Starting phenix.real_space_refine on Mon Sep 30 03:48:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/09_2024/7l1r_23116.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/09_2024/7l1r_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/09_2024/7l1r_23116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/09_2024/7l1r_23116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/09_2024/7l1r_23116.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l1r_23116/09_2024/7l1r_23116.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 14.62, per 1000 atoms: 0.60 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: 5.97 Conformation dependent library (CDL) restraints added in 2.9 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: 2.64 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: 7.74 Time building geometry restraints manager: 7.03 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 499 or resid 600 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: 0.870 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: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 52.590 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.900 ------------------------------------------------------------------------------- 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= 0.746 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (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 HIS 0.024 0.004 HIS F 173 PHE 0.093 0.009 PHE A 395 TYR 0.110 0.012 TYR D 199 ARG 0.105 0.005 ARG F 270 *********************** 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 fitting. rotamer outliers: 85 poor density : 1210 time to evaluate : 2.685 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: 0.6872 (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: 0.6051 (mtp85) 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: 0.6951 (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: 0.6218 (m) REVERT: B 67 GLU cc_start: 0.6538 (mm-30) cc_final: 0.6061 (mm-30) REVERT: B 127 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6855 (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: 0.6574 (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: 0.6627 (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: 0.7487 (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: 0.6230 (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: 0.6429 (mmt) REVERT: D 74 MET cc_start: 0.7380 (mtt) cc_final: 0.6905 (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: 0.7306 (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: 0.6722 (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: 0.5672 (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: 0.7814 (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: 0.8242 (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: 0.6267 (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: 0.6187 (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: 0.7317 (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: 0.7419 (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: 0.8247 (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: 0.6858 (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: 0.6871 (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: 0.7371 (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: 0.6801 (mt-10) REVERT: F 442 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6600 (mt-10) REVERT: F 444 LYS cc_start: 0.7986 (tttt) cc_final: 0.7378 (tttt) REVERT: F 445 TYR cc_start: 0.8263 (m-80) cc_final: 0.7550 (m-80) REVERT: F 451 ASP cc_start: 0.7794 (m-30) cc_final: 0.7591 (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: 0.6476 (mtm) cc_final: 0.5772 (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: 0.4308 time to fit residues: 775.8815 Evaluate side-chains 1136 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1103 time to evaluate : 2.748 ------------------------------------------------------------------------------- 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 261 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 488 ASN B 33 GLN B 185 ASN 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 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: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24604 Z= 0.245 Angle : 0.685 10.219 33364 Z= 0.372 Chirality : 0.047 0.161 3840 Planarity : 0.005 0.062 4349 Dihedral : 10.187 141.017 3632 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.83 % Allowed : 16.34 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3104 helix: 0.93 (0.14), residues: 1264 sheet: 0.24 (0.23), residues: 492 loop : -0.66 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 179 PHE 0.021 0.002 PHE C 236 TYR 0.025 0.002 TYR C 248 ARG 0.010 0.001 ARG C 415 *********************** 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 1171 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1073 time to evaluate : 2.590 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 89 ARG cc_start: 0.6070 (mtm-85) cc_final: 0.5768 (mtm-85) REVERT: A 93 ARG cc_start: 0.6810 (ptt180) cc_final: 0.6596 (ptt180) REVERT: A 127 ARG cc_start: 0.6815 (mtp85) cc_final: 0.6245 (mtp85) REVERT: A 140 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6870 (ttt90) REVERT: A 144 GLU cc_start: 0.7240 (pt0) cc_final: 0.6751 (pt0) REVERT: A 181 ASP cc_start: 0.7374 (m-30) cc_final: 0.7161 (m-30) REVERT: A 200 GLN cc_start: 0.7402 (mt0) cc_final: 0.7156 (mt0) REVERT: A 272 GLU cc_start: 0.6667 (tt0) cc_final: 0.6250 (tt0) REVERT: A 296 ARG cc_start: 0.7248 (mtm180) cc_final: 0.6893 (mtm-85) REVERT: A 299 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 303 LYS cc_start: 0.7547 (tptp) cc_final: 0.7251 (tttp) REVERT: A 358 ASN cc_start: 0.7288 (t0) cc_final: 0.7026 (t0) REVERT: A 375 MET cc_start: 0.7301 (tpp) cc_final: 0.6645 (tpp) REVERT: A 426 GLN cc_start: 0.7004 (mm-40) cc_final: 0.6683 (mm-40) REVERT: A 427 PRO cc_start: 0.7995 (Cg_endo) cc_final: 0.7692 (Cg_exo) REVERT: A 458 LYS cc_start: 0.7016 (ttmt) cc_final: 0.6814 (tmmt) REVERT: A 489 LYS cc_start: 0.7258 (tttt) cc_final: 0.6998 (tttt) REVERT: B 33 GLN cc_start: 0.6956 (mt0) cc_final: 0.6668 (mt0) REVERT: B 51 GLU cc_start: 0.7055 (tt0) cc_final: 0.6219 (mt-10) REVERT: B 67 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6428 (mm-30) REVERT: B 95 MET cc_start: 0.6950 (tpt) cc_final: 0.6477 (tpt) REVERT: B 127 ARG cc_start: 0.7302 (mtp85) cc_final: 0.7095 (mtp85) REVERT: B 159 ILE cc_start: 0.7473 (mt) cc_final: 0.7236 (mt) REVERT: B 177 SER cc_start: 0.6488 (p) cc_final: 0.5826 (p) REVERT: B 181 ASP cc_start: 0.7283 (m-30) cc_final: 0.7053 (m-30) REVERT: B 185 ASN cc_start: 0.7626 (t0) cc_final: 0.7292 (t0) REVERT: B 200 GLN cc_start: 0.8055 (mm-40) cc_final: 0.6962 (mp10) REVERT: B 202 GLU cc_start: 0.6223 (tp30) cc_final: 0.5740 (tp30) REVERT: B 211 THR cc_start: 0.4874 (m) cc_final: 0.4672 (p) REVERT: B 229 SER cc_start: 0.7259 (t) cc_final: 0.6945 (p) REVERT: B 272 GLU cc_start: 0.6758 (tt0) cc_final: 0.6379 (tt0) REVERT: B 312 SER cc_start: 0.8397 (t) cc_final: 0.7938 (p) REVERT: B 345 GLN cc_start: 0.6000 (OUTLIER) cc_final: 0.5669 (tt0) REVERT: B 385 ASP cc_start: 0.7011 (m-30) cc_final: 0.6713 (m-30) REVERT: B 391 GLU cc_start: 0.7134 (tp30) cc_final: 0.6770 (tp30) REVERT: B 428 ILE cc_start: 0.7734 (mt) cc_final: 0.7408 (mm) REVERT: B 442 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.7137 (mmt-90) REVERT: B 467 ASN cc_start: 0.8367 (t0) cc_final: 0.8100 (t0) REVERT: B 478 THR cc_start: 0.7157 (OUTLIER) cc_final: 0.6911 (t) REVERT: C 34 VAL cc_start: 0.7686 (t) cc_final: 0.7341 (p) REVERT: C 51 GLU cc_start: 0.7414 (tt0) cc_final: 0.6974 (tt0) REVERT: C 60 MET cc_start: 0.6263 (mmt) cc_final: 0.5991 (mmt) REVERT: C 62 MET cc_start: 0.6616 (ttt) cc_final: 0.6375 (ttp) REVERT: C 90 ARG cc_start: 0.7527 (ttp80) cc_final: 0.7162 (ttp-110) REVERT: C 101 GLU cc_start: 0.7485 (mp0) cc_final: 0.7199 (mp0) REVERT: C 109 ASN cc_start: 0.7020 (t0) cc_final: 0.6708 (t0) REVERT: C 122 GLU cc_start: 0.7497 (tp30) cc_final: 0.6938 (tp30) REVERT: C 127 ARG cc_start: 0.7443 (mtp85) cc_final: 0.6953 (mtp-110) REVERT: C 137 MET cc_start: 0.8016 (mmm) cc_final: 0.7792 (mmm) REVERT: C 144 GLU cc_start: 0.6860 (pt0) cc_final: 0.6242 (pt0) REVERT: C 147 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7136 (mm110) REVERT: C 181 ASP cc_start: 0.7674 (m-30) cc_final: 0.7318 (m-30) REVERT: C 196 VAL cc_start: 0.7823 (t) cc_final: 0.7478 (m) REVERT: C 200 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6796 (mm-40) REVERT: C 222 ILE cc_start: 0.7223 (mt) cc_final: 0.7000 (mt) REVERT: C 229 SER cc_start: 0.7314 (t) cc_final: 0.7016 (p) REVERT: C 254 LYS cc_start: 0.7323 (mmtm) cc_final: 0.6944 (mtmm) REVERT: C 272 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6574 (mt-10) REVERT: C 279 ARG cc_start: 0.7187 (mtt180) cc_final: 0.6591 (mtt-85) REVERT: C 361 LEU cc_start: 0.7614 (mp) cc_final: 0.7331 (mp) REVERT: C 385 ASP cc_start: 0.6572 (m-30) cc_final: 0.6360 (m-30) REVERT: C 442 ARG cc_start: 0.7400 (mmt-90) cc_final: 0.7124 (mmt90) REVERT: C 451 GLU cc_start: 0.7561 (mp0) cc_final: 0.7045 (mp0) REVERT: C 452 ASP cc_start: 0.7161 (m-30) cc_final: 0.6821 (m-30) REVERT: C 467 ASN cc_start: 0.8429 (t0) cc_final: 0.8138 (t0) REVERT: C 496 LYS cc_start: 0.8583 (mttt) cc_final: 0.8044 (mttt) REVERT: D 3 ARG cc_start: 0.6423 (mtm-85) cc_final: 0.6028 (mtm-85) REVERT: D 5 ARG cc_start: 0.6166 (mtm-85) cc_final: 0.5878 (mtm-85) REVERT: D 7 ILE cc_start: 0.7681 (mt) cc_final: 0.7323 (mm) REVERT: D 10 MET cc_start: 0.6260 (mtm) cc_final: 0.5773 (mtm) REVERT: D 15 ASP cc_start: 0.6928 (m-30) cc_final: 0.6724 (m-30) REVERT: D 17 LYS cc_start: 0.7055 (tttt) cc_final: 0.6611 (tttm) REVERT: D 26 ILE cc_start: 0.8016 (mt) cc_final: 0.7762 (mp) REVERT: D 64 MET cc_start: 0.6746 (mmt) cc_final: 0.6379 (mmt) REVERT: D 74 MET cc_start: 0.7376 (mtt) cc_final: 0.6938 (mtt) REVERT: D 75 GLU cc_start: 0.7433 (tt0) cc_final: 0.7138 (tt0) REVERT: D 84 SER cc_start: 0.7807 (m) cc_final: 0.7428 (p) REVERT: D 101 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6819 (mt-10) REVERT: D 114 ARG cc_start: 0.7226 (ttt180) cc_final: 0.6743 (ttp80) REVERT: D 116 ASP cc_start: 0.7059 (m-30) cc_final: 0.6484 (m-30) REVERT: D 133 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6622 (mt-10) REVERT: D 190 ASP cc_start: 0.6534 (m-30) cc_final: 0.5508 (m-30) REVERT: D 197 ASP cc_start: 0.6825 (t0) cc_final: 0.6572 (t0) REVERT: D 214 VAL cc_start: 0.7792 (t) cc_final: 0.7442 (p) REVERT: D 227 ARG cc_start: 0.6784 (mmt180) cc_final: 0.6208 (mmt90) REVERT: D 228 VAL cc_start: 0.6983 (OUTLIER) cc_final: 0.6724 (p) REVERT: D 237 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6566 (mt-10) REVERT: D 241 ASP cc_start: 0.7215 (m-30) cc_final: 0.6823 (m-30) REVERT: D 252 ASP cc_start: 0.6404 (t0) cc_final: 0.6019 (t0) REVERT: D 270 ARG cc_start: 0.7352 (mtt180) cc_final: 0.6908 (mtt-85) REVERT: D 271 MET cc_start: 0.7865 (mtt) cc_final: 0.7589 (ttm) REVERT: D 284 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5630 (mt-10) REVERT: D 285 MET cc_start: 0.6535 (ttm) cc_final: 0.6232 (ttm) REVERT: D 326 ASP cc_start: 0.7184 (m-30) cc_final: 0.6242 (m-30) REVERT: D 337 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6680 (mt-10) REVERT: D 352 ARG cc_start: 0.7077 (mtp180) cc_final: 0.6737 (mtp180) REVERT: D 387 LEU cc_start: 0.7815 (mt) cc_final: 0.7537 (mp) REVERT: D 427 TYR cc_start: 0.7806 (t80) cc_final: 0.7538 (t80) REVERT: D 428 VAL cc_start: 0.8464 (t) cc_final: 0.8166 (m) REVERT: D 439 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6866 (mm-30) REVERT: E 1 MET cc_start: 0.3431 (mmt) cc_final: 0.3040 (mmt) REVERT: E 3 ARG cc_start: 0.6698 (mtm-85) cc_final: 0.6399 (mtm-85) REVERT: E 5 ARG cc_start: 0.6529 (ptp-110) cc_final: 0.6112 (ptp-110) REVERT: E 10 MET cc_start: 0.5907 (ptp) cc_final: 0.5430 (ptp) REVERT: E 43 ASP cc_start: 0.6951 (m-30) cc_final: 0.6512 (m-30) REVERT: E 71 ILE cc_start: 0.7696 (mt) cc_final: 0.7484 (mt) REVERT: E 91 THR cc_start: 0.7721 (p) cc_final: 0.7513 (t) REVERT: E 120 ARG cc_start: 0.6762 (mtp85) cc_final: 0.6542 (ttp80) REVERT: E 127 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6402 (mt-10) REVERT: E 134 ILE cc_start: 0.8230 (mt) cc_final: 0.7897 (tt) REVERT: E 170 GLU cc_start: 0.7002 (tp30) cc_final: 0.6739 (tt0) REVERT: E 210 LYS cc_start: 0.7524 (mttt) cc_final: 0.7140 (mttt) REVERT: E 227 ARG cc_start: 0.6360 (mmt180) cc_final: 0.6073 (mmt90) REVERT: E 237 GLU cc_start: 0.6972 (tt0) cc_final: 0.6737 (mt-10) REVERT: E 256 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6448 (mtt180) REVERT: E 278 GLN cc_start: 0.7021 (pm20) cc_final: 0.6675 (pt0) REVERT: E 284 GLU cc_start: 0.6183 (mt-10) cc_final: 0.5404 (mt-10) REVERT: E 312 ASP cc_start: 0.7271 (t0) cc_final: 0.6895 (t0) REVERT: E 315 ASP cc_start: 0.7077 (OUTLIER) cc_final: 0.6802 (t70) REVERT: E 362 GLU cc_start: 0.7662 (pm20) cc_final: 0.7307 (pm20) REVERT: E 365 GLN cc_start: 0.7535 (mt0) cc_final: 0.7121 (mt0) REVERT: E 376 ARG cc_start: 0.7701 (tpt170) cc_final: 0.7177 (tpt170) REVERT: E 402 ARG cc_start: 0.7573 (mmm-85) cc_final: 0.7045 (mtt-85) REVERT: E 405 ARG cc_start: 0.7514 (mpt180) cc_final: 0.7266 (mmt-90) REVERT: E 407 GLN cc_start: 0.7578 (tt0) cc_final: 0.7075 (tp-100) REVERT: E 418 GLU cc_start: 0.7545 (tt0) cc_final: 0.7058 (tt0) REVERT: E 420 PHE cc_start: 0.7583 (m-10) cc_final: 0.7373 (m-10) REVERT: E 423 GLN cc_start: 0.7306 (mm-40) cc_final: 0.7049 (mm-40) REVERT: E 431 LYS cc_start: 0.7694 (ptmm) cc_final: 0.7437 (ptmm) REVERT: E 435 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7138 (ttp80) REVERT: E 438 LYS cc_start: 0.7792 (ttpt) cc_final: 0.6856 (ttpt) REVERT: E 439 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6780 (mm-30) REVERT: E 442 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7186 (mt-10) REVERT: E 450 GLU cc_start: 0.7814 (pm20) cc_final: 0.7268 (pm20) REVERT: F 3 ARG cc_start: 0.6603 (mtt180) cc_final: 0.6343 (mtt180) REVERT: F 5 ARG cc_start: 0.5955 (mmt180) cc_final: 0.5416 (mmt180) REVERT: F 10 MET cc_start: 0.6898 (mtm) cc_final: 0.6668 (mtm) REVERT: F 15 ASP cc_start: 0.6950 (m-30) cc_final: 0.6460 (m-30) REVERT: F 23 LEU cc_start: 0.8241 (mp) cc_final: 0.8033 (mt) REVERT: F 33 GLN cc_start: 0.7491 (mt0) cc_final: 0.7180 (mt0) REVERT: F 39 GLU cc_start: 0.7478 (mp0) cc_final: 0.6939 (mp0) REVERT: F 74 MET cc_start: 0.6878 (mtt) cc_final: 0.6406 (mtt) REVERT: F 89 GLU cc_start: 0.7450 (tp30) cc_final: 0.7158 (tp30) REVERT: F 114 ARG cc_start: 0.7260 (ttp-170) cc_final: 0.6892 (ttp80) REVERT: F 120 ARG cc_start: 0.7041 (ptm-80) cc_final: 0.6691 (ptt90) REVERT: F 124 LYS cc_start: 0.7057 (mttm) cc_final: 0.6734 (mttm) REVERT: F 127 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6883 (mt-10) REVERT: F 213 MET cc_start: 0.7284 (mtp) cc_final: 0.7026 (mtm) REVERT: F 218 MET cc_start: 0.7482 (mtm) cc_final: 0.7234 (mtp) REVERT: F 220 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6566 (mm-30) REVERT: F 277 TYR cc_start: 0.6902 (m-80) cc_final: 0.6543 (m-80) REVERT: F 285 MET cc_start: 0.6966 (ttm) cc_final: 0.6736 (ttm) REVERT: F 290 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6946 (mm-30) REVERT: F 303 ILE cc_start: 0.7240 (mt) cc_final: 0.7033 (mm) REVERT: F 326 ASP cc_start: 0.7171 (m-30) cc_final: 0.6888 (m-30) REVERT: F 345 ASP cc_start: 0.7409 (t70) cc_final: 0.7093 (t70) REVERT: F 352 ARG cc_start: 0.7291 (ttm-80) cc_final: 0.7068 (ttm-80) REVERT: F 389 MET cc_start: 0.7212 (mtm) cc_final: 0.6693 (mtm) REVERT: F 397 LYS cc_start: 0.7441 (tttm) cc_final: 0.7144 (tttm) REVERT: F 423 GLN cc_start: 0.7475 (pt0) cc_final: 0.7252 (pt0) REVERT: F 438 LYS cc_start: 0.7543 (tttt) cc_final: 0.7160 (tttt) REVERT: F 439 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6632 (mt-10) REVERT: F 442 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6411 (mt-10) REVERT: F 444 LYS cc_start: 0.7976 (tttt) cc_final: 0.7287 (tttt) REVERT: F 445 TYR cc_start: 0.8318 (m-80) cc_final: 0.7574 (m-80) REVERT: F 451 ASP cc_start: 0.7916 (m-30) cc_final: 0.7698 (m-30) REVERT: F 460 GLU cc_start: 0.7883 (mp0) cc_final: 0.7676 (mp0) REVERT: G 17 THR cc_start: 0.6613 (p) cc_final: 0.6370 (t) REVERT: G 33 SER cc_start: 0.7740 (t) cc_final: 0.7408 (p) REVERT: G 54 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8423 (mt-10) REVERT: G 70 MET cc_start: 0.7733 (mmm) cc_final: 0.7263 (mmm) REVERT: G 88 ARG cc_start: 0.6952 (ptt180) cc_final: 0.6673 (ptt180) REVERT: G 95 ASN cc_start: 0.7826 (m-40) cc_final: 0.7587 (m110) REVERT: G 115 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7538 (mm-30) REVERT: G 116 TYR cc_start: 0.7625 (p90) cc_final: 0.7169 (p90) REVERT: G 134 MET cc_start: 0.6457 (mtm) cc_final: 0.5998 (mtm) REVERT: G 173 MET cc_start: 0.7148 (mtm) cc_final: 0.6786 (mtm) REVERT: G 185 GLU cc_start: 0.6490 (mm-30) cc_final: 0.6259 (mm-30) REVERT: G 188 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5583 (tt0) REVERT: G 225 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8290 (mt-10) REVERT: G 227 LEU cc_start: 0.8086 (mm) cc_final: 0.7816 (mm) REVERT: G 256 GLU cc_start: 0.6692 (tp30) cc_final: 0.6415 (tp30) REVERT: G 270 GLN cc_start: 0.7107 (mt0) cc_final: 0.6731 (mt0) outliers start: 98 outliers final: 52 residues processed: 1115 average time/residue: 0.4225 time to fit residues: 685.0946 Evaluate side-chains 1087 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1030 time to evaluate : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 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 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 305 SER 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 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 177 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 491 ILE 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 369 LYS Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 459 ILE 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 293 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 380 LEU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 278 GLN 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 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 148 SER Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 264 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 191 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 282 optimal weight: 0.9980 chunk 304 optimal weight: 8.9990 chunk 251 optimal weight: 2.9990 chunk 279 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 294 HIS A 345 GLN A 469 GLN B 185 ASN C 345 GLN C 358 ASN C 466 GLN C 474 HIS E 375 GLN E 412 GLN F 324 HIS G 110 HIS G 266 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 24604 Z= 0.381 Angle : 0.697 8.875 33364 Z= 0.377 Chirality : 0.050 0.183 3840 Planarity : 0.006 0.068 4349 Dihedral : 9.595 138.810 3589 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.96 % Allowed : 19.66 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 3104 helix: 0.76 (0.14), residues: 1256 sheet: -0.00 (0.22), residues: 528 loop : -0.88 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS B 294 PHE 0.022 0.002 PHE A 343 TYR 0.025 0.002 TYR F 307 ARG 0.012 0.001 ARG C 415 *********************** 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 1219 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1092 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7257 (mtp85) cc_final: 0.6881 (mtt90) REVERT: A 89 ARG cc_start: 0.6209 (mtm-85) cc_final: 0.5898 (mtm-85) REVERT: A 93 ARG cc_start: 0.7127 (ptt180) cc_final: 0.6729 (ptt180) REVERT: A 140 ARG cc_start: 0.7282 (ttt-90) cc_final: 0.6875 (ttt90) REVERT: A 144 GLU cc_start: 0.7218 (pt0) cc_final: 0.6669 (pt0) REVERT: A 165 GLU cc_start: 0.7515 (tp30) cc_final: 0.7268 (tp30) REVERT: A 251 TYR cc_start: 0.7169 (m-80) cc_final: 0.6686 (m-80) REVERT: A 272 GLU cc_start: 0.6664 (tt0) cc_final: 0.6196 (tt0) REVERT: A 296 ARG cc_start: 0.7321 (mtm180) cc_final: 0.7017 (mtm-85) REVERT: A 299 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7431 (mm-30) REVERT: A 375 MET cc_start: 0.7358 (tpp) cc_final: 0.6711 (tpp) REVERT: A 385 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6907 (t0) REVERT: A 421 LYS cc_start: 0.7273 (mttp) cc_final: 0.6995 (mttm) REVERT: A 426 GLN cc_start: 0.7161 (mm-40) cc_final: 0.6796 (mm-40) REVERT: A 427 PRO cc_start: 0.8148 (Cg_endo) cc_final: 0.7907 (Cg_exo) REVERT: A 476 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7770 (ttm110) REVERT: A 478 THR cc_start: 0.7606 (t) cc_final: 0.7355 (p) REVERT: A 489 LYS cc_start: 0.7532 (tttt) cc_final: 0.7262 (tttt) REVERT: B 33 GLN cc_start: 0.7055 (mt0) cc_final: 0.6766 (mt0) REVERT: B 40 ARG cc_start: 0.6512 (mtt90) cc_final: 0.6270 (mtt90) REVERT: B 51 GLU cc_start: 0.7140 (tt0) cc_final: 0.6044 (mt-10) REVERT: B 67 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6663 (mm-30) REVERT: B 95 MET cc_start: 0.6908 (tpt) cc_final: 0.6186 (tpt) REVERT: B 127 ARG cc_start: 0.7318 (mtp85) cc_final: 0.7045 (mtp85) REVERT: B 144 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.5970 (pt0) REVERT: B 159 ILE cc_start: 0.7288 (mt) cc_final: 0.7053 (mt) REVERT: B 171 ARG cc_start: 0.7132 (mtm110) cc_final: 0.6924 (mtm110) REVERT: B 177 SER cc_start: 0.6301 (p) cc_final: 0.5871 (m) REVERT: B 181 ASP cc_start: 0.7408 (m-30) cc_final: 0.7106 (m-30) REVERT: B 185 ASN cc_start: 0.7677 (t0) cc_final: 0.7351 (t0) REVERT: B 200 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7729 (mm110) REVERT: B 202 GLU cc_start: 0.6148 (tp30) cc_final: 0.5857 (tp30) REVERT: B 272 GLU cc_start: 0.6736 (tt0) cc_final: 0.6396 (tt0) REVERT: B 345 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.6057 (tt0) REVERT: B 378 VAL cc_start: 0.7962 (t) cc_final: 0.7719 (p) REVERT: B 385 ASP cc_start: 0.7291 (m-30) cc_final: 0.6934 (m-30) REVERT: B 423 ASP cc_start: 0.6432 (p0) cc_final: 0.6116 (p0) REVERT: B 449 PRO cc_start: 0.7386 (Cg_exo) cc_final: 0.7109 (Cg_endo) REVERT: B 467 ASN cc_start: 0.8386 (t0) cc_final: 0.8103 (t0) REVERT: B 479 LYS cc_start: 0.7334 (mptt) cc_final: 0.6804 (mptt) REVERT: B 480 ASP cc_start: 0.6717 (t0) cc_final: 0.6495 (t0) REVERT: B 481 LEU cc_start: 0.8269 (tp) cc_final: 0.7794 (mp) REVERT: C 34 VAL cc_start: 0.7675 (t) cc_final: 0.7348 (p) REVERT: C 51 GLU cc_start: 0.7506 (tt0) cc_final: 0.7142 (tt0) REVERT: C 62 MET cc_start: 0.6647 (ttt) cc_final: 0.6292 (ttp) REVERT: C 80 THR cc_start: 0.7920 (p) cc_final: 0.7681 (m) REVERT: C 90 ARG cc_start: 0.7574 (ttp80) cc_final: 0.7142 (ttt-90) REVERT: C 127 ARG cc_start: 0.7465 (mtp85) cc_final: 0.7060 (mtp85) REVERT: C 137 MET cc_start: 0.7985 (mmm) cc_final: 0.7771 (mmm) REVERT: C 144 GLU cc_start: 0.7009 (pt0) cc_final: 0.6368 (pt0) REVERT: C 147 GLN cc_start: 0.7472 (mm-40) cc_final: 0.7154 (mm110) REVERT: C 181 ASP cc_start: 0.7654 (m-30) cc_final: 0.7293 (m-30) REVERT: C 185 ASN cc_start: 0.7879 (t0) cc_final: 0.7568 (t0) REVERT: C 196 VAL cc_start: 0.7806 (t) cc_final: 0.7472 (m) REVERT: C 224 VAL cc_start: 0.7490 (t) cc_final: 0.7174 (m) REVERT: C 254 LYS cc_start: 0.7468 (mmtm) cc_final: 0.7046 (mtmm) REVERT: C 260 TYR cc_start: 0.6672 (m-80) cc_final: 0.6400 (m-80) REVERT: C 272 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6555 (mt-10) REVERT: C 314 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7023 (p) REVERT: C 361 LEU cc_start: 0.7663 (mp) cc_final: 0.7433 (mp) REVERT: C 372 ILE cc_start: 0.7506 (mt) cc_final: 0.7271 (mm) REVERT: C 376 LYS cc_start: 0.7398 (ttpt) cc_final: 0.7144 (ttpt) REVERT: C 385 ASP cc_start: 0.6457 (m-30) cc_final: 0.6199 (m-30) REVERT: C 422 GLN cc_start: 0.7499 (tt0) cc_final: 0.7294 (tt0) REVERT: C 442 ARG cc_start: 0.7415 (mmt-90) cc_final: 0.7127 (mmt90) REVERT: C 451 GLU cc_start: 0.7571 (mp0) cc_final: 0.7051 (mp0) REVERT: C 452 ASP cc_start: 0.7380 (m-30) cc_final: 0.7075 (m-30) REVERT: C 473 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7850 (mm-30) REVERT: C 496 LYS cc_start: 0.8566 (mttt) cc_final: 0.8045 (mttt) REVERT: D 5 ARG cc_start: 0.6150 (mtm-85) cc_final: 0.5838 (mtm-85) REVERT: D 7 ILE cc_start: 0.7624 (mt) cc_final: 0.7317 (mm) REVERT: D 10 MET cc_start: 0.6570 (mtm) cc_final: 0.5948 (mtm) REVERT: D 15 ASP cc_start: 0.6984 (m-30) cc_final: 0.6707 (m-30) REVERT: D 17 LYS cc_start: 0.7090 (tttt) cc_final: 0.6607 (tttm) REVERT: D 37 ARG cc_start: 0.6906 (mtm180) cc_final: 0.6467 (mtm180) REVERT: D 64 MET cc_start: 0.6792 (mmt) cc_final: 0.6437 (mmt) REVERT: D 74 MET cc_start: 0.7524 (mtt) cc_final: 0.7078 (mtt) REVERT: D 75 GLU cc_start: 0.7396 (tt0) cc_final: 0.6991 (tt0) REVERT: D 84 SER cc_start: 0.7827 (m) cc_final: 0.7400 (p) REVERT: D 101 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6931 (mt-10) REVERT: D 114 ARG cc_start: 0.7260 (ttt180) cc_final: 0.6864 (ttp80) REVERT: D 116 ASP cc_start: 0.7060 (m-30) cc_final: 0.6488 (m-30) REVERT: D 120 ARG cc_start: 0.7276 (ttt90) cc_final: 0.6918 (ptm160) REVERT: D 133 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6693 (mt-10) REVERT: D 170 GLU cc_start: 0.7141 (tp30) cc_final: 0.6789 (tt0) REVERT: D 173 HIS cc_start: 0.8295 (t70) cc_final: 0.8076 (t70) REVERT: D 190 ASP cc_start: 0.6891 (m-30) cc_final: 0.5487 (m-30) REVERT: D 191 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.5886 (mtt-85) REVERT: D 197 ASP cc_start: 0.6907 (t0) cc_final: 0.6651 (t0) REVERT: D 214 VAL cc_start: 0.7832 (t) cc_final: 0.7505 (p) REVERT: D 227 ARG cc_start: 0.6848 (mmt180) cc_final: 0.6282 (mmt90) REVERT: D 237 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6524 (mt-10) REVERT: D 241 ASP cc_start: 0.7156 (m-30) cc_final: 0.6842 (m-30) REVERT: D 246 ASP cc_start: 0.7517 (m-30) cc_final: 0.6973 (m-30) REVERT: D 252 ASP cc_start: 0.6407 (t0) cc_final: 0.5901 (t0) REVERT: D 284 GLU cc_start: 0.6142 (mt-10) cc_final: 0.5621 (mt-10) REVERT: D 285 MET cc_start: 0.6485 (ttm) cc_final: 0.6182 (ttm) REVERT: D 326 ASP cc_start: 0.7138 (m-30) cc_final: 0.6391 (m-30) REVERT: D 337 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6729 (mt-10) REVERT: D 345 ASP cc_start: 0.7155 (t0) cc_final: 0.6949 (t0) REVERT: D 352 ARG cc_start: 0.7108 (mtp180) cc_final: 0.6817 (mtp180) REVERT: D 387 LEU cc_start: 0.7808 (mt) cc_final: 0.7561 (mp) REVERT: D 428 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8028 (m) REVERT: D 439 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6854 (mm-30) REVERT: E 1 MET cc_start: 0.3451 (mmt) cc_final: 0.3071 (mmt) REVERT: E 3 ARG cc_start: 0.6708 (mtm-85) cc_final: 0.6414 (mtm-85) REVERT: E 5 ARG cc_start: 0.6536 (ptp-110) cc_final: 0.6158 (ptp-110) REVERT: E 10 MET cc_start: 0.5987 (ptp) cc_final: 0.5488 (ptp) REVERT: E 17 LYS cc_start: 0.7659 (tttt) cc_final: 0.7101 (ttmm) REVERT: E 43 ASP cc_start: 0.7115 (m-30) cc_final: 0.6768 (m-30) REVERT: E 71 ILE cc_start: 0.7696 (mt) cc_final: 0.7421 (mt) REVERT: E 91 THR cc_start: 0.7681 (p) cc_final: 0.7401 (t) REVERT: E 104 ASP cc_start: 0.7366 (m-30) cc_final: 0.6820 (m-30) REVERT: E 120 ARG cc_start: 0.6876 (mtp85) cc_final: 0.6595 (ttp80) REVERT: E 127 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6528 (mt-10) REVERT: E 134 ILE cc_start: 0.8284 (mt) cc_final: 0.7940 (tt) REVERT: E 170 GLU cc_start: 0.7054 (tp30) cc_final: 0.6716 (tt0) REVERT: E 178 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6920 (mm-30) REVERT: E 210 LYS cc_start: 0.7610 (mttt) cc_final: 0.7227 (mttt) REVERT: E 227 ARG cc_start: 0.6497 (mmt180) cc_final: 0.6156 (mmt90) REVERT: E 247 VAL cc_start: 0.7446 (t) cc_final: 0.6897 (m) REVERT: E 256 ARG cc_start: 0.6820 (mtm-85) cc_final: 0.6591 (mtt90) REVERT: E 284 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5787 (mt-10) REVERT: E 312 ASP cc_start: 0.7160 (t0) cc_final: 0.6708 (t70) REVERT: E 315 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6930 (t70) REVERT: E 334 LYS cc_start: 0.7390 (mmmm) cc_final: 0.7170 (mmmm) REVERT: E 362 GLU cc_start: 0.7664 (pm20) cc_final: 0.7358 (pm20) REVERT: E 365 GLN cc_start: 0.7606 (mt0) cc_final: 0.7203 (mt0) REVERT: E 375 GLN cc_start: 0.7656 (tp40) cc_final: 0.7377 (tp-100) REVERT: E 376 ARG cc_start: 0.7764 (tpt170) cc_final: 0.7276 (tpt170) REVERT: E 402 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.7179 (mtt-85) REVERT: E 405 ARG cc_start: 0.7541 (mpt180) cc_final: 0.7197 (mmt-90) REVERT: E 407 GLN cc_start: 0.7425 (tt0) cc_final: 0.7015 (tp-100) REVERT: E 408 PHE cc_start: 0.6995 (m-80) cc_final: 0.6708 (m-80) REVERT: E 421 THR cc_start: 0.7667 (t) cc_final: 0.7457 (t) REVERT: E 431 LYS cc_start: 0.7758 (ptmm) cc_final: 0.7484 (ptmm) REVERT: E 435 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7108 (ttp80) REVERT: E 438 LYS cc_start: 0.7728 (ttpt) cc_final: 0.7108 (ttpt) REVERT: E 439 GLU cc_start: 0.7579 (mm-30) cc_final: 0.6707 (mm-30) REVERT: E 442 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7417 (mt-10) REVERT: E 445 TYR cc_start: 0.7513 (m-80) cc_final: 0.6657 (m-80) REVERT: E 446 ASP cc_start: 0.7714 (m-30) cc_final: 0.7485 (m-30) REVERT: E 450 GLU cc_start: 0.7842 (pm20) cc_final: 0.7284 (pm20) REVERT: E 461 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7248 (mt-10) REVERT: F 3 ARG cc_start: 0.6757 (mtt180) cc_final: 0.6159 (mtt180) REVERT: F 5 ARG cc_start: 0.6021 (mmt180) cc_final: 0.5447 (mmt180) REVERT: F 8 GLN cc_start: 0.7323 (mt0) cc_final: 0.6943 (mt0) REVERT: F 10 MET cc_start: 0.7073 (mtm) cc_final: 0.6866 (mtm) REVERT: F 15 ASP cc_start: 0.6992 (m-30) cc_final: 0.6607 (m-30) REVERT: F 33 GLN cc_start: 0.7437 (mt0) cc_final: 0.7077 (mt0) REVERT: F 37 ARG cc_start: 0.7340 (ttm170) cc_final: 0.7111 (ttm170) REVERT: F 39 GLU cc_start: 0.7523 (mp0) cc_final: 0.7083 (mp0) REVERT: F 74 MET cc_start: 0.6850 (mtt) cc_final: 0.6407 (mtt) REVERT: F 75 GLU cc_start: 0.6894 (tt0) cc_final: 0.5188 (tt0) REVERT: F 89 GLU cc_start: 0.7498 (tp30) cc_final: 0.7210 (tp30) REVERT: F 114 ARG cc_start: 0.7481 (ttp-170) cc_final: 0.7085 (ttp80) REVERT: F 115 ARG cc_start: 0.7429 (mtt90) cc_final: 0.7057 (mtt90) REVERT: F 116 ASP cc_start: 0.7417 (m-30) cc_final: 0.7004 (m-30) REVERT: F 124 LYS cc_start: 0.7124 (mttm) cc_final: 0.6723 (mttm) REVERT: F 127 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6892 (mt-10) REVERT: F 213 MET cc_start: 0.7325 (mtp) cc_final: 0.6813 (mtp) REVERT: F 220 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6567 (mm-30) REVERT: F 237 GLU cc_start: 0.6670 (tt0) cc_final: 0.6185 (mt-10) REVERT: F 254 ILE cc_start: 0.7857 (tp) cc_final: 0.7616 (mt) REVERT: F 285 MET cc_start: 0.6888 (ttm) cc_final: 0.6649 (ttm) REVERT: F 300 ILE cc_start: 0.7785 (mt) cc_final: 0.7504 (tt) REVERT: F 303 ILE cc_start: 0.7273 (mt) cc_final: 0.6995 (mp) REVERT: F 345 ASP cc_start: 0.7427 (t70) cc_final: 0.6992 (t70) REVERT: F 357 GLU cc_start: 0.7296 (pm20) cc_final: 0.7081 (pm20) REVERT: F 389 MET cc_start: 0.7407 (mtm) cc_final: 0.6923 (mtm) REVERT: F 397 LYS cc_start: 0.7413 (tttm) cc_final: 0.7136 (tttm) REVERT: F 423 GLN cc_start: 0.7562 (pt0) cc_final: 0.7354 (pt0) REVERT: F 438 LYS cc_start: 0.7619 (tttt) cc_final: 0.7108 (tttt) REVERT: F 439 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6717 (mt-10) REVERT: F 442 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6517 (mt-10) REVERT: F 444 LYS cc_start: 0.7943 (tttt) cc_final: 0.7387 (tttt) REVERT: F 445 TYR cc_start: 0.8290 (m-80) cc_final: 0.7643 (m-80) REVERT: F 451 ASP cc_start: 0.7899 (m-30) cc_final: 0.7681 (m-30) REVERT: F 460 GLU cc_start: 0.7981 (mp0) cc_final: 0.7727 (mp0) REVERT: G 11 LYS cc_start: 0.7401 (tptt) cc_final: 0.6755 (tptt) REVERT: G 15 ASN cc_start: 0.7354 (m-40) cc_final: 0.6985 (m-40) REVERT: G 33 SER cc_start: 0.7773 (t) cc_final: 0.7421 (p) REVERT: G 54 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8413 (mt-10) REVERT: G 70 MET cc_start: 0.7885 (mmm) cc_final: 0.7292 (mmm) REVERT: G 85 THR cc_start: 0.7807 (OUTLIER) cc_final: 0.7277 (t) REVERT: G 88 ARG cc_start: 0.7062 (ptt180) cc_final: 0.6633 (ptt180) REVERT: G 115 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7662 (mm-30) REVERT: G 116 TYR cc_start: 0.7651 (p90) cc_final: 0.7309 (p90) REVERT: G 134 MET cc_start: 0.6604 (mtm) cc_final: 0.6395 (mtm) REVERT: G 170 GLU cc_start: 0.6747 (tt0) cc_final: 0.6475 (tt0) REVERT: G 173 MET cc_start: 0.7049 (mtm) cc_final: 0.6790 (mtm) REVERT: G 185 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6209 (mm-30) REVERT: G 188 GLU cc_start: 0.5978 (tt0) cc_final: 0.5637 (tt0) REVERT: G 225 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8303 (mt-10) REVERT: G 227 LEU cc_start: 0.7987 (mm) cc_final: 0.7717 (mm) REVERT: G 229 TYR cc_start: 0.7795 (t80) cc_final: 0.7422 (t80) REVERT: G 256 GLU cc_start: 0.6781 (tp30) cc_final: 0.6539 (tp30) outliers start: 127 outliers final: 75 residues processed: 1135 average time/residue: 0.4290 time to fit residues: 711.5099 Evaluate side-chains 1145 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1062 time to evaluate : 2.808 ------------------------------------------------------------------------------- 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 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR 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 144 GLU 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 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 C residue 28 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 129 ILE 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 C residue 491 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU 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 248 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 226 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 357 GLU 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 E residue 456 VAL Chi-restraints excluded: chain E residue 469 MET 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 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 267 LEU Chi-restraints excluded: chain F residue 273 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 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 127 SER Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 299 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 185 ASN A 215 HIS A 358 ASN C 172 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 371 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 ASN E 412 GLN E 423 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24604 Z= 0.290 Angle : 0.614 8.650 33364 Z= 0.329 Chirality : 0.046 0.175 3840 Planarity : 0.005 0.071 4349 Dihedral : 8.968 130.499 3579 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.93 % Allowed : 21.74 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3104 helix: 0.95 (0.14), residues: 1265 sheet: 0.00 (0.22), residues: 529 loop : -0.84 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 401 PHE 0.026 0.002 PHE A 494 TYR 0.024 0.002 TYR E 238 ARG 0.009 0.001 ARG C 140 *********************** 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 1201 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1075 time to evaluate : 2.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6658 (mp) REVERT: A 89 ARG cc_start: 0.6084 (mtm-85) cc_final: 0.5727 (mtm-85) REVERT: A 93 ARG cc_start: 0.7055 (ptt180) cc_final: 0.6647 (ptt180) REVERT: A 96 GLU cc_start: 0.6463 (tt0) cc_final: 0.6119 (tt0) REVERT: A 125 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.6075 (pt0) REVERT: A 127 ARG cc_start: 0.6960 (mtp85) cc_final: 0.6446 (mtp85) REVERT: A 140 ARG cc_start: 0.7273 (ttt-90) cc_final: 0.6959 (ttt90) REVERT: A 144 GLU cc_start: 0.7219 (pt0) cc_final: 0.6678 (pt0) REVERT: A 165 GLU cc_start: 0.7525 (tp30) cc_final: 0.7108 (tp30) REVERT: A 251 TYR cc_start: 0.7176 (m-80) cc_final: 0.6863 (m-80) REVERT: A 272 GLU cc_start: 0.6671 (tt0) cc_final: 0.6180 (tt0) REVERT: A 296 ARG cc_start: 0.7359 (mtm180) cc_final: 0.6982 (mtm-85) REVERT: A 299 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7414 (mm-30) REVERT: A 303 LYS cc_start: 0.7508 (tptp) cc_final: 0.7220 (tptp) REVERT: A 375 MET cc_start: 0.7344 (tpp) cc_final: 0.6669 (tpp) REVERT: A 385 ASP cc_start: 0.7245 (OUTLIER) cc_final: 0.6925 (t0) REVERT: A 426 GLN cc_start: 0.7257 (mm-40) cc_final: 0.6904 (mm-40) REVERT: A 478 THR cc_start: 0.7342 (t) cc_final: 0.6971 (p) REVERT: A 486 ASP cc_start: 0.8347 (t0) cc_final: 0.8141 (t0) REVERT: A 487 LEU cc_start: 0.7952 (tp) cc_final: 0.7714 (mm) REVERT: A 489 LYS cc_start: 0.7640 (tttt) cc_final: 0.7359 (tttt) REVERT: B 40 ARG cc_start: 0.6576 (mtt90) cc_final: 0.6355 (mtt90) REVERT: B 48 MET cc_start: 0.7664 (mtm) cc_final: 0.7423 (mtp) REVERT: B 67 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6637 (mm-30) REVERT: B 95 MET cc_start: 0.6841 (tpt) cc_final: 0.6590 (tpp) REVERT: B 144 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.5981 (pt0) REVERT: B 159 ILE cc_start: 0.7303 (mt) cc_final: 0.7062 (mt) REVERT: B 177 SER cc_start: 0.6365 (p) cc_final: 0.5880 (m) REVERT: B 181 ASP cc_start: 0.7364 (m-30) cc_final: 0.7085 (m-30) REVERT: B 185 ASN cc_start: 0.7570 (t0) cc_final: 0.7341 (t0) REVERT: B 200 GLN cc_start: 0.8034 (mm-40) cc_final: 0.7751 (mm110) REVERT: B 210 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6555 (mm-30) REVERT: B 272 GLU cc_start: 0.6742 (tt0) cc_final: 0.6405 (tt0) REVERT: B 336 SER cc_start: 0.7776 (t) cc_final: 0.7460 (p) REVERT: B 385 ASP cc_start: 0.7213 (m-30) cc_final: 0.6835 (m-30) REVERT: B 428 ILE cc_start: 0.7557 (mm) cc_final: 0.7292 (mt) REVERT: B 442 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7057 (mmp80) REVERT: B 449 PRO cc_start: 0.7477 (Cg_exo) cc_final: 0.7186 (Cg_endo) REVERT: B 467 ASN cc_start: 0.8362 (t0) cc_final: 0.8088 (t0) REVERT: B 479 LYS cc_start: 0.7207 (mptt) cc_final: 0.6729 (mptt) REVERT: B 481 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7995 (mp) REVERT: B 484 GLU cc_start: 0.7710 (mp0) cc_final: 0.7474 (mp0) REVERT: C 34 VAL cc_start: 0.7690 (OUTLIER) cc_final: 0.7351 (p) REVERT: C 51 GLU cc_start: 0.7458 (tt0) cc_final: 0.7174 (tt0) REVERT: C 62 MET cc_start: 0.6672 (ttt) cc_final: 0.6417 (ttp) REVERT: C 80 THR cc_start: 0.7924 (p) cc_final: 0.7682 (m) REVERT: C 90 ARG cc_start: 0.7555 (ttp80) cc_final: 0.7234 (ttt-90) REVERT: C 96 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6331 (mt-10) REVERT: C 127 ARG cc_start: 0.7467 (mtp85) cc_final: 0.7016 (mtp85) REVERT: C 137 MET cc_start: 0.7972 (mmm) cc_final: 0.7763 (mmm) REVERT: C 140 ARG cc_start: 0.7760 (ttt90) cc_final: 0.7488 (ttt-90) REVERT: C 147 GLN cc_start: 0.7477 (mm-40) cc_final: 0.6991 (mm110) REVERT: C 181 ASP cc_start: 0.7631 (m-30) cc_final: 0.7269 (m-30) REVERT: C 185 ASN cc_start: 0.7853 (t0) cc_final: 0.7470 (t0) REVERT: C 196 VAL cc_start: 0.7782 (t) cc_final: 0.7455 (m) REVERT: C 224 VAL cc_start: 0.7498 (t) cc_final: 0.7205 (m) REVERT: C 254 LYS cc_start: 0.7450 (mmtm) cc_final: 0.7022 (mtmm) REVERT: C 272 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6543 (mt-10) REVERT: C 314 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7020 (p) REVERT: C 349 PHE cc_start: 0.7602 (t80) cc_final: 0.7377 (t80) REVERT: C 354 ARG cc_start: 0.7124 (mtt90) cc_final: 0.6587 (mtt90) REVERT: C 361 LEU cc_start: 0.7640 (mp) cc_final: 0.7369 (mp) REVERT: C 385 ASP cc_start: 0.6478 (m-30) cc_final: 0.6243 (m-30) REVERT: C 442 ARG cc_start: 0.7305 (mmt-90) cc_final: 0.7094 (mmt90) REVERT: C 451 GLU cc_start: 0.7608 (mp0) cc_final: 0.7111 (mp0) REVERT: C 452 ASP cc_start: 0.7372 (m-30) cc_final: 0.7063 (m-30) REVERT: C 473 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7852 (mm-30) REVERT: C 496 LYS cc_start: 0.8526 (mttt) cc_final: 0.7984 (mttt) REVERT: D 5 ARG cc_start: 0.6135 (mtm-85) cc_final: 0.5879 (mtm-85) REVERT: D 7 ILE cc_start: 0.7599 (mt) cc_final: 0.7384 (mm) REVERT: D 10 MET cc_start: 0.6339 (mtm) cc_final: 0.5791 (mtm) REVERT: D 15 ASP cc_start: 0.7008 (m-30) cc_final: 0.6717 (m-30) REVERT: D 17 LYS cc_start: 0.7070 (tttt) cc_final: 0.6752 (tttm) REVERT: D 37 ARG cc_start: 0.6888 (mtm180) cc_final: 0.6407 (mtm180) REVERT: D 64 MET cc_start: 0.6808 (mmt) cc_final: 0.6468 (mmt) REVERT: D 74 MET cc_start: 0.7504 (mtt) cc_final: 0.7031 (mtt) REVERT: D 75 GLU cc_start: 0.7361 (tt0) cc_final: 0.6906 (tt0) REVERT: D 84 SER cc_start: 0.7829 (m) cc_final: 0.7400 (p) REVERT: D 101 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6911 (mt-10) REVERT: D 114 ARG cc_start: 0.7281 (ttt180) cc_final: 0.6793 (ttp80) REVERT: D 116 ASP cc_start: 0.7051 (m-30) cc_final: 0.6425 (m-30) REVERT: D 120 ARG cc_start: 0.7234 (ttt90) cc_final: 0.6878 (ptm160) REVERT: D 133 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6620 (mt-10) REVERT: D 169 GLN cc_start: 0.7320 (mt0) cc_final: 0.6838 (mm-40) REVERT: D 170 GLU cc_start: 0.7177 (tp30) cc_final: 0.6809 (tt0) REVERT: D 190 ASP cc_start: 0.6855 (m-30) cc_final: 0.5513 (m-30) REVERT: D 191 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.5967 (mtt-85) REVERT: D 197 ASP cc_start: 0.6905 (t0) cc_final: 0.6662 (t0) REVERT: D 214 VAL cc_start: 0.7842 (t) cc_final: 0.7506 (p) REVERT: D 227 ARG cc_start: 0.6932 (mmt180) cc_final: 0.6349 (mmt90) REVERT: D 237 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6488 (mt-10) REVERT: D 241 ASP cc_start: 0.7113 (m-30) cc_final: 0.6811 (m-30) REVERT: D 246 ASP cc_start: 0.7518 (m-30) cc_final: 0.7010 (m-30) REVERT: D 252 ASP cc_start: 0.6369 (t0) cc_final: 0.5881 (t0) REVERT: D 270 ARG cc_start: 0.7583 (mtt180) cc_final: 0.6971 (mtt-85) REVERT: D 284 GLU cc_start: 0.6228 (mt-10) cc_final: 0.5647 (mt-10) REVERT: D 285 MET cc_start: 0.6408 (ttm) cc_final: 0.6100 (ttm) REVERT: D 326 ASP cc_start: 0.7213 (m-30) cc_final: 0.6360 (m-30) REVERT: D 352 ARG cc_start: 0.7121 (mtp180) cc_final: 0.6835 (mtp180) REVERT: D 387 LEU cc_start: 0.7709 (mt) cc_final: 0.7482 (mp) REVERT: D 428 VAL cc_start: 0.8372 (t) cc_final: 0.8040 (m) REVERT: D 439 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6720 (mm-30) REVERT: E 1 MET cc_start: 0.3447 (mmt) cc_final: 0.3092 (mmt) REVERT: E 3 ARG cc_start: 0.6679 (mtm-85) cc_final: 0.6405 (mtm-85) REVERT: E 5 ARG cc_start: 0.6545 (ptp-110) cc_final: 0.6232 (ptp-110) REVERT: E 10 MET cc_start: 0.5963 (ptp) cc_final: 0.5563 (ptp) REVERT: E 17 LYS cc_start: 0.7641 (tttt) cc_final: 0.7081 (ttmm) REVERT: E 43 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: E 71 ILE cc_start: 0.7662 (mt) cc_final: 0.7376 (mt) REVERT: E 91 THR cc_start: 0.7650 (p) cc_final: 0.7374 (t) REVERT: E 120 ARG cc_start: 0.6907 (mtp85) cc_final: 0.6605 (ttp80) REVERT: E 127 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6454 (mt-10) REVERT: E 134 ILE cc_start: 0.8285 (mt) cc_final: 0.7925 (tt) REVERT: E 149 ILE cc_start: 0.7673 (mt) cc_final: 0.7422 (mm) REVERT: E 170 GLU cc_start: 0.7086 (tp30) cc_final: 0.6697 (tt0) REVERT: E 178 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6650 (mm-30) REVERT: E 203 LYS cc_start: 0.7581 (tppt) cc_final: 0.7343 (tppt) REVERT: E 210 LYS cc_start: 0.7561 (mttt) cc_final: 0.7187 (mttt) REVERT: E 227 ARG cc_start: 0.6491 (mmt180) cc_final: 0.6125 (mmt90) REVERT: E 284 GLU cc_start: 0.6281 (mt-10) cc_final: 0.5877 (mt-10) REVERT: E 312 ASP cc_start: 0.7193 (t0) cc_final: 0.6769 (t0) REVERT: E 315 ASP cc_start: 0.7026 (t70) cc_final: 0.6795 (t70) REVERT: E 334 LYS cc_start: 0.7394 (mmmm) cc_final: 0.7132 (mmmm) REVERT: E 354 LEU cc_start: 0.7618 (tp) cc_final: 0.7359 (tt) REVERT: E 365 GLN cc_start: 0.7556 (mt0) cc_final: 0.7186 (mt0) REVERT: E 376 ARG cc_start: 0.7764 (tpt170) cc_final: 0.7483 (tpt170) REVERT: E 379 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7180 (mt-10) REVERT: E 401 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6323 (t70) REVERT: E 402 ARG cc_start: 0.7611 (mmm-85) cc_final: 0.7260 (mtt-85) REVERT: E 405 ARG cc_start: 0.7507 (mpt180) cc_final: 0.7021 (mmt-90) REVERT: E 407 GLN cc_start: 0.7435 (tt0) cc_final: 0.7057 (tp-100) REVERT: E 427 TYR cc_start: 0.8304 (t80) cc_final: 0.8072 (t80) REVERT: E 431 LYS cc_start: 0.7744 (ptmm) cc_final: 0.7433 (ptmm) REVERT: E 435 ARG cc_start: 0.7484 (ttp80) cc_final: 0.6954 (ttp80) REVERT: E 438 LYS cc_start: 0.7716 (ttpt) cc_final: 0.7045 (ttpt) REVERT: E 439 GLU cc_start: 0.7525 (mm-30) cc_final: 0.6560 (mm-30) REVERT: E 442 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7213 (mt-10) REVERT: E 445 TYR cc_start: 0.7498 (m-80) cc_final: 0.6747 (m-80) REVERT: E 446 ASP cc_start: 0.7689 (m-30) cc_final: 0.7376 (m-30) REVERT: E 450 GLU cc_start: 0.7858 (pm20) cc_final: 0.7292 (pm20) REVERT: F 5 ARG cc_start: 0.6062 (mmt180) cc_final: 0.5458 (mmt180) REVERT: F 8 GLN cc_start: 0.7294 (mt0) cc_final: 0.6854 (mt0) REVERT: F 15 ASP cc_start: 0.6954 (m-30) cc_final: 0.6540 (m-30) REVERT: F 23 LEU cc_start: 0.8338 (mp) cc_final: 0.8073 (mt) REVERT: F 33 GLN cc_start: 0.7467 (mt0) cc_final: 0.7240 (mt0) REVERT: F 37 ARG cc_start: 0.7340 (ttm170) cc_final: 0.7106 (ttm170) REVERT: F 39 GLU cc_start: 0.7528 (mp0) cc_final: 0.7093 (mp0) REVERT: F 49 GLU cc_start: 0.6852 (tt0) cc_final: 0.6070 (tt0) REVERT: F 74 MET cc_start: 0.6863 (mtt) cc_final: 0.6377 (mtt) REVERT: F 75 GLU cc_start: 0.7001 (tt0) cc_final: 0.5326 (tt0) REVERT: F 89 GLU cc_start: 0.7515 (tp30) cc_final: 0.7218 (tp30) REVERT: F 114 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.7126 (ttp80) REVERT: F 115 ARG cc_start: 0.7413 (mtt90) cc_final: 0.7088 (mtt90) REVERT: F 116 ASP cc_start: 0.7416 (m-30) cc_final: 0.7027 (m-30) REVERT: F 120 ARG cc_start: 0.7109 (ptm-80) cc_final: 0.6820 (tmm-80) REVERT: F 124 LYS cc_start: 0.7157 (mttm) cc_final: 0.6748 (mttm) REVERT: F 127 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6840 (mt-10) REVERT: F 148 TYR cc_start: 0.7969 (m-10) cc_final: 0.7691 (m-10) REVERT: F 213 MET cc_start: 0.7312 (mtp) cc_final: 0.7069 (mtm) REVERT: F 220 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6591 (mm-30) REVERT: F 237 GLU cc_start: 0.6659 (tt0) cc_final: 0.6125 (mt-10) REVERT: F 285 MET cc_start: 0.6896 (ttm) cc_final: 0.6625 (ttm) REVERT: F 300 ILE cc_start: 0.7707 (mt) cc_final: 0.7505 (tt) REVERT: F 345 ASP cc_start: 0.7501 (t70) cc_final: 0.7015 (t70) REVERT: F 357 GLU cc_start: 0.7226 (pm20) cc_final: 0.7015 (pm20) REVERT: F 389 MET cc_start: 0.7457 (mtm) cc_final: 0.7102 (mtm) REVERT: F 397 LYS cc_start: 0.7337 (tttm) cc_final: 0.7049 (tttm) REVERT: F 423 GLN cc_start: 0.7646 (pt0) cc_final: 0.7440 (pt0) REVERT: F 438 LYS cc_start: 0.7556 (tttt) cc_final: 0.7077 (tttt) REVERT: F 439 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6679 (mt-10) REVERT: F 442 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6458 (mt-10) REVERT: F 444 LYS cc_start: 0.7961 (tttt) cc_final: 0.7330 (tttt) REVERT: F 445 TYR cc_start: 0.8278 (m-80) cc_final: 0.7559 (m-80) REVERT: F 448 LEU cc_start: 0.8131 (mm) cc_final: 0.7756 (mp) REVERT: F 451 ASP cc_start: 0.7917 (m-30) cc_final: 0.7679 (m-30) REVERT: F 460 GLU cc_start: 0.7973 (mp0) cc_final: 0.7772 (mp0) REVERT: G 11 LYS cc_start: 0.7287 (tptt) cc_final: 0.6632 (tptt) REVERT: G 15 ASN cc_start: 0.7381 (m-40) cc_final: 0.7006 (m-40) REVERT: G 32 THR cc_start: 0.7667 (m) cc_final: 0.7350 (p) REVERT: G 33 SER cc_start: 0.7790 (t) cc_final: 0.7311 (p) REVERT: G 54 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8452 (mt-10) REVERT: G 70 MET cc_start: 0.7876 (mmm) cc_final: 0.7283 (mmm) REVERT: G 85 THR cc_start: 0.7749 (OUTLIER) cc_final: 0.7335 (t) REVERT: G 95 ASN cc_start: 0.7992 (m-40) cc_final: 0.7702 (m110) REVERT: G 116 TYR cc_start: 0.7631 (p90) cc_final: 0.7176 (p90) REVERT: G 134 MET cc_start: 0.6627 (mtm) cc_final: 0.5764 (mtm) REVERT: G 173 MET cc_start: 0.6984 (mtm) cc_final: 0.6716 (mtm) REVERT: G 185 GLU cc_start: 0.6555 (mm-30) cc_final: 0.6108 (mm-30) REVERT: G 188 GLU cc_start: 0.5819 (OUTLIER) cc_final: 0.5527 (tt0) REVERT: G 223 TYR cc_start: 0.8151 (t80) cc_final: 0.7792 (t80) REVERT: G 225 GLU cc_start: 0.8571 (mt-10) cc_final: 0.8275 (mt-10) REVERT: G 227 LEU cc_start: 0.7962 (mm) cc_final: 0.7738 (mm) REVERT: G 256 GLU cc_start: 0.6971 (tp30) cc_final: 0.6618 (tp30) outliers start: 126 outliers final: 85 residues processed: 1122 average time/residue: 0.4451 time to fit residues: 729.1329 Evaluate side-chains 1147 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1050 time to evaluate : 2.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 LEU 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 243 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 299 GLU Chi-restraints excluded: chain B residue 306 ASP 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 481 LEU Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 171 ARG 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 375 MET Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 30 LEU 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 203 LYS Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 299 SER 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 384 ILE Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 218 MET Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 290 GLU 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 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 401 HIS Chi-restraints excluded: chain E residue 456 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 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 273 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 455 LEU Chi-restraints excluded: chain F residue 462 VAL Chi-restraints excluded: chain G residue 12 THR 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 186 VAL Chi-restraints excluded: chain G residue 188 GLU 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 249 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 223 optimal weight: 8.9990 chunk 123 optimal weight: 0.9990 chunk 255 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 268 optimal weight: 6.9990 chunk 75 optimal weight: 0.0870 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 172 GLN A 215 HIS A 358 ASN B 333 ASN C 172 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN D 219 ASN D 330 ASN D 401 HIS E 423 GLN F 28 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24604 Z= 0.221 Angle : 0.578 8.810 33364 Z= 0.304 Chirality : 0.045 0.173 3840 Planarity : 0.005 0.068 4349 Dihedral : 8.443 117.927 3577 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.46 % Allowed : 22.83 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3104 helix: 1.22 (0.14), residues: 1253 sheet: 0.02 (0.22), residues: 535 loop : -0.76 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 401 PHE 0.020 0.001 PHE G 45 TYR 0.022 0.001 TYR C 248 ARG 0.008 0.001 ARG C 140 *********************** 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 1181 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1067 time to evaluate : 3.045 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 52 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6593 (mp) REVERT: A 57 ASN cc_start: 0.7958 (m-40) cc_final: 0.7664 (m-40) REVERT: A 93 ARG cc_start: 0.6944 (ptt180) cc_final: 0.6548 (ptt180) REVERT: A 96 GLU cc_start: 0.6449 (tt0) cc_final: 0.6142 (tt0) REVERT: A 125 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5952 (pt0) REVERT: A 127 ARG cc_start: 0.7039 (mtp85) cc_final: 0.6535 (mtp85) REVERT: A 140 ARG cc_start: 0.7285 (ttt-90) cc_final: 0.6966 (ttt90) REVERT: A 144 GLU cc_start: 0.7181 (pt0) cc_final: 0.6621 (pt0) REVERT: A 147 GLN cc_start: 0.7623 (mm-40) cc_final: 0.6836 (mm-40) REVERT: A 165 GLU cc_start: 0.7505 (tp30) cc_final: 0.7164 (tp30) REVERT: A 186 GLN cc_start: 0.7209 (mm-40) cc_final: 0.6941 (mm-40) REVERT: A 200 GLN cc_start: 0.7592 (mt0) cc_final: 0.7385 (mt0) REVERT: A 251 TYR cc_start: 0.7150 (m-80) cc_final: 0.6800 (m-80) REVERT: A 272 GLU cc_start: 0.6671 (tt0) cc_final: 0.6173 (tt0) REVERT: A 296 ARG cc_start: 0.7366 (mtm180) cc_final: 0.7103 (mtm-85) REVERT: A 299 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 303 LYS cc_start: 0.7507 (tptp) cc_final: 0.7203 (tptp) REVERT: A 375 MET cc_start: 0.7374 (tpp) cc_final: 0.6827 (tpp) REVERT: A 377 LYS cc_start: 0.7295 (mtmm) cc_final: 0.6848 (mtmm) REVERT: A 385 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6946 (t0) REVERT: A 426 GLN cc_start: 0.7284 (mm-40) cc_final: 0.6931 (mm-40) REVERT: A 486 ASP cc_start: 0.8311 (t0) cc_final: 0.8110 (t0) REVERT: A 487 LEU cc_start: 0.7945 (tp) cc_final: 0.7682 (mm) REVERT: A 489 LYS cc_start: 0.7677 (tttt) cc_final: 0.7385 (tttt) REVERT: B 48 MET cc_start: 0.7679 (mtm) cc_final: 0.7398 (mtp) REVERT: B 67 GLU cc_start: 0.7070 (mm-30) cc_final: 0.6617 (mm-30) REVERT: B 95 MET cc_start: 0.6863 (tpt) cc_final: 0.6500 (tpt) REVERT: B 137 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7229 (mtm) REVERT: B 144 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.5919 (pt0) REVERT: B 159 ILE cc_start: 0.7335 (mt) cc_final: 0.7099 (mt) REVERT: B 164 ARG cc_start: 0.7167 (mtm180) cc_final: 0.6895 (mtm-85) REVERT: B 177 SER cc_start: 0.6369 (p) cc_final: 0.5872 (m) REVERT: B 181 ASP cc_start: 0.7375 (m-30) cc_final: 0.7078 (m-30) REVERT: B 200 GLN cc_start: 0.8064 (mm-40) cc_final: 0.7788 (mm110) REVERT: B 210 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6550 (mm-30) REVERT: B 272 GLU cc_start: 0.6741 (tt0) cc_final: 0.6405 (tt0) REVERT: B 336 SER cc_start: 0.7767 (t) cc_final: 0.7447 (p) REVERT: B 385 ASP cc_start: 0.7196 (m-30) cc_final: 0.6810 (m-30) REVERT: B 428 ILE cc_start: 0.7498 (mm) cc_final: 0.7226 (mt) REVERT: B 442 ARG cc_start: 0.7556 (mmt-90) cc_final: 0.6942 (mmp80) REVERT: B 449 PRO cc_start: 0.7481 (Cg_exo) cc_final: 0.7204 (Cg_endo) REVERT: B 467 ASN cc_start: 0.8299 (t0) cc_final: 0.8030 (t0) REVERT: B 476 ARG cc_start: 0.7942 (ptp-110) cc_final: 0.7558 (ptp-110) REVERT: B 479 LYS cc_start: 0.7152 (mptt) cc_final: 0.6656 (mptt) REVERT: B 481 LEU cc_start: 0.8154 (tp) cc_final: 0.7920 (mp) REVERT: B 484 GLU cc_start: 0.7750 (mp0) cc_final: 0.7518 (mp0) REVERT: C 34 VAL cc_start: 0.7718 (OUTLIER) cc_final: 0.7355 (p) REVERT: C 51 GLU cc_start: 0.7448 (tt0) cc_final: 0.7044 (tt0) REVERT: C 62 MET cc_start: 0.6684 (ttt) cc_final: 0.6368 (ttp) REVERT: C 68 GLU cc_start: 0.7206 (mt-10) cc_final: 0.6832 (mt-10) REVERT: C 80 THR cc_start: 0.7925 (p) cc_final: 0.7689 (m) REVERT: C 90 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7130 (ttp-110) REVERT: C 127 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7065 (mtp85) REVERT: C 137 MET cc_start: 0.7962 (mmm) cc_final: 0.7739 (mmm) REVERT: C 140 ARG cc_start: 0.7750 (ttt90) cc_final: 0.7513 (ttt90) REVERT: C 147 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7078 (mm110) REVERT: C 181 ASP cc_start: 0.7626 (m-30) cc_final: 0.7253 (m-30) REVERT: C 185 ASN cc_start: 0.7801 (t0) cc_final: 0.7420 (t0) REVERT: C 196 VAL cc_start: 0.7758 (t) cc_final: 0.7446 (m) REVERT: C 222 ILE cc_start: 0.7224 (mt) cc_final: 0.6978 (mt) REVERT: C 224 VAL cc_start: 0.7481 (t) cc_final: 0.7235 (m) REVERT: C 229 SER cc_start: 0.7323 (t) cc_final: 0.6976 (p) REVERT: C 254 LYS cc_start: 0.7381 (mmtm) cc_final: 0.6944 (mtmm) REVERT: C 262 ASP cc_start: 0.6798 (m-30) cc_final: 0.6583 (t0) REVERT: C 272 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6542 (mt-10) REVERT: C 314 THR cc_start: 0.7515 (OUTLIER) cc_final: 0.7023 (p) REVERT: C 354 ARG cc_start: 0.7090 (mtt90) cc_final: 0.6577 (mtt90) REVERT: C 361 LEU cc_start: 0.7604 (mp) cc_final: 0.7240 (mp) REVERT: C 376 LYS cc_start: 0.7460 (ttpt) cc_final: 0.7231 (ttpt) REVERT: C 385 ASP cc_start: 0.6498 (m-30) cc_final: 0.6250 (m-30) REVERT: C 451 GLU cc_start: 0.7621 (mp0) cc_final: 0.7149 (mp0) REVERT: C 452 ASP cc_start: 0.7350 (m-30) cc_final: 0.7038 (m-30) REVERT: C 473 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7764 (mm-30) REVERT: C 496 LYS cc_start: 0.8508 (mttt) cc_final: 0.7959 (mttt) REVERT: D 5 ARG cc_start: 0.6159 (mtm-85) cc_final: 0.5902 (mtm-85) REVERT: D 10 MET cc_start: 0.6343 (mtm) cc_final: 0.5806 (mtm) REVERT: D 15 ASP cc_start: 0.7021 (m-30) cc_final: 0.6722 (m-30) REVERT: D 17 LYS cc_start: 0.7039 (tttt) cc_final: 0.6705 (tttm) REVERT: D 37 ARG cc_start: 0.6878 (mtm180) cc_final: 0.6397 (mtm180) REVERT: D 64 MET cc_start: 0.6816 (mmt) cc_final: 0.6504 (mmt) REVERT: D 74 MET cc_start: 0.7495 (mtt) cc_final: 0.7036 (mtt) REVERT: D 75 GLU cc_start: 0.7354 (tt0) cc_final: 0.6890 (tt0) REVERT: D 84 SER cc_start: 0.7823 (m) cc_final: 0.7317 (p) REVERT: D 101 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6881 (mt-10) REVERT: D 114 ARG cc_start: 0.7317 (ttt180) cc_final: 0.6854 (ttp80) REVERT: D 115 ARG cc_start: 0.7669 (mtt-85) cc_final: 0.7285 (mtt-85) REVERT: D 116 ASP cc_start: 0.7094 (m-30) cc_final: 0.6479 (m-30) REVERT: D 120 ARG cc_start: 0.7204 (ttt90) cc_final: 0.6904 (ptm160) REVERT: D 133 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6663 (mt-10) REVERT: D 153 LYS cc_start: 0.6554 (mttp) cc_final: 0.6282 (mttt) REVERT: D 169 GLN cc_start: 0.7291 (mt0) cc_final: 0.6822 (mm-40) REVERT: D 170 GLU cc_start: 0.7174 (tp30) cc_final: 0.6838 (tt0) REVERT: D 190 ASP cc_start: 0.6915 (m-30) cc_final: 0.5632 (m-30) REVERT: D 191 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.5707 (mtt-85) REVERT: D 197 ASP cc_start: 0.6921 (t0) cc_final: 0.6697 (t70) REVERT: D 214 VAL cc_start: 0.7851 (t) cc_final: 0.7549 (p) REVERT: D 227 ARG cc_start: 0.6927 (mmt180) cc_final: 0.6346 (mmt90) REVERT: D 237 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6478 (mt-10) REVERT: D 241 ASP cc_start: 0.7121 (m-30) cc_final: 0.6808 (m-30) REVERT: D 246 ASP cc_start: 0.7507 (m-30) cc_final: 0.7032 (m-30) REVERT: D 252 ASP cc_start: 0.6365 (t0) cc_final: 0.5887 (t0) REVERT: D 270 ARG cc_start: 0.7577 (mtt180) cc_final: 0.6968 (mtt-85) REVERT: D 284 GLU cc_start: 0.6225 (mt-10) cc_final: 0.5617 (mt-10) REVERT: D 285 MET cc_start: 0.6350 (ttm) cc_final: 0.6038 (ttm) REVERT: D 326 ASP cc_start: 0.7268 (m-30) cc_final: 0.6469 (m-30) REVERT: D 352 ARG cc_start: 0.7101 (mtp180) cc_final: 0.6832 (mtp180) REVERT: D 387 LEU cc_start: 0.7688 (mt) cc_final: 0.7475 (mp) REVERT: D 428 VAL cc_start: 0.8354 (t) cc_final: 0.8038 (m) REVERT: D 439 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6685 (mm-30) REVERT: E 1 MET cc_start: 0.3439 (mmt) cc_final: 0.3103 (mmt) REVERT: E 3 ARG cc_start: 0.6669 (mtm-85) cc_final: 0.6390 (mtm-85) REVERT: E 5 ARG cc_start: 0.6526 (ptp-110) cc_final: 0.6190 (ptp-110) REVERT: E 10 MET cc_start: 0.5906 (ptp) cc_final: 0.5599 (ptp) REVERT: E 17 LYS cc_start: 0.7594 (tttt) cc_final: 0.7018 (ttmm) REVERT: E 43 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6760 (m-30) REVERT: E 91 THR cc_start: 0.7633 (p) cc_final: 0.7368 (t) REVERT: E 101 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6519 (mp0) REVERT: E 127 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6457 (mt-10) REVERT: E 134 ILE cc_start: 0.8281 (mt) cc_final: 0.7901 (tt) REVERT: E 149 ILE cc_start: 0.7642 (mt) cc_final: 0.7399 (mm) REVERT: E 170 GLU cc_start: 0.7117 (tp30) cc_final: 0.6710 (tt0) REVERT: E 178 GLU cc_start: 0.7202 (mm-30) cc_final: 0.6637 (mm-30) REVERT: E 203 LYS cc_start: 0.7595 (tppt) cc_final: 0.7371 (tppt) REVERT: E 210 LYS cc_start: 0.7555 (mttt) cc_final: 0.7168 (mttt) REVERT: E 256 ARG cc_start: 0.6641 (mtt180) cc_final: 0.6359 (mtm-85) REVERT: E 284 GLU cc_start: 0.6289 (mt-10) cc_final: 0.5898 (mt-10) REVERT: E 285 MET cc_start: 0.6715 (tpp) cc_final: 0.6054 (mmm) REVERT: E 312 ASP cc_start: 0.7066 (t0) cc_final: 0.6653 (t0) REVERT: E 315 ASP cc_start: 0.7021 (t70) cc_final: 0.6785 (t70) REVERT: E 334 LYS cc_start: 0.7389 (mmmm) cc_final: 0.7144 (mmmm) REVERT: E 354 LEU cc_start: 0.7605 (tp) cc_final: 0.7374 (tt) REVERT: E 362 GLU cc_start: 0.7765 (pm20) cc_final: 0.7481 (pm20) REVERT: E 365 GLN cc_start: 0.7516 (mt0) cc_final: 0.7104 (mt0) REVERT: E 402 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.7222 (mtt-85) REVERT: E 407 GLN cc_start: 0.7419 (tt0) cc_final: 0.7022 (tp40) REVERT: E 427 TYR cc_start: 0.8273 (t80) cc_final: 0.8027 (t80) REVERT: E 431 LYS cc_start: 0.7754 (ptmm) cc_final: 0.7420 (ptmm) REVERT: E 435 ARG cc_start: 0.7489 (ttp80) cc_final: 0.6925 (ttp80) REVERT: E 438 LYS cc_start: 0.7688 (ttpt) cc_final: 0.6995 (ttpt) REVERT: E 439 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6580 (mm-30) REVERT: E 442 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7188 (mt-10) REVERT: E 446 ASP cc_start: 0.7752 (m-30) cc_final: 0.7408 (m-30) REVERT: E 450 GLU cc_start: 0.7856 (pm20) cc_final: 0.7293 (pm20) REVERT: F 5 ARG cc_start: 0.6067 (mmt180) cc_final: 0.5436 (mmt180) REVERT: F 8 GLN cc_start: 0.7268 (mt0) cc_final: 0.6792 (mt0) REVERT: F 15 ASP cc_start: 0.6927 (m-30) cc_final: 0.6537 (m-30) REVERT: F 23 LEU cc_start: 0.8328 (mp) cc_final: 0.8063 (mt) REVERT: F 33 GLN cc_start: 0.7438 (mt0) cc_final: 0.7222 (mt0) REVERT: F 37 ARG cc_start: 0.7338 (ttm170) cc_final: 0.7108 (ttm170) REVERT: F 39 GLU cc_start: 0.7585 (mp0) cc_final: 0.7144 (mp0) REVERT: F 74 MET cc_start: 0.6854 (mtt) cc_final: 0.6381 (mtt) REVERT: F 75 GLU cc_start: 0.7010 (tt0) cc_final: 0.5400 (tt0) REVERT: F 89 GLU cc_start: 0.7482 (tp30) cc_final: 0.7183 (tp30) REVERT: F 114 ARG cc_start: 0.7532 (ttp-170) cc_final: 0.7264 (ttp80) REVERT: F 115 ARG cc_start: 0.7417 (mtt90) cc_final: 0.7073 (mtt90) REVERT: F 116 ASP cc_start: 0.7417 (m-30) cc_final: 0.7133 (m-30) REVERT: F 124 LYS cc_start: 0.7075 (mttm) cc_final: 0.6723 (mttm) REVERT: F 127 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6811 (mt-10) REVERT: F 213 MET cc_start: 0.7303 (mtp) cc_final: 0.7067 (mtm) REVERT: F 220 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6596 (mm-30) REVERT: F 237 GLU cc_start: 0.6635 (tt0) cc_final: 0.5780 (mt-10) REVERT: F 241 ASP cc_start: 0.6638 (m-30) cc_final: 0.6193 (m-30) REVERT: F 285 MET cc_start: 0.6852 (ttm) cc_final: 0.6560 (ttm) REVERT: F 303 ILE cc_start: 0.7222 (mt) cc_final: 0.7003 (mp) REVERT: F 345 ASP cc_start: 0.7505 (t70) cc_final: 0.7023 (t70) REVERT: F 357 GLU cc_start: 0.7273 (pm20) cc_final: 0.7040 (pm20) REVERT: F 389 MET cc_start: 0.7405 (mtm) cc_final: 0.7107 (mtm) REVERT: F 397 LYS cc_start: 0.7334 (tttm) cc_final: 0.6965 (tttm) REVERT: F 439 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6687 (mt-10) REVERT: F 442 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6454 (mt-10) REVERT: F 444 LYS cc_start: 0.7896 (tttt) cc_final: 0.7279 (tttt) REVERT: F 445 TYR cc_start: 0.8236 (m-80) cc_final: 0.7513 (m-80) REVERT: F 451 ASP cc_start: 0.7926 (m-30) cc_final: 0.7687 (m-30) REVERT: G 11 LYS cc_start: 0.7256 (tptt) cc_final: 0.6596 (tptt) REVERT: G 15 ASN cc_start: 0.7417 (m-40) cc_final: 0.7062 (m-40) REVERT: G 32 THR cc_start: 0.7548 (m) cc_final: 0.7288 (p) REVERT: G 33 SER cc_start: 0.7767 (t) cc_final: 0.7281 (p) REVERT: G 54 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8483 (mt-10) REVERT: G 70 MET cc_start: 0.7863 (mmm) cc_final: 0.7252 (mmm) REVERT: G 85 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7366 (t) REVERT: G 95 ASN cc_start: 0.7969 (m-40) cc_final: 0.7700 (m110) REVERT: G 116 TYR cc_start: 0.7620 (p90) cc_final: 0.7041 (p90) REVERT: G 134 MET cc_start: 0.6554 (mtm) cc_final: 0.5771 (mtm) REVERT: G 173 MET cc_start: 0.6936 (mtm) cc_final: 0.6675 (mtm) REVERT: G 185 GLU cc_start: 0.6532 (mm-30) cc_final: 0.6087 (mm-30) REVERT: G 188 GLU cc_start: 0.5782 (OUTLIER) cc_final: 0.5547 (tt0) REVERT: G 223 TYR cc_start: 0.8076 (t80) cc_final: 0.7706 (t80) REVERT: G 225 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8251 (mt-10) REVERT: G 227 LEU cc_start: 0.7902 (mm) cc_final: 0.7668 (mm) REVERT: G 256 GLU cc_start: 0.6956 (tp30) cc_final: 0.6609 (tp30) outliers start: 114 outliers final: 86 residues processed: 1111 average time/residue: 0.4290 time to fit residues: 691.8689 Evaluate side-chains 1164 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1067 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP 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 97 VAL 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 294 HIS Chi-restraints excluded: chain A residue 314 THR 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 125 GLU Chi-restraints excluded: chain B residue 132 ARG Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 333 ASN 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 495 LYS 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 104 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 171 ARG 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 375 MET Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain C residue 491 ILE 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 126 GLU Chi-restraints excluded: chain D residue 131 GLU 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 299 SER Chi-restraints excluded: chain D residue 311 ASP 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 456 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 218 MET 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 384 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 399 VAL Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 1 MET 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 149 ILE Chi-restraints excluded: chain F residue 183 SER Chi-restraints excluded: chain F residue 233 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 462 VAL Chi-restraints excluded: chain G residue 12 THR 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 186 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.0170 chunk 157 optimal weight: 2.9990 overall best weight: 1.6024 ------------------------------------------------------------------------------- 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 ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN C 469 GLN C 474 HIS D 173 HIS D 330 ASN E 169 GLN G 110 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24604 Z= 0.219 Angle : 0.570 8.647 33364 Z= 0.301 Chirality : 0.044 0.155 3840 Planarity : 0.005 0.066 4349 Dihedral : 8.238 108.250 3577 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.61 % Allowed : 23.53 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.15), residues: 3104 helix: 1.32 (0.14), residues: 1262 sheet: 0.07 (0.22), residues: 544 loop : -0.72 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS G 110 PHE 0.017 0.001 PHE G 45 TYR 0.021 0.001 TYR C 248 ARG 0.008 0.001 ARG E 115 *********************** 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 1183 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1065 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6678 (mp) REVERT: A 57 ASN cc_start: 0.7983 (m-40) cc_final: 0.7705 (m-40) REVERT: A 89 ARG cc_start: 0.6228 (mtm-85) cc_final: 0.5819 (mtm-85) REVERT: A 93 ARG cc_start: 0.6891 (ptt180) cc_final: 0.6318 (ptt180) REVERT: A 96 GLU cc_start: 0.6485 (tt0) cc_final: 0.6266 (tt0) REVERT: A 125 GLU cc_start: 0.6057 (pt0) cc_final: 0.5618 (pt0) REVERT: A 127 ARG cc_start: 0.7027 (mtp85) cc_final: 0.6558 (mtp85) REVERT: A 140 ARG cc_start: 0.7299 (ttt-90) cc_final: 0.7006 (ttt90) REVERT: A 144 GLU cc_start: 0.7152 (pt0) cc_final: 0.6617 (pt0) REVERT: A 147 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7238 (mm110) REVERT: A 165 GLU cc_start: 0.7576 (tp30) cc_final: 0.7153 (tp30) REVERT: A 186 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6926 (mm-40) REVERT: A 200 GLN cc_start: 0.7595 (mt0) cc_final: 0.7373 (mt0) REVERT: A 251 TYR cc_start: 0.7187 (m-80) cc_final: 0.6863 (m-80) REVERT: A 254 LYS cc_start: 0.7219 (mmtm) cc_final: 0.6861 (mmtm) REVERT: A 272 GLU cc_start: 0.6672 (tt0) cc_final: 0.6182 (tt0) REVERT: A 296 ARG cc_start: 0.7337 (mtm180) cc_final: 0.7084 (mtm-85) REVERT: A 299 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7413 (mm-30) REVERT: A 303 LYS cc_start: 0.7489 (tptp) cc_final: 0.7173 (tptp) REVERT: A 375 MET cc_start: 0.7376 (tpp) cc_final: 0.6860 (tpp) REVERT: A 377 LYS cc_start: 0.7335 (mtmm) cc_final: 0.6940 (mtmm) REVERT: A 385 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6978 (t0) REVERT: A 426 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6964 (mm-40) REVERT: A 478 THR cc_start: 0.7337 (t) cc_final: 0.7080 (t) REVERT: A 480 ASP cc_start: 0.6280 (t0) cc_final: 0.6078 (m-30) REVERT: A 487 LEU cc_start: 0.7989 (tp) cc_final: 0.7723 (mm) REVERT: A 489 LYS cc_start: 0.7745 (tttt) cc_final: 0.7456 (tttt) REVERT: B 48 MET cc_start: 0.7624 (mtm) cc_final: 0.7343 (mtp) REVERT: B 67 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6604 (mm-30) REVERT: B 95 MET cc_start: 0.6870 (tpt) cc_final: 0.6612 (tpp) REVERT: B 137 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7242 (mtm) REVERT: B 144 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.5909 (pt0) REVERT: B 159 ILE cc_start: 0.7348 (mt) cc_final: 0.7114 (mt) REVERT: B 164 ARG cc_start: 0.7185 (mtm180) cc_final: 0.6909 (mtm-85) REVERT: B 177 SER cc_start: 0.6314 (p) cc_final: 0.5847 (m) REVERT: B 181 ASP cc_start: 0.7371 (m-30) cc_final: 0.7080 (m-30) REVERT: B 200 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7777 (mm110) REVERT: B 210 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6534 (mm-30) REVERT: B 245 MET cc_start: 0.6788 (mtt) cc_final: 0.6516 (mmt) REVERT: B 257 LEU cc_start: 0.6961 (tt) cc_final: 0.6738 (tt) REVERT: B 272 GLU cc_start: 0.6739 (tt0) cc_final: 0.6413 (tt0) REVERT: B 336 SER cc_start: 0.7834 (t) cc_final: 0.7505 (p) REVERT: B 385 ASP cc_start: 0.7199 (m-30) cc_final: 0.6791 (m-30) REVERT: B 423 ASP cc_start: 0.6426 (p0) cc_final: 0.6124 (p0) REVERT: B 428 ILE cc_start: 0.7500 (mm) cc_final: 0.7217 (mt) REVERT: B 442 ARG cc_start: 0.7541 (mmt-90) cc_final: 0.6922 (mmp80) REVERT: B 449 PRO cc_start: 0.7493 (Cg_exo) cc_final: 0.7212 (Cg_endo) REVERT: B 467 ASN cc_start: 0.8291 (t0) cc_final: 0.8029 (t0) REVERT: B 476 ARG cc_start: 0.7959 (ptp-110) cc_final: 0.7637 (ptp-110) REVERT: B 479 LYS cc_start: 0.7030 (mptt) cc_final: 0.6592 (mptt) REVERT: B 484 GLU cc_start: 0.7744 (mp0) cc_final: 0.7516 (mp0) REVERT: C 34 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7365 (p) REVERT: C 51 GLU cc_start: 0.7412 (tt0) cc_final: 0.7033 (tt0) REVERT: C 62 MET cc_start: 0.6686 (ttt) cc_final: 0.6359 (ttp) REVERT: C 68 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6813 (mt-10) REVERT: C 80 THR cc_start: 0.7923 (p) cc_final: 0.7691 (m) REVERT: C 90 ARG cc_start: 0.7545 (ttp80) cc_final: 0.7085 (ttp-110) REVERT: C 127 ARG cc_start: 0.7479 (mtp85) cc_final: 0.7068 (mtp85) REVERT: C 137 MET cc_start: 0.7967 (mmm) cc_final: 0.7744 (mmm) REVERT: C 147 GLN cc_start: 0.7450 (mm-40) cc_final: 0.7089 (mm110) REVERT: C 181 ASP cc_start: 0.7627 (m-30) cc_final: 0.7253 (m-30) REVERT: C 185 ASN cc_start: 0.7779 (t0) cc_final: 0.7384 (t0) REVERT: C 196 VAL cc_start: 0.7749 (t) cc_final: 0.7440 (m) REVERT: C 222 ILE cc_start: 0.7223 (mt) cc_final: 0.6977 (mt) REVERT: C 224 VAL cc_start: 0.7480 (t) cc_final: 0.7239 (m) REVERT: C 229 SER cc_start: 0.7364 (t) cc_final: 0.7021 (p) REVERT: C 254 LYS cc_start: 0.7368 (mmtm) cc_final: 0.6908 (mtmm) REVERT: C 262 ASP cc_start: 0.6811 (m-30) cc_final: 0.6590 (t0) REVERT: C 272 GLU cc_start: 0.6961 (mt-10) cc_final: 0.6542 (mt-10) REVERT: C 314 THR cc_start: 0.7513 (OUTLIER) cc_final: 0.7024 (p) REVERT: C 354 ARG cc_start: 0.7091 (mtt90) cc_final: 0.6603 (mtt90) REVERT: C 361 LEU cc_start: 0.7559 (mp) cc_final: 0.7193 (mp) REVERT: C 376 LYS cc_start: 0.7477 (ttpt) cc_final: 0.7213 (ttpt) REVERT: C 385 ASP cc_start: 0.6528 (m-30) cc_final: 0.6300 (m-30) REVERT: C 451 GLU cc_start: 0.7625 (mp0) cc_final: 0.7157 (mp0) REVERT: C 452 ASP cc_start: 0.7356 (m-30) cc_final: 0.7061 (m-30) REVERT: C 473 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7749 (mm-30) REVERT: C 496 LYS cc_start: 0.8495 (mttt) cc_final: 0.7961 (mttt) REVERT: D 10 MET cc_start: 0.6316 (mtm) cc_final: 0.5766 (mtm) REVERT: D 15 ASP cc_start: 0.6972 (m-30) cc_final: 0.6696 (m-30) REVERT: D 17 LYS cc_start: 0.7001 (tttt) cc_final: 0.6678 (tttm) REVERT: D 37 ARG cc_start: 0.6858 (mtm180) cc_final: 0.6376 (mtm180) REVERT: D 64 MET cc_start: 0.6820 (mmt) cc_final: 0.6526 (mmt) REVERT: D 74 MET cc_start: 0.7504 (mtt) cc_final: 0.7014 (mtt) REVERT: D 75 GLU cc_start: 0.7321 (tt0) cc_final: 0.6857 (tt0) REVERT: D 84 SER cc_start: 0.7829 (m) cc_final: 0.7310 (p) REVERT: D 96 PHE cc_start: 0.7167 (m-80) cc_final: 0.6474 (m-80) REVERT: D 101 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6857 (mt-10) REVERT: D 114 ARG cc_start: 0.7332 (ttt180) cc_final: 0.6891 (ttp80) REVERT: D 115 ARG cc_start: 0.7662 (mtt-85) cc_final: 0.7274 (mtt-85) REVERT: D 116 ASP cc_start: 0.7100 (m-30) cc_final: 0.6495 (m-30) REVERT: D 120 ARG cc_start: 0.7210 (ttt90) cc_final: 0.6932 (ptm160) REVERT: D 133 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6666 (mt-10) REVERT: D 153 LYS cc_start: 0.6569 (mttp) cc_final: 0.6293 (mttt) REVERT: D 169 GLN cc_start: 0.7289 (mt0) cc_final: 0.6830 (mm-40) REVERT: D 170 GLU cc_start: 0.7194 (tp30) cc_final: 0.6880 (tt0) REVERT: D 190 ASP cc_start: 0.6938 (m-30) cc_final: 0.5647 (m-30) REVERT: D 191 ARG cc_start: 0.6942 (OUTLIER) cc_final: 0.5527 (mtt-85) REVERT: D 197 ASP cc_start: 0.6917 (t0) cc_final: 0.6694 (t0) REVERT: D 214 VAL cc_start: 0.7844 (t) cc_final: 0.7572 (p) REVERT: D 227 ARG cc_start: 0.6919 (mmt180) cc_final: 0.6389 (mmt90) REVERT: D 237 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6490 (mt-10) REVERT: D 241 ASP cc_start: 0.7104 (m-30) cc_final: 0.6776 (m-30) REVERT: D 246 ASP cc_start: 0.7495 (m-30) cc_final: 0.7009 (m-30) REVERT: D 252 ASP cc_start: 0.6366 (t0) cc_final: 0.5891 (t0) REVERT: D 270 ARG cc_start: 0.7546 (mtt180) cc_final: 0.6953 (mtt-85) REVERT: D 284 GLU cc_start: 0.6229 (mt-10) cc_final: 0.5617 (mt-10) REVERT: D 285 MET cc_start: 0.6335 (ttm) cc_final: 0.6026 (ttm) REVERT: D 326 ASP cc_start: 0.7268 (m-30) cc_final: 0.6401 (m-30) REVERT: D 352 ARG cc_start: 0.7103 (mtp180) cc_final: 0.6813 (mtp180) REVERT: D 387 LEU cc_start: 0.7604 (mt) cc_final: 0.7380 (mp) REVERT: D 428 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8051 (m) REVERT: D 439 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6665 (mm-30) REVERT: E 1 MET cc_start: 0.3440 (mmt) cc_final: 0.3098 (mmt) REVERT: E 3 ARG cc_start: 0.6661 (mtm-85) cc_final: 0.6401 (mtm-85) REVERT: E 5 ARG cc_start: 0.6534 (ptp-110) cc_final: 0.6217 (ptp-110) REVERT: E 10 MET cc_start: 0.5923 (ptp) cc_final: 0.5625 (ptp) REVERT: E 17 LYS cc_start: 0.7563 (tttt) cc_final: 0.6993 (ttmm) REVERT: E 43 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6765 (m-30) REVERT: E 60 ARG cc_start: 0.7024 (ttm-80) cc_final: 0.6646 (ttm-80) REVERT: E 91 THR cc_start: 0.7621 (p) cc_final: 0.7363 (t) REVERT: E 101 GLU cc_start: 0.6941 (mt-10) cc_final: 0.6573 (mp0) REVERT: E 127 GLU cc_start: 0.6814 (mt-10) cc_final: 0.6439 (mt-10) REVERT: E 134 ILE cc_start: 0.8269 (mt) cc_final: 0.7887 (tt) REVERT: E 149 ILE cc_start: 0.7676 (mt) cc_final: 0.7428 (mm) REVERT: E 170 GLU cc_start: 0.7120 (tp30) cc_final: 0.6686 (tt0) REVERT: E 178 GLU cc_start: 0.7158 (mm-30) cc_final: 0.6682 (mm-30) REVERT: E 203 LYS cc_start: 0.7596 (tppt) cc_final: 0.7364 (tppt) REVERT: E 210 LYS cc_start: 0.7593 (mttt) cc_final: 0.7215 (mttt) REVERT: E 284 GLU cc_start: 0.6290 (mt-10) cc_final: 0.5868 (mt-10) REVERT: E 285 MET cc_start: 0.6708 (tpp) cc_final: 0.6020 (mmm) REVERT: E 312 ASP cc_start: 0.7055 (t0) cc_final: 0.6639 (t0) REVERT: E 315 ASP cc_start: 0.7011 (t70) cc_final: 0.6769 (t70) REVERT: E 334 LYS cc_start: 0.7391 (mmmm) cc_final: 0.7147 (mmmm) REVERT: E 354 LEU cc_start: 0.7586 (tp) cc_final: 0.7363 (tt) REVERT: E 362 GLU cc_start: 0.7771 (pm20) cc_final: 0.7564 (pm20) REVERT: E 402 ARG cc_start: 0.7510 (mmm-85) cc_final: 0.7209 (mtt-85) REVERT: E 407 GLN cc_start: 0.7437 (tt0) cc_final: 0.7016 (tp40) REVERT: E 427 TYR cc_start: 0.8282 (t80) cc_final: 0.8072 (t80) REVERT: E 431 LYS cc_start: 0.7754 (ptmm) cc_final: 0.7432 (ptmm) REVERT: E 435 ARG cc_start: 0.7510 (ttp80) cc_final: 0.6872 (ttp80) REVERT: E 438 LYS cc_start: 0.7689 (ttpt) cc_final: 0.6983 (ttpt) REVERT: E 439 GLU cc_start: 0.7518 (mm-30) cc_final: 0.6447 (mm-30) REVERT: E 445 TYR cc_start: 0.7458 (m-80) cc_final: 0.6780 (m-80) REVERT: E 446 ASP cc_start: 0.7768 (m-30) cc_final: 0.7457 (m-30) REVERT: E 450 GLU cc_start: 0.7863 (pm20) cc_final: 0.7315 (pm20) REVERT: F 5 ARG cc_start: 0.6060 (mmt180) cc_final: 0.5456 (mmt180) REVERT: F 8 GLN cc_start: 0.7261 (mt0) cc_final: 0.6750 (mt0) REVERT: F 15 ASP cc_start: 0.6920 (m-30) cc_final: 0.6532 (m-30) REVERT: F 23 LEU cc_start: 0.8318 (mp) cc_final: 0.8072 (mt) REVERT: F 33 GLN cc_start: 0.7450 (mt0) cc_final: 0.7232 (mt0) REVERT: F 37 ARG cc_start: 0.7352 (ttm170) cc_final: 0.7113 (ttm170) REVERT: F 39 GLU cc_start: 0.7602 (mp0) cc_final: 0.7183 (mp0) REVERT: F 74 MET cc_start: 0.6862 (mtt) cc_final: 0.6386 (mtt) REVERT: F 75 GLU cc_start: 0.7050 (tt0) cc_final: 0.5496 (tt0) REVERT: F 89 GLU cc_start: 0.7501 (tp30) cc_final: 0.7195 (tp30) REVERT: F 114 ARG cc_start: 0.7540 (ttp-170) cc_final: 0.7282 (ttp80) REVERT: F 115 ARG cc_start: 0.7451 (mtt90) cc_final: 0.7133 (mtt90) REVERT: F 116 ASP cc_start: 0.7392 (m-30) cc_final: 0.7118 (m-30) REVERT: F 124 LYS cc_start: 0.7062 (mttm) cc_final: 0.6690 (mttm) REVERT: F 127 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6726 (mt-10) REVERT: F 213 MET cc_start: 0.7301 (mtp) cc_final: 0.7069 (mtm) REVERT: F 218 MET cc_start: 0.7463 (mtm) cc_final: 0.7249 (mtp) REVERT: F 220 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6587 (mm-30) REVERT: F 237 GLU cc_start: 0.6641 (tt0) cc_final: 0.5771 (mt-10) REVERT: F 241 ASP cc_start: 0.6698 (m-30) cc_final: 0.6214 (m-30) REVERT: F 345 ASP cc_start: 0.7504 (t70) cc_final: 0.7025 (t70) REVERT: F 357 GLU cc_start: 0.7267 (pm20) cc_final: 0.7058 (pm20) REVERT: F 389 MET cc_start: 0.7352 (mtm) cc_final: 0.6951 (mtm) REVERT: F 439 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6746 (mt-10) REVERT: F 442 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6455 (mt-10) REVERT: F 444 LYS cc_start: 0.7894 (tttt) cc_final: 0.7284 (tttt) REVERT: F 445 TYR cc_start: 0.8259 (m-80) cc_final: 0.7551 (m-80) REVERT: F 451 ASP cc_start: 0.7935 (m-30) cc_final: 0.7691 (m-30) REVERT: G 11 LYS cc_start: 0.7243 (tptt) cc_final: 0.6596 (tptt) REVERT: G 15 ASN cc_start: 0.7409 (m-40) cc_final: 0.7058 (m-40) REVERT: G 32 THR cc_start: 0.7508 (m) cc_final: 0.7263 (p) REVERT: G 33 SER cc_start: 0.7734 (t) cc_final: 0.7253 (p) REVERT: G 54 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8528 (mt-10) REVERT: G 70 MET cc_start: 0.7866 (mmm) cc_final: 0.7246 (mmm) REVERT: G 85 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7392 (t) REVERT: G 90 LEU cc_start: 0.7777 (tp) cc_final: 0.7405 (tp) REVERT: G 95 ASN cc_start: 0.7957 (m-40) cc_final: 0.7626 (m-40) REVERT: G 134 MET cc_start: 0.6534 (mtm) cc_final: 0.6145 (mtm) REVERT: G 173 MET cc_start: 0.6947 (mtm) cc_final: 0.6658 (mtm) REVERT: G 185 GLU cc_start: 0.6521 (mm-30) cc_final: 0.6113 (mm-30) REVERT: G 188 GLU cc_start: 0.5770 (OUTLIER) cc_final: 0.5526 (tt0) REVERT: G 223 TYR cc_start: 0.8068 (t80) cc_final: 0.7703 (t80) REVERT: G 225 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8242 (mt-10) REVERT: G 227 LEU cc_start: 0.7908 (mm) cc_final: 0.7676 (mm) REVERT: G 256 GLU cc_start: 0.7004 (tp30) cc_final: 0.6645 (tp30) outliers start: 118 outliers final: 89 residues processed: 1110 average time/residue: 0.4222 time to fit residues: 680.0922 Evaluate side-chains 1155 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1055 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP 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 62 MET Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 136 VAL 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 314 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 445 LEU 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 137 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 375 MET Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 495 LYS 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 104 ILE Chi-restraints excluded: chain C residue 129 ILE 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 469 GLN 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 126 GLU Chi-restraints excluded: chain D residue 131 GLU 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 299 SER Chi-restraints excluded: chain D residue 311 ASP 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 428 VAL Chi-restraints excluded: chain D residue 431 LYS Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 103 ILE 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 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 1 MET 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 149 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 265 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 384 ILE 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 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 186 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 186 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 172 GLN A 358 ASN A 371 GLN B 46 ASN B 333 ASN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS F 324 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 24604 Z= 0.391 Angle : 0.658 7.984 33364 Z= 0.351 Chirality : 0.048 0.171 3840 Planarity : 0.006 0.067 4349 Dihedral : 8.445 98.307 3577 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.96 % Allowed : 24.08 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.15), residues: 3104 helix: 1.00 (0.14), residues: 1260 sheet: -0.21 (0.22), residues: 540 loop : -0.92 (0.17), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS D 173 PHE 0.022 0.002 PHE B 463 TYR 0.020 0.002 TYR F 307 ARG 0.009 0.001 ARG E 115 *********************** 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 1215 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1088 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7946 (tt0) cc_final: 0.7620 (tt0) REVERT: A 52 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6649 (mp) REVERT: A 57 ASN cc_start: 0.7990 (m-40) cc_final: 0.7737 (m-40) REVERT: A 93 ARG cc_start: 0.6850 (ptt180) cc_final: 0.6187 (ppt170) REVERT: A 94 ILE cc_start: 0.7929 (mm) cc_final: 0.7684 (mt) REVERT: A 96 GLU cc_start: 0.6613 (tt0) cc_final: 0.6351 (tt0) REVERT: A 125 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5796 (pt0) REVERT: A 127 ARG cc_start: 0.6982 (mtp85) cc_final: 0.6543 (mtp85) REVERT: A 140 ARG cc_start: 0.7328 (ttt-90) cc_final: 0.7059 (ttt90) REVERT: A 147 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7182 (mm110) REVERT: A 170 ASP cc_start: 0.6219 (t0) cc_final: 0.5988 (t0) REVERT: A 186 GLN cc_start: 0.7201 (mm-40) cc_final: 0.6882 (mm-40) REVERT: A 251 TYR cc_start: 0.7325 (m-80) cc_final: 0.7026 (m-80) REVERT: A 254 LYS cc_start: 0.7305 (mmtm) cc_final: 0.6924 (mmtm) REVERT: A 272 GLU cc_start: 0.6636 (tt0) cc_final: 0.6159 (tt0) REVERT: A 296 ARG cc_start: 0.7302 (mtm180) cc_final: 0.7052 (mtm-85) REVERT: A 299 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7406 (mm-30) REVERT: A 303 LYS cc_start: 0.7524 (tptp) cc_final: 0.7219 (tptp) REVERT: A 375 MET cc_start: 0.7460 (tpp) cc_final: 0.7113 (tpp) REVERT: A 377 LYS cc_start: 0.7424 (mtmm) cc_final: 0.6998 (mtmm) REVERT: A 426 GLN cc_start: 0.7382 (mm-40) cc_final: 0.7084 (mm-40) REVERT: A 446 ASP cc_start: 0.6871 (p0) cc_final: 0.6623 (p0) REVERT: A 467 ASN cc_start: 0.7530 (t0) cc_final: 0.7115 (t0) REVERT: A 478 THR cc_start: 0.7330 (t) cc_final: 0.6863 (p) REVERT: A 480 ASP cc_start: 0.6546 (t0) cc_final: 0.6284 (m-30) REVERT: A 488 ASN cc_start: 0.7570 (m-40) cc_final: 0.7339 (m-40) REVERT: A 489 LYS cc_start: 0.7867 (tttt) cc_final: 0.7553 (tttt) REVERT: B 48 MET cc_start: 0.7630 (mtm) cc_final: 0.7354 (mtp) REVERT: B 67 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6534 (mm-30) REVERT: B 95 MET cc_start: 0.6863 (tpt) cc_final: 0.6594 (tpp) REVERT: B 137 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7295 (mtm) REVERT: B 144 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5988 (pt0) REVERT: B 159 ILE cc_start: 0.7272 (mt) cc_final: 0.7043 (mt) REVERT: B 177 SER cc_start: 0.6238 (p) cc_final: 0.5849 (m) REVERT: B 181 ASP cc_start: 0.7358 (m-30) cc_final: 0.7080 (m-30) REVERT: B 200 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7819 (mm110) REVERT: B 210 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6439 (mm-30) REVERT: B 245 MET cc_start: 0.6775 (mtt) cc_final: 0.6487 (mmt) REVERT: B 272 GLU cc_start: 0.6728 (tt0) cc_final: 0.6411 (tt0) REVERT: B 336 SER cc_start: 0.7777 (t) cc_final: 0.7440 (p) REVERT: B 385 ASP cc_start: 0.7271 (m-30) cc_final: 0.6836 (m-30) REVERT: B 418 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7123 (mm-30) REVERT: B 423 ASP cc_start: 0.6503 (p0) cc_final: 0.6209 (p0) REVERT: B 428 ILE cc_start: 0.7577 (mm) cc_final: 0.7162 (mt) REVERT: B 442 ARG cc_start: 0.7579 (mmt-90) cc_final: 0.6968 (mmp80) REVERT: B 449 PRO cc_start: 0.7721 (Cg_exo) cc_final: 0.7466 (Cg_endo) REVERT: B 476 ARG cc_start: 0.7889 (ptp-110) cc_final: 0.7509 (ptp-110) REVERT: B 479 LYS cc_start: 0.7018 (mptt) cc_final: 0.6574 (mptt) REVERT: B 494 PHE cc_start: 0.8331 (t80) cc_final: 0.8073 (t80) REVERT: C 34 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7420 (p) REVERT: C 51 GLU cc_start: 0.7507 (tt0) cc_final: 0.7149 (tt0) REVERT: C 62 MET cc_start: 0.6688 (ttt) cc_final: 0.6391 (ttp) REVERT: C 68 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6891 (mt-10) REVERT: C 80 THR cc_start: 0.7918 (p) cc_final: 0.7687 (m) REVERT: C 90 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7264 (ttt-90) REVERT: C 96 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6391 (mt-10) REVERT: C 127 ARG cc_start: 0.7495 (mtp85) cc_final: 0.7037 (mtp85) REVERT: C 137 MET cc_start: 0.7967 (mmm) cc_final: 0.7760 (mmm) REVERT: C 147 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7041 (mm110) REVERT: C 171 ARG cc_start: 0.7443 (ptm-80) cc_final: 0.7060 (ptm-80) REVERT: C 181 ASP cc_start: 0.7668 (m-30) cc_final: 0.7285 (m-30) REVERT: C 185 ASN cc_start: 0.7858 (t0) cc_final: 0.7453 (t0) REVERT: C 196 VAL cc_start: 0.7771 (t) cc_final: 0.7459 (m) REVERT: C 224 VAL cc_start: 0.7539 (t) cc_final: 0.7257 (m) REVERT: C 254 LYS cc_start: 0.7598 (mmtm) cc_final: 0.7128 (mtmm) REVERT: C 272 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6490 (mt-10) REVERT: C 296 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6912 (mtm180) REVERT: C 314 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.6993 (p) REVERT: C 354 ARG cc_start: 0.7108 (mtt90) cc_final: 0.6620 (mtt90) REVERT: C 361 LEU cc_start: 0.7591 (mp) cc_final: 0.7236 (mp) REVERT: C 376 LYS cc_start: 0.7512 (ttpt) cc_final: 0.7090 (tppt) REVERT: C 385 ASP cc_start: 0.6477 (m-30) cc_final: 0.6232 (m-30) REVERT: C 451 GLU cc_start: 0.7604 (mp0) cc_final: 0.7140 (mp0) REVERT: C 452 ASP cc_start: 0.7458 (m-30) cc_final: 0.7174 (m-30) REVERT: C 473 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7759 (mm-30) REVERT: D 5 ARG cc_start: 0.6156 (mtm-85) cc_final: 0.5920 (mtm-85) REVERT: D 10 MET cc_start: 0.6387 (mtm) cc_final: 0.5857 (mtm) REVERT: D 15 ASP cc_start: 0.6970 (m-30) cc_final: 0.6666 (m-30) REVERT: D 17 LYS cc_start: 0.7048 (tttt) cc_final: 0.6756 (tttm) REVERT: D 23 LEU cc_start: 0.8378 (mt) cc_final: 0.8094 (mt) REVERT: D 37 ARG cc_start: 0.6867 (mtm180) cc_final: 0.6401 (mtm180) REVERT: D 64 MET cc_start: 0.6875 (mmt) cc_final: 0.6536 (mmt) REVERT: D 74 MET cc_start: 0.7541 (mtt) cc_final: 0.7308 (mtt) REVERT: D 75 GLU cc_start: 0.7318 (tt0) cc_final: 0.6860 (tt0) REVERT: D 101 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6878 (mt-10) REVERT: D 114 ARG cc_start: 0.7331 (ttt180) cc_final: 0.6915 (ttp80) REVERT: D 116 ASP cc_start: 0.7060 (m-30) cc_final: 0.6464 (m-30) REVERT: D 120 ARG cc_start: 0.7280 (ttt90) cc_final: 0.7041 (ptm160) REVERT: D 133 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6682 (mt-10) REVERT: D 153 LYS cc_start: 0.6543 (mttp) cc_final: 0.6154 (mttt) REVERT: D 169 GLN cc_start: 0.7266 (mt0) cc_final: 0.6823 (mm-40) REVERT: D 190 ASP cc_start: 0.6918 (m-30) cc_final: 0.5600 (m-30) REVERT: D 191 ARG cc_start: 0.6967 (OUTLIER) cc_final: 0.5545 (mtt-85) REVERT: D 197 ASP cc_start: 0.6972 (t0) cc_final: 0.6746 (t0) REVERT: D 214 VAL cc_start: 0.7834 (t) cc_final: 0.7501 (p) REVERT: D 227 ARG cc_start: 0.7019 (mmt180) cc_final: 0.6463 (mmt90) REVERT: D 237 GLU cc_start: 0.7111 (mt-10) cc_final: 0.6536 (mt-10) REVERT: D 241 ASP cc_start: 0.7133 (m-30) cc_final: 0.6810 (m-30) REVERT: D 246 ASP cc_start: 0.7540 (m-30) cc_final: 0.7036 (m-30) REVERT: D 252 ASP cc_start: 0.6400 (t0) cc_final: 0.5848 (t0) REVERT: D 270 ARG cc_start: 0.7613 (mtt180) cc_final: 0.6979 (mtt-85) REVERT: D 284 GLU cc_start: 0.6182 (mt-10) cc_final: 0.5571 (mt-10) REVERT: D 285 MET cc_start: 0.6417 (ttm) cc_final: 0.6138 (ttm) REVERT: D 326 ASP cc_start: 0.7230 (m-30) cc_final: 0.6462 (m-30) REVERT: D 352 ARG cc_start: 0.7107 (mtp180) cc_final: 0.6833 (mtp180) REVERT: D 387 LEU cc_start: 0.7692 (mt) cc_final: 0.7474 (mp) REVERT: D 428 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.8049 (m) REVERT: D 435 ARG cc_start: 0.7125 (mtp85) cc_final: 0.6747 (mtp85) REVERT: D 439 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6664 (mm-30) REVERT: E 1 MET cc_start: 0.3459 (mmt) cc_final: 0.3124 (mmt) REVERT: E 3 ARG cc_start: 0.6659 (mtm-85) cc_final: 0.6380 (mtm-85) REVERT: E 5 ARG cc_start: 0.6609 (ptp-110) cc_final: 0.6254 (ptp-110) REVERT: E 10 MET cc_start: 0.6007 (ptp) cc_final: 0.5712 (ptp) REVERT: E 17 LYS cc_start: 0.7623 (tttt) cc_final: 0.6975 (ttmm) REVERT: E 43 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: E 58 THR cc_start: 0.7093 (t) cc_final: 0.6867 (p) REVERT: E 60 ARG cc_start: 0.7119 (ttm-80) cc_final: 0.6738 (ttm-80) REVERT: E 91 THR cc_start: 0.7622 (p) cc_final: 0.7343 (t) REVERT: E 101 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6660 (mp0) REVERT: E 104 ASP cc_start: 0.7486 (m-30) cc_final: 0.7147 (m-30) REVERT: E 127 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6443 (mt-10) REVERT: E 134 ILE cc_start: 0.8297 (mt) cc_final: 0.7904 (tt) REVERT: E 149 ILE cc_start: 0.7725 (mt) cc_final: 0.7432 (mm) REVERT: E 170 GLU cc_start: 0.7132 (tp30) cc_final: 0.6686 (tt0) REVERT: E 178 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6697 (mm-30) REVERT: E 203 LYS cc_start: 0.7617 (tppt) cc_final: 0.7298 (tppt) REVERT: E 210 LYS cc_start: 0.7590 (mttt) cc_final: 0.7314 (mttt) REVERT: E 270 ARG cc_start: 0.7178 (mtt90) cc_final: 0.6684 (mtt180) REVERT: E 284 GLU cc_start: 0.6273 (mt-10) cc_final: 0.5870 (mt-10) REVERT: E 312 ASP cc_start: 0.7012 (t0) cc_final: 0.6500 (t0) REVERT: E 315 ASP cc_start: 0.7124 (t70) cc_final: 0.6836 (t70) REVERT: E 334 LYS cc_start: 0.7381 (mmmm) cc_final: 0.7115 (mmmm) REVERT: E 354 LEU cc_start: 0.7546 (tp) cc_final: 0.7329 (tt) REVERT: E 362 GLU cc_start: 0.7765 (pm20) cc_final: 0.7552 (pm20) REVERT: E 402 ARG cc_start: 0.7523 (mmm-85) cc_final: 0.7213 (mtt-85) REVERT: E 407 GLN cc_start: 0.7527 (tt0) cc_final: 0.7092 (tp40) REVERT: E 418 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7621 (mt-10) REVERT: E 423 GLN cc_start: 0.7540 (mm-40) cc_final: 0.7282 (mt0) REVERT: E 427 TYR cc_start: 0.8331 (t80) cc_final: 0.8099 (t80) REVERT: E 431 LYS cc_start: 0.7811 (ptmm) cc_final: 0.7463 (ptmm) REVERT: E 438 LYS cc_start: 0.7624 (ttpt) cc_final: 0.7043 (ttpt) REVERT: E 439 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6632 (mm-30) REVERT: E 442 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6947 (mt-10) REVERT: E 446 ASP cc_start: 0.7814 (m-30) cc_final: 0.7447 (m-30) REVERT: E 450 GLU cc_start: 0.7917 (pm20) cc_final: 0.7382 (pm20) REVERT: F 3 ARG cc_start: 0.6789 (mtt180) cc_final: 0.6232 (mtt180) REVERT: F 5 ARG cc_start: 0.6067 (mmt180) cc_final: 0.5493 (mmt180) REVERT: F 8 GLN cc_start: 0.7386 (mt0) cc_final: 0.6968 (mt0) REVERT: F 15 ASP cc_start: 0.6955 (m-30) cc_final: 0.6583 (m-30) REVERT: F 33 GLN cc_start: 0.7453 (mt0) cc_final: 0.7244 (mt0) REVERT: F 37 ARG cc_start: 0.7370 (ttm170) cc_final: 0.7144 (ttm170) REVERT: F 39 GLU cc_start: 0.7615 (mp0) cc_final: 0.7195 (mp0) REVERT: F 49 GLU cc_start: 0.6882 (tt0) cc_final: 0.6151 (tt0) REVERT: F 74 MET cc_start: 0.6845 (mtt) cc_final: 0.6386 (mtt) REVERT: F 75 GLU cc_start: 0.7075 (tt0) cc_final: 0.5485 (tt0) REVERT: F 89 GLU cc_start: 0.7537 (tp30) cc_final: 0.7231 (tp30) REVERT: F 114 ARG cc_start: 0.7573 (ttp-170) cc_final: 0.7332 (ttp80) REVERT: F 115 ARG cc_start: 0.7500 (mtt90) cc_final: 0.7143 (mtt90) REVERT: F 116 ASP cc_start: 0.7422 (m-30) cc_final: 0.7156 (m-30) REVERT: F 120 ARG cc_start: 0.7081 (ptm-80) cc_final: 0.6774 (tmm-80) REVERT: F 124 LYS cc_start: 0.7063 (mttm) cc_final: 0.6657 (mttm) REVERT: F 127 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6734 (mt-10) REVERT: F 213 MET cc_start: 0.7318 (mtp) cc_final: 0.7078 (mtm) REVERT: F 220 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6628 (mm-30) REVERT: F 237 GLU cc_start: 0.6716 (tt0) cc_final: 0.5763 (mt-10) REVERT: F 241 ASP cc_start: 0.6771 (m-30) cc_final: 0.6269 (m-30) REVERT: F 254 ILE cc_start: 0.7872 (tp) cc_final: 0.7597 (mt) REVERT: F 389 MET cc_start: 0.7261 (mtm) cc_final: 0.6991 (mtm) REVERT: F 439 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6718 (mt-10) REVERT: F 442 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6492 (mt-10) REVERT: F 444 LYS cc_start: 0.7909 (tttt) cc_final: 0.7305 (tttt) REVERT: F 445 TYR cc_start: 0.8224 (m-80) cc_final: 0.7518 (m-80) REVERT: F 448 LEU cc_start: 0.8187 (mm) cc_final: 0.7802 (mp) REVERT: F 451 ASP cc_start: 0.7908 (m-30) cc_final: 0.7671 (m-30) REVERT: G 11 LYS cc_start: 0.7290 (tptt) cc_final: 0.6683 (tptt) REVERT: G 15 ASN cc_start: 0.7365 (m-40) cc_final: 0.7046 (m-40) REVERT: G 54 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8558 (mt-10) REVERT: G 70 MET cc_start: 0.7892 (mmm) cc_final: 0.7263 (mmm) REVERT: G 85 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7369 (t) REVERT: G 95 ASN cc_start: 0.7968 (m-40) cc_final: 0.7642 (m-40) REVERT: G 134 MET cc_start: 0.6612 (mtm) cc_final: 0.6195 (mtm) REVERT: G 173 MET cc_start: 0.6916 (mtm) cc_final: 0.6630 (mtm) REVERT: G 184 GLN cc_start: 0.6946 (mp10) cc_final: 0.6468 (mp10) REVERT: G 185 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6116 (mm-30) REVERT: G 188 GLU cc_start: 0.5711 (tt0) cc_final: 0.5462 (tt0) REVERT: G 223 TYR cc_start: 0.8119 (t80) cc_final: 0.7777 (t80) REVERT: G 225 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8279 (mt-10) REVERT: G 227 LEU cc_start: 0.7932 (mm) cc_final: 0.7703 (mm) REVERT: G 244 MET cc_start: 0.7299 (ttm) cc_final: 0.7058 (ttp) REVERT: G 256 GLU cc_start: 0.6945 (tp30) cc_final: 0.6594 (tp30) outliers start: 127 outliers final: 97 residues processed: 1140 average time/residue: 0.4288 time to fit residues: 713.2881 Evaluate side-chains 1193 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1084 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL 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 163 GLN 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 381 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 46 ASN 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 137 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain B residue 375 MET 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 34 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 296 ARG 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 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 126 GLU Chi-restraints excluded: chain D residue 131 GLU 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 273 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 419 GLN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 66 SER 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 218 MET 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 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 1 MET 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 149 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 273 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 329 THR Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 384 ILE 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 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 333 ASN C 172 GLN C 433 GLN C 467 ASN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 287 GLN D 447 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 24604 Z= 0.317 Angle : 0.631 7.730 33364 Z= 0.335 Chirality : 0.047 0.175 3840 Planarity : 0.006 0.070 4349 Dihedral : 8.318 93.468 3577 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.16 % Allowed : 24.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.15), residues: 3104 helix: 1.12 (0.14), residues: 1249 sheet: -0.15 (0.22), residues: 544 loop : -0.92 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 173 PHE 0.018 0.002 PHE B 463 TYR 0.022 0.002 TYR G 116 ARG 0.008 0.001 ARG E 333 *********************** 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 1210 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1078 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.7897 (tt0) cc_final: 0.7666 (tt0) REVERT: A 57 ASN cc_start: 0.7977 (m-40) cc_final: 0.7723 (m-40) REVERT: A 93 ARG cc_start: 0.6855 (ptt180) cc_final: 0.6293 (ppt170) REVERT: A 125 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5686 (pt0) REVERT: A 127 ARG cc_start: 0.6969 (mtp85) cc_final: 0.6569 (mtp85) REVERT: A 140 ARG cc_start: 0.7300 (ttt-90) cc_final: 0.7081 (ttt90) REVERT: A 144 GLU cc_start: 0.7239 (pt0) cc_final: 0.6901 (pt0) REVERT: A 147 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7183 (mm110) REVERT: A 170 ASP cc_start: 0.6233 (t0) cc_final: 0.5998 (t0) REVERT: A 186 GLN cc_start: 0.7219 (mm-40) cc_final: 0.6883 (mm-40) REVERT: A 251 TYR cc_start: 0.7329 (m-80) cc_final: 0.7014 (m-80) REVERT: A 254 LYS cc_start: 0.7328 (mmtm) cc_final: 0.6958 (mmtm) REVERT: A 272 GLU cc_start: 0.6643 (tt0) cc_final: 0.6153 (tt0) REVERT: A 296 ARG cc_start: 0.7293 (mtm180) cc_final: 0.7054 (mtm-85) REVERT: A 299 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7401 (mm-30) REVERT: A 303 LYS cc_start: 0.7515 (tptp) cc_final: 0.7181 (tptp) REVERT: A 375 MET cc_start: 0.7448 (tpp) cc_final: 0.6797 (tpp) REVERT: A 377 LYS cc_start: 0.7457 (mtmm) cc_final: 0.7043 (mtmm) REVERT: A 421 LYS cc_start: 0.6990 (mttm) cc_final: 0.6401 (mtpp) REVERT: A 426 GLN cc_start: 0.7390 (mm-40) cc_final: 0.7124 (mm-40) REVERT: A 467 ASN cc_start: 0.7569 (t0) cc_final: 0.7168 (t0) REVERT: A 478 THR cc_start: 0.7277 (t) cc_final: 0.7006 (t) REVERT: A 480 ASP cc_start: 0.6646 (t0) cc_final: 0.6385 (m-30) REVERT: A 489 LYS cc_start: 0.7896 (tttt) cc_final: 0.7587 (tttt) REVERT: B 48 MET cc_start: 0.7625 (mtm) cc_final: 0.7355 (mtp) REVERT: B 67 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6534 (mm-30) REVERT: B 95 MET cc_start: 0.6908 (tpt) cc_final: 0.6264 (tpt) REVERT: B 137 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7258 (mtm) REVERT: B 144 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.5974 (pt0) REVERT: B 159 ILE cc_start: 0.7273 (mt) cc_final: 0.6967 (mt) REVERT: B 177 SER cc_start: 0.6226 (p) cc_final: 0.5802 (m) REVERT: B 181 ASP cc_start: 0.7356 (m-30) cc_final: 0.7075 (m-30) REVERT: B 200 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7760 (mm-40) REVERT: B 210 GLU cc_start: 0.6809 (mm-30) cc_final: 0.6450 (mm-30) REVERT: B 245 MET cc_start: 0.6745 (mtt) cc_final: 0.6483 (mmt) REVERT: B 272 GLU cc_start: 0.6734 (tt0) cc_final: 0.6416 (tt0) REVERT: B 336 SER cc_start: 0.7728 (t) cc_final: 0.7378 (p) REVERT: B 385 ASP cc_start: 0.7203 (m-30) cc_final: 0.6765 (m-30) REVERT: B 418 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7168 (mm-30) REVERT: B 423 ASP cc_start: 0.6483 (p0) cc_final: 0.6193 (p0) REVERT: B 442 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6945 (mmp80) REVERT: B 449 PRO cc_start: 0.7756 (Cg_exo) cc_final: 0.7496 (Cg_endo) REVERT: B 463 PHE cc_start: 0.8121 (t80) cc_final: 0.7860 (t80) REVERT: B 476 ARG cc_start: 0.7886 (ptp-110) cc_final: 0.7531 (ptp-110) REVERT: B 479 LYS cc_start: 0.7085 (mptt) cc_final: 0.6616 (mptt) REVERT: B 494 PHE cc_start: 0.8348 (t80) cc_final: 0.8053 (t80) REVERT: C 34 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7406 (p) REVERT: C 51 GLU cc_start: 0.7474 (tt0) cc_final: 0.7147 (tt0) REVERT: C 62 MET cc_start: 0.6682 (ttt) cc_final: 0.6383 (ttp) REVERT: C 68 GLU cc_start: 0.7226 (tt0) cc_final: 0.6950 (mt-10) REVERT: C 80 THR cc_start: 0.7912 (p) cc_final: 0.7689 (m) REVERT: C 90 ARG cc_start: 0.7555 (ttp80) cc_final: 0.7228 (ttt-90) REVERT: C 96 GLU cc_start: 0.6746 (mt-10) cc_final: 0.6403 (mt-10) REVERT: C 127 ARG cc_start: 0.7522 (mtp85) cc_final: 0.7070 (mtp85) REVERT: C 137 MET cc_start: 0.7967 (mmm) cc_final: 0.7757 (mmm) REVERT: C 147 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7013 (mm110) REVERT: C 171 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7073 (ptm-80) REVERT: C 181 ASP cc_start: 0.7632 (m-30) cc_final: 0.7266 (m-30) REVERT: C 185 ASN cc_start: 0.7826 (t0) cc_final: 0.7428 (t0) REVERT: C 196 VAL cc_start: 0.7758 (t) cc_final: 0.7458 (m) REVERT: C 224 VAL cc_start: 0.7521 (t) cc_final: 0.7245 (m) REVERT: C 272 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6513 (mt-10) REVERT: C 296 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6902 (mtm180) REVERT: C 314 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7002 (p) REVERT: C 354 ARG cc_start: 0.7084 (mtt90) cc_final: 0.6606 (mtt90) REVERT: C 361 LEU cc_start: 0.7561 (mp) cc_final: 0.7177 (mp) REVERT: C 376 LYS cc_start: 0.7502 (ttpt) cc_final: 0.7209 (ttpt) REVERT: C 385 ASP cc_start: 0.6511 (m-30) cc_final: 0.6267 (m-30) REVERT: C 421 LYS cc_start: 0.7289 (mttp) cc_final: 0.7039 (mttm) REVERT: C 451 GLU cc_start: 0.7605 (mp0) cc_final: 0.7133 (mp0) REVERT: C 452 ASP cc_start: 0.7389 (m-30) cc_final: 0.7103 (m-30) REVERT: C 473 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7767 (mm-30) REVERT: D 10 MET cc_start: 0.6376 (mtm) cc_final: 0.5821 (mtm) REVERT: D 15 ASP cc_start: 0.7019 (m-30) cc_final: 0.6708 (m-30) REVERT: D 17 LYS cc_start: 0.7030 (tttt) cc_final: 0.6705 (tttm) REVERT: D 23 LEU cc_start: 0.8387 (mt) cc_final: 0.8106 (mt) REVERT: D 37 ARG cc_start: 0.6868 (mtm180) cc_final: 0.6402 (mtm180) REVERT: D 64 MET cc_start: 0.6824 (mmt) cc_final: 0.6486 (mmt) REVERT: D 74 MET cc_start: 0.7524 (mtt) cc_final: 0.7257 (mtt) REVERT: D 75 GLU cc_start: 0.7294 (tt0) cc_final: 0.6812 (tt0) REVERT: D 96 PHE cc_start: 0.7110 (m-80) cc_final: 0.6526 (m-80) REVERT: D 101 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6874 (mt-10) REVERT: D 114 ARG cc_start: 0.7327 (ttt180) cc_final: 0.6808 (ttp80) REVERT: D 116 ASP cc_start: 0.7057 (m-30) cc_final: 0.6385 (m-30) REVERT: D 120 ARG cc_start: 0.7277 (ttt90) cc_final: 0.6991 (ptm160) REVERT: D 133 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6620 (mt-10) REVERT: D 153 LYS cc_start: 0.6537 (mttp) cc_final: 0.6265 (mttt) REVERT: D 169 GLN cc_start: 0.7252 (mt0) cc_final: 0.6819 (mm-40) REVERT: D 190 ASP cc_start: 0.6909 (m-30) cc_final: 0.5637 (m-30) REVERT: D 191 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.5670 (mtt-85) REVERT: D 197 ASP cc_start: 0.6959 (t0) cc_final: 0.6732 (t0) REVERT: D 214 VAL cc_start: 0.7830 (t) cc_final: 0.7538 (p) REVERT: D 237 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6544 (mt-10) REVERT: D 241 ASP cc_start: 0.7091 (m-30) cc_final: 0.6736 (m-30) REVERT: D 246 ASP cc_start: 0.7543 (m-30) cc_final: 0.7045 (m-30) REVERT: D 252 ASP cc_start: 0.6359 (t0) cc_final: 0.5833 (t0) REVERT: D 270 ARG cc_start: 0.7607 (mtt180) cc_final: 0.6987 (mtt-85) REVERT: D 284 GLU cc_start: 0.6270 (mt-10) cc_final: 0.5634 (mt-10) REVERT: D 285 MET cc_start: 0.6380 (ttm) cc_final: 0.6078 (ttm) REVERT: D 326 ASP cc_start: 0.7192 (m-30) cc_final: 0.6367 (m-30) REVERT: D 352 ARG cc_start: 0.7120 (mtp180) cc_final: 0.6854 (mtp180) REVERT: D 387 LEU cc_start: 0.7605 (mt) cc_final: 0.7376 (mp) REVERT: D 428 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.8047 (m) REVERT: D 439 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6643 (mm-30) REVERT: E 1 MET cc_start: 0.3465 (mmt) cc_final: 0.3109 (mmt) REVERT: E 3 ARG cc_start: 0.6653 (mtm-85) cc_final: 0.6384 (mtm-85) REVERT: E 5 ARG cc_start: 0.6601 (ptp-110) cc_final: 0.6224 (ptp-110) REVERT: E 10 MET cc_start: 0.5999 (ptp) cc_final: 0.5696 (ptp) REVERT: E 17 LYS cc_start: 0.7604 (tttt) cc_final: 0.7016 (ttmm) REVERT: E 41 GLU cc_start: 0.6456 (mt-10) cc_final: 0.6191 (mt-10) REVERT: E 43 ASP cc_start: 0.7140 (OUTLIER) cc_final: 0.6812 (m-30) REVERT: E 56 ASP cc_start: 0.6816 (t0) cc_final: 0.6222 (t0) REVERT: E 58 THR cc_start: 0.7074 (t) cc_final: 0.6805 (p) REVERT: E 91 THR cc_start: 0.7614 (p) cc_final: 0.7331 (t) REVERT: E 101 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6644 (mp0) REVERT: E 104 ASP cc_start: 0.7479 (m-30) cc_final: 0.7187 (m-30) REVERT: E 120 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6456 (ttp80) REVERT: E 127 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6425 (mt-10) REVERT: E 134 ILE cc_start: 0.8288 (mt) cc_final: 0.7898 (tt) REVERT: E 149 ILE cc_start: 0.7732 (mt) cc_final: 0.7443 (mm) REVERT: E 170 GLU cc_start: 0.7135 (tp30) cc_final: 0.6710 (tt0) REVERT: E 178 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6594 (mm-30) REVERT: E 203 LYS cc_start: 0.7681 (tppt) cc_final: 0.7425 (tppt) REVERT: E 210 LYS cc_start: 0.7602 (mttt) cc_final: 0.7318 (mttt) REVERT: E 256 ARG cc_start: 0.6690 (mtt180) cc_final: 0.6441 (mtm180) REVERT: E 284 GLU cc_start: 0.6277 (mt-10) cc_final: 0.5855 (mt-10) REVERT: E 312 ASP cc_start: 0.7028 (t0) cc_final: 0.6528 (t0) REVERT: E 315 ASP cc_start: 0.7080 (t70) cc_final: 0.6805 (t70) REVERT: E 334 LYS cc_start: 0.7384 (mmmm) cc_final: 0.7112 (mmmm) REVERT: E 402 ARG cc_start: 0.7511 (mmm-85) cc_final: 0.7228 (mtt-85) REVERT: E 405 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7353 (mmt-90) REVERT: E 407 GLN cc_start: 0.7496 (tt0) cc_final: 0.7068 (tp40) REVERT: E 418 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: E 423 GLN cc_start: 0.7529 (mm-40) cc_final: 0.7278 (mt0) REVERT: E 427 TYR cc_start: 0.8353 (t80) cc_final: 0.8104 (t80) REVERT: E 431 LYS cc_start: 0.7789 (ptmm) cc_final: 0.7451 (ptmm) REVERT: E 438 LYS cc_start: 0.7610 (ttpt) cc_final: 0.7004 (ttpt) REVERT: E 439 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6611 (mm-30) REVERT: E 442 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6970 (mt-10) REVERT: E 446 ASP cc_start: 0.7823 (m-30) cc_final: 0.7543 (m-30) REVERT: E 450 GLU cc_start: 0.7887 (pm20) cc_final: 0.7380 (pm20) REVERT: F 3 ARG cc_start: 0.6766 (mtt180) cc_final: 0.6201 (mtt180) REVERT: F 5 ARG cc_start: 0.6070 (mmt180) cc_final: 0.5478 (mmt180) REVERT: F 8 GLN cc_start: 0.7313 (mt0) cc_final: 0.6909 (mt0) REVERT: F 15 ASP cc_start: 0.6939 (m-30) cc_final: 0.6561 (m-30) REVERT: F 33 GLN cc_start: 0.7454 (mt0) cc_final: 0.7244 (mt0) REVERT: F 37 ARG cc_start: 0.7356 (ttm170) cc_final: 0.7141 (ttm170) REVERT: F 39 GLU cc_start: 0.7605 (mp0) cc_final: 0.7197 (mp0) REVERT: F 49 GLU cc_start: 0.6923 (tt0) cc_final: 0.6151 (tt0) REVERT: F 74 MET cc_start: 0.6842 (mtt) cc_final: 0.6361 (mtt) REVERT: F 75 GLU cc_start: 0.7092 (tt0) cc_final: 0.5488 (tt0) REVERT: F 89 GLU cc_start: 0.7538 (tp30) cc_final: 0.7232 (tp30) REVERT: F 114 ARG cc_start: 0.7579 (ttp-170) cc_final: 0.7144 (ttp80) REVERT: F 115 ARG cc_start: 0.7488 (mtt90) cc_final: 0.7083 (mtt90) REVERT: F 116 ASP cc_start: 0.7416 (m-30) cc_final: 0.6957 (m-30) REVERT: F 120 ARG cc_start: 0.7069 (ptm-80) cc_final: 0.6778 (tmm-80) REVERT: F 124 LYS cc_start: 0.7028 (mttm) cc_final: 0.6648 (mttm) REVERT: F 127 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6724 (mt-10) REVERT: F 213 MET cc_start: 0.7305 (mtp) cc_final: 0.7069 (mtm) REVERT: F 220 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6647 (mm-30) REVERT: F 237 GLU cc_start: 0.6746 (tt0) cc_final: 0.5807 (mt-10) REVERT: F 241 ASP cc_start: 0.6795 (m-30) cc_final: 0.6306 (m-30) REVERT: F 254 ILE cc_start: 0.7850 (tp) cc_final: 0.7564 (mt) REVERT: F 389 MET cc_start: 0.7340 (mtm) cc_final: 0.7004 (mtm) REVERT: F 439 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6579 (mt-10) REVERT: F 442 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6467 (mt-10) REVERT: F 444 LYS cc_start: 0.7901 (tttt) cc_final: 0.7658 (tttt) REVERT: F 445 TYR cc_start: 0.8228 (m-80) cc_final: 0.7676 (m-80) REVERT: F 448 LEU cc_start: 0.8188 (mm) cc_final: 0.7807 (mp) REVERT: F 451 ASP cc_start: 0.7898 (m-30) cc_final: 0.7659 (m-30) REVERT: G 11 LYS cc_start: 0.7284 (tptt) cc_final: 0.6687 (tptt) REVERT: G 15 ASN cc_start: 0.7388 (m-40) cc_final: 0.7066 (m-40) REVERT: G 28 GLU cc_start: 0.7535 (tt0) cc_final: 0.7226 (tt0) REVERT: G 54 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8553 (mt-10) REVERT: G 70 MET cc_start: 0.7888 (mmm) cc_final: 0.7243 (mmm) REVERT: G 85 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7394 (t) REVERT: G 90 LEU cc_start: 0.7861 (tp) cc_final: 0.7389 (tp) REVERT: G 95 ASN cc_start: 0.7960 (m-40) cc_final: 0.7654 (m-40) REVERT: G 134 MET cc_start: 0.6544 (mtm) cc_final: 0.6117 (mtm) REVERT: G 173 MET cc_start: 0.6927 (mtm) cc_final: 0.6613 (mtm) REVERT: G 185 GLU cc_start: 0.6537 (mm-30) cc_final: 0.6095 (mm-30) REVERT: G 188 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.5448 (tt0) REVERT: G 223 TYR cc_start: 0.8110 (t80) cc_final: 0.7770 (t80) REVERT: G 225 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8258 (mt-10) REVERT: G 227 LEU cc_start: 0.7876 (mm) cc_final: 0.7645 (mm) REVERT: G 244 MET cc_start: 0.7294 (ttm) cc_final: 0.6945 (ttp) REVERT: G 256 GLU cc_start: 0.6940 (tp30) cc_final: 0.6594 (tp30) outliers start: 132 outliers final: 100 residues processed: 1130 average time/residue: 0.4248 time to fit residues: 700.9376 Evaluate side-chains 1185 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1069 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASP 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 125 GLU Chi-restraints excluded: chain A residue 136 VAL 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 290 ILE Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 46 ASN 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 136 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 333 ASN 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 34 VAL Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 296 ARG 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 450 VAL 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 57 ASP Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 162 VAL 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 299 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 419 GLN Chi-restraints excluded: chain D residue 423 GLN Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 43 ASP Chi-restraints excluded: chain E residue 66 SER Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 120 ARG Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 218 MET 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 381 GLN Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 400 VAL Chi-restraints excluded: chain E residue 405 ARG Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 1 MET 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 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 273 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain F residue 407 GLN Chi-restraints excluded: chain F residue 462 VAL 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 85 THR Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 148 SER Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 281 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 4.9990 chunk 286 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 167 optimal weight: 0.0770 chunk 121 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 251 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN B 46 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 172 GLN C 433 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 GLN F 217 GLN F 412 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24604 Z= 0.171 Angle : 0.570 8.006 33364 Z= 0.299 Chirality : 0.044 0.164 3840 Planarity : 0.005 0.067 4349 Dihedral : 7.836 84.978 3577 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.44 % Allowed : 26.58 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3104 helix: 1.50 (0.15), residues: 1247 sheet: 0.17 (0.22), residues: 535 loop : -0.77 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 173 PHE 0.018 0.001 PHE G 45 TYR 0.023 0.001 TYR C 248 ARG 0.009 0.001 ARG E 333 *********************** 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 1157 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1069 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.7945 (m-40) cc_final: 0.7683 (m-40) REVERT: A 67 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6198 (mm-30) REVERT: A 93 ARG cc_start: 0.6803 (ptt180) cc_final: 0.6272 (ppt170) REVERT: A 95 MET cc_start: 0.6807 (tpt) cc_final: 0.6497 (tpt) REVERT: A 125 GLU cc_start: 0.5776 (OUTLIER) cc_final: 0.5377 (pt0) REVERT: A 127 ARG cc_start: 0.7071 (mtp85) cc_final: 0.6676 (mtp85) REVERT: A 140 ARG cc_start: 0.7287 (ttt-90) cc_final: 0.7036 (ttt90) REVERT: A 144 GLU cc_start: 0.7271 (pt0) cc_final: 0.6929 (pt0) REVERT: A 170 ASP cc_start: 0.6247 (t0) cc_final: 0.6026 (t0) REVERT: A 251 TYR cc_start: 0.7250 (m-80) cc_final: 0.6973 (m-80) REVERT: A 254 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6921 (mmtm) REVERT: A 272 GLU cc_start: 0.6678 (tt0) cc_final: 0.6201 (tt0) REVERT: A 296 ARG cc_start: 0.7249 (mtm180) cc_final: 0.7027 (mtm-85) REVERT: A 299 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 375 MET cc_start: 0.7307 (tpp) cc_final: 0.6800 (tpp) REVERT: A 377 LYS cc_start: 0.7351 (mtmm) cc_final: 0.6977 (mtmm) REVERT: A 385 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.7035 (t0) REVERT: A 421 LYS cc_start: 0.6978 (mttm) cc_final: 0.6489 (mtpp) REVERT: A 426 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7116 (mm-40) REVERT: A 467 ASN cc_start: 0.7413 (t0) cc_final: 0.7035 (t0) REVERT: A 476 ARG cc_start: 0.8047 (ttm-80) cc_final: 0.7829 (ttm-80) REVERT: A 478 THR cc_start: 0.7213 (t) cc_final: 0.6934 (t) REVERT: A 480 ASP cc_start: 0.6540 (t0) cc_final: 0.6264 (m-30) REVERT: A 489 LYS cc_start: 0.7876 (tttt) cc_final: 0.7577 (tttt) REVERT: B 48 MET cc_start: 0.7583 (mtm) cc_final: 0.7352 (mtp) REVERT: B 67 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6542 (mm-30) REVERT: B 95 MET cc_start: 0.6903 (tpt) cc_final: 0.6636 (tpp) REVERT: B 137 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.7280 (mtm) REVERT: B 144 GLU cc_start: 0.7008 (pt0) cc_final: 0.5978 (pt0) REVERT: B 164 ARG cc_start: 0.7309 (mtm180) cc_final: 0.6999 (mtm-85) REVERT: B 177 SER cc_start: 0.6242 (p) cc_final: 0.5718 (m) REVERT: B 181 ASP cc_start: 0.7288 (m-30) cc_final: 0.7034 (m-30) REVERT: B 210 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6468 (mm-30) REVERT: B 245 MET cc_start: 0.6734 (mtt) cc_final: 0.6526 (mmt) REVERT: B 272 GLU cc_start: 0.6769 (tt0) cc_final: 0.6435 (tt0) REVERT: B 333 ASN cc_start: 0.7369 (t0) cc_final: 0.6608 (t0) REVERT: B 336 SER cc_start: 0.7878 (t) cc_final: 0.7546 (p) REVERT: B 371 GLN cc_start: 0.7246 (mt0) cc_final: 0.6975 (mt0) REVERT: B 385 ASP cc_start: 0.7201 (m-30) cc_final: 0.6766 (m-30) REVERT: B 423 ASP cc_start: 0.6434 (p0) cc_final: 0.6137 (p0) REVERT: B 433 GLN cc_start: 0.7488 (mt0) cc_final: 0.7266 (mt0) REVERT: B 442 ARG cc_start: 0.7473 (mmt-90) cc_final: 0.7153 (mmp80) REVERT: B 449 PRO cc_start: 0.7620 (Cg_exo) cc_final: 0.7341 (Cg_endo) REVERT: B 463 PHE cc_start: 0.8076 (t80) cc_final: 0.7829 (t80) REVERT: B 476 ARG cc_start: 0.7888 (ptp-110) cc_final: 0.7584 (ptp-110) REVERT: B 479 LYS cc_start: 0.7089 (mptt) cc_final: 0.6626 (mptt) REVERT: B 494 PHE cc_start: 0.8302 (t80) cc_final: 0.8062 (t80) REVERT: C 34 VAL cc_start: 0.7801 (OUTLIER) cc_final: 0.7417 (p) REVERT: C 51 GLU cc_start: 0.7384 (tt0) cc_final: 0.6949 (tt0) REVERT: C 62 MET cc_start: 0.6672 (ttt) cc_final: 0.6337 (ttp) REVERT: C 68 GLU cc_start: 0.7243 (tt0) cc_final: 0.6907 (mt-10) REVERT: C 80 THR cc_start: 0.7911 (p) cc_final: 0.7683 (m) REVERT: C 90 ARG cc_start: 0.7505 (ttp80) cc_final: 0.7078 (ttp-110) REVERT: C 96 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6406 (mt-10) REVERT: C 127 ARG cc_start: 0.7474 (mtp85) cc_final: 0.7026 (mtp85) REVERT: C 137 MET cc_start: 0.7956 (mmm) cc_final: 0.7747 (mmm) REVERT: C 147 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7054 (mm110) REVERT: C 163 GLN cc_start: 0.7786 (tt0) cc_final: 0.7574 (tt0) REVERT: C 181 ASP cc_start: 0.7593 (m-30) cc_final: 0.7232 (m-30) REVERT: C 185 ASN cc_start: 0.7790 (t0) cc_final: 0.7411 (t0) REVERT: C 196 VAL cc_start: 0.7737 (t) cc_final: 0.7452 (m) REVERT: C 222 ILE cc_start: 0.7188 (mt) cc_final: 0.6943 (mt) REVERT: C 224 VAL cc_start: 0.7458 (t) cc_final: 0.7244 (m) REVERT: C 229 SER cc_start: 0.7362 (t) cc_final: 0.7041 (p) REVERT: C 262 ASP cc_start: 0.6836 (m-30) cc_final: 0.6628 (t0) REVERT: C 272 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6597 (mt-10) REVERT: C 314 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7021 (p) REVERT: C 354 ARG cc_start: 0.7031 (mtt90) cc_final: 0.6592 (mtt90) REVERT: C 358 ASN cc_start: 0.7030 (t0) cc_final: 0.6802 (t0) REVERT: C 361 LEU cc_start: 0.7507 (mp) cc_final: 0.7117 (mp) REVERT: C 376 LYS cc_start: 0.7492 (ttpt) cc_final: 0.7148 (ttpt) REVERT: C 385 ASP cc_start: 0.6485 (m-30) cc_final: 0.6252 (m-30) REVERT: C 421 LYS cc_start: 0.7230 (mttp) cc_final: 0.6977 (mttm) REVERT: C 451 GLU cc_start: 0.7589 (mp0) cc_final: 0.7113 (mp0) REVERT: C 452 ASP cc_start: 0.7368 (m-30) cc_final: 0.7062 (m-30) REVERT: C 473 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7737 (mm-30) REVERT: D 10 MET cc_start: 0.6294 (mtm) cc_final: 0.5773 (mtm) REVERT: D 15 ASP cc_start: 0.6982 (m-30) cc_final: 0.6713 (m-30) REVERT: D 17 LYS cc_start: 0.6987 (tttt) cc_final: 0.6626 (tttm) REVERT: D 64 MET cc_start: 0.6796 (mmt) cc_final: 0.6476 (mmt) REVERT: D 74 MET cc_start: 0.7508 (mtt) cc_final: 0.7034 (mtt) REVERT: D 75 GLU cc_start: 0.7250 (tt0) cc_final: 0.6790 (tt0) REVERT: D 96 PHE cc_start: 0.7109 (m-80) cc_final: 0.6556 (m-80) REVERT: D 101 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6821 (mt-10) REVERT: D 114 ARG cc_start: 0.7326 (ttt180) cc_final: 0.6797 (ttp80) REVERT: D 115 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.7253 (mtt-85) REVERT: D 116 ASP cc_start: 0.7091 (m-30) cc_final: 0.6411 (m-30) REVERT: D 120 ARG cc_start: 0.7219 (ttt90) cc_final: 0.6928 (ptm160) REVERT: D 153 LYS cc_start: 0.6615 (mttp) cc_final: 0.6200 (mttt) REVERT: D 169 GLN cc_start: 0.7269 (mt0) cc_final: 0.6845 (mm-40) REVERT: D 170 GLU cc_start: 0.7210 (tp30) cc_final: 0.6862 (tt0) REVERT: D 190 ASP cc_start: 0.7030 (m-30) cc_final: 0.5786 (m-30) REVERT: D 197 ASP cc_start: 0.6930 (t0) cc_final: 0.6715 (t0) REVERT: D 214 VAL cc_start: 0.7859 (t) cc_final: 0.7601 (p) REVERT: D 227 ARG cc_start: 0.6904 (mmt180) cc_final: 0.6354 (mmt90) REVERT: D 237 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6488 (mt-10) REVERT: D 241 ASP cc_start: 0.7074 (m-30) cc_final: 0.6750 (m-30) REVERT: D 246 ASP cc_start: 0.7488 (m-30) cc_final: 0.7011 (m-30) REVERT: D 252 ASP cc_start: 0.6353 (t0) cc_final: 0.5859 (t0) REVERT: D 270 ARG cc_start: 0.7580 (mtt180) cc_final: 0.6953 (mtt-85) REVERT: D 284 GLU cc_start: 0.6233 (mt-10) cc_final: 0.5577 (mt-10) REVERT: D 285 MET cc_start: 0.6249 (ttm) cc_final: 0.5958 (ttm) REVERT: D 304 GLN cc_start: 0.7504 (mt0) cc_final: 0.7050 (mt0) REVERT: D 326 ASP cc_start: 0.7275 (m-30) cc_final: 0.6561 (m-30) REVERT: D 352 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6879 (mtp180) REVERT: D 387 LEU cc_start: 0.7522 (mt) cc_final: 0.7303 (mp) REVERT: D 428 VAL cc_start: 0.8332 (t) cc_final: 0.8029 (m) REVERT: D 455 LEU cc_start: 0.7766 (mp) cc_final: 0.7545 (mm) REVERT: E 1 MET cc_start: 0.3495 (mmt) cc_final: 0.3170 (mmt) REVERT: E 3 ARG cc_start: 0.6640 (mtm-85) cc_final: 0.6429 (mtm-85) REVERT: E 5 ARG cc_start: 0.6606 (ptp-110) cc_final: 0.6147 (ptp-110) REVERT: E 10 MET cc_start: 0.5896 (ptp) cc_final: 0.5554 (ptp) REVERT: E 17 LYS cc_start: 0.7561 (tttt) cc_final: 0.7018 (ttmm) REVERT: E 43 ASP cc_start: 0.7174 (m-30) cc_final: 0.6904 (m-30) REVERT: E 56 ASP cc_start: 0.6850 (t0) cc_final: 0.6318 (t0) REVERT: E 60 ARG cc_start: 0.7001 (ttm-80) cc_final: 0.6649 (ttm-80) REVERT: E 91 THR cc_start: 0.7592 (p) cc_final: 0.7338 (t) REVERT: E 101 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6617 (mp0) REVERT: E 104 ASP cc_start: 0.7445 (m-30) cc_final: 0.7175 (m-30) REVERT: E 120 ARG cc_start: 0.6972 (mtp85) cc_final: 0.6542 (ttp80) REVERT: E 127 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6368 (mt-10) REVERT: E 132 VAL cc_start: 0.7829 (m) cc_final: 0.7535 (p) REVERT: E 134 ILE cc_start: 0.8284 (mt) cc_final: 0.7851 (tt) REVERT: E 149 ILE cc_start: 0.7708 (mt) cc_final: 0.7480 (mm) REVERT: E 170 GLU cc_start: 0.7210 (tp30) cc_final: 0.6755 (tt0) REVERT: E 178 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6611 (mm-30) REVERT: E 203 LYS cc_start: 0.7619 (tppt) cc_final: 0.7376 (tppt) REVERT: E 210 LYS cc_start: 0.7611 (mttt) cc_final: 0.7303 (mttt) REVERT: E 215 PHE cc_start: 0.7783 (m-10) cc_final: 0.7559 (m-10) REVERT: E 284 GLU cc_start: 0.6256 (mt-10) cc_final: 0.5999 (mt-10) REVERT: E 285 MET cc_start: 0.6692 (tpp) cc_final: 0.5975 (mmm) REVERT: E 312 ASP cc_start: 0.7045 (t0) cc_final: 0.6652 (t0) REVERT: E 315 ASP cc_start: 0.6928 (t70) cc_final: 0.6712 (t70) REVERT: E 334 LYS cc_start: 0.7419 (mmmm) cc_final: 0.7143 (mmmm) REVERT: E 402 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.7295 (mtt-85) REVERT: E 405 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7201 (mmt-90) REVERT: E 407 GLN cc_start: 0.7387 (tt0) cc_final: 0.6983 (tp40) REVERT: E 423 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7269 (mt0) REVERT: E 427 TYR cc_start: 0.8313 (t80) cc_final: 0.8076 (t80) REVERT: E 431 LYS cc_start: 0.7758 (ptmm) cc_final: 0.7447 (ptmm) REVERT: E 438 LYS cc_start: 0.7603 (ttpt) cc_final: 0.6984 (ttpt) REVERT: E 439 GLU cc_start: 0.7409 (mm-30) cc_final: 0.6592 (mm-30) REVERT: E 442 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6871 (mt-10) REVERT: E 446 ASP cc_start: 0.7808 (m-30) cc_final: 0.7419 (m-30) REVERT: E 450 GLU cc_start: 0.7858 (pm20) cc_final: 0.7346 (pm20) REVERT: F 5 ARG cc_start: 0.6076 (mmt180) cc_final: 0.5454 (mmt180) REVERT: F 8 GLN cc_start: 0.7173 (mt0) cc_final: 0.6755 (mt0) REVERT: F 15 ASP cc_start: 0.6808 (m-30) cc_final: 0.6417 (m-30) REVERT: F 33 GLN cc_start: 0.7494 (mt0) cc_final: 0.7278 (mt0) REVERT: F 37 ARG cc_start: 0.7352 (ttm170) cc_final: 0.7141 (ttm170) REVERT: F 39 GLU cc_start: 0.7615 (mp0) cc_final: 0.7204 (mp0) REVERT: F 74 MET cc_start: 0.6869 (mtt) cc_final: 0.6368 (mtt) REVERT: F 75 GLU cc_start: 0.7105 (tt0) cc_final: 0.5615 (tt0) REVERT: F 89 GLU cc_start: 0.7548 (tp30) cc_final: 0.7230 (tp30) REVERT: F 114 ARG cc_start: 0.7594 (ttp-170) cc_final: 0.7169 (ttp80) REVERT: F 115 ARG cc_start: 0.7455 (mtt90) cc_final: 0.7124 (mtt90) REVERT: F 116 ASP cc_start: 0.7364 (m-30) cc_final: 0.6903 (m-30) REVERT: F 124 LYS cc_start: 0.7071 (mttm) cc_final: 0.6699 (mttm) REVERT: F 127 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6608 (mt-10) REVERT: F 213 MET cc_start: 0.7252 (mtp) cc_final: 0.6732 (mtp) REVERT: F 220 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6670 (mm-30) REVERT: F 237 GLU cc_start: 0.6666 (tt0) cc_final: 0.5880 (mt-10) REVERT: F 241 ASP cc_start: 0.6770 (m-30) cc_final: 0.6272 (m-30) REVERT: F 345 ASP cc_start: 0.7511 (t70) cc_final: 0.6999 (t70) REVERT: F 389 MET cc_start: 0.7401 (mtm) cc_final: 0.6989 (mtm) REVERT: F 439 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6614 (mt-10) REVERT: F 442 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6439 (mt-10) REVERT: F 444 LYS cc_start: 0.7868 (tttt) cc_final: 0.7618 (tttt) REVERT: F 445 TYR cc_start: 0.8256 (m-80) cc_final: 0.7748 (m-80) REVERT: G 11 LYS cc_start: 0.7217 (tptt) cc_final: 0.6605 (tptt) REVERT: G 15 ASN cc_start: 0.7412 (m-40) cc_final: 0.7087 (m-40) REVERT: G 28 GLU cc_start: 0.7536 (tt0) cc_final: 0.7182 (tt0) REVERT: G 32 THR cc_start: 0.7586 (m) cc_final: 0.7251 (p) REVERT: G 54 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8540 (mt-10) REVERT: G 70 MET cc_start: 0.7876 (mmm) cc_final: 0.7217 (mmm) REVERT: G 85 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7532 (t) REVERT: G 88 ARG cc_start: 0.6866 (ptt180) cc_final: 0.6528 (ptt180) REVERT: G 95 ASN cc_start: 0.7941 (m-40) cc_final: 0.7640 (m-40) REVERT: G 134 MET cc_start: 0.6482 (mtm) cc_final: 0.6071 (mtm) REVERT: G 173 MET cc_start: 0.6956 (mtm) cc_final: 0.6628 (mtm) REVERT: G 185 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6101 (mm-30) REVERT: G 223 TYR cc_start: 0.8079 (t80) cc_final: 0.7743 (t80) REVERT: G 225 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8197 (mt-10) REVERT: G 227 LEU cc_start: 0.7828 (mm) cc_final: 0.7571 (mm) REVERT: G 256 GLU cc_start: 0.6949 (tp30) cc_final: 0.6615 (tp30) outliers start: 88 outliers final: 63 residues processed: 1105 average time/residue: 0.4506 time to fit residues: 726.3037 Evaluate side-chains 1122 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1052 time to evaluate : 2.562 ------------------------------------------------------------------------------- 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 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 261 ASP 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 70 ASN Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 166 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 450 VAL Chi-restraints excluded: chain C residue 470 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 162 VAL 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 299 SER 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 D residue 456 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 142 VAL 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 405 ARG Chi-restraints excluded: chain E residue 421 THR Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 106 GLU 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 290 GLU Chi-restraints excluded: chain F residue 308 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 464 GLU 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 186 VAL 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 182 optimal weight: 5.9990 chunk 294 optimal weight: 5.9990 chunk 179 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 0.0970 chunk 308 optimal weight: 1.9990 chunk 284 optimal weight: 6.9990 chunk 245 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 150 optimal weight: 0.0670 overall best weight: 1.0320 ------------------------------------------------------------------------------- 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 172 GLN A 358 ASN B 163 GLN B 200 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 GLN C 172 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 287 GLN E 169 GLN F 412 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.4701 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= 0.187 Angle : 0.579 8.529 33364 Z= 0.301 Chirality : 0.044 0.164 3840 Planarity : 0.005 0.066 4349 Dihedral : 7.728 82.471 3576 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.74 % Allowed : 28.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3104 helix: 1.53 (0.15), residues: 1252 sheet: 0.23 (0.22), residues: 540 loop : -0.73 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 173 PHE 0.028 0.001 PHE F 409 TYR 0.020 0.001 TYR C 248 ARG 0.009 0.001 ARG B 89 ********************** 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 1118 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1048 time to evaluate : 2.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 ASN cc_start: 0.7944 (m-40) cc_final: 0.7686 (m-40) REVERT: A 67 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6338 (mm-30) REVERT: A 93 ARG cc_start: 0.6775 (ptt180) cc_final: 0.6240 (ppt170) REVERT: A 95 MET cc_start: 0.6851 (tpt) cc_final: 0.6507 (tpt) REVERT: A 125 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5334 (pt0) REVERT: A 127 ARG cc_start: 0.7048 (mtp85) cc_final: 0.6655 (mtp85) REVERT: A 140 ARG cc_start: 0.7296 (ttt-90) cc_final: 0.7017 (ttt90) REVERT: A 170 ASP cc_start: 0.6298 (t0) cc_final: 0.6075 (t0) REVERT: A 251 TYR cc_start: 0.7228 (m-80) cc_final: 0.6993 (m-80) REVERT: A 254 LYS cc_start: 0.7250 (mmtm) cc_final: 0.6862 (mmtm) REVERT: A 272 GLU cc_start: 0.6679 (tt0) cc_final: 0.6203 (tt0) REVERT: A 296 ARG cc_start: 0.7243 (mtm180) cc_final: 0.7021 (mtm-85) REVERT: A 299 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7405 (mm-30) REVERT: A 303 LYS cc_start: 0.7460 (tptp) cc_final: 0.7168 (tptp) REVERT: A 375 MET cc_start: 0.7295 (tpp) cc_final: 0.6793 (tpp) REVERT: A 377 LYS cc_start: 0.7354 (mtmm) cc_final: 0.7039 (mtmm) REVERT: A 426 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7130 (mm-40) REVERT: A 467 ASN cc_start: 0.7461 (t0) cc_final: 0.7071 (t0) REVERT: A 478 THR cc_start: 0.7211 (t) cc_final: 0.6941 (t) REVERT: A 480 ASP cc_start: 0.6591 (t0) cc_final: 0.6288 (m-30) REVERT: A 489 LYS cc_start: 0.7880 (tttt) cc_final: 0.7587 (tttt) REVERT: B 48 MET cc_start: 0.7591 (mtm) cc_final: 0.7356 (mtp) REVERT: B 67 GLU cc_start: 0.7046 (mm-30) cc_final: 0.6588 (mm-30) REVERT: B 95 MET cc_start: 0.6902 (tpt) cc_final: 0.6636 (tpp) REVERT: B 137 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7266 (mtm) REVERT: B 144 GLU cc_start: 0.6997 (pt0) cc_final: 0.5956 (pt0) REVERT: B 164 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6989 (mtm-85) REVERT: B 177 SER cc_start: 0.6254 (p) cc_final: 0.5743 (m) REVERT: B 181 ASP cc_start: 0.7298 (m-30) cc_final: 0.7041 (m-30) REVERT: B 200 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7689 (mm110) REVERT: B 210 GLU cc_start: 0.6774 (mm-30) cc_final: 0.6451 (mm-30) REVERT: B 245 MET cc_start: 0.6742 (mtt) cc_final: 0.6530 (mmt) REVERT: B 272 GLU cc_start: 0.6748 (tt0) cc_final: 0.6414 (tt0) REVERT: B 336 SER cc_start: 0.7819 (t) cc_final: 0.7476 (p) REVERT: B 385 ASP cc_start: 0.7204 (m-30) cc_final: 0.6765 (m-30) REVERT: B 423 ASP cc_start: 0.6438 (p0) cc_final: 0.6143 (p0) REVERT: B 442 ARG cc_start: 0.7434 (mmt-90) cc_final: 0.7033 (mmt-90) REVERT: B 449 PRO cc_start: 0.7638 (Cg_exo) cc_final: 0.7357 (Cg_endo) REVERT: B 463 PHE cc_start: 0.8038 (t80) cc_final: 0.7802 (t80) REVERT: B 479 LYS cc_start: 0.7087 (mptt) cc_final: 0.6631 (mptt) REVERT: B 494 PHE cc_start: 0.8338 (t80) cc_final: 0.8108 (t80) REVERT: C 34 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7404 (p) REVERT: C 51 GLU cc_start: 0.7411 (tt0) cc_final: 0.7011 (tt0) REVERT: C 62 MET cc_start: 0.6681 (ttt) cc_final: 0.6349 (ttp) REVERT: C 68 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6858 (mt-10) REVERT: C 80 THR cc_start: 0.7899 (p) cc_final: 0.7669 (m) REVERT: C 90 ARG cc_start: 0.7478 (ttp80) cc_final: 0.6929 (ttp-110) REVERT: C 96 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6439 (mt-10) REVERT: C 127 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7020 (mtp85) REVERT: C 137 MET cc_start: 0.7958 (mmm) cc_final: 0.7749 (mmm) REVERT: C 147 GLN cc_start: 0.7479 (mm-40) cc_final: 0.7037 (mm110) REVERT: C 163 GLN cc_start: 0.7797 (tt0) cc_final: 0.7573 (tt0) REVERT: C 171 ARG cc_start: 0.7486 (ptm-80) cc_final: 0.7111 (ptm-80) REVERT: C 181 ASP cc_start: 0.7598 (m-30) cc_final: 0.7220 (m-30) REVERT: C 185 ASN cc_start: 0.7780 (t0) cc_final: 0.7394 (t0) REVERT: C 196 VAL cc_start: 0.7732 (t) cc_final: 0.7435 (m) REVERT: C 222 ILE cc_start: 0.7197 (mt) cc_final: 0.6953 (mt) REVERT: C 224 VAL cc_start: 0.7456 (t) cc_final: 0.7244 (m) REVERT: C 229 SER cc_start: 0.7349 (t) cc_final: 0.7035 (p) REVERT: C 272 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6603 (mt-10) REVERT: C 314 THR cc_start: 0.7461 (OUTLIER) cc_final: 0.7020 (p) REVERT: C 354 ARG cc_start: 0.7047 (mtt90) cc_final: 0.6612 (mtt90) REVERT: C 361 LEU cc_start: 0.7510 (mp) cc_final: 0.7176 (mp) REVERT: C 376 LYS cc_start: 0.7486 (ttpt) cc_final: 0.7214 (ttpt) REVERT: C 385 ASP cc_start: 0.6490 (m-30) cc_final: 0.6242 (m-30) REVERT: C 451 GLU cc_start: 0.7621 (mp0) cc_final: 0.7154 (mp0) REVERT: C 452 ASP cc_start: 0.7370 (m-30) cc_final: 0.7074 (m-30) REVERT: C 473 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7744 (mm-30) REVERT: D 10 MET cc_start: 0.6287 (mtm) cc_final: 0.5770 (mtm) REVERT: D 15 ASP cc_start: 0.6972 (m-30) cc_final: 0.6699 (m-30) REVERT: D 17 LYS cc_start: 0.6980 (tttt) cc_final: 0.6597 (tttm) REVERT: D 64 MET cc_start: 0.6799 (mmt) cc_final: 0.6479 (mmt) REVERT: D 74 MET cc_start: 0.7517 (mtt) cc_final: 0.7254 (mtt) REVERT: D 75 GLU cc_start: 0.7259 (tt0) cc_final: 0.6796 (tt0) REVERT: D 96 PHE cc_start: 0.7132 (m-80) cc_final: 0.6588 (m-80) REVERT: D 101 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6795 (mt-10) REVERT: D 114 ARG cc_start: 0.7330 (ttt180) cc_final: 0.6802 (ttp80) REVERT: D 115 ARG cc_start: 0.7659 (mtt-85) cc_final: 0.7273 (mtt-85) REVERT: D 116 ASP cc_start: 0.7094 (m-30) cc_final: 0.6440 (m-30) REVERT: D 120 ARG cc_start: 0.7219 (ttt90) cc_final: 0.6926 (ptm160) REVERT: D 153 LYS cc_start: 0.6619 (mttp) cc_final: 0.6200 (mttt) REVERT: D 169 GLN cc_start: 0.7238 (mt0) cc_final: 0.6826 (mm-40) REVERT: D 170 GLU cc_start: 0.7189 (tp30) cc_final: 0.6853 (tt0) REVERT: D 190 ASP cc_start: 0.7045 (m-30) cc_final: 0.5812 (m-30) REVERT: D 197 ASP cc_start: 0.6918 (t0) cc_final: 0.6705 (t0) REVERT: D 214 VAL cc_start: 0.7834 (t) cc_final: 0.7573 (p) REVERT: D 227 ARG cc_start: 0.6891 (mmt180) cc_final: 0.6336 (mmt90) REVERT: D 237 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6504 (mt-10) REVERT: D 241 ASP cc_start: 0.7092 (m-30) cc_final: 0.6768 (m-30) REVERT: D 246 ASP cc_start: 0.7478 (m-30) cc_final: 0.7005 (m-30) REVERT: D 252 ASP cc_start: 0.6388 (t0) cc_final: 0.5903 (t0) REVERT: D 270 ARG cc_start: 0.7572 (mtt180) cc_final: 0.6935 (mtt-85) REVERT: D 284 GLU cc_start: 0.6235 (mt-10) cc_final: 0.5581 (mt-10) REVERT: D 285 MET cc_start: 0.6277 (ttm) cc_final: 0.5980 (ttm) REVERT: D 304 GLN cc_start: 0.7400 (mt0) cc_final: 0.7039 (mt0) REVERT: D 326 ASP cc_start: 0.7277 (m-30) cc_final: 0.6583 (m-30) REVERT: D 352 ARG cc_start: 0.7128 (mtp180) cc_final: 0.6895 (mtp180) REVERT: D 387 LEU cc_start: 0.7500 (mt) cc_final: 0.7268 (mp) REVERT: D 428 VAL cc_start: 0.8339 (t) cc_final: 0.8044 (m) REVERT: D 455 LEU cc_start: 0.7752 (mp) cc_final: 0.7537 (mm) REVERT: E 1 MET cc_start: 0.3532 (mmt) cc_final: 0.3183 (mmt) REVERT: E 3 ARG cc_start: 0.6627 (mtm-85) cc_final: 0.6399 (mtm-85) REVERT: E 5 ARG cc_start: 0.6603 (ptp-110) cc_final: 0.6132 (ptp-110) REVERT: E 10 MET cc_start: 0.5885 (ptp) cc_final: 0.5545 (ptp) REVERT: E 17 LYS cc_start: 0.7555 (tttt) cc_final: 0.7020 (ttmm) REVERT: E 43 ASP cc_start: 0.7192 (m-30) cc_final: 0.6905 (m-30) REVERT: E 56 ASP cc_start: 0.6865 (t0) cc_final: 0.6340 (t0) REVERT: E 60 ARG cc_start: 0.7032 (ttm-80) cc_final: 0.6672 (ttm-80) REVERT: E 91 THR cc_start: 0.7582 (p) cc_final: 0.7342 (t) REVERT: E 101 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6614 (mp0) REVERT: E 104 ASP cc_start: 0.7454 (m-30) cc_final: 0.7187 (m-30) REVERT: E 120 ARG cc_start: 0.6961 (mtp85) cc_final: 0.6533 (ttp80) REVERT: E 127 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6440 (mt-10) REVERT: E 132 VAL cc_start: 0.7824 (m) cc_final: 0.7526 (p) REVERT: E 134 ILE cc_start: 0.8286 (mt) cc_final: 0.7858 (tt) REVERT: E 149 ILE cc_start: 0.7706 (mt) cc_final: 0.7476 (mm) REVERT: E 170 GLU cc_start: 0.7232 (tp30) cc_final: 0.6771 (tt0) REVERT: E 178 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6616 (mm-30) REVERT: E 203 LYS cc_start: 0.7623 (tppt) cc_final: 0.7386 (tppt) REVERT: E 210 LYS cc_start: 0.7610 (mttt) cc_final: 0.7285 (mttt) REVERT: E 215 PHE cc_start: 0.7801 (m-10) cc_final: 0.7559 (m-10) REVERT: E 284 GLU cc_start: 0.6280 (mt-10) cc_final: 0.6015 (mt-10) REVERT: E 285 MET cc_start: 0.6691 (tpp) cc_final: 0.6011 (mmm) REVERT: E 312 ASP cc_start: 0.7012 (t0) cc_final: 0.6636 (t0) REVERT: E 315 ASP cc_start: 0.6979 (t70) cc_final: 0.6748 (t70) REVERT: E 334 LYS cc_start: 0.7401 (mmmm) cc_final: 0.7125 (mmmm) REVERT: E 402 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7317 (mtt-85) REVERT: E 405 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7161 (mmt-90) REVERT: E 407 GLN cc_start: 0.7421 (tt0) cc_final: 0.7000 (tp40) REVERT: E 427 TYR cc_start: 0.8306 (t80) cc_final: 0.8068 (t80) REVERT: E 431 LYS cc_start: 0.7784 (ptmm) cc_final: 0.7470 (ptmm) REVERT: E 435 ARG cc_start: 0.7563 (ttp80) cc_final: 0.6864 (ttp80) REVERT: E 438 LYS cc_start: 0.7593 (ttpt) cc_final: 0.7000 (ttpt) REVERT: E 439 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6476 (mm-30) REVERT: E 446 ASP cc_start: 0.7769 (m-30) cc_final: 0.7407 (m-30) REVERT: E 450 GLU cc_start: 0.7857 (pm20) cc_final: 0.7321 (pm20) REVERT: F 1 MET cc_start: 0.4405 (mmm) cc_final: 0.4033 (mmm) REVERT: F 5 ARG cc_start: 0.6083 (mmt180) cc_final: 0.5456 (mmt180) REVERT: F 8 GLN cc_start: 0.7236 (mt0) cc_final: 0.6745 (mt0) REVERT: F 15 ASP cc_start: 0.6806 (m-30) cc_final: 0.6411 (m-30) REVERT: F 33 GLN cc_start: 0.7503 (mt0) cc_final: 0.7297 (mt0) REVERT: F 37 ARG cc_start: 0.7358 (ttm170) cc_final: 0.7135 (ttm170) REVERT: F 39 GLU cc_start: 0.7619 (mp0) cc_final: 0.7182 (mp0) REVERT: F 74 MET cc_start: 0.6858 (mtt) cc_final: 0.6356 (mtt) REVERT: F 75 GLU cc_start: 0.7129 (tt0) cc_final: 0.5632 (tt0) REVERT: F 89 GLU cc_start: 0.7572 (tp30) cc_final: 0.7250 (tp30) REVERT: F 114 ARG cc_start: 0.7599 (ttp-170) cc_final: 0.7180 (ttp80) REVERT: F 115 ARG cc_start: 0.7489 (mtt90) cc_final: 0.7190 (mtt90) REVERT: F 116 ASP cc_start: 0.7391 (m-30) cc_final: 0.6965 (m-30) REVERT: F 120 ARG cc_start: 0.7217 (tmm-80) cc_final: 0.6925 (ptt90) REVERT: F 124 LYS cc_start: 0.6981 (mttm) cc_final: 0.6656 (mttm) REVERT: F 127 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6583 (mt-10) REVERT: F 213 MET cc_start: 0.7263 (mtp) cc_final: 0.6746 (mtp) REVERT: F 220 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6667 (mm-30) REVERT: F 241 ASP cc_start: 0.6806 (m-30) cc_final: 0.6303 (m-30) REVERT: F 345 ASP cc_start: 0.7504 (t70) cc_final: 0.7019 (t70) REVERT: F 389 MET cc_start: 0.7382 (mtm) cc_final: 0.6971 (mtm) REVERT: F 435 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7571 (ttp80) REVERT: F 439 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6603 (mt-10) REVERT: F 442 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6443 (mt-10) REVERT: F 444 LYS cc_start: 0.7870 (tttt) cc_final: 0.7612 (tttt) REVERT: F 445 TYR cc_start: 0.8247 (m-80) cc_final: 0.7693 (m-80) REVERT: G 11 LYS cc_start: 0.7204 (tptt) cc_final: 0.6876 (tptt) REVERT: G 28 GLU cc_start: 0.7526 (tt0) cc_final: 0.7184 (tt0) REVERT: G 32 THR cc_start: 0.7372 (m) cc_final: 0.7132 (p) REVERT: G 54 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8557 (mt-10) REVERT: G 70 MET cc_start: 0.7889 (mmm) cc_final: 0.7236 (mmm) REVERT: G 85 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7510 (t) REVERT: G 88 ARG cc_start: 0.6900 (ptt180) cc_final: 0.6566 (ptt180) REVERT: G 90 LEU cc_start: 0.7831 (tp) cc_final: 0.7196 (tp) REVERT: G 95 ASN cc_start: 0.7948 (m-40) cc_final: 0.7649 (m-40) REVERT: G 134 MET cc_start: 0.6493 (mtm) cc_final: 0.6097 (mtm) REVERT: G 173 MET cc_start: 0.6978 (mtm) cc_final: 0.6678 (mtm) REVERT: G 185 GLU cc_start: 0.6552 (mm-30) cc_final: 0.6115 (mm-30) REVERT: G 188 GLU cc_start: 0.5772 (tt0) cc_final: 0.5433 (tt0) REVERT: G 223 TYR cc_start: 0.8073 (t80) cc_final: 0.7744 (t80) REVERT: G 225 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8192 (mt-10) REVERT: G 227 LEU cc_start: 0.7823 (mm) cc_final: 0.7562 (mm) REVERT: G 256 GLU cc_start: 0.6997 (tp30) cc_final: 0.6658 (tp30) outliers start: 70 outliers final: 62 residues processed: 1078 average time/residue: 0.4464 time to fit residues: 702.7299 Evaluate side-chains 1113 residues out of total 2558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1045 time to evaluate : 2.527 ------------------------------------------------------------------------------- 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 136 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 261 ASP 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 104 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 166 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 470 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 126 GLU Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 162 VAL 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 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 D residue 456 VAL Chi-restraints excluded: chain E residue 76 VAL 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 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 405 ARG Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 GLU 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 233 LEU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 290 GLU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain F residue 464 GLU 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 186 VAL 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 195 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 226 optimal weight: 0.0370 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 246 optimal weight: 0.0970 chunk 103 optimal weight: 8.9990 chunk 252 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- 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 ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN C 172 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS D 287 GLN F 412 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.130685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115850 restraints weight = 34931.105| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.18 r_work: 0.3365 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4808 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= 0.178 Angle : 0.572 10.960 33364 Z= 0.296 Chirality : 0.043 0.159 3840 Planarity : 0.005 0.065 4349 Dihedral : 7.468 80.495 3572 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.93 % Allowed : 28.19 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.15), residues: 3104 helix: 1.60 (0.15), residues: 1257 sheet: 0.24 (0.22), residues: 547 loop : -0.69 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 173 PHE 0.015 0.001 PHE G 45 TYR 0.022 0.001 TYR C 248 ARG 0.009 0.001 ARG F 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10328.22 seconds wall clock time: 180 minutes 9.14 seconds (10809.14 seconds total)