3.616A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.519A pdb=" N ALA B 387 " --> pdb=" O ARG B 383 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.516A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 443 Processing helix chain 'B' and resid 444 through 447 removed outlier: 3.765A pdb=" N ASP B 447 " --> pdb=" O PHE B 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 444 through 447' Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 467 Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.838A pdb=" N LEU B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG B 476 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.607A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.844A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 253 removed outlier: 3.651A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.845A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 322 through 325 removed outlier: 3.625A pdb=" N ASP C 325 " --> pdb=" O GLN C 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 322 through 325' Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'C' and resid 381 through 397 Processing helix chain 'C' and resid 403 through 420 Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 removed outlier: 3.503A pdb=" N LYS C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.880A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 164 through 179 removed outlier: 3.867A pdb=" N GLU D 170 " --> pdb=" O VAL D 166 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLN D 177 " --> pdb=" O HIS D 173 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 206 removed outlier: 3.670A pdb=" N GLY D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN D 196 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP D 197 " --> pdb=" O ARG D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 227 removed outlier: 3.525A pdb=" N ARG D 225 " --> pdb=" O PRO D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.666A pdb=" N THR D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 232 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET D 235 " --> pdb=" O THR D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.611A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 263 " --> pdb=" O GLN D 259 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.709A pdb=" N GLU D 284 " --> pdb=" O THR D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 323 removed outlier: 4.003A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 4.149A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.622A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 4.305A pdb=" N PHE D 420 " --> pdb=" O VAL D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.685A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N MET D 469 " --> pdb=" O LYS D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 178 Processing helix chain 'E' and resid 191 through 205 removed outlier: 3.797A pdb=" N ASN E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP E 197 " --> pdb=" O ARG E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 209 removed outlier: 4.066A pdb=" N SER E 209 " --> pdb=" O GLY E 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 206 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 4.960A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 4.027A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 315 through 325 removed outlier: 3.586A pdb=" N THR E 320 " --> pdb=" O PRO E 316 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 325 " --> pdb=" O THR E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 355 through 360 Processing helix chain 'E' and resid 360 through 387 removed outlier: 4.098A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 392 Processing helix chain 'E' and resid 393 through 411 removed outlier: 3.962A pdb=" N ARG E 402 " --> pdb=" O LEU E 398 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER E 411 " --> pdb=" O GLN E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 420 removed outlier: 3.766A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.848A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET E 469 " --> pdb=" O LYS E 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 179 removed outlier: 3.602A pdb=" N LEU F 167 " --> pdb=" O GLY F 163 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.730A pdb=" N ARG F 225 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET F 226 " --> pdb=" O PRO F 222 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 removed outlier: 4.025A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 292 removed outlier: 3.614A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG F 291 " --> pdb=" O GLN F 287 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE F 292 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 323 removed outlier: 3.549A pdb=" N THR F 320 " --> pdb=" O PRO F 316 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 385 removed outlier: 4.986A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 410 Processing helix chain 'F' and resid 414 through 418 removed outlier: 3.503A pdb=" N GLU F 418 " --> pdb=" O HIS F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.933A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.625A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET F 469 " --> pdb=" O LYS F 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 62 Proline residue: G 47 - end of helix Processing helix chain 'G' and resid 93 through 110 removed outlier: 3.569A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 122 through 131 Processing helix chain 'G' and resid 148 through 165 removed outlier: 4.325A pdb=" N ILE G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU G 154 " --> pdb=" O ALA G 150 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 287 removed outlier: 3.596A pdb=" N VAL G 218 " --> pdb=" O GLU G 214 " (cutoff:3.500A) Proline residue: G 221 - end of helix removed outlier: 3.523A pdb=" N SER G 264 " --> pdb=" O THR G 260 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE G 277 " --> pdb=" O ILE G 273 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 5.736A pdb=" N VAL A 31 " --> pdb=" O HIS A 42 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N HIS A 42 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 33 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA A 63 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.620A pdb=" N VAL A 108 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.917A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE B 73 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 91 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 7.078A pdb=" N VAL B 108 " --> pdb=" O THR B 225 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LEU B 316 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N VAL B 258 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N PHE B 318 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N TYR B 260 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N GLU B 320 " --> pdb=" O TYR B 260 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.675A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASN C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N LEU C 66 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 63 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.484A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.728A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.557A pdb=" N SER D 183 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N VAL D 214 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE D 185 " --> pdb=" O VAL D 214 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLY D 216 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY D 187 " --> pdb=" O GLY D 216 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS D 153 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N THR D 329 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLY D 155 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N LEU D 331 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE D 157 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 10 removed outlier: 5.671A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.370A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU E 331 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N PHE E 157 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 10 removed outlier: 6.621A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 54 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.623A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 138 through 140 removed outlier: 4.054A pdb=" N LEU G 138 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR G 79 " --> pdb=" O ALA G 117 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N ILE G 119 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TYR G 81 " --> pdb=" O ILE G 119 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE G 121 " --> pdb=" O TYR G 81 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL G 83 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ASN G 176 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU G 171 " --> pdb=" O LEU G 191 " (cutoff:3.500A) 1124 hydrogen bonds defined for protein. 3222 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: 4.02 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4272 1.31 - 1.44: 5802 1.44 - 1.57: 14343 1.57 - 1.69: 33 1.69 - 1.82: 154 Bond restraints: 24604 Sorted by residual: bond pdb=" C PRO B 280 " pdb=" O PRO B 280 " ideal model delta sigma weight residual 1.246 1.196 0.049 8.50e-03 1.38e+04 3.34e+01 bond pdb=" C4 ADP E 501 " pdb=" C5 ADP E 501 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" CA SER A 295 " pdb=" CB SER A 295 " ideal model delta sigma weight residual 1.528 1.463 0.066 1.56e-02 4.11e+03 1.76e+01 bond pdb=" C5 ADP E 501 " pdb=" C6 ADP E 501 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C ARG B 40 " pdb=" O ARG B 40 " ideal model delta sigma weight residual 1.234 1.184 0.050 1.22e-02 6.72e+03 1.71e+01 ... (remaining 24599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 31084 3.31 - 6.62: 2167 6.62 - 9.92: 99 9.92 - 13.23: 11 13.23 - 16.54: 3 Bond angle restraints: 33364 Sorted by residual: angle pdb=" PB ATP D 500 " pdb=" O3B ATP D 500 " pdb=" PG ATP D 500 " ideal model delta sigma weight residual 139.87 123.33 16.54 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 125.52 14.35 1.00e+00 1.00e+00 2.06e+02 angle pdb=" PB ATP F 500 " pdb=" O3B ATP F 500 " pdb=" PG ATP F 500 " ideal model delta sigma weight residual 139.87 126.51 13.36 1.00e+00 1.00e+00 1.78e+02 angle pdb=" PA ATP D 500 " pdb=" O3A ATP D 500 " pdb=" PB ATP D 500 " ideal model delta sigma weight residual 136.83 123.69 13.14 1.00e+00 1.00e+00 1.73e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 127.16 12.71 1.00e+00 1.00e+00 1.62e+02 ... (remaining 33359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.03: 14488 30.03 - 60.07: 486 60.07 - 90.10: 68 90.10 - 120.13: 0 120.13 - 150.16: 2 Dihedral angle restraints: 15044 sinusoidal: 6152 harmonic: 8892 Sorted by residual: dihedral pdb=" C ARG A 283 " pdb=" N ARG A 283 " pdb=" CA ARG A 283 " pdb=" CB ARG A 283 " ideal model delta harmonic sigma weight residual -122.60 -140.28 17.68 0 2.50e+00 1.60e-01 5.00e+01 dihedral pdb=" C ASP C 261 " pdb=" N ASP C 261 " pdb=" CA ASP C 261 " pdb=" CB ASP C 261 " ideal model delta harmonic sigma weight residual -122.60 -139.55 16.95 0 2.50e+00 1.60e-01 4.60e+01 dihedral pdb=" O1B ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PB ADP E 501 " pdb=" PA ADP E 501 " ideal model delta sinusoidal sigma weight residual 300.00 149.83 150.16 1 2.00e+01 2.50e-03 4.48e+01 ... (remaining 15041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3061 0.133 - 0.266: 685 0.266 - 0.399: 76 0.399 - 0.531: 15 0.531 - 0.664: 3 Chirality restraints: 3840 Sorted by residual: chirality pdb=" CA ASP C 261 " pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CB ASP C 261 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA ARG A 283 " pdb=" N ARG A 283 " pdb=" C ARG A 283 " pdb=" CB ARG A 283 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA TYR D 27 " pdb=" N TYR D 27 " pdb=" C TYR D 27 " pdb=" CB TYR D 27 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.58e+00 ... (remaining 3837 not shown) Planarity restraints: 4349 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 220 " -0.101 2.00e-02 2.50e+03 6.26e-02 7.84e+01 pdb=" CG TYR A 220 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 220 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TYR A 220 " 0.072 2.00e-02 2.50e+03 pdb=" CE1 TYR A 220 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 TYR A 220 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 220 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 220 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 199 " 0.110 2.00e-02 2.50e+03 6.02e-02 7.25e+01 pdb=" CG TYR D 199 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR D 199 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR D 199 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR D 199 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR D 199 " -0.039 2.00e-02 2.50e+03 pdb=" CZ TYR D 199 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 199 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 313 " 0.081 2.00e-02 2.50e+03 5.47e-02 5.97e+01 pdb=" CG TYR D 313 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR D 313 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR D 313 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR D 313 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR D 313 " -0.050 2.00e-02 2.50e+03 pdb=" CZ TYR D 313 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR D 313 " 0.102 2.00e-02 2.50e+03 ... (remaining 4346 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 97 2.55 - 3.14: 18686 3.14 - 3.73: 34453 3.73 - 4.31: 50848 4.31 - 4.90: 84559 Nonbonded interactions: 188643 Sorted by model distance: nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.965 2.170 nonbonded pdb=" O THR F 192 " pdb=" OG1 THR F 192 " model vdw 2.043 3.040 nonbonded pdb=" O1G ATP D 500 " pdb="MG MG D 501 " model vdw 2.098 2.170 nonbonded pdb=" O1G ATP F 500 " pdb="MG MG F 501 " model vdw 2.107 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.201 2.170 ... (remaining 188638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 601) selection = (chain 'B' and (resid 27 through 499 or resid 600 through 601)) selection = (chain 'C' and (resid 27 through 499 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 2 through 470 or resid 501)) selection = (chain 'E' and (resid 2 through 470 or resid 502)) selection = (chain 'F' and (resid 2 through 470 or resid 501)) } 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: 1.030 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.000 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 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 : 0.011 0.111 24604 Z= 0.691 Angle : 1.763 16.538 33364 Z= 1.202 Chirality : 0.111 0.664 3840 Planarity : 0.010 0.089 4349 Dihedral : 14.952 150.162 9354 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 3.32 % Allowed : 9.73 % Favored : 86.94 % Cbeta Deviations : 0.98 % Peptide Plane: Cis-proline : 4.83 % 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: -0.59 (0.14), residues: 3104 helix: -0.08 (0.14), residues: 1225 sheet: 0.26 (0.24), residues: 461 loop : -0.79 (0.16), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.105 0.005 ARG F 270 TYR 0.110 0.012 TYR D 199 PHE 0.093 0.009 PHE A 395 HIS 0.024 0.004 HIS F 173 Details of bonding type rmsd covalent geometry : bond 0.01135 (24604) covalent geometry : angle 1.76338 (33364) hydrogen bonds : bond 0.24764 ( 1124) hydrogen bonds : angle 7.75056 ( 3222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1210 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6611 (m-30) cc_final: 0.6241 (m-30) REVERT: A 38 ILE cc_start: 0.7211 (mm) cc_final: 0.6931 (mm) REVERT: A 48 MET cc_start: 0.7287 (mtm) cc_final: 0.6871 (mtm) REVERT: A 60 MET cc_start: 0.6973 (mmt) cc_final: 0.6750 (mmm) REVERT: A 93 ARG cc_start: 0.6450 (ptt180) cc_final: 0.6067 (ptt180) REVERT: A 127 ARG cc_start: 0.6613 (mtp85) cc_final: 0.6098 (mtp-110) REVERT: A 140 ARG cc_start: 0.7288 (ttt180) cc_final: 0.6960 (ttt90) REVERT: A 144 GLU cc_start: 0.7080 (pt0) cc_final: 0.6673 (pt0) REVERT: A 163 GLN cc_start: 0.7617 (tt0) cc_final: 0.7397 (tt0) REVERT: A 181 ASP cc_start: 0.7614 (m-30) cc_final: 0.7384 (m-30) REVERT: A 185 ASN cc_start: 0.7455 (t0) cc_final: 0.7087 (t0) REVERT: A 272 GLU cc_start: 0.6724 (tt0) cc_final: 0.6331 (tt0) REVERT: A 296 ARG cc_start: 0.7316 (mtm180) cc_final: 0.7040 (mtm-85) REVERT: A 299 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 313 LEU cc_start: 0.6879 (tp) cc_final: 0.6671 (tp) REVERT: A 341 GLN cc_start: 0.6849 (pm20) cc_final: 0.6520 (pm20) REVERT: A 358 ASN cc_start: 0.7107 (t0) cc_final: 0.6808 (t0) REVERT: A 375 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6952 (tpp) REVERT: A 391 GLU cc_start: 0.6866 (tp30) cc_final: 0.6651 (tp30) REVERT: A 426 GLN cc_start: 0.6986 (mm-40) cc_final: 0.6629 (mm-40) REVERT: A 427 PRO cc_start: 0.8032 (Cg_endo) cc_final: 0.7770 (Cg_exo) REVERT: A 431 GLU cc_start: 0.7501 (pm20) cc_final: 0.7144 (pm20) REVERT: A 474 HIS cc_start: 0.6589 (t-90) cc_final: 0.5753 (t-170) REVERT: A 478 THR cc_start: 0.7293 (m) cc_final: 0.7059 (t) REVERT: B 49 SER cc_start: 0.7711 (t) cc_final: 0.7133 (m) REVERT: B 51 GLU cc_start: 0.7006 (tt0) cc_final: 0.6248 (mt-10) REVERT: B 53 VAL cc_start: 0.6475 (OUTLIER) cc_final: 0.6219 (m) REVERT: B 67 GLU cc_start: 0.6538 (mm-30) cc_final: 0.6060 (mm-30) REVERT: B 127 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6856 (mtp85) REVERT: B 159 ILE cc_start: 0.7544 (mt) cc_final: 0.7192 (mt) REVERT: B 163 GLN cc_start: 0.8093 (tt0) cc_final: 0.7829 (tt0) REVERT: B 177 SER cc_start: 0.6777 (p) cc_final: 0.6462 (m) REVERT: B 181 ASP cc_start: 0.7620 (m-30) cc_final: 0.7311 (m-30) REVERT: B 185 ASN cc_start: 0.8070 (t0) cc_final: 0.7623 (t0) REVERT: B 202 GLU cc_start: 0.6651 (tp30) cc_final: 0.6283 (tp30) REVERT: B 222 ILE cc_start: 0.7288 (mt) cc_final: 0.7087 (mt) REVERT: B 227 SER cc_start: 0.7298 (p) cc_final: 0.6609 (p) REVERT: B 229 SER cc_start: 0.7132 (t) cc_final: 0.6748 (p) REVERT: B 230 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6442 (mm-40) REVERT: B 272 GLU cc_start: 0.6834 (tt0) cc_final: 0.6361 (tt0) REVERT: B 312 SER cc_start: 0.8155 (t) cc_final: 0.7701 (p) REVERT: B 320 GLU cc_start: 0.7190 (tt0) cc_final: 0.6925 (tt0) REVERT: B 385 ASP cc_start: 0.7003 (m-30) cc_final: 0.6575 (m-30) REVERT: B 428 ILE cc_start: 0.7848 (mt) cc_final: 0.7594 (mm) REVERT: B 449 PRO cc_start: 0.6591 (Cg_exo) cc_final: 0.6251 (Cg_endo) REVERT: B 467 ASN cc_start: 0.8260 (t0) cc_final: 0.7934 (t0) REVERT: B 478 THR cc_start: 0.7397 (OUTLIER) cc_final: 0.7163 (t) REVERT: C 34 VAL cc_start: 0.7563 (OUTLIER) cc_final: 0.7239 (p) REVERT: C 53 VAL cc_start: 0.6816 (p) cc_final: 0.6570 (m) REVERT: C 60 MET cc_start: 0.6349 (mmt) cc_final: 0.5976 (mmt) REVERT: C 62 MET cc_start: 0.6628 (ttt) cc_final: 0.6258 (ptm) REVERT: C 90 ARG cc_start: 0.7552 (ttp80) cc_final: 0.7155 (mtp-110) REVERT: C 109 ASN cc_start: 0.6996 (t0) cc_final: 0.6669 (t0) REVERT: C 122 GLU cc_start: 0.7579 (tp30) cc_final: 0.6938 (tp30) REVERT: C 127 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6888 (mtp-110) REVERT: C 137 MET cc_start: 0.8068 (mmm) cc_final: 0.7788 (mmm) REVERT: C 139 ARG cc_start: 0.7775 (mtt-85) cc_final: 0.7353 (mtt180) REVERT: C 144 GLU cc_start: 0.6740 (pt0) cc_final: 0.6374 (pt0) REVERT: C 147 GLN cc_start: 0.7571 (mm-40) cc_final: 0.7320 (mm110) REVERT: C 163 GLN cc_start: 0.7828 (tt0) cc_final: 0.7577 (tt0) REVERT: C 181 ASP cc_start: 0.7816 (m-30) cc_final: 0.7486 (m-30) REVERT: C 185 ASN cc_start: 0.7869 (t0) cc_final: 0.7569 (t0) REVERT: C 196 VAL cc_start: 0.7816 (t) cc_final: 0.7445 (m) REVERT: C 206 ARG cc_start: 0.7232 (ttt180) cc_final: 0.7019 (ttm-80) REVERT: C 210 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6525 (mm-30) REVERT: C 222 ILE cc_start: 0.7332 (mt) cc_final: 0.7108 (mt) REVERT: C 254 LYS cc_start: 0.7538 (mmtm) cc_final: 0.7273 (mtmm) REVERT: C 260 TYR cc_start: 0.7308 (m-80) cc_final: 0.7029 (m-80) REVERT: C 272 GLU cc_start: 0.7030 (mt-10) cc_final: 0.6701 (mt-10) REVERT: C 279 ARG cc_start: 0.7262 (mtt180) cc_final: 0.6568 (mtt-85) REVERT: C 361 LEU cc_start: 0.7587 (mp) cc_final: 0.7294 (mp) REVERT: C 385 ASP cc_start: 0.6920 (m-30) cc_final: 0.6661 (m-30) REVERT: C 409 LYS cc_start: 0.7461 (tptt) cc_final: 0.6883 (tptt) REVERT: C 418 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6847 (mm-30) REVERT: C 419 VAL cc_start: 0.7328 (t) cc_final: 0.7045 (p) REVERT: C 452 ASP cc_start: 0.7317 (m-30) cc_final: 0.7026 (m-30) REVERT: C 486 ASP cc_start: 0.7732 (m-30) cc_final: 0.7513 (m-30) REVERT: C 496 LYS cc_start: 0.8668 (mttt) cc_final: 0.8364 (mttt) REVERT: D 3 ARG cc_start: 0.6321 (mtm-85) cc_final: 0.5888 (mtm-85) REVERT: D 5 ARG cc_start: 0.6400 (mtm-85) cc_final: 0.6046 (mtm-85) REVERT: D 10 MET cc_start: 0.6669 (mtm) cc_final: 0.6229 (mtm) REVERT: D 26 ILE cc_start: 0.8149 (mt) cc_final: 0.7900 (mp) REVERT: D 37 ARG cc_start: 0.6856 (mtm180) cc_final: 0.6504 (mtm180) REVERT: D 64 MET cc_start: 0.6719 (mmt) cc_final: 0.6430 (mmt) REVERT: D 74 MET cc_start: 0.7380 (mtt) cc_final: 0.6906 (mtt) REVERT: D 75 GLU cc_start: 0.7476 (tt0) cc_final: 0.7178 (tt0) REVERT: D 84 SER cc_start: 0.7837 (m) cc_final: 0.7399 (p) REVERT: D 101 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6499 (mt-10) REVERT: D 114 ARG cc_start: 0.7071 (ttt180) cc_final: 0.6572 (ttt180) REVERT: D 115 ARG cc_start: 0.7495 (mtt-85) cc_final: 0.7123 (mtt-85) REVERT: D 116 ASP cc_start: 0.6914 (m-30) cc_final: 0.6344 (m-30) REVERT: D 125 PHE cc_start: 0.7641 (t80) cc_final: 0.7319 (t80) REVERT: D 133 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6618 (mt-10) REVERT: D 190 ASP cc_start: 0.6741 (m-30) cc_final: 0.5862 (m-30) REVERT: D 197 ASP cc_start: 0.6863 (t0) cc_final: 0.6571 (t0) REVERT: D 214 VAL cc_start: 0.7615 (t) cc_final: 0.7055 (p) REVERT: D 227 ARG cc_start: 0.7107 (mmt180) cc_final: 0.6590 (mmt90) REVERT: D 228 VAL cc_start: 0.7594 (OUTLIER) cc_final: 0.7307 (p) REVERT: D 237 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6760 (mt-10) REVERT: D 241 ASP cc_start: 0.7116 (m-30) cc_final: 0.6899 (m-30) REVERT: D 252 ASP cc_start: 0.6631 (t0) cc_final: 0.6335 (t0) REVERT: D 270 ARG cc_start: 0.7165 (mtt180) cc_final: 0.6851 (mtt-85) REVERT: D 271 MET cc_start: 0.7818 (mtt) cc_final: 0.7561 (ttm) REVERT: D 284 GLU cc_start: 0.6253 (mt-10) cc_final: 0.5673 (mt-10) REVERT: D 285 MET cc_start: 0.6711 (ttm) cc_final: 0.6310 (ttm) REVERT: D 307 TYR cc_start: 0.7769 (t80) cc_final: 0.7472 (t80) REVERT: D 326 ASP cc_start: 0.6757 (m-30) cc_final: 0.6162 (m-30) REVERT: D 352 ARG cc_start: 0.7040 (mtp180) cc_final: 0.6810 (mtp180) REVERT: D 356 PRO cc_start: 0.7859 (Cg_endo) cc_final: 0.7489 (Cg_exo) REVERT: D 364 TYR cc_start: 0.7658 (t80) cc_final: 0.7426 (t80) REVERT: D 375 GLN cc_start: 0.7210 (tp40) cc_final: 0.6911 (tp40) REVERT: D 378 LYS cc_start: 0.6824 (tttt) cc_final: 0.6589 (ttmm) REVERT: D 386 ILE cc_start: 0.7625 (mt) cc_final: 0.7346 (mp) REVERT: D 389 MET cc_start: 0.7813 (ttt) cc_final: 0.7376 (ttt) REVERT: D 404 ARG cc_start: 0.6966 (mmm160) cc_final: 0.6667 (mmm-85) REVERT: D 427 TYR cc_start: 0.7611 (t80) cc_final: 0.7154 (t80) REVERT: D 428 VAL cc_start: 0.8536 (t) cc_final: 0.8243 (m) REVERT: D 431 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7562 (mtpt) REVERT: D 450 GLU cc_start: 0.7079 (pt0) cc_final: 0.6642 (pt0) REVERT: E 1 MET cc_start: 0.3442 (mmt) cc_final: 0.3033 (mmt) REVERT: E 3 ARG cc_start: 0.6700 (mtm-85) cc_final: 0.6413 (mtm-85) REVERT: E 5 ARG cc_start: 0.6445 (ptp-110) cc_final: 0.6168 (ptp-110) REVERT: E 17 LYS cc_start: 0.7530 (tttt) cc_final: 0.7326 (tttt) REVERT: E 43 ASP cc_start: 0.7123 (m-30) cc_final: 0.6844 (m-30) REVERT: E 71 ILE cc_start: 0.7720 (mt) cc_final: 0.7437 (mt) REVERT: E 74 MET cc_start: 0.7241 (ttm) cc_final: 0.7031 (ttm) REVERT: E 89 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7164 (mm-30) REVERT: E 120 ARG cc_start: 0.6820 (mtp85) cc_final: 0.6562 (mtp85) REVERT: E 127 GLU cc_start: 0.6579 (mt-10) cc_final: 0.6266 (mt-10) REVERT: E 134 ILE cc_start: 0.8200 (mt) cc_final: 0.7970 (tt) REVERT: E 143 ASP cc_start: 0.5987 (m-30) cc_final: 0.5711 (m-30) REVERT: E 178 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7019 (mm-30) REVERT: E 202 MET cc_start: 0.7675 (mmt) cc_final: 0.7416 (mmt) REVERT: E 227 ARG cc_start: 0.6623 (mmt180) cc_final: 0.6158 (mmt90) REVERT: E 234 THR cc_start: 0.7331 (OUTLIER) cc_final: 0.7020 (m) REVERT: E 240 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6188 (ttp80) REVERT: E 247 VAL cc_start: 0.7787 (t) cc_final: 0.7294 (m) REVERT: E 256 ARG cc_start: 0.6877 (mtm-85) cc_final: 0.6674 (mtm-85) REVERT: E 284 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5658 (mt-10) REVERT: E 290 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7169 (mm-30) REVERT: E 304 GLN cc_start: 0.7289 (mt0) cc_final: 0.7071 (mt0) REVERT: E 307 TYR cc_start: 0.7993 (t80) cc_final: 0.7045 (t80) REVERT: E 312 ASP cc_start: 0.6943 (t0) cc_final: 0.6665 (t0) REVERT: E 359 VAL cc_start: 0.7648 (m) cc_final: 0.7400 (m) REVERT: E 365 GLN cc_start: 0.7711 (mt0) cc_final: 0.7316 (mt0) REVERT: E 375 GLN cc_start: 0.7521 (tp-100) cc_final: 0.7273 (tp-100) REVERT: E 376 ARG cc_start: 0.7601 (tpt170) cc_final: 0.6961 (tpt170) REVERT: E 379 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7274 (mt-10) REVERT: E 387 LEU cc_start: 0.7482 (mt) cc_final: 0.7098 (mt) REVERT: E 391 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7457 (mt-10) REVERT: E 405 ARG cc_start: 0.7578 (mpt180) cc_final: 0.7297 (mpt180) REVERT: E 406 ILE cc_start: 0.7679 (mt) cc_final: 0.7476 (mt) REVERT: E 418 GLU cc_start: 0.7468 (tt0) cc_final: 0.7033 (tt0) REVERT: E 423 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7278 (mm-40) REVERT: E 430 VAL cc_start: 0.7233 (p) cc_final: 0.6985 (m) REVERT: E 431 LYS cc_start: 0.7715 (ptmm) cc_final: 0.7420 (ptmm) REVERT: E 435 ARG cc_start: 0.7333 (ttp80) cc_final: 0.6912 (ttp80) REVERT: E 438 LYS cc_start: 0.7792 (ttpt) cc_final: 0.6907 (ttpt) REVERT: E 439 GLU cc_start: 0.7549 (mm-30) cc_final: 0.6933 (mm-30) REVERT: E 442 GLU cc_start: 0.7792 (mt-10) cc_final: 0.6984 (mt-10) REVERT: E 450 GLU cc_start: 0.7830 (pm20) cc_final: 0.7253 (pm20) REVERT: E 464 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7405 (mt-10) REVERT: F 5 ARG cc_start: 0.5986 (mmt180) cc_final: 0.5393 (mmt180) REVERT: F 10 MET cc_start: 0.6740 (mtm) cc_final: 0.6524 (mtm) REVERT: F 15 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6458 (m-30) REVERT: F 23 LEU cc_start: 0.8248 (mp) cc_final: 0.8020 (mt) REVERT: F 33 GLN cc_start: 0.7626 (mt0) cc_final: 0.7400 (mt0) REVERT: F 62 ILE cc_start: 0.7232 (mt) cc_final: 0.6995 (mt) REVERT: F 74 MET cc_start: 0.6824 (mtt) cc_final: 0.6353 (mtt) REVERT: F 89 GLU cc_start: 0.7493 (tp30) cc_final: 0.7264 (tp30) REVERT: F 114 ARG cc_start: 0.7199 (ttp-170) cc_final: 0.6845 (ttp80) REVERT: F 120 ARG cc_start: 0.7261 (ptm-80) cc_final: 0.6828 (ptt90) REVERT: F 124 LYS cc_start: 0.6851 (mttm) cc_final: 0.6459 (mttm) REVERT: F 127 GLU cc_start: 0.7384 (mt-10) cc_final: 0.6859 (mt-10) REVERT: F 170 GLU cc_start: 0.6940 (tp30) cc_final: 0.6731 (tp30) REVERT: F 201 GLU cc_start: 0.6761 (tp30) cc_final: 0.6496 (tp30) REVERT: F 202 MET cc_start: 0.6807 (mmp) cc_final: 0.6600 (mmp) REVERT: F 213 MET cc_start: 0.7479 (mtp) cc_final: 0.7179 (mtm) REVERT: F 215 PHE cc_start: 0.7665 (m-80) cc_final: 0.7352 (m-10) REVERT: F 237 GLU cc_start: 0.7072 (tt0) cc_final: 0.6618 (tt0) REVERT: F 242 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6747 (mm-30) REVERT: F 262 SER cc_start: 0.7086 (t) cc_final: 0.6870 (t) REVERT: F 271 MET cc_start: 0.8202 (mtp) cc_final: 0.7984 (mtm) REVERT: F 290 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6956 (mm-30) REVERT: F 292 ILE cc_start: 0.7601 (mt) cc_final: 0.7354 (mt) REVERT: F 303 ILE cc_start: 0.7677 (mt) cc_final: 0.7354 (mp) REVERT: F 364 TYR cc_start: 0.7314 (t80) cc_final: 0.6445 (t80) REVERT: F 378 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.7218 (ttmm) REVERT: F 381 GLN cc_start: 0.6986 (tt0) cc_final: 0.6728 (tt0) REVERT: F 389 MET cc_start: 0.7450 (mtm) cc_final: 0.6913 (mtm) REVERT: F 397 LYS cc_start: 0.7388 (tttm) cc_final: 0.7174 (tttm) REVERT: F 432 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6883 (mm-30) REVERT: F 435 ARG cc_start: 0.7965 (ttp80) cc_final: 0.7372 (ttp80) REVERT: F 438 LYS cc_start: 0.7533 (tttt) cc_final: 0.7158 (tttt) REVERT: F 439 GLU cc_start: 0.7694 (mt-10) cc_final: 0.6802 (mt-10) REVERT: F 442 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6599 (mt-10) REVERT: F 444 LYS cc_start: 0.7986 (tttt) cc_final: 0.7377 (tttt) REVERT: F 445 TYR cc_start: 0.8263 (m-80) cc_final: 0.7550 (m-80) REVERT: F 451 ASP cc_start: 0.7793 (m-30) cc_final: 0.7590 (m-30) REVERT: F 454 ARG cc_start: 0.7676 (mtp180) cc_final: 0.7412 (mtp85) REVERT: F 460 GLU cc_start: 0.8025 (mp0) cc_final: 0.7726 (mp0) REVERT: G 17 THR cc_start: 0.6796 (p) cc_final: 0.6580 (t) REVERT: G 18 LYS cc_start: 0.7552 (mttm) cc_final: 0.7323 (mttm) REVERT: G 25 LYS cc_start: 0.7149 (tptt) cc_final: 0.6907 (tptt) REVERT: G 27 MET cc_start: 0.7973 (mtp) cc_final: 0.7679 (mtp) REVERT: G 28 GLU cc_start: 0.7559 (tt0) cc_final: 0.7204 (tt0) REVERT: G 29 MET cc_start: 0.7112 (mmm) cc_final: 0.6615 (mmm) REVERT: G 31 SER cc_start: 0.8140 (t) cc_final: 0.7819 (p) REVERT: G 33 SER cc_start: 0.7994 (t) cc_final: 0.7663 (p) REVERT: G 39 GLU cc_start: 0.8506 (tt0) cc_final: 0.8198 (tt0) REVERT: G 70 MET cc_start: 0.7754 (mmm) cc_final: 0.7161 (mmm) REVERT: G 88 ARG cc_start: 0.7077 (ptt180) cc_final: 0.6690 (ptt180) REVERT: G 99 LEU cc_start: 0.8077 (mt) cc_final: 0.7866 (mt) REVERT: G 105 THR cc_start: 0.7059 (m) cc_final: 0.6609 (m) REVERT: G 109 ARG cc_start: 0.6789 (ptt90) cc_final: 0.6327 (ptt90) REVERT: G 116 TYR cc_start: 0.7674 (p90) cc_final: 0.7126 (p90) REVERT: G 134 MET cc_start: 0.6477 (mtm) cc_final: 0.5771 (mtm) REVERT: G 173 MET cc_start: 0.7328 (mtm) cc_final: 0.7058 (mtm) REVERT: G 174 TYR cc_start: 0.7327 (m-80) cc_final: 0.5851 (m-80) REVERT: G 188 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.6000 (tt0) REVERT: G 220 LEU cc_start: 0.8563 (mm) cc_final: 0.8342 (mm) REVERT: G 256 GLU cc_start: 0.6806 (tp30) cc_final: 0.6517 (tp30) REVERT: G 269 ARG cc_start: 0.7127 (ttp80) cc_final: 0.6879 (ttp-110) outliers start: 85 outliers final: 23 residues processed: 1252 average time/residue: 0.2100 time to fit residues: 380.7287 Evaluate side-chains 1134 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 1101 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 390 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 240 ARG Chi-restraints excluded: chain E residue 254 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain F residue 15 ASP Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 447 HIS Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 192 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 200 GLN A 266 GLN A 345 GLN A 371 GLN A 425 HIS A 466 GLN A 474 HIS A 488 ASN B 33 GLN B 186 GLN B 371 GLN B 397 GLN B 488 ASN C 46 ASN C 345 GLN C 397 GLN C 407 GLN C 422 GLN C 425 HIS C 488 ASN D 8 GLN D 33 GLN D 169 GLN D 253 ASN D 365 GLN E 33 GLN E 119 HIS E 169 GLN E 412 GLN F 8 GLN F 173 HIS F 217 GLN F 324 HIS F 371 GLN F 372 GLN F 423 GLN G 41 ASN G 183 GLN G 240 HIS G 249 ASN G 253 ASN G 285 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.136325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.121064 restraints weight = 35394.577| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.24 r_work: 0.3443 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24604 Z= 0.151 Angle : 0.662 9.745 33364 Z= 0.358 Chirality : 0.047 0.167 3840 Planarity : 0.005 0.060 4349 Dihedral : 9.922 137.090 3632 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.36 % Allowed : 16.50 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.35 (0.15), residues: 3104 helix: 1.04 (0.14), residues: 1255 sheet: 0.35 (0.23), residues: 485 loop : -0.50 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 270 TYR 0.025 0.002 TYR C 248 PHE 0.017 0.001 PHE C 236 HIS 0.009 0.001 HIS F 179 Details of bonding type rmsd covalent geometry : bond 0.00302 (24604) covalent geometry : angle 0.66175 (33364) hydrogen bonds : bond 0.06572 ( 1124) hydrogen bonds : angle 5.21963 ( 3222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 1086 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.6926 (m-30) cc_final: 0.6705 (m-30) REVERT: A 31 VAL cc_start: 0.7766 (p) cc_final: 0.7566 (m) REVERT: A 38 ILE cc_start: 0.8046 (mm) cc_final: 0.7817 (mm) REVERT: A 55 PHE cc_start: 0.7573 (m-80) cc_final: 0.7336 (m-10) REVERT: A 60 MET cc_start: 0.7654 (mmt) cc_final: 0.7446 (mmt) REVERT: A 89 ARG cc_start: 0.7060 (mtm-85) cc_final: 0.6765 (mtm-85) REVERT: A 127 ARG cc_start: 0.7483 (mtp85) cc_final: 0.7244 (mtp85) REVERT: A 170 ASP cc_start: 0.7392 (t70) cc_final: 0.7184 (t0) REVERT: A 181 ASP cc_start: 0.7634 (m-30) cc_final: 0.7423 (m-30) REVERT: A 211 THR cc_start: 0.7019 (m) cc_final: 0.6699 (p) REVERT: A 272 GLU cc_start: 0.7733 (tt0) cc_final: 0.7472 (tt0) REVERT: A 375 MET cc_start: 0.7983 (tpp) cc_final: 0.7663 (tpp) REVERT: A 376 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7799 (ttmm) REVERT: A 389 TYR cc_start: 0.8478 (t80) cc_final: 0.8106 (t80) REVERT: A 407 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7468 (mt0) REVERT: A 417 VAL cc_start: 0.8881 (m) cc_final: 0.8614 (t) REVERT: A 421 LYS cc_start: 0.8262 (mttp) cc_final: 0.7961 (mttp) REVERT: A 426 GLN cc_start: 0.7517 (mm-40) cc_final: 0.7232 (mm-40) REVERT: A 427 PRO cc_start: 0.8561 (Cg_endo) cc_final: 0.8311 (Cg_exo) REVERT: A 433 GLN cc_start: 0.7782 (mt0) cc_final: 0.7553 (mt0) REVERT: A 475 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8491 (tp) REVERT: A 476 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.8060 (ttm-80) REVERT: A 489 LYS cc_start: 0.7753 (tttt) cc_final: 0.7552 (tttt) REVERT: B 47 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8432 (p) REVERT: B 51 GLU cc_start: 0.8077 (tt0) cc_final: 0.7676 (mt-10) REVERT: B 53 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7877 (m) REVERT: B 67 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7441 (mm-30) REVERT: B 159 ILE cc_start: 0.8582 (mt) cc_final: 0.8337 (mt) REVERT: B 164 ARG cc_start: 0.8300 (mtm180) cc_final: 0.8098 (mtm-85) REVERT: B 177 SER cc_start: 0.8165 (p) cc_final: 0.7597 (p) REVERT: B 181 ASP cc_start: 0.7930 (m-30) cc_final: 0.7635 (m-30) REVERT: B 185 ASN cc_start: 0.8872 (t0) cc_final: 0.8454 (t0) REVERT: B 200 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7745 (mp10) REVERT: B 202 GLU cc_start: 0.7270 (tp30) cc_final: 0.6885 (tp30) REVERT: B 211 THR cc_start: 0.6274 (m) cc_final: 0.5700 (p) REVERT: B 213 ARG cc_start: 0.7881 (ttm110) cc_final: 0.7664 (ttp-110) REVERT: B 229 SER cc_start: 0.7731 (t) cc_final: 0.7344 (p) REVERT: B 272 GLU cc_start: 0.7841 (tt0) cc_final: 0.7605 (tt0) REVERT: B 312 SER cc_start: 0.8608 (t) cc_final: 0.8335 (p) REVERT: B 345 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.6588 (tt0) REVERT: B 385 ASP cc_start: 0.7082 (m-30) cc_final: 0.6812 (m-30) REVERT: B 428 ILE cc_start: 0.8551 (mt) cc_final: 0.8257 (mm) REVERT: B 442 ARG cc_start: 0.8230 (mmt-90) cc_final: 0.7606 (mmt-90) REVERT: B 458 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8235 (ttmt) REVERT: B 478 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8142 (t) REVERT: C 34 VAL cc_start: 0.8593 (t) cc_final: 0.8307 (p) REVERT: C 62 MET cc_start: 0.7827 (ttt) cc_final: 0.7581 (ttp) REVERT: C 90 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7838 (ttp-110) REVERT: C 101 GLU cc_start: 0.7978 (mp0) cc_final: 0.7688 (mp0) REVERT: C 122 GLU cc_start: 0.7677 (tp30) cc_final: 0.7310 (tp30) REVERT: C 137 MET cc_start: 0.8198 (mmm) cc_final: 0.7955 (mmm) REVERT: C 147 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7470 (mm110) REVERT: C 181 ASP cc_start: 0.7913 (m-30) cc_final: 0.7614 (m-30) REVERT: C 196 VAL cc_start: 0.8530 (t) cc_final: 0.8316 (m) REVERT: C 279 ARG cc_start: 0.7814 (mtt180) cc_final: 0.7403 (mtt-85) REVERT: C 372 ILE cc_start: 0.8790 (pt) cc_final: 0.8561 (mt) REVERT: C 451 GLU cc_start: 0.7922 (mp0) cc_final: 0.7602 (mp0) REVERT: C 452 ASP cc_start: 0.7530 (m-30) cc_final: 0.7313 (m-30) REVERT: D 10 MET cc_start: 0.7531 (mtm) cc_final: 0.7314 (mtm) REVERT: D 37 ARG cc_start: 0.7467 (mtm180) cc_final: 0.7097 (mtm180) REVERT: D 41 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7838 (mt-10) REVERT: D 84 SER cc_start: 0.8425 (m) cc_final: 0.8031 (p) REVERT: D 114 ARG cc_start: 0.7609 (ttt180) cc_final: 0.7390 (ttp80) REVERT: D 116 ASP cc_start: 0.7861 (m-30) cc_final: 0.7598 (m-30) REVERT: D 125 PHE cc_start: 0.8169 (t80) cc_final: 0.7960 (t80) REVERT: D 133 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7772 (mt-10) REVERT: D 190 ASP cc_start: 0.6804 (m-30) cc_final: 0.6005 (m-30) REVERT: D 227 ARG cc_start: 0.7963 (mmt180) cc_final: 0.7532 (mmt90) REVERT: D 228 VAL cc_start: 0.8211 (OUTLIER) cc_final: 0.7962 (p) REVERT: D 237 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7230 (mt-10) REVERT: D 241 ASP cc_start: 0.7887 (m-30) cc_final: 0.7654 (m-30) REVERT: D 284 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7067 (mt-10) REVERT: D 337 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7524 (mt-10) REVERT: D 387 LEU cc_start: 0.8521 (mt) cc_final: 0.8247 (mp) REVERT: D 439 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7648 (mm-30) REVERT: E 1 MET cc_start: 0.3507 (mmt) cc_final: 0.3122 (mmt) REVERT: E 5 ARG cc_start: 0.7699 (ptp-110) cc_final: 0.7483 (ptp-110) REVERT: E 64 MET cc_start: 0.7463 (mmt) cc_final: 0.7190 (mmm) REVERT: E 91 THR cc_start: 0.8074 (p) cc_final: 0.7773 (t) REVERT: E 127 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7396 (mt-10) REVERT: E 134 ILE cc_start: 0.8675 (mt) cc_final: 0.8452 (tt) REVERT: E 210 LYS cc_start: 0.8085 (mttt) cc_final: 0.7719 (mttt) REVERT: E 227 ARG cc_start: 0.7874 (mmt180) cc_final: 0.7590 (mmt90) REVERT: E 256 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7566 (mtt180) REVERT: E 283 THR cc_start: 0.8158 (t) cc_final: 0.7947 (m) REVERT: E 284 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6789 (mt-10) REVERT: E 307 TYR cc_start: 0.8702 (t80) cc_final: 0.8078 (t80) REVERT: E 334 LYS cc_start: 0.8416 (mmmm) cc_final: 0.8122 (mmmm) REVERT: E 362 GLU cc_start: 0.8069 (pm20) cc_final: 0.7800 (pm20) REVERT: E 365 GLN cc_start: 0.7964 (mt0) cc_final: 0.7692 (mt0) REVERT: E 376 ARG cc_start: 0.8543 (tpt170) cc_final: 0.8226 (tpt170) REVERT: E 402 ARG cc_start: 0.8241 (mmm-85) cc_final: 0.7794 (mtt-85) REVERT: E 405 ARG cc_start: 0.8378 (mpt180) cc_final: 0.8153 (mmt-90) REVERT: E 406 ILE cc_start: 0.8636 (mt) cc_final: 0.8430 (mt) REVERT: E 407 GLN cc_start: 0.8300 (tt0) cc_final: 0.8083 (tp-100) REVERT: E 418 GLU cc_start: 0.7825 (tt0) cc_final: 0.7421 (tt0) REVERT: E 419 GLN cc_start: 0.8022 (pt0) cc_final: 0.7783 (pt0) REVERT: E 431 LYS cc_start: 0.7987 (ptmm) cc_final: 0.7732 (ptmm) REVERT: E 435 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7672 (ttp80) REVERT: E 438 LYS cc_start: 0.8601 (ttpt) cc_final: 0.7972 (ttpt) REVERT: E 439 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7346 (mm-30) REVERT: E 441 LEU cc_start: 0.8617 (mt) cc_final: 0.8355 (mt) REVERT: E 442 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7572 (mt-10) REVERT: E 450 GLU cc_start: 0.8020 (pm20) cc_final: 0.7636 (pm20) REVERT: E 461 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7669 (mt-10) REVERT: E 464 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7624 (mt-10) REVERT: F 5 ARG cc_start: 0.7305 (mmt180) cc_final: 0.6920 (mmt180) REVERT: F 39 GLU cc_start: 0.7689 (mp0) cc_final: 0.7145 (mp0) REVERT: F 74 MET cc_start: 0.7774 (mtt) cc_final: 0.7573 (mtt) REVERT: F 89 GLU cc_start: 0.7848 (tp30) cc_final: 0.7559 (tp30) REVERT: F 95 VAL cc_start: 0.8302 (t) cc_final: 0.8003 (p) REVERT: F 99 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8122 (mt) REVERT: F 124 LYS cc_start: 0.8021 (mttm) cc_final: 0.7731 (mttm) REVERT: F 125 PHE cc_start: 0.8567 (t80) cc_final: 0.8363 (t80) REVERT: F 127 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7890 (mt-10) REVERT: F 202 MET cc_start: 0.8016 (mmp) cc_final: 0.7806 (mmp) REVERT: F 237 GLU cc_start: 0.7727 (tt0) cc_final: 0.7439 (tt0) REVERT: F 242 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7494 (mm-30) REVERT: F 326 ASP cc_start: 0.7974 (m-30) cc_final: 0.7754 (m-30) REVERT: F 335 LEU cc_start: 0.8119 (mt) cc_final: 0.7904 (mp) REVERT: F 352 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7391 (ttm-80) REVERT: F 389 MET cc_start: 0.7470 (mtm) cc_final: 0.7222 (mtm) REVERT: F 405 ARG cc_start: 0.8013 (mpt180) cc_final: 0.7804 (mpt180) REVERT: F 438 LYS cc_start: 0.8533 (tttt) cc_final: 0.8172 (tttt) REVERT: F 439 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7625 (mt-10) REVERT: F 442 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7528 (mt-10) REVERT: F 444 LYS cc_start: 0.8496 (tttt) cc_final: 0.8094 (tttt) REVERT: F 445 TYR cc_start: 0.8713 (m-80) cc_final: 0.8106 (m-80) REVERT: G 17 THR cc_start: 0.8189 (p) cc_final: 0.7810 (t) REVERT: G 33 SER cc_start: 0.8992 (t) cc_final: 0.8624 (p) REVERT: G 54 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7913 (mt-10) REVERT: G 70 MET cc_start: 0.7647 (mmm) cc_final: 0.7151 (mmm) REVERT: G 99 LEU cc_start: 0.8598 (mt) cc_final: 0.8366 (mt) REVERT: G 109 ARG cc_start: 0.7392 (ptt90) cc_final: 0.7186 (ptt90) REVERT: G 116 TYR cc_start: 0.7673 (p90) cc_final: 0.7251 (p90) REVERT: G 134 MET cc_start: 0.6286 (mtm) cc_final: 0.6055 (mtm) REVERT: G 173 MET cc_start: 0.8146 (mtm) cc_final: 0.7880 (mtm) REVERT: G 185 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7179 (mm-30) REVERT: G 188 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: G 192 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7554 (mm) REVERT: G 225 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8157 (mt-10) REVERT: G 229 TYR cc_start: 0.7562 (t80) cc_final: 0.7350 (t80) REVERT: G 256 GLU cc_start: 0.8042 (tp30) cc_final: 0.7821 (tp30) REVERT: G 263 LEU cc_start: 0.8556 (mp) cc_final: 0.8298 (mt) REVERT: G 269 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8335 (ttp-170) outliers start: 86 outliers final: 43 residues processed: 1121 average time/residue: 0.2029 time to fit residues: 333.7927 Evaluate side-chains 1097 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1044 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 334 LYS Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 302 optimal weight: 40.0000 chunk 87 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 256 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 307 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS A 163 GLN A 294 HIS A 358 ASN B 46 ASN B 230 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 GLN C 358 ASN C 371 GLN C 466 GLN C 474 HIS E 375 GLN E 412 GLN F 324 HIS G 95 ASN G 110 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116433 restraints weight = 35491.266| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.19 r_work: 0.3374 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24604 Z= 0.169 Angle : 0.623 7.874 33364 Z= 0.335 Chirality : 0.046 0.200 3840 Planarity : 0.005 0.062 4349 Dihedral : 9.314 125.040 3592 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.30 % Allowed : 20.72 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.40 (0.15), residues: 3104 helix: 1.19 (0.14), residues: 1251 sheet: 0.18 (0.22), residues: 544 loop : -0.53 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 161 TYR 0.025 0.002 TYR D 364 PHE 0.018 0.002 PHE A 343 HIS 0.009 0.001 HIS C 474 Details of bonding type rmsd covalent geometry : bond 0.00367 (24604) covalent geometry : angle 0.62334 (33364) hydrogen bonds : bond 0.06444 ( 1124) hydrogen bonds : angle 4.97408 ( 3222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1070 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8281 (ptp) cc_final: 0.7999 (ptt) REVERT: A 70 ASN cc_start: 0.8006 (p0) cc_final: 0.7749 (p0) REVERT: A 89 ARG cc_start: 0.7270 (mtm-85) cc_final: 0.7032 (mtm-85) REVERT: A 110 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.8076 (Cg_endo) REVERT: A 200 GLN cc_start: 0.7912 (mt0) cc_final: 0.7681 (mt0) REVERT: A 272 GLU cc_start: 0.7751 (tt0) cc_final: 0.7444 (tt0) REVERT: A 314 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.7828 (p) REVERT: A 375 MET cc_start: 0.8008 (tpp) cc_final: 0.7729 (tpp) REVERT: A 385 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7811 (t0) REVERT: A 386 LEU cc_start: 0.8674 (tp) cc_final: 0.8388 (tt) REVERT: A 409 LYS cc_start: 0.8341 (mtpp) cc_final: 0.8080 (mtpp) REVERT: A 417 VAL cc_start: 0.8827 (m) cc_final: 0.8587 (t) REVERT: A 426 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7309 (mm-40) REVERT: A 427 PRO cc_start: 0.8563 (Cg_endo) cc_final: 0.8311 (Cg_exo) REVERT: A 489 LYS cc_start: 0.8029 (tttt) cc_final: 0.7785 (tttt) REVERT: B 51 GLU cc_start: 0.8079 (tt0) cc_final: 0.7641 (mt-10) REVERT: B 67 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 159 ILE cc_start: 0.8515 (mt) cc_final: 0.8220 (mt) REVERT: B 177 SER cc_start: 0.8245 (p) cc_final: 0.7753 (m) REVERT: B 181 ASP cc_start: 0.8068 (m-30) cc_final: 0.7791 (m-30) REVERT: B 185 ASN cc_start: 0.8826 (t0) cc_final: 0.8460 (t0) REVERT: B 345 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: B 385 ASP cc_start: 0.7444 (m-30) cc_final: 0.7096 (m-30) REVERT: B 415 ARG cc_start: 0.8589 (mmt90) cc_final: 0.8237 (mtt90) REVERT: B 458 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8257 (ttmt) REVERT: B 478 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8092 (p) REVERT: B 479 LYS cc_start: 0.8517 (mptt) cc_final: 0.8061 (mptt) REVERT: B 481 LEU cc_start: 0.8435 (tp) cc_final: 0.8034 (mp) REVERT: C 34 VAL cc_start: 0.8578 (t) cc_final: 0.8301 (p) REVERT: C 62 MET cc_start: 0.7861 (ttt) cc_final: 0.7618 (ttp) REVERT: C 88 VAL cc_start: 0.7937 (p) cc_final: 0.7665 (t) REVERT: C 137 MET cc_start: 0.8312 (mmm) cc_final: 0.8065 (mmm) REVERT: C 181 ASP cc_start: 0.8013 (m-30) cc_final: 0.7779 (m-30) REVERT: C 185 ASN cc_start: 0.8660 (t0) cc_final: 0.8364 (t0) REVERT: C 196 VAL cc_start: 0.8497 (t) cc_final: 0.8262 (m) REVERT: C 224 VAL cc_start: 0.8528 (t) cc_final: 0.8322 (m) REVERT: C 274 SER cc_start: 0.8492 (p) cc_final: 0.8194 (m) REVERT: C 279 ARG cc_start: 0.7929 (mtt180) cc_final: 0.7580 (mtt-85) REVERT: C 314 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8016 (p) REVERT: C 372 ILE cc_start: 0.8791 (pt) cc_final: 0.8563 (mt) REVERT: C 390 ARG cc_start: 0.8256 (mmt180) cc_final: 0.7930 (mmm160) REVERT: C 451 GLU cc_start: 0.7949 (mp0) cc_final: 0.7636 (mp0) REVERT: C 462 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8561 (mm) REVERT: D 3 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.6622 (mtm-85) REVERT: D 10 MET cc_start: 0.7637 (mtm) cc_final: 0.7379 (mtm) REVERT: D 37 ARG cc_start: 0.7564 (mtm180) cc_final: 0.7150 (mtm180) REVERT: D 84 SER cc_start: 0.8410 (m) cc_final: 0.7957 (p) REVERT: D 101 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7879 (mp0) REVERT: D 114 ARG cc_start: 0.7658 (ttt180) cc_final: 0.7424 (ttp80) REVERT: D 116 ASP cc_start: 0.7828 (m-30) cc_final: 0.7519 (m-30) REVERT: D 120 ARG cc_start: 0.7990 (ttt90) cc_final: 0.7656 (ptm160) REVERT: D 133 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7743 (mt-10) REVERT: D 153 LYS cc_start: 0.7919 (mttp) cc_final: 0.7647 (mttt) REVERT: D 190 ASP cc_start: 0.6906 (m-30) cc_final: 0.6599 (m-30) REVERT: D 191 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7340 (mtt-85) REVERT: D 202 MET cc_start: 0.8051 (mmt) cc_final: 0.7829 (mmt) REVERT: D 227 ARG cc_start: 0.7954 (mmt180) cc_final: 0.7610 (mmt90) REVERT: D 228 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7903 (p) REVERT: D 237 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7043 (mt-10) REVERT: D 241 ASP cc_start: 0.7994 (m-30) cc_final: 0.7749 (m-30) REVERT: D 270 ARG cc_start: 0.8447 (mtt-85) cc_final: 0.8210 (mtt-85) REVERT: D 284 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7009 (mt-10) REVERT: D 337 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7565 (mt-10) REVERT: D 387 LEU cc_start: 0.8470 (mt) cc_final: 0.8181 (mp) REVERT: D 427 TYR cc_start: 0.8492 (t80) cc_final: 0.8267 (t80) REVERT: D 439 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7706 (mm-30) REVERT: D 464 GLU cc_start: 0.7818 (tp30) cc_final: 0.7610 (tp30) REVERT: E 1 MET cc_start: 0.3651 (mmt) cc_final: 0.3257 (mmt) REVERT: E 3 ARG cc_start: 0.7317 (mtm-85) cc_final: 0.7038 (mtm-85) REVERT: E 15 ASP cc_start: 0.7296 (m-30) cc_final: 0.7071 (m-30) REVERT: E 17 LYS cc_start: 0.8680 (tttt) cc_final: 0.8367 (ttmm) REVERT: E 91 THR cc_start: 0.7985 (p) cc_final: 0.7669 (t) REVERT: E 127 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7407 (mt-10) REVERT: E 134 ILE cc_start: 0.8682 (mt) cc_final: 0.8430 (tt) REVERT: E 170 GLU cc_start: 0.7860 (tp30) cc_final: 0.7567 (tt0) REVERT: E 178 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7388 (mm-30) REVERT: E 200 HIS cc_start: 0.7910 (m90) cc_final: 0.7699 (m-70) REVERT: E 210 LYS cc_start: 0.8176 (mttt) cc_final: 0.7812 (mttt) REVERT: E 283 THR cc_start: 0.8118 (t) cc_final: 0.7827 (m) REVERT: E 284 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6742 (mt-10) REVERT: E 301 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8202 (m) REVERT: E 334 LYS cc_start: 0.8400 (mmmm) cc_final: 0.8146 (mmmm) REVERT: E 376 ARG cc_start: 0.8610 (tpt170) cc_final: 0.8176 (tpt170) REVERT: E 379 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7721 (mt-10) REVERT: E 387 LEU cc_start: 0.8014 (mt) cc_final: 0.7577 (tp) REVERT: E 402 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.7877 (mtt-85) REVERT: E 405 ARG cc_start: 0.8471 (mpt180) cc_final: 0.8214 (mmt-90) REVERT: E 406 ILE cc_start: 0.8725 (mt) cc_final: 0.8486 (mt) REVERT: E 407 GLN cc_start: 0.8290 (tt0) cc_final: 0.8013 (tp40) REVERT: E 408 PHE cc_start: 0.8308 (m-80) cc_final: 0.8052 (m-80) REVERT: E 427 TYR cc_start: 0.8458 (t80) cc_final: 0.8195 (t80) REVERT: E 431 LYS cc_start: 0.8192 (ptmm) cc_final: 0.7885 (ptmm) REVERT: E 435 ARG cc_start: 0.8117 (ttp80) cc_final: 0.7784 (ttp80) REVERT: E 438 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8008 (ttpt) REVERT: E 439 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7307 (mm-30) REVERT: E 445 TYR cc_start: 0.7508 (m-80) cc_final: 0.7034 (m-80) REVERT: E 450 GLU cc_start: 0.8113 (pm20) cc_final: 0.7736 (pm20) REVERT: E 461 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7743 (mt-10) REVERT: E 464 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7626 (mt-10) REVERT: F 39 GLU cc_start: 0.7770 (mp0) cc_final: 0.7313 (mp0) REVERT: F 75 GLU cc_start: 0.7677 (tt0) cc_final: 0.7316 (tt0) REVERT: F 89 GLU cc_start: 0.7918 (tp30) cc_final: 0.7625 (tp30) REVERT: F 99 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8213 (mt) REVERT: F 114 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7559 (ttp80) REVERT: F 116 ASP cc_start: 0.8135 (m-30) cc_final: 0.7887 (m-30) REVERT: F 124 LYS cc_start: 0.8011 (mttm) cc_final: 0.7708 (mttm) REVERT: F 202 MET cc_start: 0.7801 (mmp) cc_final: 0.7480 (mmp) REVERT: F 242 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7454 (mm-30) REVERT: F 300 ILE cc_start: 0.8530 (mt) cc_final: 0.8262 (tt) REVERT: F 389 MET cc_start: 0.7469 (mtm) cc_final: 0.7224 (mtm) REVERT: F 392 LEU cc_start: 0.8387 (mt) cc_final: 0.8071 (mt) REVERT: F 423 GLN cc_start: 0.7779 (pt0) cc_final: 0.7548 (pm20) REVERT: F 438 LYS cc_start: 0.8653 (tttt) cc_final: 0.8107 (tttt) REVERT: F 439 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7751 (mt-10) REVERT: F 442 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7573 (mt-10) REVERT: F 444 LYS cc_start: 0.8543 (tttt) cc_final: 0.8242 (tttt) REVERT: F 445 TYR cc_start: 0.8686 (m-80) cc_final: 0.8255 (m-80) REVERT: G 11 LYS cc_start: 0.8225 (tptt) cc_final: 0.7928 (tptt) REVERT: G 17 THR cc_start: 0.8244 (p) cc_final: 0.7855 (t) REVERT: G 32 THR cc_start: 0.8905 (m) cc_final: 0.8569 (p) REVERT: G 33 SER cc_start: 0.8987 (t) cc_final: 0.8537 (p) REVERT: G 37 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8041 (ttp80) REVERT: G 54 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7990 (mt-10) REVERT: G 70 MET cc_start: 0.7687 (mmm) cc_final: 0.7129 (mmm) REVERT: G 82 LEU cc_start: 0.8318 (tp) cc_final: 0.8114 (tp) REVERT: G 85 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8057 (t) REVERT: G 95 ASN cc_start: 0.8357 (m-40) cc_final: 0.8135 (m-40) REVERT: G 99 LEU cc_start: 0.8586 (mt) cc_final: 0.8353 (mt) REVERT: G 134 MET cc_start: 0.6330 (mtm) cc_final: 0.5740 (mtm) REVERT: G 173 MET cc_start: 0.8125 (mtm) cc_final: 0.7867 (mtm) REVERT: G 184 GLN cc_start: 0.7810 (mp10) cc_final: 0.7414 (mp10) REVERT: G 185 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7300 (mm-30) REVERT: G 188 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: G 192 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7608 (mm) REVERT: G 225 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8208 (mt-10) REVERT: G 256 GLU cc_start: 0.8031 (tp30) cc_final: 0.7808 (tp30) REVERT: G 263 LEU cc_start: 0.8576 (mp) cc_final: 0.8318 (mt) outliers start: 110 outliers final: 64 residues processed: 1103 average time/residue: 0.2001 time to fit residues: 324.2435 Evaluate side-chains 1124 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1047 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 295 optimal weight: 20.0000 chunk 4 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN B 33 GLN B 163 GLN B 371 GLN C 147 GLN C 172 GLN C 371 GLN C 474 HIS D 174 ASN ** E 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 324 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.111695 restraints weight = 35634.861| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.14 r_work: 0.3301 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 24604 Z= 0.303 Angle : 0.716 8.516 33364 Z= 0.386 Chirality : 0.051 0.206 3840 Planarity : 0.006 0.078 4349 Dihedral : 9.007 124.702 3584 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 5.00 % Allowed : 22.17 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: -0.14 (0.15), residues: 3104 helix: 0.76 (0.14), residues: 1257 sheet: -0.02 (0.22), residues: 525 loop : -0.88 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 476 TYR 0.029 0.003 TYR E 238 PHE 0.022 0.002 PHE C 236 HIS 0.014 0.002 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00676 (24604) covalent geometry : angle 0.71596 (33364) hydrogen bonds : bond 0.07584 ( 1124) hydrogen bonds : angle 5.17396 ( 3222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1089 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.8476 (t) cc_final: 0.8156 (m) REVERT: A 54 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6858 (pt0) REVERT: A 87 GLU cc_start: 0.7574 (pt0) cc_final: 0.7372 (pt0) REVERT: A 89 ARG cc_start: 0.7295 (mtm-85) cc_final: 0.7021 (mtm-85) REVERT: A 101 GLU cc_start: 0.7584 (mp0) cc_final: 0.7375 (mp0) REVERT: A 125 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7286 (pt0) REVERT: A 127 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7489 (mtp85) REVERT: A 211 THR cc_start: 0.7824 (m) cc_final: 0.7438 (p) REVERT: A 272 GLU cc_start: 0.7744 (tt0) cc_final: 0.7471 (tt0) REVERT: A 303 LYS cc_start: 0.8221 (tptp) cc_final: 0.8019 (tptp) REVERT: A 375 MET cc_start: 0.8294 (tpp) cc_final: 0.7944 (tpp) REVERT: A 377 LYS cc_start: 0.8223 (mtmm) cc_final: 0.8004 (mtmm) REVERT: A 385 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7820 (t0) REVERT: A 386 LEU cc_start: 0.8730 (tp) cc_final: 0.8471 (tt) REVERT: A 426 GLN cc_start: 0.7711 (mm-40) cc_final: 0.7401 (mm-40) REVERT: A 446 ASP cc_start: 0.7475 (p0) cc_final: 0.7267 (p0) REVERT: A 489 LYS cc_start: 0.8446 (tttt) cc_final: 0.8223 (tttt) REVERT: B 67 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7671 (mm-30) REVERT: B 137 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8032 (mtm) REVERT: B 144 GLU cc_start: 0.7343 (pt0) cc_final: 0.6983 (pt0) REVERT: B 177 SER cc_start: 0.8191 (p) cc_final: 0.7828 (m) REVERT: B 181 ASP cc_start: 0.8084 (m-30) cc_final: 0.7823 (m-30) REVERT: B 185 ASN cc_start: 0.8901 (t0) cc_final: 0.8609 (t0) REVERT: B 202 GLU cc_start: 0.7307 (tp30) cc_final: 0.7065 (tp30) REVERT: B 208 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8149 (p) REVERT: B 218 LEU cc_start: 0.8588 (tp) cc_final: 0.8351 (mt) REVERT: B 272 GLU cc_start: 0.7629 (tt0) cc_final: 0.7297 (tt0) REVERT: B 336 SER cc_start: 0.8888 (t) cc_final: 0.8634 (p) REVERT: B 353 VAL cc_start: 0.8481 (t) cc_final: 0.8043 (m) REVERT: B 385 ASP cc_start: 0.7636 (m-30) cc_final: 0.7214 (m-30) REVERT: B 423 ASP cc_start: 0.7570 (p0) cc_final: 0.7244 (p0) REVERT: B 442 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7805 (mmp80) REVERT: B 478 THR cc_start: 0.8232 (m) cc_final: 0.7926 (p) REVERT: B 479 LYS cc_start: 0.8414 (mptt) cc_final: 0.8020 (mptt) REVERT: B 480 ASP cc_start: 0.7489 (t0) cc_final: 0.7234 (t0) REVERT: B 481 LEU cc_start: 0.8549 (tp) cc_final: 0.8288 (mp) REVERT: B 484 GLU cc_start: 0.7920 (mp0) cc_final: 0.7686 (mp0) REVERT: C 34 VAL cc_start: 0.8619 (t) cc_final: 0.8292 (p) REVERT: C 62 MET cc_start: 0.7931 (ttt) cc_final: 0.7680 (ttp) REVERT: C 80 THR cc_start: 0.8353 (p) cc_final: 0.8051 (m) REVERT: C 88 VAL cc_start: 0.7974 (p) cc_final: 0.7759 (t) REVERT: C 137 MET cc_start: 0.8297 (mmm) cc_final: 0.8067 (mmm) REVERT: C 147 GLN cc_start: 0.7835 (mm-40) cc_final: 0.7603 (mm110) REVERT: C 181 ASP cc_start: 0.8073 (m-30) cc_final: 0.7813 (m-30) REVERT: C 196 VAL cc_start: 0.8528 (t) cc_final: 0.8305 (m) REVERT: C 260 TYR cc_start: 0.7892 (m-80) cc_final: 0.7645 (m-80) REVERT: C 272 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7387 (mt-10) REVERT: C 274 SER cc_start: 0.8490 (p) cc_final: 0.8251 (m) REVERT: C 314 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.7974 (p) REVERT: C 349 PHE cc_start: 0.8507 (t80) cc_final: 0.8259 (t80) REVERT: C 372 ILE cc_start: 0.8766 (pt) cc_final: 0.8487 (mm) REVERT: C 451 GLU cc_start: 0.7990 (mp0) cc_final: 0.7686 (mp0) REVERT: C 462 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8529 (mm) REVERT: C 467 ASN cc_start: 0.8556 (t0) cc_final: 0.7856 (t0) REVERT: D 10 MET cc_start: 0.7749 (mtm) cc_final: 0.7453 (mtm) REVERT: D 37 ARG cc_start: 0.7630 (mtm180) cc_final: 0.7170 (mtm180) REVERT: D 70 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8547 (mt) REVERT: D 84 SER cc_start: 0.8433 (m) cc_final: 0.7982 (p) REVERT: D 114 ARG cc_start: 0.7673 (ttt180) cc_final: 0.7432 (ttp80) REVERT: D 116 ASP cc_start: 0.7815 (m-30) cc_final: 0.7521 (m-30) REVERT: D 133 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7698 (mt-10) REVERT: D 190 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6613 (m-30) REVERT: D 191 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7266 (mtt-85) REVERT: D 227 ARG cc_start: 0.8129 (mmt180) cc_final: 0.7776 (mmt90) REVERT: D 237 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7153 (mt-10) REVERT: D 241 ASP cc_start: 0.7992 (m-30) cc_final: 0.7755 (m-30) REVERT: D 246 ASP cc_start: 0.7725 (m-30) cc_final: 0.7465 (m-30) REVERT: D 284 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7097 (mt-10) REVERT: D 352 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7503 (mtp180) REVERT: D 387 LEU cc_start: 0.8443 (mt) cc_final: 0.8225 (mp) REVERT: D 439 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7769 (mm-30) REVERT: D 464 GLU cc_start: 0.7844 (tp30) cc_final: 0.7604 (tp30) REVERT: E 1 MET cc_start: 0.3604 (mmt) cc_final: 0.3242 (mmt) REVERT: E 3 ARG cc_start: 0.7225 (mtm-85) cc_final: 0.6939 (mtm-85) REVERT: E 15 ASP cc_start: 0.7339 (m-30) cc_final: 0.7052 (m-30) REVERT: E 17 LYS cc_start: 0.8726 (tttt) cc_final: 0.8370 (ttmm) REVERT: E 91 THR cc_start: 0.7940 (p) cc_final: 0.7596 (t) REVERT: E 127 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7573 (mt-10) REVERT: E 134 ILE cc_start: 0.8745 (mt) cc_final: 0.8468 (tt) REVERT: E 170 GLU cc_start: 0.7908 (tp30) cc_final: 0.7566 (tt0) REVERT: E 178 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7167 (mm-30) REVERT: E 203 LYS cc_start: 0.8396 (tppt) cc_final: 0.8176 (tppt) REVERT: E 210 LYS cc_start: 0.8236 (mttt) cc_final: 0.7879 (mttt) REVERT: E 256 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7843 (mtm-85) REVERT: E 284 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6749 (mt-10) REVERT: E 312 ASP cc_start: 0.7895 (t0) cc_final: 0.7671 (t0) REVERT: E 334 LYS cc_start: 0.8414 (mmmm) cc_final: 0.8139 (mmmm) REVERT: E 335 LEU cc_start: 0.8881 (mt) cc_final: 0.8675 (mt) REVERT: E 354 LEU cc_start: 0.8485 (tp) cc_final: 0.8267 (tt) REVERT: E 365 GLN cc_start: 0.8166 (mt0) cc_final: 0.7887 (mt0) REVERT: E 379 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7942 (mt-10) REVERT: E 387 LEU cc_start: 0.8016 (mt) cc_final: 0.7665 (mt) REVERT: E 402 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.7976 (mtt-85) REVERT: E 405 ARG cc_start: 0.8507 (mpt180) cc_final: 0.8136 (mpt180) REVERT: E 406 ILE cc_start: 0.8833 (mt) cc_final: 0.8604 (mt) REVERT: E 421 THR cc_start: 0.8301 (t) cc_final: 0.8028 (p) REVERT: E 423 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7406 (mm-40) REVERT: E 427 TYR cc_start: 0.8580 (t80) cc_final: 0.8270 (t80) REVERT: E 431 LYS cc_start: 0.8213 (ptmm) cc_final: 0.7888 (ptmm) REVERT: E 435 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7766 (ttp80) REVERT: E 438 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8008 (ttpt) REVERT: E 439 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7296 (mm-30) REVERT: E 450 GLU cc_start: 0.8119 (pm20) cc_final: 0.7723 (pm20) REVERT: E 464 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7611 (mt-10) REVERT: F 39 GLU cc_start: 0.7825 (mp0) cc_final: 0.7410 (mp0) REVERT: F 49 GLU cc_start: 0.7606 (tt0) cc_final: 0.7206 (tt0) REVERT: F 75 GLU cc_start: 0.7796 (tt0) cc_final: 0.7418 (tt0) REVERT: F 89 GLU cc_start: 0.8037 (tp30) cc_final: 0.7741 (tp30) REVERT: F 114 ARG cc_start: 0.7870 (ttp80) cc_final: 0.7604 (ttp80) REVERT: F 116 ASP cc_start: 0.8129 (m-30) cc_final: 0.7864 (m-30) REVERT: F 124 LYS cc_start: 0.8095 (mttm) cc_final: 0.7832 (mttm) REVERT: F 241 ASP cc_start: 0.7513 (m-30) cc_final: 0.6967 (m-30) REVERT: F 254 ILE cc_start: 0.8660 (tp) cc_final: 0.8349 (mt) REVERT: F 300 ILE cc_start: 0.8545 (mt) cc_final: 0.8307 (tt) REVERT: F 356 PRO cc_start: 0.8562 (Cg_exo) cc_final: 0.8282 (Cg_endo) REVERT: F 368 ARG cc_start: 0.8399 (mmt180) cc_final: 0.8168 (mpt180) REVERT: F 380 LEU cc_start: 0.8401 (mt) cc_final: 0.8185 (mt) REVERT: F 389 MET cc_start: 0.7505 (mtm) cc_final: 0.7173 (mtm) REVERT: F 439 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7705 (mt-10) REVERT: F 442 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7558 (mt-10) REVERT: F 444 LYS cc_start: 0.8519 (tttt) cc_final: 0.8184 (tttt) REVERT: F 445 TYR cc_start: 0.8637 (m-80) cc_final: 0.8285 (m-80) REVERT: F 448 LEU cc_start: 0.9047 (mm) cc_final: 0.8701 (mp) REVERT: G 11 LYS cc_start: 0.8378 (tptt) cc_final: 0.7848 (tptt) REVERT: G 15 ASN cc_start: 0.8076 (m-40) cc_final: 0.7772 (m-40) REVERT: G 17 THR cc_start: 0.8293 (p) cc_final: 0.7919 (t) REVERT: G 33 SER cc_start: 0.9018 (t) cc_final: 0.8658 (p) REVERT: G 36 ASN cc_start: 0.8789 (t0) cc_final: 0.8377 (t0) REVERT: G 37 ARG cc_start: 0.8338 (ttp80) cc_final: 0.8071 (ttp80) REVERT: G 54 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8071 (mt-10) REVERT: G 70 MET cc_start: 0.7708 (mmm) cc_final: 0.7206 (mmm) REVERT: G 85 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8231 (t) REVERT: G 88 ARG cc_start: 0.7630 (ptt180) cc_final: 0.7414 (ptm160) REVERT: G 99 LEU cc_start: 0.8616 (mt) cc_final: 0.8366 (mt) REVERT: G 119 ILE cc_start: 0.7858 (mt) cc_final: 0.7616 (mt) REVERT: G 173 MET cc_start: 0.8120 (mtm) cc_final: 0.7895 (mtm) REVERT: G 185 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7387 (mm-30) REVERT: G 188 GLU cc_start: 0.7718 (tt0) cc_final: 0.7328 (tt0) REVERT: G 192 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7533 (mm) REVERT: G 225 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8238 (mt-10) REVERT: G 256 GLU cc_start: 0.8070 (tp30) cc_final: 0.7820 (tp30) REVERT: G 259 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8352 (ttp80) outliers start: 128 outliers final: 87 residues processed: 1138 average time/residue: 0.2029 time to fit residues: 338.1902 Evaluate side-chains 1170 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1070 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 54 GLU Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 366 VAL Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 172 TYR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 169 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 283 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN C 172 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN C 474 HIS D 173 HIS D 219 ASN D 330 ASN E 375 GLN E 407 GLN F 28 ASN G 95 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.129125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114498 restraints weight = 35333.344| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.16 r_work: 0.3345 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24604 Z= 0.137 Angle : 0.575 7.447 33364 Z= 0.304 Chirality : 0.044 0.149 3840 Planarity : 0.005 0.073 4349 Dihedral : 8.296 111.925 3579 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.10 % Allowed : 24.00 % Favored : 71.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.36 (0.15), residues: 3104 helix: 1.31 (0.15), residues: 1251 sheet: 0.09 (0.22), residues: 546 loop : -0.69 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 476 TYR 0.022 0.001 TYR C 248 PHE 0.023 0.001 PHE A 494 HIS 0.008 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00297 (24604) covalent geometry : angle 0.57532 (33364) hydrogen bonds : bond 0.05424 ( 1124) hydrogen bonds : angle 4.75846 ( 3222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1072 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 SER cc_start: 0.8448 (t) cc_final: 0.8130 (m) REVERT: A 54 GLU cc_start: 0.7892 (pt0) cc_final: 0.7025 (pt0) REVERT: A 84 GLU cc_start: 0.7669 (tt0) cc_final: 0.7369 (tm-30) REVERT: A 89 ARG cc_start: 0.7270 (mtm-85) cc_final: 0.6964 (mtm-85) REVERT: A 101 GLU cc_start: 0.7540 (mp0) cc_final: 0.7331 (mp0) REVERT: A 125 GLU cc_start: 0.7405 (pt0) cc_final: 0.7142 (pt0) REVERT: A 127 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7492 (mtp85) REVERT: A 186 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7898 (mm-40) REVERT: A 251 TYR cc_start: 0.8380 (m-80) cc_final: 0.8140 (m-80) REVERT: A 272 GLU cc_start: 0.7795 (tt0) cc_final: 0.7472 (tt0) REVERT: A 344 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8371 (mp) REVERT: A 375 MET cc_start: 0.8177 (tpp) cc_final: 0.7780 (tpp) REVERT: A 385 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7849 (t0) REVERT: A 386 LEU cc_start: 0.8686 (tp) cc_final: 0.8406 (tt) REVERT: A 426 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7429 (mm-40) REVERT: A 474 HIS cc_start: 0.8240 (t70) cc_final: 0.7970 (t-90) REVERT: A 476 ARG cc_start: 0.8509 (ttm110) cc_final: 0.8297 (ttm-80) REVERT: A 480 ASP cc_start: 0.7191 (t0) cc_final: 0.6899 (m-30) REVERT: A 489 LYS cc_start: 0.8414 (tttt) cc_final: 0.8207 (tttt) REVERT: B 144 GLU cc_start: 0.7322 (pt0) cc_final: 0.6893 (pt0) REVERT: B 154 ASP cc_start: 0.7706 (t0) cc_final: 0.7500 (t0) REVERT: B 177 SER cc_start: 0.8196 (p) cc_final: 0.7739 (m) REVERT: B 181 ASP cc_start: 0.8059 (m-30) cc_final: 0.7794 (m-30) REVERT: B 185 ASN cc_start: 0.8881 (t0) cc_final: 0.8555 (t0) REVERT: B 208 VAL cc_start: 0.8362 (t) cc_final: 0.8131 (p) REVERT: B 272 GLU cc_start: 0.7604 (tt0) cc_final: 0.7225 (tt0) REVERT: B 336 SER cc_start: 0.8892 (t) cc_final: 0.8629 (p) REVERT: B 385 ASP cc_start: 0.7564 (m-30) cc_final: 0.7120 (m-30) REVERT: B 415 ARG cc_start: 0.8592 (mmt90) cc_final: 0.8280 (mtt90) REVERT: B 442 ARG cc_start: 0.8090 (mmt-90) cc_final: 0.7664 (mmp80) REVERT: B 476 ARG cc_start: 0.8414 (ptp-110) cc_final: 0.7771 (ptp-110) REVERT: B 478 THR cc_start: 0.8264 (m) cc_final: 0.7979 (p) REVERT: B 479 LYS cc_start: 0.8416 (mptt) cc_final: 0.7963 (mptt) REVERT: B 484 GLU cc_start: 0.7889 (mp0) cc_final: 0.7618 (mp0) REVERT: C 34 VAL cc_start: 0.8623 (t) cc_final: 0.8302 (p) REVERT: C 62 MET cc_start: 0.7860 (ttt) cc_final: 0.7649 (ttp) REVERT: C 68 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7184 (mt-10) REVERT: C 80 THR cc_start: 0.8345 (p) cc_final: 0.8055 (m) REVERT: C 88 VAL cc_start: 0.7924 (p) cc_final: 0.7715 (t) REVERT: C 137 MET cc_start: 0.8358 (mmm) cc_final: 0.8104 (mmm) REVERT: C 147 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7393 (mm110) REVERT: C 154 ASP cc_start: 0.8321 (m-30) cc_final: 0.8058 (t0) REVERT: C 181 ASP cc_start: 0.8030 (m-30) cc_final: 0.7722 (m-30) REVERT: C 185 ASN cc_start: 0.8647 (t0) cc_final: 0.8384 (t0) REVERT: C 247 GLU cc_start: 0.7535 (pt0) cc_final: 0.7270 (pt0) REVERT: C 272 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7440 (mt-10) REVERT: C 274 SER cc_start: 0.8461 (p) cc_final: 0.8240 (m) REVERT: C 314 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8004 (p) REVERT: C 354 ARG cc_start: 0.7956 (mtt90) cc_final: 0.7651 (mtt180) REVERT: C 451 GLU cc_start: 0.7980 (mp0) cc_final: 0.7690 (mp0) REVERT: C 462 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8463 (mm) REVERT: D 10 MET cc_start: 0.7688 (mtm) cc_final: 0.7397 (mtm) REVERT: D 37 ARG cc_start: 0.7622 (mtm180) cc_final: 0.7121 (mtm180) REVERT: D 84 SER cc_start: 0.8433 (m) cc_final: 0.7997 (p) REVERT: D 101 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7821 (mp0) REVERT: D 114 ARG cc_start: 0.7649 (ttt180) cc_final: 0.7435 (ttp80) REVERT: D 116 ASP cc_start: 0.7802 (m-30) cc_final: 0.7519 (m-30) REVERT: D 133 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7722 (mt-10) REVERT: D 169 GLN cc_start: 0.8617 (mt0) cc_final: 0.8260 (mm-40) REVERT: D 170 GLU cc_start: 0.7921 (tp30) cc_final: 0.7700 (tt0) REVERT: D 227 ARG cc_start: 0.8120 (mmt180) cc_final: 0.7823 (mmt90) REVERT: D 237 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7000 (mt-10) REVERT: D 241 ASP cc_start: 0.7935 (m-30) cc_final: 0.7695 (m-30) REVERT: D 246 ASP cc_start: 0.7652 (m-30) cc_final: 0.7391 (m-30) REVERT: D 284 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7050 (mt-10) REVERT: D 287 GLN cc_start: 0.8463 (mm110) cc_final: 0.8250 (mt0) REVERT: D 352 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7544 (mtp180) REVERT: D 387 LEU cc_start: 0.8430 (mt) cc_final: 0.8210 (mp) REVERT: D 427 TYR cc_start: 0.8529 (t80) cc_final: 0.8272 (t80) REVERT: D 439 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7650 (mm-30) REVERT: D 464 GLU cc_start: 0.7836 (tp30) cc_final: 0.7564 (tp30) REVERT: E 1 MET cc_start: 0.3666 (mmt) cc_final: 0.3308 (mmt) REVERT: E 3 ARG cc_start: 0.7237 (mtm-85) cc_final: 0.6931 (mtm-85) REVERT: E 17 LYS cc_start: 0.8699 (tttt) cc_final: 0.8338 (ttmm) REVERT: E 91 THR cc_start: 0.7894 (p) cc_final: 0.7583 (t) REVERT: E 101 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7637 (mp0) REVERT: E 127 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7534 (mt-10) REVERT: E 134 ILE cc_start: 0.8719 (mt) cc_final: 0.8446 (tt) REVERT: E 170 GLU cc_start: 0.7816 (tp30) cc_final: 0.7462 (tt0) REVERT: E 178 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7237 (mm-30) REVERT: E 210 LYS cc_start: 0.8194 (mttt) cc_final: 0.7844 (mttt) REVERT: E 227 ARG cc_start: 0.7910 (mmt180) cc_final: 0.7610 (mmt90) REVERT: E 256 ARG cc_start: 0.7874 (mtt90) cc_final: 0.7662 (mtt90) REVERT: E 284 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6739 (mt-10) REVERT: E 301 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8188 (m) REVERT: E 333 ARG cc_start: 0.7942 (ttm-80) cc_final: 0.7740 (ttm-80) REVERT: E 334 LYS cc_start: 0.8385 (mmmm) cc_final: 0.8105 (mmmm) REVERT: E 354 LEU cc_start: 0.8484 (tp) cc_final: 0.8183 (tt) REVERT: E 387 LEU cc_start: 0.8014 (mt) cc_final: 0.7508 (tp) REVERT: E 402 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.8047 (mtt-85) REVERT: E 405 ARG cc_start: 0.8434 (mpt180) cc_final: 0.8157 (mmt-90) REVERT: E 406 ILE cc_start: 0.8774 (mt) cc_final: 0.8535 (mt) REVERT: E 421 THR cc_start: 0.8229 (t) cc_final: 0.7972 (p) REVERT: E 423 GLN cc_start: 0.7558 (mm-40) cc_final: 0.7315 (mm-40) REVERT: E 427 TYR cc_start: 0.8498 (t80) cc_final: 0.8167 (t80) REVERT: E 431 LYS cc_start: 0.8176 (ptmm) cc_final: 0.7866 (ptmm) REVERT: E 435 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7587 (ttp80) REVERT: E 438 LYS cc_start: 0.8534 (ttpt) cc_final: 0.7941 (ttpt) REVERT: E 439 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7158 (mm-30) REVERT: E 450 GLU cc_start: 0.8149 (pm20) cc_final: 0.7753 (pm20) REVERT: E 461 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7734 (mt-10) REVERT: E 464 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7604 (mt-10) REVERT: F 8 GLN cc_start: 0.8428 (mt0) cc_final: 0.8133 (mt0) REVERT: F 39 GLU cc_start: 0.7809 (mp0) cc_final: 0.7371 (mp0) REVERT: F 49 GLU cc_start: 0.7631 (tt0) cc_final: 0.7242 (tt0) REVERT: F 75 GLU cc_start: 0.7846 (tt0) cc_final: 0.7506 (tt0) REVERT: F 89 GLU cc_start: 0.8014 (tp30) cc_final: 0.7725 (tp30) REVERT: F 114 ARG cc_start: 0.7880 (ttp80) cc_final: 0.7626 (ttp80) REVERT: F 116 ASP cc_start: 0.8187 (m-30) cc_final: 0.7949 (m-30) REVERT: F 124 LYS cc_start: 0.8050 (mttm) cc_final: 0.7708 (mttm) REVERT: F 127 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7778 (mp0) REVERT: F 254 ILE cc_start: 0.8607 (tp) cc_final: 0.8300 (mt) REVERT: F 300 ILE cc_start: 0.8512 (mt) cc_final: 0.8285 (tt) REVERT: F 356 PRO cc_start: 0.8512 (Cg_exo) cc_final: 0.8294 (Cg_endo) REVERT: F 439 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7607 (mt-10) REVERT: F 442 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7501 (mt-10) REVERT: F 444 LYS cc_start: 0.8443 (tttt) cc_final: 0.8070 (tttt) REVERT: F 445 TYR cc_start: 0.8619 (m-80) cc_final: 0.8191 (m-80) REVERT: F 448 LEU cc_start: 0.9007 (mm) cc_final: 0.8707 (mp) REVERT: G 11 LYS cc_start: 0.8223 (tptt) cc_final: 0.7935 (tptt) REVERT: G 17 THR cc_start: 0.8195 (p) cc_final: 0.7815 (t) REVERT: G 28 GLU cc_start: 0.8366 (tt0) cc_final: 0.8124 (tt0) REVERT: G 32 THR cc_start: 0.8949 (m) cc_final: 0.8538 (p) REVERT: G 33 SER cc_start: 0.8975 (t) cc_final: 0.8494 (p) REVERT: G 36 ASN cc_start: 0.8689 (t0) cc_final: 0.8192 (t0) REVERT: G 37 ARG cc_start: 0.8331 (ttp80) cc_final: 0.8056 (ttp80) REVERT: G 54 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8100 (mt-10) REVERT: G 70 MET cc_start: 0.7697 (mmm) cc_final: 0.7182 (mmm) REVERT: G 88 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7310 (ptm160) REVERT: G 119 ILE cc_start: 0.7833 (mt) cc_final: 0.7588 (mt) REVERT: G 173 MET cc_start: 0.8072 (mtm) cc_final: 0.7791 (mtm) REVERT: G 184 GLN cc_start: 0.7870 (mp10) cc_final: 0.7417 (mp10) REVERT: G 185 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7317 (mm-30) REVERT: G 188 GLU cc_start: 0.7752 (tt0) cc_final: 0.7502 (tt0) REVERT: G 192 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7526 (mm) REVERT: G 223 TYR cc_start: 0.7779 (t80) cc_final: 0.7499 (t80) REVERT: G 225 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 256 GLU cc_start: 0.8066 (tp30) cc_final: 0.7819 (tp30) REVERT: G 259 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8286 (ttp80) REVERT: G 263 LEU cc_start: 0.8573 (mp) cc_final: 0.8285 (mt) outliers start: 105 outliers final: 74 residues processed: 1109 average time/residue: 0.2012 time to fit residues: 325.4539 Evaluate side-chains 1133 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1052 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain F residue 464 GLU Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 111 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 309 optimal weight: 4.9990 chunk 290 optimal weight: 7.9990 chunk 118 optimal weight: 3.9990 chunk 173 optimal weight: 8.9990 chunk 151 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN ** B 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN C 172 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 401 HIS F 8 GLN F 33 GLN F 324 HIS G 95 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.126235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.111688 restraints weight = 35278.824| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.13 r_work: 0.3300 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 24604 Z= 0.283 Angle : 0.675 7.945 33364 Z= 0.361 Chirality : 0.049 0.172 3840 Planarity : 0.006 0.074 4349 Dihedral : 8.481 102.322 3575 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.85 % Allowed : 24.98 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: -0.06 (0.15), residues: 3104 helix: 0.95 (0.14), residues: 1258 sheet: -0.16 (0.22), residues: 537 loop : -0.90 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 140 TYR 0.021 0.002 TYR C 248 PHE 0.020 0.002 PHE A 494 HIS 0.008 0.002 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00631 (24604) covalent geometry : angle 0.67521 (33364) hydrogen bonds : bond 0.07104 ( 1124) hydrogen bonds : angle 5.05494 ( 3222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1083 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8326 (ptp) cc_final: 0.8098 (mtm) REVERT: A 49 SER cc_start: 0.8461 (t) cc_final: 0.8167 (m) REVERT: A 89 ARG cc_start: 0.7357 (mtm-85) cc_final: 0.7042 (mtm-85) REVERT: A 125 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.6910 (pt0) REVERT: A 127 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7495 (mtp85) REVERT: A 251 TYR cc_start: 0.8513 (m-80) cc_final: 0.8189 (m-80) REVERT: A 254 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7782 (mmtm) REVERT: A 272 GLU cc_start: 0.7762 (tt0) cc_final: 0.7476 (tt0) REVERT: A 375 MET cc_start: 0.8363 (tpp) cc_final: 0.7673 (tpp) REVERT: A 386 LEU cc_start: 0.8735 (tp) cc_final: 0.8498 (tt) REVERT: A 426 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7411 (mm-40) REVERT: A 488 ASN cc_start: 0.8396 (m-40) cc_final: 0.8149 (m-40) REVERT: B 144 GLU cc_start: 0.7365 (pt0) cc_final: 0.6939 (pt0) REVERT: B 177 SER cc_start: 0.8111 (p) cc_final: 0.7767 (m) REVERT: B 181 ASP cc_start: 0.8088 (m-30) cc_final: 0.7802 (m-30) REVERT: B 185 ASN cc_start: 0.8897 (t0) cc_final: 0.8645 (t0) REVERT: B 230 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7905 (mt0) REVERT: B 272 GLU cc_start: 0.7587 (tt0) cc_final: 0.7298 (tt0) REVERT: B 336 SER cc_start: 0.8818 (t) cc_final: 0.8564 (p) REVERT: B 385 ASP cc_start: 0.7642 (m-30) cc_final: 0.7249 (m-30) REVERT: B 423 ASP cc_start: 0.7524 (p0) cc_final: 0.7211 (p0) REVERT: B 442 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7673 (mmp80) REVERT: B 464 LEU cc_start: 0.8078 (mt) cc_final: 0.7690 (mt) REVERT: B 478 THR cc_start: 0.8276 (m) cc_final: 0.7979 (p) REVERT: B 479 LYS cc_start: 0.8338 (mptt) cc_final: 0.7941 (mptt) REVERT: B 480 ASP cc_start: 0.7687 (t0) cc_final: 0.7485 (t0) REVERT: B 484 GLU cc_start: 0.7911 (mp0) cc_final: 0.7655 (mp0) REVERT: C 34 VAL cc_start: 0.8681 (t) cc_final: 0.8351 (p) REVERT: C 62 MET cc_start: 0.7900 (ttt) cc_final: 0.7685 (ttp) REVERT: C 68 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7277 (mt-10) REVERT: C 80 THR cc_start: 0.8366 (p) cc_final: 0.8063 (m) REVERT: C 88 VAL cc_start: 0.7940 (p) cc_final: 0.7730 (t) REVERT: C 96 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7186 (mt-10) REVERT: C 107 VAL cc_start: 0.8633 (t) cc_final: 0.8089 (p) REVERT: C 137 MET cc_start: 0.8383 (mmm) cc_final: 0.8127 (mmm) REVERT: C 147 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7292 (mm-40) REVERT: C 181 ASP cc_start: 0.8092 (m-30) cc_final: 0.7827 (m-30) REVERT: C 201 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6947 (mtmt) REVERT: C 272 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7362 (mt-10) REVERT: C 274 SER cc_start: 0.8492 (p) cc_final: 0.8255 (m) REVERT: C 314 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.7933 (p) REVERT: C 354 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7682 (mtt180) REVERT: C 376 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8127 (tppt) REVERT: C 451 GLU cc_start: 0.7973 (mp0) cc_final: 0.7656 (mp0) REVERT: C 462 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8439 (mm) REVERT: D 10 MET cc_start: 0.7634 (mtm) cc_final: 0.7334 (mtm) REVERT: D 15 ASP cc_start: 0.7643 (m-30) cc_final: 0.7441 (m-30) REVERT: D 37 ARG cc_start: 0.7637 (mtm180) cc_final: 0.7188 (mtm180) REVERT: D 101 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7822 (mp0) REVERT: D 114 ARG cc_start: 0.7662 (ttt180) cc_final: 0.7446 (ttp80) REVERT: D 116 ASP cc_start: 0.7805 (m-30) cc_final: 0.7540 (m-30) REVERT: D 133 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 169 GLN cc_start: 0.8599 (mt0) cc_final: 0.8237 (mm-40) REVERT: D 190 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6695 (m-30) REVERT: D 227 ARG cc_start: 0.8222 (mmt180) cc_final: 0.7896 (mmt90) REVERT: D 237 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7153 (mt-10) REVERT: D 241 ASP cc_start: 0.7932 (m-30) cc_final: 0.7699 (m-30) REVERT: D 246 ASP cc_start: 0.7668 (m-30) cc_final: 0.7421 (m-30) REVERT: D 265 SER cc_start: 0.8684 (OUTLIER) cc_final: 0.8455 (p) REVERT: D 352 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7503 (mtp180) REVERT: D 439 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7604 (mm-30) REVERT: D 464 GLU cc_start: 0.7883 (tp30) cc_final: 0.7613 (tp30) REVERT: E 1 MET cc_start: 0.3546 (mmt) cc_final: 0.3218 (mmt) REVERT: E 3 ARG cc_start: 0.7344 (mtm-85) cc_final: 0.7056 (mtm-85) REVERT: E 15 ASP cc_start: 0.7256 (m-30) cc_final: 0.7043 (m-30) REVERT: E 17 LYS cc_start: 0.8723 (tttt) cc_final: 0.8359 (ttmm) REVERT: E 91 THR cc_start: 0.7894 (p) cc_final: 0.7548 (t) REVERT: E 127 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7501 (mt-10) REVERT: E 134 ILE cc_start: 0.8749 (mt) cc_final: 0.8466 (tt) REVERT: E 170 GLU cc_start: 0.7897 (tp30) cc_final: 0.7535 (tt0) REVERT: E 178 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7211 (mm-30) REVERT: E 193 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8193 (ttp80) REVERT: E 210 LYS cc_start: 0.8274 (mttt) cc_final: 0.8001 (mttt) REVERT: E 256 ARG cc_start: 0.7984 (mtt90) cc_final: 0.7774 (mtm-85) REVERT: E 270 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7454 (mtt180) REVERT: E 284 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6817 (mt-10) REVERT: E 333 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7767 (ttm-80) REVERT: E 334 LYS cc_start: 0.8381 (mmmm) cc_final: 0.8094 (mmmm) REVERT: E 387 LEU cc_start: 0.8022 (mt) cc_final: 0.7558 (tp) REVERT: E 402 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.7947 (mtt-85) REVERT: E 405 ARG cc_start: 0.8464 (mpt180) cc_final: 0.8023 (mpt180) REVERT: E 406 ILE cc_start: 0.8804 (mt) cc_final: 0.8599 (mt) REVERT: E 421 THR cc_start: 0.8333 (t) cc_final: 0.8079 (p) REVERT: E 423 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7331 (mm-40) REVERT: E 427 TYR cc_start: 0.8620 (t80) cc_final: 0.8238 (t80) REVERT: E 431 LYS cc_start: 0.8234 (ptmm) cc_final: 0.7894 (ptmm) REVERT: E 435 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7692 (ttp80) REVERT: E 438 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8010 (ttpt) REVERT: E 439 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7219 (mm-30) REVERT: E 450 GLU cc_start: 0.8170 (pm20) cc_final: 0.7799 (pm20) REVERT: E 461 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7782 (mt-10) REVERT: E 463 VAL cc_start: 0.8775 (t) cc_final: 0.8542 (p) REVERT: E 464 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7588 (mt-10) REVERT: F 8 GLN cc_start: 0.8453 (mt0) cc_final: 0.8144 (mt0) REVERT: F 39 GLU cc_start: 0.7790 (mp0) cc_final: 0.7393 (mp0) REVERT: F 49 GLU cc_start: 0.7674 (tt0) cc_final: 0.7260 (tt0) REVERT: F 62 ILE cc_start: 0.8250 (mt) cc_final: 0.8016 (mt) REVERT: F 75 GLU cc_start: 0.7767 (tt0) cc_final: 0.7410 (tt0) REVERT: F 89 GLU cc_start: 0.8022 (tp30) cc_final: 0.7739 (tp30) REVERT: F 114 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7649 (ttp80) REVERT: F 124 LYS cc_start: 0.8051 (mttm) cc_final: 0.7804 (mttm) REVERT: F 148 TYR cc_start: 0.8525 (m-10) cc_final: 0.8211 (m-10) REVERT: F 241 ASP cc_start: 0.7459 (m-30) cc_final: 0.6987 (m-30) REVERT: F 254 ILE cc_start: 0.8678 (tp) cc_final: 0.8356 (mt) REVERT: F 300 ILE cc_start: 0.8524 (mt) cc_final: 0.8285 (tt) REVERT: F 356 PRO cc_start: 0.8570 (Cg_exo) cc_final: 0.8319 (Cg_endo) REVERT: F 368 ARG cc_start: 0.8314 (mmt180) cc_final: 0.8061 (mpt180) REVERT: F 439 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7682 (mt-10) REVERT: F 442 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7520 (mt-10) REVERT: F 444 LYS cc_start: 0.8503 (tttt) cc_final: 0.8161 (tttt) REVERT: F 445 TYR cc_start: 0.8638 (m-80) cc_final: 0.8261 (m-80) REVERT: F 448 LEU cc_start: 0.9088 (mm) cc_final: 0.8761 (mp) REVERT: G 11 LYS cc_start: 0.8352 (tptt) cc_final: 0.7788 (tptt) REVERT: G 15 ASN cc_start: 0.8027 (m-40) cc_final: 0.7775 (m-40) REVERT: G 17 THR cc_start: 0.8246 (p) cc_final: 0.7843 (t) REVERT: G 28 GLU cc_start: 0.8396 (tt0) cc_final: 0.8149 (tt0) REVERT: G 32 THR cc_start: 0.8948 (m) cc_final: 0.8563 (p) REVERT: G 33 SER cc_start: 0.9032 (t) cc_final: 0.8529 (p) REVERT: G 37 ARG cc_start: 0.8384 (ttp80) cc_final: 0.8117 (ttp80) REVERT: G 54 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8127 (mt-10) REVERT: G 70 MET cc_start: 0.7704 (mmm) cc_final: 0.7215 (mmm) REVERT: G 119 ILE cc_start: 0.7830 (mt) cc_final: 0.7577 (mt) REVERT: G 173 MET cc_start: 0.8066 (mtm) cc_final: 0.7792 (mtm) REVERT: G 185 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7366 (mm-30) REVERT: G 188 GLU cc_start: 0.7662 (tt0) cc_final: 0.7407 (tt0) REVERT: G 192 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7546 (mm) REVERT: G 223 TYR cc_start: 0.7839 (t80) cc_final: 0.7574 (t80) REVERT: G 225 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8203 (mt-10) REVERT: G 256 GLU cc_start: 0.8136 (tp30) cc_final: 0.7872 (tp30) outliers start: 124 outliers final: 92 residues processed: 1127 average time/residue: 0.2085 time to fit residues: 341.3946 Evaluate side-chains 1176 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1076 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 442 ARG Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 278 GLN Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 378 LYS Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 172 TYR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 258 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 260 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 230 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 167 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 283 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 272 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN ** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 ASN C 172 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN D 401 HIS D 447 HIS F 217 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.129102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.114484 restraints weight = 35405.026| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.19 r_work: 0.3346 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24604 Z= 0.125 Angle : 0.578 10.300 33364 Z= 0.304 Chirality : 0.044 0.161 3840 Planarity : 0.005 0.069 4349 Dihedral : 8.024 96.186 3575 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.79 % Allowed : 27.09 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.42 (0.15), residues: 3104 helix: 1.45 (0.15), residues: 1242 sheet: 0.09 (0.22), residues: 547 loop : -0.74 (0.17), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 60 TYR 0.022 0.001 TYR C 248 PHE 0.028 0.001 PHE C 494 HIS 0.007 0.001 HIS F 401 Details of bonding type rmsd covalent geometry : bond 0.00266 (24604) covalent geometry : angle 0.57787 (33364) hydrogen bonds : bond 0.05179 ( 1124) hydrogen bonds : angle 4.73064 ( 3222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 1063 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.6852 (m-30) cc_final: 0.6329 (m-30) REVERT: A 67 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 84 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7267 (tm-30) REVERT: A 89 ARG cc_start: 0.7324 (mtm-85) cc_final: 0.6969 (mtm-85) REVERT: A 95 MET cc_start: 0.7379 (tpt) cc_final: 0.7045 (tpt) REVERT: A 125 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6790 (pt0) REVERT: A 127 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7590 (mtp85) REVERT: A 251 TYR cc_start: 0.8404 (m-80) cc_final: 0.8160 (m-80) REVERT: A 254 LYS cc_start: 0.8218 (mmtm) cc_final: 0.7768 (mmtm) REVERT: A 272 GLU cc_start: 0.7787 (tt0) cc_final: 0.7464 (tt0) REVERT: A 375 MET cc_start: 0.8247 (tpp) cc_final: 0.7880 (tpp) REVERT: A 385 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7849 (t0) REVERT: A 386 LEU cc_start: 0.8696 (tp) cc_final: 0.8435 (tt) REVERT: A 421 LYS cc_start: 0.8303 (mttm) cc_final: 0.7814 (mtpp) REVERT: A 480 ASP cc_start: 0.7397 (m-30) cc_final: 0.7127 (m-30) REVERT: A 488 ASN cc_start: 0.8411 (m-40) cc_final: 0.8180 (m-40) REVERT: B 144 GLU cc_start: 0.7332 (pt0) cc_final: 0.6933 (pt0) REVERT: B 177 SER cc_start: 0.8117 (p) cc_final: 0.7687 (m) REVERT: B 181 ASP cc_start: 0.7995 (m-30) cc_final: 0.7710 (m-30) REVERT: B 185 ASN cc_start: 0.8892 (t0) cc_final: 0.8572 (t0) REVERT: B 230 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7850 (mt0) REVERT: B 272 GLU cc_start: 0.7592 (tt0) cc_final: 0.7275 (tt0) REVERT: B 330 ILE cc_start: 0.8054 (mm) cc_final: 0.7805 (mm) REVERT: B 336 SER cc_start: 0.8846 (t) cc_final: 0.8582 (p) REVERT: B 385 ASP cc_start: 0.7616 (m-30) cc_final: 0.7196 (m-30) REVERT: B 415 ARG cc_start: 0.8547 (mmt90) cc_final: 0.8219 (mtt90) REVERT: B 423 ASP cc_start: 0.7439 (p0) cc_final: 0.7118 (p0) REVERT: B 442 ARG cc_start: 0.8031 (mmt-90) cc_final: 0.7580 (mmp80) REVERT: B 464 LEU cc_start: 0.7978 (mt) cc_final: 0.7571 (mt) REVERT: B 478 THR cc_start: 0.8228 (m) cc_final: 0.7969 (p) REVERT: B 479 LYS cc_start: 0.8357 (mptt) cc_final: 0.7935 (mptt) REVERT: B 484 GLU cc_start: 0.7897 (mp0) cc_final: 0.7634 (mp0) REVERT: C 34 VAL cc_start: 0.8673 (t) cc_final: 0.8341 (p) REVERT: C 62 MET cc_start: 0.7791 (ttt) cc_final: 0.7566 (ttp) REVERT: C 68 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7223 (mt-10) REVERT: C 80 THR cc_start: 0.8348 (p) cc_final: 0.8058 (m) REVERT: C 88 VAL cc_start: 0.7938 (p) cc_final: 0.7722 (t) REVERT: C 96 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7237 (mt-10) REVERT: C 107 VAL cc_start: 0.8551 (t) cc_final: 0.8065 (p) REVERT: C 137 MET cc_start: 0.8310 (mmm) cc_final: 0.8062 (mmm) REVERT: C 147 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7257 (mm-40) REVERT: C 181 ASP cc_start: 0.8019 (m-30) cc_final: 0.7715 (m-30) REVERT: C 185 ASN cc_start: 0.8670 (t0) cc_final: 0.8410 (t0) REVERT: C 272 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7459 (mt-10) REVERT: C 376 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8251 (ttpt) REVERT: C 451 GLU cc_start: 0.7994 (mp0) cc_final: 0.7692 (mp0) REVERT: C 462 LEU cc_start: 0.8679 (mt) cc_final: 0.8399 (mm) REVERT: D 10 MET cc_start: 0.7599 (mtm) cc_final: 0.7317 (mtm) REVERT: D 84 SER cc_start: 0.8446 (m) cc_final: 0.8010 (p) REVERT: D 101 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7780 (mp0) REVERT: D 114 ARG cc_start: 0.7701 (ttt180) cc_final: 0.7486 (ttp80) REVERT: D 116 ASP cc_start: 0.7793 (m-30) cc_final: 0.7511 (m-30) REVERT: D 133 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7725 (mt-10) REVERT: D 169 GLN cc_start: 0.8575 (mt0) cc_final: 0.8254 (mm-40) REVERT: D 170 GLU cc_start: 0.7898 (tp30) cc_final: 0.7675 (tt0) REVERT: D 190 ASP cc_start: 0.6931 (OUTLIER) cc_final: 0.6639 (m-30) REVERT: D 227 ARG cc_start: 0.8164 (mmt180) cc_final: 0.7847 (mmt90) REVERT: D 237 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6978 (mt-10) REVERT: D 241 ASP cc_start: 0.7931 (m-30) cc_final: 0.7712 (m-30) REVERT: D 246 ASP cc_start: 0.7563 (m-30) cc_final: 0.7330 (m-30) REVERT: D 333 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7819 (ttm170) REVERT: D 352 ARG cc_start: 0.7845 (mtp180) cc_final: 0.7520 (mtp180) REVERT: D 380 LEU cc_start: 0.8451 (mt) cc_final: 0.8234 (tp) REVERT: D 427 TYR cc_start: 0.8536 (t80) cc_final: 0.8279 (t80) REVERT: D 464 GLU cc_start: 0.7806 (tp30) cc_final: 0.7502 (tp30) REVERT: E 1 MET cc_start: 0.3638 (mmt) cc_final: 0.3294 (mmt) REVERT: E 3 ARG cc_start: 0.7228 (mtm-85) cc_final: 0.6918 (mtm-85) REVERT: E 17 LYS cc_start: 0.8664 (tttt) cc_final: 0.8290 (ttmm) REVERT: E 85 VAL cc_start: 0.8378 (m) cc_final: 0.8159 (p) REVERT: E 91 THR cc_start: 0.7854 (p) cc_final: 0.7520 (t) REVERT: E 101 GLU cc_start: 0.7947 (mp0) cc_final: 0.7677 (mp0) REVERT: E 127 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7521 (mt-10) REVERT: E 134 ILE cc_start: 0.8732 (mt) cc_final: 0.8440 (tt) REVERT: E 170 GLU cc_start: 0.7815 (tp30) cc_final: 0.7463 (tt0) REVERT: E 178 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7189 (mm-30) REVERT: E 210 LYS cc_start: 0.8150 (mttt) cc_final: 0.7893 (mttt) REVERT: E 256 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7489 (mtm-85) REVERT: E 280 THR cc_start: 0.8131 (p) cc_final: 0.6813 (t) REVERT: E 333 ARG cc_start: 0.7964 (ttm-80) cc_final: 0.7724 (ttm-80) REVERT: E 334 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8078 (mmmm) REVERT: E 387 LEU cc_start: 0.8003 (mt) cc_final: 0.7561 (tp) REVERT: E 402 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.7936 (mtt-85) REVERT: E 406 ILE cc_start: 0.8732 (mt) cc_final: 0.8499 (mt) REVERT: E 421 THR cc_start: 0.8208 (t) cc_final: 0.7943 (p) REVERT: E 423 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7370 (mm-40) REVERT: E 427 TYR cc_start: 0.8534 (t80) cc_final: 0.8172 (t80) REVERT: E 431 LYS cc_start: 0.8203 (ptmm) cc_final: 0.7896 (ptmm) REVERT: E 435 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7539 (ttp80) REVERT: E 438 LYS cc_start: 0.8509 (ttpt) cc_final: 0.7934 (ttpt) REVERT: E 439 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7063 (mm-30) REVERT: E 450 GLU cc_start: 0.8148 (pm20) cc_final: 0.7794 (pm20) REVERT: E 461 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7759 (mt-10) REVERT: F 8 GLN cc_start: 0.8380 (mt0) cc_final: 0.8074 (mt0) REVERT: F 39 GLU cc_start: 0.7772 (mp0) cc_final: 0.7354 (mp0) REVERT: F 49 GLU cc_start: 0.7627 (tt0) cc_final: 0.7227 (tt0) REVERT: F 75 GLU cc_start: 0.7835 (tt0) cc_final: 0.7496 (tt0) REVERT: F 89 GLU cc_start: 0.8023 (tp30) cc_final: 0.7743 (tp30) REVERT: F 114 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7643 (ttp80) REVERT: F 124 LYS cc_start: 0.7990 (mttm) cc_final: 0.7697 (mttm) REVERT: F 127 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7820 (mp0) REVERT: F 241 ASP cc_start: 0.7548 (m-30) cc_final: 0.7089 (m-30) REVERT: F 254 ILE cc_start: 0.8620 (tp) cc_final: 0.8297 (mt) REVERT: F 300 ILE cc_start: 0.8484 (mt) cc_final: 0.8262 (tt) REVERT: F 356 PRO cc_start: 0.8456 (Cg_exo) cc_final: 0.8247 (Cg_endo) REVERT: F 439 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7644 (mt-10) REVERT: F 442 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7468 (mt-10) REVERT: F 444 LYS cc_start: 0.8453 (tttt) cc_final: 0.8074 (tttt) REVERT: F 445 TYR cc_start: 0.8615 (m-80) cc_final: 0.8205 (m-80) REVERT: G 17 THR cc_start: 0.8143 (p) cc_final: 0.7762 (t) REVERT: G 28 GLU cc_start: 0.8385 (tt0) cc_final: 0.8142 (tt0) REVERT: G 32 THR cc_start: 0.8900 (m) cc_final: 0.8503 (p) REVERT: G 33 SER cc_start: 0.8988 (t) cc_final: 0.8488 (p) REVERT: G 54 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8111 (mt-10) REVERT: G 70 MET cc_start: 0.7622 (mmm) cc_final: 0.7091 (mmm) REVERT: G 119 ILE cc_start: 0.7797 (mt) cc_final: 0.7547 (mt) REVERT: G 173 MET cc_start: 0.8104 (mtm) cc_final: 0.7802 (mtm) REVERT: G 185 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7383 (mm-30) REVERT: G 188 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: G 192 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7494 (mm) REVERT: G 223 TYR cc_start: 0.7764 (t80) cc_final: 0.7476 (t80) REVERT: G 225 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8134 (mt-10) REVERT: G 256 GLU cc_start: 0.8062 (tp30) cc_final: 0.7822 (tp30) REVERT: G 263 LEU cc_start: 0.8578 (mp) cc_final: 0.8303 (mt) outliers start: 97 outliers final: 73 residues processed: 1090 average time/residue: 0.2031 time to fit residues: 323.3854 Evaluate side-chains 1132 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 1054 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 172 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 178 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 308 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 266 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN C 163 GLN C 172 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN C 474 HIS D 173 HIS D 330 ASN F 324 HIS G 95 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.127934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.113437 restraints weight = 35058.925| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.14 r_work: 0.3326 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24604 Z= 0.190 Angle : 0.615 8.613 33364 Z= 0.325 Chirality : 0.046 0.167 3840 Planarity : 0.006 0.067 4349 Dihedral : 8.126 88.839 3575 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.26 % Allowed : 27.33 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.32 (0.15), residues: 3104 helix: 1.34 (0.14), residues: 1248 sheet: 0.03 (0.22), residues: 547 loop : -0.75 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 270 TYR 0.020 0.002 TYR C 248 PHE 0.027 0.002 PHE C 494 HIS 0.007 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00427 (24604) covalent geometry : angle 0.61526 (33364) hydrogen bonds : bond 0.05946 ( 1124) hydrogen bonds : angle 4.82980 ( 3222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1076 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.6747 (m-30) cc_final: 0.6184 (m-30) REVERT: A 67 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7314 (mm-30) REVERT: A 89 ARG cc_start: 0.7431 (mtm-85) cc_final: 0.7065 (mtm-85) REVERT: A 95 MET cc_start: 0.7438 (tpt) cc_final: 0.7153 (tpt) REVERT: A 125 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6707 (pt0) REVERT: A 127 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7520 (mtp85) REVERT: A 251 TYR cc_start: 0.8472 (m-80) cc_final: 0.8226 (m-80) REVERT: A 254 LYS cc_start: 0.8246 (mmtm) cc_final: 0.7785 (mmtm) REVERT: A 272 GLU cc_start: 0.7752 (tt0) cc_final: 0.7441 (tt0) REVERT: A 375 MET cc_start: 0.8300 (tpp) cc_final: 0.7626 (tpp) REVERT: A 386 LEU cc_start: 0.8717 (tp) cc_final: 0.8468 (tt) REVERT: A 478 THR cc_start: 0.8528 (t) cc_final: 0.8256 (p) REVERT: A 480 ASP cc_start: 0.7404 (m-30) cc_final: 0.7113 (m-30) REVERT: A 488 ASN cc_start: 0.8434 (m-40) cc_final: 0.8210 (m-40) REVERT: B 144 GLU cc_start: 0.7333 (pt0) cc_final: 0.6925 (pt0) REVERT: B 177 SER cc_start: 0.8111 (p) cc_final: 0.7754 (m) REVERT: B 181 ASP cc_start: 0.8064 (m-30) cc_final: 0.7783 (m-30) REVERT: B 185 ASN cc_start: 0.8913 (t0) cc_final: 0.8626 (t0) REVERT: B 230 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7860 (mt0) REVERT: B 330 ILE cc_start: 0.8110 (mm) cc_final: 0.7855 (mm) REVERT: B 336 SER cc_start: 0.8815 (t) cc_final: 0.8552 (p) REVERT: B 385 ASP cc_start: 0.7670 (m-30) cc_final: 0.7240 (m-30) REVERT: B 415 ARG cc_start: 0.8593 (mmt90) cc_final: 0.8295 (mtt90) REVERT: B 423 ASP cc_start: 0.7477 (p0) cc_final: 0.7151 (p0) REVERT: B 442 ARG cc_start: 0.7987 (mmt-90) cc_final: 0.7781 (mmp80) REVERT: B 464 LEU cc_start: 0.8023 (mt) cc_final: 0.7622 (mt) REVERT: B 478 THR cc_start: 0.8195 (m) cc_final: 0.7968 (p) REVERT: B 479 LYS cc_start: 0.8348 (mptt) cc_final: 0.7969 (mptt) REVERT: B 484 GLU cc_start: 0.7906 (mp0) cc_final: 0.7655 (mp0) REVERT: C 34 VAL cc_start: 0.8685 (t) cc_final: 0.8354 (p) REVERT: C 62 MET cc_start: 0.7857 (ttt) cc_final: 0.7609 (ttp) REVERT: C 68 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7261 (mt-10) REVERT: C 80 THR cc_start: 0.8360 (p) cc_final: 0.8062 (m) REVERT: C 88 VAL cc_start: 0.7938 (p) cc_final: 0.7725 (t) REVERT: C 96 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7221 (mt-10) REVERT: C 107 VAL cc_start: 0.8582 (t) cc_final: 0.8111 (p) REVERT: C 137 MET cc_start: 0.8306 (mmm) cc_final: 0.8053 (mmm) REVERT: C 147 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7258 (mm-40) REVERT: C 181 ASP cc_start: 0.8082 (m-30) cc_final: 0.7800 (m-30) REVERT: C 185 ASN cc_start: 0.8643 (t0) cc_final: 0.8356 (t0) REVERT: C 272 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7452 (mt-10) REVERT: C 314 THR cc_start: 0.8495 (OUTLIER) cc_final: 0.7964 (p) REVERT: C 451 GLU cc_start: 0.8019 (mp0) cc_final: 0.7707 (mp0) REVERT: C 459 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7894 (mm-30) REVERT: C 462 LEU cc_start: 0.8708 (mt) cc_final: 0.8420 (mm) REVERT: D 3 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.7043 (mtm-85) REVERT: D 10 MET cc_start: 0.7659 (mtm) cc_final: 0.7383 (mtm) REVERT: D 84 SER cc_start: 0.8462 (m) cc_final: 0.8008 (p) REVERT: D 101 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7787 (mp0) REVERT: D 114 ARG cc_start: 0.7680 (ttt180) cc_final: 0.7428 (ttp80) REVERT: D 116 ASP cc_start: 0.7818 (m-30) cc_final: 0.7489 (m-30) REVERT: D 133 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7730 (mt-10) REVERT: D 169 GLN cc_start: 0.8587 (mt0) cc_final: 0.8257 (mm-40) REVERT: D 190 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6692 (m-30) REVERT: D 227 ARG cc_start: 0.8183 (mmt180) cc_final: 0.7888 (mmt90) REVERT: D 237 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6941 (mt-10) REVERT: D 241 ASP cc_start: 0.7934 (m-30) cc_final: 0.7672 (m-30) REVERT: D 246 ASP cc_start: 0.7611 (m-30) cc_final: 0.7387 (m-30) REVERT: D 270 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.8065 (mtt-85) REVERT: D 333 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7827 (ttm170) REVERT: D 352 ARG cc_start: 0.7856 (mtp180) cc_final: 0.7524 (mtp180) REVERT: D 427 TYR cc_start: 0.8513 (t80) cc_final: 0.8244 (t80) REVERT: D 464 GLU cc_start: 0.7853 (tp30) cc_final: 0.7547 (tp30) REVERT: E 1 MET cc_start: 0.3548 (mmt) cc_final: 0.3181 (mmt) REVERT: E 3 ARG cc_start: 0.7361 (mtm-85) cc_final: 0.7086 (mtm-85) REVERT: E 17 LYS cc_start: 0.8726 (tttt) cc_final: 0.8356 (ttmm) REVERT: E 91 THR cc_start: 0.7862 (p) cc_final: 0.7542 (t) REVERT: E 101 GLU cc_start: 0.7932 (mp0) cc_final: 0.7599 (mp0) REVERT: E 127 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7481 (mt-10) REVERT: E 134 ILE cc_start: 0.8738 (mt) cc_final: 0.8446 (tt) REVERT: E 170 GLU cc_start: 0.7881 (tp30) cc_final: 0.7509 (tt0) REVERT: E 178 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7297 (mm-30) REVERT: E 210 LYS cc_start: 0.8253 (mttt) cc_final: 0.7982 (mttt) REVERT: E 256 ARG cc_start: 0.7906 (mtt90) cc_final: 0.7535 (mtm-85) REVERT: E 270 ARG cc_start: 0.7760 (mtt90) cc_final: 0.7452 (mtt180) REVERT: E 280 THR cc_start: 0.8147 (p) cc_final: 0.7028 (t) REVERT: E 333 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7712 (ttm-80) REVERT: E 334 LYS cc_start: 0.8377 (mmmm) cc_final: 0.8080 (mmmm) REVERT: E 387 LEU cc_start: 0.8018 (mt) cc_final: 0.7558 (tp) REVERT: E 402 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.7945 (mtt-85) REVERT: E 406 ILE cc_start: 0.8772 (mt) cc_final: 0.8555 (mt) REVERT: E 421 THR cc_start: 0.8242 (t) cc_final: 0.8011 (p) REVERT: E 427 TYR cc_start: 0.8604 (t80) cc_final: 0.8249 (t80) REVERT: E 431 LYS cc_start: 0.8260 (ptmm) cc_final: 0.7952 (ptmm) REVERT: E 435 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7615 (ttp80) REVERT: E 438 LYS cc_start: 0.8582 (ttpt) cc_final: 0.7988 (ttpt) REVERT: E 439 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7119 (mm-30) REVERT: E 450 GLU cc_start: 0.8149 (pm20) cc_final: 0.7817 (pm20) REVERT: E 463 VAL cc_start: 0.8802 (t) cc_final: 0.8574 (p) REVERT: F 8 GLN cc_start: 0.8451 (mt0) cc_final: 0.8176 (mt0) REVERT: F 39 GLU cc_start: 0.7778 (mp0) cc_final: 0.7358 (mp0) REVERT: F 49 GLU cc_start: 0.7666 (tt0) cc_final: 0.7278 (tt0) REVERT: F 62 ILE cc_start: 0.8235 (mt) cc_final: 0.7992 (mt) REVERT: F 89 GLU cc_start: 0.7960 (tp30) cc_final: 0.7672 (tp30) REVERT: F 114 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7618 (ttp80) REVERT: F 124 LYS cc_start: 0.8053 (mttm) cc_final: 0.7749 (mttm) REVERT: F 127 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7769 (mp0) REVERT: F 148 TYR cc_start: 0.8525 (m-10) cc_final: 0.8212 (m-10) REVERT: F 241 ASP cc_start: 0.7475 (m-30) cc_final: 0.7011 (m-30) REVERT: F 254 ILE cc_start: 0.8660 (tp) cc_final: 0.8345 (mt) REVERT: F 300 ILE cc_start: 0.8495 (mt) cc_final: 0.8278 (tt) REVERT: F 439 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7624 (mt-10) REVERT: F 442 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7476 (mt-10) REVERT: F 444 LYS cc_start: 0.8462 (tttt) cc_final: 0.8259 (tttt) REVERT: F 445 TYR cc_start: 0.8623 (m-80) cc_final: 0.8341 (m-80) REVERT: G 17 THR cc_start: 0.8173 (p) cc_final: 0.7786 (t) REVERT: G 28 GLU cc_start: 0.8448 (tt0) cc_final: 0.8211 (tt0) REVERT: G 32 THR cc_start: 0.8916 (m) cc_final: 0.8529 (p) REVERT: G 33 SER cc_start: 0.9016 (t) cc_final: 0.8502 (p) REVERT: G 54 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8162 (mt-10) REVERT: G 70 MET cc_start: 0.7697 (mmm) cc_final: 0.7193 (mmm) REVERT: G 119 ILE cc_start: 0.7827 (mt) cc_final: 0.7578 (mt) REVERT: G 173 MET cc_start: 0.8107 (mtm) cc_final: 0.7807 (mtm) REVERT: G 185 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7413 (mm-30) REVERT: G 188 GLU cc_start: 0.7662 (tt0) cc_final: 0.7408 (tt0) REVERT: G 192 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7540 (mm) REVERT: G 223 TYR cc_start: 0.7815 (t80) cc_final: 0.7529 (t80) REVERT: G 225 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8178 (mt-10) REVERT: G 256 GLU cc_start: 0.8136 (tp30) cc_final: 0.7898 (tp30) REVERT: G 263 LEU cc_start: 0.8633 (mp) cc_final: 0.8346 (mt) outliers start: 109 outliers final: 90 residues processed: 1118 average time/residue: 0.2080 time to fit residues: 340.0168 Evaluate side-chains 1154 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1060 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 215 HIS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 377 LYS Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 13 ARG Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 172 TYR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 14 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 199 optimal weight: 0.0980 chunk 60 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 218 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN B 185 ASN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN B 433 GLN C 172 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.129753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115211 restraints weight = 35018.239| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.16 r_work: 0.3350 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24604 Z= 0.127 Angle : 0.577 8.211 33364 Z= 0.302 Chirality : 0.044 0.171 3840 Planarity : 0.005 0.068 4349 Dihedral : 7.823 83.318 3575 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.64 % Allowed : 27.64 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.56 (0.15), residues: 3104 helix: 1.56 (0.15), residues: 1255 sheet: 0.23 (0.22), residues: 543 loop : -0.72 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 60 TYR 0.024 0.001 TYR C 248 PHE 0.028 0.001 PHE C 494 HIS 0.006 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00281 (24604) covalent geometry : angle 0.57738 (33364) hydrogen bonds : bond 0.04967 ( 1124) hydrogen bonds : angle 4.66048 ( 3222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1071 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 ASP cc_start: 0.6761 (m-30) cc_final: 0.5967 (m-30) REVERT: A 67 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7311 (mm-30) REVERT: A 89 ARG cc_start: 0.7389 (mtm-85) cc_final: 0.7022 (mtm-85) REVERT: A 95 MET cc_start: 0.7484 (tpt) cc_final: 0.7174 (tpt) REVERT: A 125 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6631 (pt0) REVERT: A 127 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7525 (mtp85) REVERT: A 251 TYR cc_start: 0.8385 (m-80) cc_final: 0.8109 (m-80) REVERT: A 254 LYS cc_start: 0.8237 (mmtm) cc_final: 0.7795 (mmtm) REVERT: A 272 GLU cc_start: 0.7811 (tt0) cc_final: 0.7508 (tt0) REVERT: A 375 MET cc_start: 0.8200 (tpp) cc_final: 0.7515 (tpp) REVERT: A 386 LEU cc_start: 0.8687 (tp) cc_final: 0.8432 (tt) REVERT: A 478 THR cc_start: 0.8542 (t) cc_final: 0.8263 (p) REVERT: A 480 ASP cc_start: 0.7418 (m-30) cc_final: 0.7154 (m-30) REVERT: A 488 ASN cc_start: 0.8431 (m-40) cc_final: 0.8219 (m-40) REVERT: B 144 GLU cc_start: 0.7316 (pt0) cc_final: 0.6910 (pt0) REVERT: B 177 SER cc_start: 0.8072 (p) cc_final: 0.7606 (m) REVERT: B 181 ASP cc_start: 0.8033 (m-30) cc_final: 0.7742 (m-30) REVERT: B 185 ASN cc_start: 0.8878 (t0) cc_final: 0.8478 (t0) REVERT: B 230 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7862 (mt0) REVERT: B 272 GLU cc_start: 0.7592 (tt0) cc_final: 0.7269 (tt0) REVERT: B 330 ILE cc_start: 0.8130 (mm) cc_final: 0.7854 (mm) REVERT: B 336 SER cc_start: 0.8819 (t) cc_final: 0.8554 (p) REVERT: B 385 ASP cc_start: 0.7621 (m-30) cc_final: 0.7196 (m-30) REVERT: B 415 ARG cc_start: 0.8603 (mmt90) cc_final: 0.8335 (mtt90) REVERT: B 423 ASP cc_start: 0.7443 (p0) cc_final: 0.7116 (p0) REVERT: B 442 ARG cc_start: 0.7980 (mmt-90) cc_final: 0.7685 (mmt-90) REVERT: B 464 LEU cc_start: 0.7976 (mt) cc_final: 0.7572 (mt) REVERT: B 478 THR cc_start: 0.8215 (m) cc_final: 0.7984 (p) REVERT: B 479 LYS cc_start: 0.8349 (mptt) cc_final: 0.7961 (mptt) REVERT: B 484 GLU cc_start: 0.7895 (mp0) cc_final: 0.7651 (mp0) REVERT: C 34 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8368 (p) REVERT: C 62 MET cc_start: 0.7851 (ttt) cc_final: 0.7625 (ttp) REVERT: C 68 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7234 (mt-10) REVERT: C 80 THR cc_start: 0.8367 (p) cc_final: 0.8091 (m) REVERT: C 88 VAL cc_start: 0.7930 (p) cc_final: 0.7716 (t) REVERT: C 137 MET cc_start: 0.8370 (mmm) cc_final: 0.8104 (mmm) REVERT: C 147 GLN cc_start: 0.7566 (mm-40) cc_final: 0.7189 (mm-40) REVERT: C 181 ASP cc_start: 0.8031 (m-30) cc_final: 0.7766 (m-30) REVERT: C 185 ASN cc_start: 0.8630 (t0) cc_final: 0.8356 (t0) REVERT: C 272 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7438 (mt-10) REVERT: C 314 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.7983 (p) REVERT: C 376 LYS cc_start: 0.8443 (ttpt) cc_final: 0.8198 (ttpt) REVERT: C 451 GLU cc_start: 0.8017 (mp0) cc_final: 0.7690 (mp0) REVERT: C 459 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7926 (mm-30) REVERT: C 462 LEU cc_start: 0.8693 (mt) cc_final: 0.8413 (mm) REVERT: D 3 ARG cc_start: 0.7467 (mtm-85) cc_final: 0.7127 (mtm-85) REVERT: D 10 MET cc_start: 0.7599 (mtm) cc_final: 0.7302 (mtm) REVERT: D 32 ILE cc_start: 0.8364 (mt) cc_final: 0.8106 (tt) REVERT: D 84 SER cc_start: 0.8454 (m) cc_final: 0.7992 (p) REVERT: D 101 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7729 (mp0) REVERT: D 114 ARG cc_start: 0.7706 (ttt180) cc_final: 0.7452 (ttp80) REVERT: D 116 ASP cc_start: 0.7801 (m-30) cc_final: 0.7475 (m-30) REVERT: D 133 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7715 (mt-10) REVERT: D 169 GLN cc_start: 0.8585 (mt0) cc_final: 0.8260 (mm-40) REVERT: D 170 GLU cc_start: 0.7916 (tp30) cc_final: 0.7680 (tt0) REVERT: D 190 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6690 (m-30) REVERT: D 227 ARG cc_start: 0.8149 (mmt180) cc_final: 0.7821 (mmt90) REVERT: D 237 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6932 (mt-10) REVERT: D 241 ASP cc_start: 0.7908 (m-30) cc_final: 0.7679 (m-30) REVERT: D 246 ASP cc_start: 0.7594 (m-30) cc_final: 0.7378 (m-30) REVERT: D 304 GLN cc_start: 0.8143 (mt0) cc_final: 0.7855 (mt0) REVERT: D 333 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7816 (ttm170) REVERT: D 352 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7538 (mtp180) REVERT: D 427 TYR cc_start: 0.8496 (t80) cc_final: 0.8234 (t80) REVERT: D 464 GLU cc_start: 0.7855 (tp30) cc_final: 0.7516 (tp30) REVERT: E 1 MET cc_start: 0.3659 (mmt) cc_final: 0.3297 (mmt) REVERT: E 3 ARG cc_start: 0.7417 (mtm-85) cc_final: 0.7120 (mtm-85) REVERT: E 17 LYS cc_start: 0.8691 (tttt) cc_final: 0.8345 (ttmm) REVERT: E 56 ASP cc_start: 0.7466 (t0) cc_final: 0.7031 (t0) REVERT: E 72 ARG cc_start: 0.8199 (mtm180) cc_final: 0.7906 (ttp-110) REVERT: E 91 THR cc_start: 0.7845 (p) cc_final: 0.7531 (t) REVERT: E 101 GLU cc_start: 0.7929 (mp0) cc_final: 0.7572 (mp0) REVERT: E 127 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7442 (mt-10) REVERT: E 134 ILE cc_start: 0.8723 (mt) cc_final: 0.8438 (tt) REVERT: E 170 GLU cc_start: 0.7840 (tp30) cc_final: 0.7472 (tt0) REVERT: E 178 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7360 (mm-30) REVERT: E 210 LYS cc_start: 0.8238 (mttt) cc_final: 0.7940 (mttt) REVERT: E 256 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7440 (mtm-85) REVERT: E 280 THR cc_start: 0.8096 (p) cc_final: 0.6805 (t) REVERT: E 333 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7621 (ttm-80) REVERT: E 334 LYS cc_start: 0.8368 (mmmm) cc_final: 0.8062 (mmmm) REVERT: E 387 LEU cc_start: 0.8015 (mt) cc_final: 0.7448 (tp) REVERT: E 402 ARG cc_start: 0.8320 (mmm-85) cc_final: 0.7930 (mtt-85) REVERT: E 406 ILE cc_start: 0.8706 (mt) cc_final: 0.8484 (mt) REVERT: E 421 THR cc_start: 0.8214 (t) cc_final: 0.7990 (p) REVERT: E 427 TYR cc_start: 0.8566 (t80) cc_final: 0.8221 (t80) REVERT: E 431 LYS cc_start: 0.8214 (ptmm) cc_final: 0.7913 (ptmm) REVERT: E 435 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7485 (ttp80) REVERT: E 438 LYS cc_start: 0.8534 (ttpt) cc_final: 0.7959 (ttpt) REVERT: E 439 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7098 (mm-30) REVERT: E 450 GLU cc_start: 0.8106 (pm20) cc_final: 0.7760 (pm20) REVERT: F 8 GLN cc_start: 0.8400 (mt0) cc_final: 0.8135 (mt0) REVERT: F 39 GLU cc_start: 0.7770 (mp0) cc_final: 0.7351 (mp0) REVERT: F 49 GLU cc_start: 0.7669 (tt0) cc_final: 0.7282 (tt0) REVERT: F 89 GLU cc_start: 0.7985 (tp30) cc_final: 0.7700 (tp30) REVERT: F 124 LYS cc_start: 0.8068 (mttm) cc_final: 0.7780 (mttm) REVERT: F 127 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7689 (mp0) REVERT: F 241 ASP cc_start: 0.7458 (m-30) cc_final: 0.6998 (m-30) REVERT: F 254 ILE cc_start: 0.8615 (tp) cc_final: 0.8303 (mt) REVERT: F 300 ILE cc_start: 0.8476 (mt) cc_final: 0.8273 (tt) REVERT: F 439 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7592 (mt-10) REVERT: F 442 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7442 (mt-10) REVERT: F 445 TYR cc_start: 0.8606 (m-80) cc_final: 0.8286 (m-80) REVERT: G 17 THR cc_start: 0.8147 (p) cc_final: 0.7715 (t) REVERT: G 28 GLU cc_start: 0.8449 (tt0) cc_final: 0.8208 (tt0) REVERT: G 32 THR cc_start: 0.8891 (m) cc_final: 0.8489 (p) REVERT: G 36 ASN cc_start: 0.8697 (t0) cc_final: 0.8176 (t0) REVERT: G 54 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8168 (mt-10) REVERT: G 70 MET cc_start: 0.7695 (mmm) cc_final: 0.7199 (mmm) REVERT: G 119 ILE cc_start: 0.7837 (mt) cc_final: 0.7587 (mt) REVERT: G 173 MET cc_start: 0.8055 (mtm) cc_final: 0.7776 (mtm) REVERT: G 185 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7370 (mm-30) REVERT: G 188 GLU cc_start: 0.7660 (tt0) cc_final: 0.7437 (tt0) REVERT: G 192 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7545 (mm) REVERT: G 223 TYR cc_start: 0.7773 (t80) cc_final: 0.7450 (t80) REVERT: G 225 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8157 (mt-10) REVERT: G 256 GLU cc_start: 0.8122 (tp30) cc_final: 0.7873 (tp30) outliers start: 93 outliers final: 75 residues processed: 1106 average time/residue: 0.1978 time to fit residues: 321.2453 Evaluate side-chains 1148 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 1068 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 172 TYR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 55 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 262 optimal weight: 0.0370 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 433 GLN A 467 ASN ** B 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN B 433 GLN C 113 GLN C 172 GLN C 371 GLN D 173 HIS ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116002 restraints weight = 35159.818| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.16 r_work: 0.3364 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24604 Z= 0.118 Angle : 0.575 8.349 33364 Z= 0.298 Chirality : 0.043 0.168 3840 Planarity : 0.005 0.064 4349 Dihedral : 7.537 80.457 3574 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.17 % Allowed : 28.50 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.69 (0.15), residues: 3104 helix: 1.69 (0.15), residues: 1254 sheet: 0.31 (0.22), residues: 543 loop : -0.67 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 60 TYR 0.041 0.001 TYR B 389 PHE 0.026 0.001 PHE C 494 HIS 0.007 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00258 (24604) covalent geometry : angle 0.57501 (33364) hydrogen bonds : bond 0.04668 ( 1124) hydrogen bonds : angle 4.59035 ( 3222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1074 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 VAL cc_start: 0.8417 (t) cc_final: 0.8192 (m) REVERT: A 48 MET cc_start: 0.8250 (ptt) cc_final: 0.8014 (ptp) REVERT: A 67 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 89 ARG cc_start: 0.7382 (mtm-85) cc_final: 0.7012 (mtm-85) REVERT: A 95 MET cc_start: 0.7475 (tpt) cc_final: 0.7196 (tpt) REVERT: A 125 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6537 (pt0) REVERT: A 127 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7572 (mtp85) REVERT: A 251 TYR cc_start: 0.8356 (m-80) cc_final: 0.8113 (m-80) REVERT: A 254 LYS cc_start: 0.8212 (mmtm) cc_final: 0.7768 (mmtm) REVERT: A 272 GLU cc_start: 0.7792 (tt0) cc_final: 0.7494 (tt0) REVERT: A 375 MET cc_start: 0.8174 (tpp) cc_final: 0.7739 (tpp) REVERT: A 386 LEU cc_start: 0.8666 (tp) cc_final: 0.8410 (tt) REVERT: A 478 THR cc_start: 0.8536 (t) cc_final: 0.8329 (t) REVERT: A 480 ASP cc_start: 0.7439 (m-30) cc_final: 0.7227 (m-30) REVERT: A 488 ASN cc_start: 0.8425 (m-40) cc_final: 0.8217 (m-40) REVERT: B 83 LYS cc_start: 0.7871 (mttt) cc_final: 0.7658 (mtmm) REVERT: B 144 GLU cc_start: 0.7284 (pt0) cc_final: 0.6888 (pt0) REVERT: B 177 SER cc_start: 0.8054 (p) cc_final: 0.7594 (m) REVERT: B 181 ASP cc_start: 0.7986 (m-30) cc_final: 0.7707 (m-30) REVERT: B 185 ASN cc_start: 0.8798 (t0) cc_final: 0.8396 (t0) REVERT: B 230 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7842 (mt0) REVERT: B 272 GLU cc_start: 0.7591 (tt0) cc_final: 0.7258 (tt0) REVERT: B 336 SER cc_start: 0.8808 (t) cc_final: 0.8538 (p) REVERT: B 385 ASP cc_start: 0.7653 (m-30) cc_final: 0.7235 (m-30) REVERT: B 415 ARG cc_start: 0.8659 (mmt90) cc_final: 0.8322 (mtt90) REVERT: B 423 ASP cc_start: 0.7428 (p0) cc_final: 0.7106 (p0) REVERT: B 442 ARG cc_start: 0.7959 (mmt-90) cc_final: 0.7649 (mmt-90) REVERT: B 464 LEU cc_start: 0.7973 (mt) cc_final: 0.7568 (mt) REVERT: B 478 THR cc_start: 0.8195 (m) cc_final: 0.7967 (p) REVERT: B 479 LYS cc_start: 0.8327 (mptt) cc_final: 0.7968 (mptt) REVERT: B 484 GLU cc_start: 0.7878 (mp0) cc_final: 0.7642 (mp0) REVERT: C 34 VAL cc_start: 0.8700 (t) cc_final: 0.8365 (p) REVERT: C 62 MET cc_start: 0.7790 (ttt) cc_final: 0.7555 (ttp) REVERT: C 68 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7213 (mt-10) REVERT: C 80 THR cc_start: 0.8349 (p) cc_final: 0.8076 (m) REVERT: C 88 VAL cc_start: 0.7909 (p) cc_final: 0.7693 (t) REVERT: C 137 MET cc_start: 0.8355 (mmm) cc_final: 0.8087 (mmm) REVERT: C 181 ASP cc_start: 0.8027 (m-30) cc_final: 0.7753 (m-30) REVERT: C 185 ASN cc_start: 0.8601 (t0) cc_final: 0.8315 (t0) REVERT: C 272 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7419 (mt-10) REVERT: C 314 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.7998 (p) REVERT: C 376 LYS cc_start: 0.8473 (ttpt) cc_final: 0.8234 (ttpt) REVERT: C 451 GLU cc_start: 0.8020 (mp0) cc_final: 0.7686 (mp0) REVERT: C 459 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7909 (mm-30) REVERT: C 462 LEU cc_start: 0.8671 (mt) cc_final: 0.8410 (mm) REVERT: D 3 ARG cc_start: 0.7363 (mtm-85) cc_final: 0.7078 (mtm-85) REVERT: D 10 MET cc_start: 0.7594 (mtm) cc_final: 0.7344 (mtm) REVERT: D 41 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7634 (mt-10) REVERT: D 84 SER cc_start: 0.8435 (m) cc_final: 0.7974 (p) REVERT: D 101 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7709 (mp0) REVERT: D 114 ARG cc_start: 0.7675 (ttt180) cc_final: 0.7432 (ttp80) REVERT: D 116 ASP cc_start: 0.7771 (m-30) cc_final: 0.7455 (m-30) REVERT: D 169 GLN cc_start: 0.8569 (mt0) cc_final: 0.8250 (mm-40) REVERT: D 170 GLU cc_start: 0.7877 (tp30) cc_final: 0.7660 (tt0) REVERT: D 190 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6676 (m-30) REVERT: D 227 ARG cc_start: 0.8118 (mmt180) cc_final: 0.7802 (mmt90) REVERT: D 237 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6915 (mt-10) REVERT: D 241 ASP cc_start: 0.7902 (m-30) cc_final: 0.7670 (m-30) REVERT: D 304 GLN cc_start: 0.8114 (mt0) cc_final: 0.7817 (mt0) REVERT: D 333 ARG cc_start: 0.8123 (ttm-80) cc_final: 0.7844 (ttm170) REVERT: D 352 ARG cc_start: 0.7861 (mtp180) cc_final: 0.7525 (mtp180) REVERT: D 427 TYR cc_start: 0.8456 (t80) cc_final: 0.8202 (t80) REVERT: D 464 GLU cc_start: 0.7837 (tp30) cc_final: 0.7509 (tp30) REVERT: E 1 MET cc_start: 0.3727 (mmt) cc_final: 0.3351 (mmt) REVERT: E 3 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.7110 (mtm-85) REVERT: E 17 LYS cc_start: 0.8653 (tttt) cc_final: 0.8302 (ttmm) REVERT: E 56 ASP cc_start: 0.7477 (t0) cc_final: 0.7043 (t0) REVERT: E 72 ARG cc_start: 0.8173 (mtm180) cc_final: 0.7888 (ttp-110) REVERT: E 91 THR cc_start: 0.7820 (p) cc_final: 0.7548 (t) REVERT: E 101 GLU cc_start: 0.7909 (mp0) cc_final: 0.7521 (mp0) REVERT: E 134 ILE cc_start: 0.8755 (mt) cc_final: 0.8448 (tt) REVERT: E 156 LEU cc_start: 0.8400 (mt) cc_final: 0.8136 (mt) REVERT: E 170 GLU cc_start: 0.7864 (tp30) cc_final: 0.7506 (tt0) REVERT: E 178 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7309 (mm-30) REVERT: E 193 ARG cc_start: 0.8242 (ttp80) cc_final: 0.8027 (ttp80) REVERT: E 210 LYS cc_start: 0.8232 (mttt) cc_final: 0.7933 (mttt) REVERT: E 214 VAL cc_start: 0.8760 (t) cc_final: 0.8410 (p) REVERT: E 256 ARG cc_start: 0.7810 (mtt90) cc_final: 0.7467 (mtm-85) REVERT: E 280 THR cc_start: 0.8084 (p) cc_final: 0.6400 (t) REVERT: E 284 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6798 (mt-10) REVERT: E 333 ARG cc_start: 0.7912 (ttm-80) cc_final: 0.7610 (ttm-80) REVERT: E 334 LYS cc_start: 0.8364 (mmmm) cc_final: 0.8063 (mmmm) REVERT: E 387 LEU cc_start: 0.8024 (mt) cc_final: 0.7653 (mt) REVERT: E 402 ARG cc_start: 0.8302 (mmm-85) cc_final: 0.7913 (mtt-85) REVERT: E 406 ILE cc_start: 0.8690 (mt) cc_final: 0.8467 (mt) REVERT: E 421 THR cc_start: 0.8127 (t) cc_final: 0.7876 (p) REVERT: E 427 TYR cc_start: 0.8529 (t80) cc_final: 0.8237 (t80) REVERT: E 431 LYS cc_start: 0.8225 (ptmm) cc_final: 0.7929 (ptmm) REVERT: E 435 ARG cc_start: 0.8164 (ttp80) cc_final: 0.7403 (ttp80) REVERT: E 438 LYS cc_start: 0.8530 (ttpt) cc_final: 0.7929 (ttpt) REVERT: E 439 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7102 (mm-30) REVERT: E 450 GLU cc_start: 0.8097 (pm20) cc_final: 0.7743 (pm20) REVERT: F 8 GLN cc_start: 0.8405 (mt0) cc_final: 0.8151 (mt0) REVERT: F 39 GLU cc_start: 0.7808 (mp0) cc_final: 0.7375 (mp0) REVERT: F 62 ILE cc_start: 0.8220 (mt) cc_final: 0.7957 (mt) REVERT: F 89 GLU cc_start: 0.8047 (tp30) cc_final: 0.7767 (tp30) REVERT: F 124 LYS cc_start: 0.8097 (mttm) cc_final: 0.7810 (mttm) REVERT: F 127 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7648 (mp0) REVERT: F 241 ASP cc_start: 0.7514 (m-30) cc_final: 0.7065 (m-30) REVERT: F 254 ILE cc_start: 0.8608 (tp) cc_final: 0.8311 (mt) REVERT: F 300 ILE cc_start: 0.8453 (mt) cc_final: 0.8248 (tt) REVERT: F 320 THR cc_start: 0.8732 (t) cc_final: 0.8294 (p) REVERT: F 392 LEU cc_start: 0.8370 (mt) cc_final: 0.8088 (mt) REVERT: F 439 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7559 (mt-10) REVERT: F 442 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7425 (mt-10) REVERT: F 444 LYS cc_start: 0.8475 (tttt) cc_final: 0.8260 (tttt) REVERT: F 445 TYR cc_start: 0.8574 (m-80) cc_final: 0.8289 (m-80) REVERT: G 17 THR cc_start: 0.8122 (p) cc_final: 0.7669 (t) REVERT: G 28 GLU cc_start: 0.8428 (tt0) cc_final: 0.8181 (tt0) REVERT: G 32 THR cc_start: 0.8819 (m) cc_final: 0.8395 (p) REVERT: G 36 ASN cc_start: 0.8663 (t0) cc_final: 0.8200 (t0) REVERT: G 54 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8202 (mt-10) REVERT: G 70 MET cc_start: 0.7712 (mmm) cc_final: 0.7187 (mmm) REVERT: G 82 LEU cc_start: 0.8404 (tp) cc_final: 0.8119 (tp) REVERT: G 90 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8152 (mt) REVERT: G 119 ILE cc_start: 0.7828 (mt) cc_final: 0.7519 (mt) REVERT: G 173 MET cc_start: 0.8029 (mtm) cc_final: 0.7702 (mtm) REVERT: G 185 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7366 (mm-30) REVERT: G 192 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7560 (mm) REVERT: G 223 TYR cc_start: 0.7786 (t80) cc_final: 0.7482 (t80) REVERT: G 225 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8160 (mt-10) REVERT: G 256 GLU cc_start: 0.8094 (tp30) cc_final: 0.7857 (tp30) outliers start: 81 outliers final: 68 residues processed: 1104 average time/residue: 0.2056 time to fit residues: 332.6079 Evaluate side-chains 1131 residues out of total 2558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 1058 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 431 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 203 LYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 380 LEU Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 357 GLU Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 126 GLU Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 88 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 172 TYR Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 77 optimal weight: 0.0030 chunk 299 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 247 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN C 172 GLN C 371 GLN D 173 HIS ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.114867 restraints weight = 35102.667| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.16 r_work: 0.3342 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24604 Z= 0.143 Angle : 0.592 8.268 33364 Z= 0.309 Chirality : 0.044 0.168 3840 Planarity : 0.005 0.064 4349 Dihedral : 7.526 82.317 3574 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.09 % Allowed : 28.97 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % 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: 0.68 (0.15), residues: 3104 helix: 1.70 (0.15), residues: 1247 sheet: 0.34 (0.22), residues: 537 loop : -0.68 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 60 TYR 0.028 0.001 TYR B 389 PHE 0.023 0.001 PHE C 494 HIS 0.007 0.001 HIS D 173 Details of bonding type rmsd covalent geometry : bond 0.00324 (24604) covalent geometry : angle 0.59155 (33364) hydrogen bonds : bond 0.05037 ( 1124) hydrogen bonds : angle 4.61610 ( 3222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8300.87 seconds wall clock time: 141 minutes 52.06 seconds (8512.06 seconds total)