Starting phenix.real_space_refine on Mon Feb 19 05:22:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tji_25926/02_2024/7tji_25926_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tji_25926/02_2024/7tji_25926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tji_25926/02_2024/7tji_25926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tji_25926/02_2024/7tji_25926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tji_25926/02_2024/7tji_25926_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tji_25926/02_2024/7tji_25926_updated.pdb" } resolution = 2.7 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= 0.000 sd= 0.002 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 93 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 14944 2.51 5 N 3949 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23766 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3885 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 475} Chain breaks: 4 Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2066 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Chain: "C" Number of atoms: 4497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4497 Classifications: {'peptide': 543} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 528} Chain breaks: 5 Chain: "D" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3543 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 421} Chain breaks: 3 Chain: "E" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3562 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 3 Chain: "F" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1300 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 846 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2995 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 14, 'TRANS': 361} Chain breaks: 7 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: "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: 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: "I" 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: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 13.20, per 1000 atoms: 0.56 Number of scatterers: 23766 At special positions: 0 Unit cell: (116.96, 140.18, 178.02, 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 96 16.00 P 93 15.00 Mg 4 11.99 O 4680 8.00 N 3949 7.00 C 14944 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 - 3.50 Amino acid : False - 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: 10.20 Conformation dependent library (CDL) restraints added in 4.0 seconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 12 sheets defined 53.0% alpha, 7.7% beta 41 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 9.47 Creating SS restraints... Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 422 through 429 removed outlier: 4.173A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 468 Processing helix chain 'A' and resid 485 through 501 Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 521 through 533 removed outlier: 3.742A pdb=" N CYS A 524 " --> pdb=" O PRO A 521 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 528 " --> pdb=" O TYR A 525 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TRP A 529 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER A 533 " --> pdb=" O ASN A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 551 Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 568 through 571 Processing helix chain 'A' and resid 577 through 587 removed outlier: 3.928A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 Processing helix chain 'A' and resid 611 through 617 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 686 through 699 Processing helix chain 'A' and resid 703 through 725 removed outlier: 3.554A pdb=" N LYS A 724 " --> pdb=" O HIS A 720 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 725 " --> pdb=" O TYR A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 785 removed outlier: 4.111A pdb=" N THR A 785 " --> pdb=" O ALA A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 Processing helix chain 'A' and resid 799 through 814 Processing helix chain 'A' and resid 822 through 835 Processing helix chain 'A' and resid 840 through 851 removed outlier: 4.906A pdb=" N LYS A 847 " --> pdb=" O MET A 843 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THR A 848 " --> pdb=" O GLU A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 875 Processing helix chain 'A' and resid 898 through 907 removed outlier: 3.636A pdb=" N GLU A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 263 through 265 No H-bonds generated for 'chain 'B' and resid 263 through 265' Processing helix chain 'B' and resid 271 through 283 removed outlier: 3.632A pdb=" N SER B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 309 removed outlier: 4.090A pdb=" N LYS B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N MET B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE B 301 " --> pdb=" O GLN B 297 " (cutoff:3.500A) Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 323 through 332 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 390 through 393 No H-bonds generated for 'chain 'B' and resid 390 through 393' Processing helix chain 'B' and resid 399 through 413 removed outlier: 4.514A pdb=" N ASN B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 461 through 464 Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 489 through 492 removed outlier: 3.661A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 489 through 492' Processing helix chain 'C' and resid 17 through 19 No H-bonds generated for 'chain 'C' and resid 17 through 19' Processing helix chain 'C' and resid 51 through 92 removed outlier: 4.000A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 157 Processing helix chain 'C' and resid 186 through 189 No H-bonds generated for 'chain 'C' and resid 186 through 189' Processing helix chain 'C' and resid 191 through 195 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 213 through 228 removed outlier: 3.785A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS C 228 " --> pdb=" O LYS C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 248 No H-bonds generated for 'chain 'C' and resid 245 through 248' Processing helix chain 'C' and resid 253 through 261 removed outlier: 4.078A pdb=" N ARG C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 287 Processing helix chain 'C' and resid 296 through 308 removed outlier: 3.645A pdb=" N ASN C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 331 Processing helix chain 'C' and resid 333 through 338 removed outlier: 3.903A pdb=" N VAL C 336 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 338 " --> pdb=" O SER C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 344 removed outlier: 4.032A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 340 through 344' Processing helix chain 'C' and resid 348 through 354 Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 389 through 396 removed outlier: 3.755A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU C 396 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 415 Processing helix chain 'C' and resid 424 through 433 Processing helix chain 'C' and resid 436 through 442 removed outlier: 4.674A pdb=" N ARG C 442 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 453 No H-bonds generated for 'chain 'C' and resid 450 through 453' Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 483 through 493 Processing helix chain 'C' and resid 511 through 516 removed outlier: 3.501A pdb=" N LYS C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE C 516 " --> pdb=" O ASP C 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 511 through 516' Processing helix chain 'C' and resid 520 through 530 removed outlier: 3.504A pdb=" N LYS C 526 " --> pdb=" O GLY C 522 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 527 " --> pdb=" O GLN C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 547 Processing helix chain 'C' and resid 550 through 558 removed outlier: 3.654A pdb=" N LEU C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 571 removed outlier: 3.595A pdb=" N GLU C 571 " --> pdb=" O LEU C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 594 Processing helix chain 'D' and resid 47 through 60 Processing helix chain 'D' and resid 66 through 68 No H-bonds generated for 'chain 'D' and resid 66 through 68' Processing helix chain 'D' and resid 73 through 90 removed outlier: 5.016A pdb=" N ASP D 77 " --> pdb=" O TYR D 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYS D 78 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 86 " --> pdb=" O ASP D 83 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE D 90 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 120 Processing helix chain 'D' and resid 141 through 157 Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 229 through 239 Processing helix chain 'D' and resid 256 through 259 No H-bonds generated for 'chain 'D' and resid 256 through 259' Processing helix chain 'D' and resid 262 through 267 Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 302 through 314 Processing helix chain 'D' and resid 319 through 330 Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.546A pdb=" N SER D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Proline residue: D 343 - end of helix Processing helix chain 'D' and resid 351 through 360 Processing helix chain 'D' and resid 362 through 372 removed outlier: 3.591A pdb=" N LEU D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 382 removed outlier: 3.531A pdb=" N GLN D 381 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 408 through 423 Processing helix chain 'D' and resid 453 through 465 removed outlier: 4.453A pdb=" N ASN D 458 " --> pdb=" O LYS D 454 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL D 459 " --> pdb=" O ASP D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 489 Processing helix chain 'D' and resid 493 through 495 No H-bonds generated for 'chain 'D' and resid 493 through 495' Processing helix chain 'D' and resid 499 through 501 No H-bonds generated for 'chain 'D' and resid 499 through 501' Processing helix chain 'D' and resid 510 through 516 removed outlier: 3.645A pdb=" N ILE D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 527 Processing helix chain 'E' and resid 12 through 21 Processing helix chain 'E' and resid 26 through 28 No H-bonds generated for 'chain 'E' and resid 26 through 28' Processing helix chain 'E' and resid 43 through 53 Processing helix chain 'E' and resid 64 through 67 No H-bonds generated for 'chain 'E' and resid 64 through 67' Processing helix chain 'E' and resid 70 through 88 removed outlier: 3.786A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 105 through 118 removed outlier: 4.268A pdb=" N GLN E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 145 through 154 removed outlier: 3.667A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASN E 153 " --> pdb=" O TYR E 149 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLU E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 removed outlier: 4.209A pdb=" N TYR E 179 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N THR E 181 " --> pdb=" O GLN E 177 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N HIS E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 210 removed outlier: 5.852A pdb=" N GLY E 207 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU E 208 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 230 through 251 removed outlier: 6.179A pdb=" N SER E 249 " --> pdb=" O GLN E 245 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N TYR E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 272 Proline residue: E 267 - end of helix removed outlier: 3.666A pdb=" N ARG E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 287 Processing helix chain 'E' and resid 290 through 292 No H-bonds generated for 'chain 'E' and resid 290 through 292' Processing helix chain 'E' and resid 326 through 340 Processing helix chain 'E' and resid 343 through 348 removed outlier: 5.038A pdb=" N ALA E 347 " --> pdb=" O ARG E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 373 through 375 No H-bonds generated for 'chain 'E' and resid 373 through 375' Processing helix chain 'E' and resid 383 through 393 Processing helix chain 'E' and resid 418 through 429 Processing helix chain 'E' and resid 456 through 465 Processing helix chain 'F' and resid 282 through 292 removed outlier: 4.079A pdb=" N PHE F 292 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 Processing helix chain 'F' and resid 316 through 331 removed outlier: 3.669A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 340 through 351 removed outlier: 3.644A pdb=" N ILE F 346 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 347 " --> pdb=" O HIS F 344 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N SER F 348 " --> pdb=" O PHE F 345 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET F 350 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 372 removed outlier: 4.184A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 386 Processing helix chain 'F' and resid 394 through 402 removed outlier: 4.423A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 425 Processing helix chain 'I' and resid 55 through 61 Processing helix chain 'I' and resid 82 through 98 removed outlier: 4.004A pdb=" N GLU I 86 " --> pdb=" O THR I 82 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS I 94 " --> pdb=" O ASN I 90 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 124 Processing helix chain 'I' and resid 178 through 188 removed outlier: 4.477A pdb=" N PHE I 182 " --> pdb=" O SER I 179 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP I 187 " --> pdb=" O LYS I 184 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER I 188 " --> pdb=" O ILE I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 209 Processing helix chain 'I' and resid 225 through 228 Processing helix chain 'I' and resid 237 through 250 removed outlier: 3.629A pdb=" N ARG I 240 " --> pdb=" O GLN I 237 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N THR I 241 " --> pdb=" O SER I 238 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU I 243 " --> pdb=" O ARG I 240 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE I 246 " --> pdb=" O LEU I 243 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU I 248 " --> pdb=" O LEU I 245 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA I 249 " --> pdb=" O PHE I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 306 removed outlier: 4.911A pdb=" N SER I 306 " --> pdb=" O GLN I 302 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 324 Processing helix chain 'I' and resid 331 through 348 Processing helix chain 'I' and resid 387 through 396 Processing helix chain 'I' and resid 403 through 408 Processing helix chain 'I' and resid 412 through 427 removed outlier: 3.616A pdb=" N LYS I 426 " --> pdb=" O ILE I 422 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 445 removed outlier: 3.682A pdb=" N THR I 445 " --> pdb=" O ILE I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 468 Processing helix chain 'I' and resid 495 through 503 removed outlier: 3.580A pdb=" N TYR I 499 " --> pdb=" O MET I 495 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP I 500 " --> pdb=" O ARG I 496 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 511 No H-bonds generated for 'chain 'I' and resid 509 through 511' Processing sheet with id= A, first strand: chain 'A' and resid 621 through 624 removed outlier: 8.590A pdb=" N ILE A 622 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR A 476 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N PHE A 624 " --> pdb=" O TYR A 476 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA A 478 " --> pdb=" O PHE A 624 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 561 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE A 596 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL A 563 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL A 598 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 565 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 646 through 649 Processing sheet with id= C, first strand: chain 'A' and resid 879 through 881 Processing sheet with id= D, first strand: chain 'B' and resid 475 through 479 removed outlier: 6.402A pdb=" N SER B 313 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N HIS B 478 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 315 " --> pdb=" O HIS B 478 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 420 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL B 453 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU B 422 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER B 455 " --> pdb=" O LEU B 422 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 424 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 263 through 267 removed outlier: 6.715A pdb=" N THR C 104 " --> pdb=" O HIS C 264 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N LEU C 266 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N PHE C 106 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU C 199 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER C 235 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N MET C 201 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ILE C 237 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N PHE C 203 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASN C 239 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE C 205 " --> pdb=" O ASN C 239 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 534 through 536 Processing sheet with id= G, first strand: chain 'D' and resid 272 through 274 removed outlier: 7.980A pdb=" N ILE D 273 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE D 99 " --> pdb=" O ILE D 273 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL D 212 " --> pdb=" O CYS D 246 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE D 248 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N PHE D 214 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N CYS D 250 " --> pdb=" O PHE D 214 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE D 216 " --> pdb=" O CYS D 250 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 469 through 471 Processing sheet with id= I, first strand: chain 'E' and resid 185 through 189 removed outlier: 9.002A pdb=" N LEU E 33 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE E 166 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU E 35 " --> pdb=" O PHE E 166 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR E 168 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY E 37 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N MET E 170 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR E 126 " --> pdb=" O ASN E 163 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS E 165 " --> pdb=" O THR E 126 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU E 128 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE E 167 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU E 130 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N THR E 169 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU E 132 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N HIS E 58 " --> pdb=" O PHE E 129 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE E 131 " --> pdb=" O HIS E 58 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL E 60 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ASP E 133 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU E 62 " --> pdb=" O ASP E 133 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 433 through 435 Processing sheet with id= K, first strand: chain 'I' and resid 284 through 288 removed outlier: 6.313A pdb=" N PHE I 218 " --> pdb=" O VAL I 257 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE I 259 " --> pdb=" O PHE I 218 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL I 220 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N MET I 261 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU I 222 " --> pdb=" O MET I 261 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N VAL I 219 " --> pdb=" O SER I 164 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ALA I 166 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N VAL I 221 " --> pdb=" O ALA I 166 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR I 168 " --> pdb=" O VAL I 221 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ASP I 223 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE I 170 " --> pdb=" O ASP I 223 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL I 165 " --> pdb=" O SER I 153 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'I' and resid 471 through 477 872 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 7.90 Time building geometry restraints manager: 10.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 3655 1.29 - 1.42: 6519 1.42 - 1.56: 13740 1.56 - 1.69: 204 1.69 - 1.83: 158 Bond restraints: 24276 Sorted by residual: bond pdb=" C ILE C 240 " pdb=" O ILE C 240 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.11e-02 8.12e+03 6.01e+01 bond pdb=" C PRO E 64 " pdb=" O PRO E 64 " ideal model delta sigma weight residual 1.238 1.174 0.064 1.42e-02 4.96e+03 2.04e+01 bond pdb=" C PRO C 133 " pdb=" O PRO C 133 " ideal model delta sigma weight residual 1.237 1.186 0.051 1.16e-02 7.43e+03 1.92e+01 bond pdb=" CA SER E 137 " pdb=" CB SER E 137 " ideal model delta sigma weight residual 1.529 1.466 0.063 1.46e-02 4.69e+03 1.85e+01 bond pdb=" CA SER I 264 " pdb=" CB SER I 264 " ideal model delta sigma weight residual 1.528 1.466 0.063 1.66e-02 3.63e+03 1.43e+01 ... (remaining 24271 not shown) Histogram of bond angle deviations from ideal: 94.99 - 104.01: 513 104.01 - 113.02: 13233 113.02 - 122.03: 14788 122.03 - 131.05: 4506 131.05 - 140.06: 113 Bond angle restraints: 33153 Sorted by residual: angle pdb=" CA GLU C 495 " pdb=" CB GLU C 495 " pdb=" CG GLU C 495 " ideal model delta sigma weight residual 114.10 125.95 -11.85 2.00e+00 2.50e-01 3.51e+01 angle pdb=" N GLN E 139 " pdb=" CA GLN E 139 " pdb=" C GLN E 139 " ideal model delta sigma weight residual 111.28 105.11 6.17 1.09e+00 8.42e-01 3.20e+01 angle pdb=" CA LYS C 526 " pdb=" CB LYS C 526 " pdb=" CG LYS C 526 " ideal model delta sigma weight residual 114.10 124.67 -10.57 2.00e+00 2.50e-01 2.79e+01 angle pdb=" C PRO I 252 " pdb=" N THR I 253 " pdb=" CA THR I 253 " ideal model delta sigma weight residual 122.61 130.33 -7.72 1.56e+00 4.11e-01 2.45e+01 angle pdb=" CB LYS C 48 " pdb=" CG LYS C 48 " pdb=" CD LYS C 48 " ideal model delta sigma weight residual 111.30 122.57 -11.27 2.30e+00 1.89e-01 2.40e+01 ... (remaining 33148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11928 17.84 - 35.69: 1753 35.69 - 53.53: 708 53.53 - 71.38: 183 71.38 - 89.22: 44 Dihedral angle restraints: 14616 sinusoidal: 6675 harmonic: 7941 Sorted by residual: dihedral pdb=" CA VAL E 8 " pdb=" C VAL E 8 " pdb=" N ALA E 9 " pdb=" CA ALA E 9 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA PHE B 475 " pdb=" C PHE B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ILE D 516 " pdb=" C ILE D 516 " pdb=" N ILE D 517 " pdb=" CA ILE D 517 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 14613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3170 0.068 - 0.136: 557 0.136 - 0.205: 43 0.205 - 0.273: 10 0.273 - 0.341: 1 Chirality restraints: 3781 Sorted by residual: chirality pdb=" CA PRO I 314 " pdb=" N PRO I 314 " pdb=" C PRO I 314 " pdb=" CB PRO I 314 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL F 369 " pdb=" CA VAL F 369 " pdb=" CG1 VAL F 369 " pdb=" CG2 VAL F 369 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA TRP C 494 " pdb=" N TRP C 494 " pdb=" C TRP C 494 " pdb=" CB TRP C 494 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3778 not shown) Planarity restraints: 3861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 313 " 0.067 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO I 314 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO I 314 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO I 314 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 450 " 0.014 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP E 450 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP E 450 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP E 450 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 450 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP E 450 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 450 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 450 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 450 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP E 450 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 509 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO I 510 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO I 510 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 510 " 0.044 5.00e-02 4.00e+02 ... (remaining 3858 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 189 2.56 - 3.14: 17264 3.14 - 3.73: 39925 3.73 - 4.31: 56197 4.31 - 4.90: 87671 Nonbonded interactions: 201246 Sorted by model distance: nonbonded pdb=" NH1 ARG I 406 " pdb=" O GLY I 469 " model vdw 1.974 2.520 nonbonded pdb=" OG1 THR D 109 " pdb="MG MG D1002 " model vdw 2.039 2.170 nonbonded pdb="MG MG I1002 " pdb=" O HOH I1104 " model vdw 2.067 2.170 nonbonded pdb=" OG1 THR E 44 " pdb="MG MG E1002 " model vdw 2.076 2.170 nonbonded pdb=" O2G ATP D1001 " pdb="MG MG D1002 " model vdw 2.097 2.170 ... (remaining 201241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 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: 7.080 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 68.610 Find NCS groups from input model: 0.850 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: 0.000 Load rotamer database and sin/cos tables:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.005 0.086 24276 Z= 0.334 Angle : 0.899 12.645 33153 Z= 0.500 Chirality : 0.052 0.341 3781 Planarity : 0.007 0.097 3861 Dihedral : 20.303 89.220 9426 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.52 % Allowed : 21.50 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.44 (0.14), residues: 2616 helix: -0.85 (0.12), residues: 1421 sheet: -0.10 (0.30), residues: 258 loop : -1.12 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP E 450 HIS 0.009 0.001 HIS C 22 PHE 0.024 0.002 PHE E 239 TYR 0.030 0.003 TYR I 389 ARG 0.022 0.001 ARG E 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 443 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8324 (mmtt) REVERT: A 889 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9172 (pp) REVERT: B 291 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8465 (mt0) REVERT: C 46 SER cc_start: 0.9280 (m) cc_final: 0.8952 (p) REVERT: C 395 PHE cc_start: 0.6817 (m-80) cc_final: 0.6379 (m-10) REVERT: C 414 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8128 (tp30) REVERT: C 568 GLU cc_start: 0.8750 (tt0) cc_final: 0.8346 (tm-30) REVERT: E 221 GLU cc_start: 0.7296 (mp0) cc_final: 0.6982 (mp0) REVERT: E 234 ASN cc_start: 0.8684 (m-40) cc_final: 0.8381 (m110) REVERT: E 368 LYS cc_start: 0.8430 (ptpt) cc_final: 0.7992 (tptm) REVERT: E 376 LEU cc_start: 0.8390 (mp) cc_final: 0.8165 (pt) REVERT: E 431 LYS cc_start: 0.8859 (mptt) cc_final: 0.8640 (mptt) REVERT: F 293 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7669 (tm-30) REVERT: F 309 ASN cc_start: 0.7501 (m-40) cc_final: 0.7132 (m-40) REVERT: F 329 PHE cc_start: 0.8494 (m-80) cc_final: 0.7764 (m-80) REVERT: F 332 PHE cc_start: 0.8284 (m-80) cc_final: 0.8022 (m-10) REVERT: F 354 MET cc_start: 0.7692 (mmt) cc_final: 0.7401 (mmp) REVERT: F 370 LYS cc_start: 0.7929 (tptm) cc_final: 0.7633 (tppt) REVERT: F 386 TYR cc_start: 0.7744 (m-10) cc_final: 0.7331 (m-10) REVERT: F 392 ILE cc_start: 0.8602 (pt) cc_final: 0.8283 (pp) REVERT: I 173 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8457 (mt) REVERT: I 240 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8177 (mtm110) REVERT: I 244 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7241 (mt-10) outliers start: 62 outliers final: 32 residues processed: 495 average time/residue: 1.6000 time to fit residues: 889.8404 Evaluate side-chains 297 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 262 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 238 SER Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 331 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 6.9990 chunk 206 optimal weight: 0.0000 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 247 optimal weight: 10.0000 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 530 ASN B 425 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN C 463 GLN D 120 GLN D 350 ASN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN F 407 GLN I 206 GLN I 232 ASN I 284 GLN I 289 GLN I 411 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 24276 Z= 0.359 Angle : 0.602 8.078 33153 Z= 0.323 Chirality : 0.043 0.164 3781 Planarity : 0.005 0.061 3861 Dihedral : 18.558 88.355 4012 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.67 % Allowed : 21.21 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.11 (0.16), residues: 2616 helix: 0.44 (0.13), residues: 1437 sheet: 0.18 (0.30), residues: 257 loop : -0.81 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 450 HIS 0.006 0.001 HIS C 405 PHE 0.024 0.002 PHE I 511 TYR 0.020 0.002 TYR I 85 ARG 0.006 0.001 ARG E 344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 281 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8656 (mmpt) REVERT: A 411 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8555 (mmtt) REVERT: A 678 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7726 (ttp80) REVERT: C 46 SER cc_start: 0.9281 (m) cc_final: 0.8989 (p) REVERT: C 48 LYS cc_start: 0.8405 (tmtt) cc_final: 0.8113 (tttt) REVERT: C 347 ASN cc_start: 0.8073 (m-40) cc_final: 0.7545 (p0) REVERT: C 391 PHE cc_start: 0.8043 (t80) cc_final: 0.7838 (t80) REVERT: C 412 PHE cc_start: 0.8335 (t80) cc_final: 0.7922 (t80) REVERT: C 414 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8199 (tp30) REVERT: D 155 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7807 (tm-30) REVERT: D 270 GLN cc_start: 0.9037 (OUTLIER) cc_final: 0.7993 (mp10) REVERT: E 125 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8382 (mtpp) REVERT: E 221 GLU cc_start: 0.7219 (mp0) cc_final: 0.6982 (mp0) REVERT: E 234 ASN cc_start: 0.8751 (m-40) cc_final: 0.8453 (m110) REVERT: E 353 LYS cc_start: 0.7905 (tttt) cc_final: 0.7587 (tttt) REVERT: E 368 LYS cc_start: 0.8481 (ptpt) cc_final: 0.8018 (tptm) REVERT: E 376 LEU cc_start: 0.8379 (mp) cc_final: 0.7973 (pt) REVERT: F 279 LYS cc_start: 0.7036 (mmtt) cc_final: 0.6824 (mmpt) REVERT: F 285 ILE cc_start: 0.8345 (mm) cc_final: 0.8041 (tp) REVERT: F 290 ASN cc_start: 0.7821 (m-40) cc_final: 0.7486 (m110) REVERT: F 329 PHE cc_start: 0.8691 (m-80) cc_final: 0.8418 (m-80) REVERT: F 367 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7977 (mtmm) REVERT: F 396 GLU cc_start: 0.7799 (tp30) cc_final: 0.7256 (tp30) REVERT: I 173 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8728 (mt) REVERT: I 201 ASN cc_start: 0.7806 (p0) cc_final: 0.7485 (p0) REVERT: I 228 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8745 (mm) REVERT: I 240 ARG cc_start: 0.8535 (mtm-85) cc_final: 0.8281 (mtm110) REVERT: I 387 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8786 (tt) REVERT: I 423 GLN cc_start: 0.8656 (tt0) cc_final: 0.8313 (tt0) REVERT: I 426 LYS cc_start: 0.8678 (mmmt) cc_final: 0.8219 (mtmt) outliers start: 115 outliers final: 41 residues processed: 373 average time/residue: 1.5493 time to fit residues: 653.2250 Evaluate side-chains 295 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 247 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 238 SER Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 388 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 137 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 chunk 168 optimal weight: 0.0870 chunk 68 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 267 optimal weight: 0.7980 chunk 220 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 84 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN B 261 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 76 GLN D 489 ASN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 411 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24276 Z= 0.207 Angle : 0.525 14.451 33153 Z= 0.282 Chirality : 0.040 0.158 3781 Planarity : 0.004 0.050 3861 Dihedral : 18.244 87.220 3983 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.62 % Allowed : 22.51 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.16), residues: 2616 helix: 0.96 (0.14), residues: 1442 sheet: 0.24 (0.31), residues: 256 loop : -0.61 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 494 HIS 0.004 0.001 HIS C 405 PHE 0.026 0.001 PHE F 345 TYR 0.013 0.001 TYR I 85 ARG 0.010 0.000 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 274 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8640 (mmpt) REVERT: A 411 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8593 (mmtt) REVERT: A 420 GLU cc_start: 0.7079 (mp0) cc_final: 0.6557 (mp0) REVERT: A 678 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7770 (ttp80) REVERT: B 260 ARG cc_start: 0.6471 (ptp-110) cc_final: 0.6184 (ptp90) REVERT: C 46 SER cc_start: 0.9268 (m) cc_final: 0.8982 (p) REVERT: C 48 LYS cc_start: 0.8458 (tmtt) cc_final: 0.8167 (tttt) REVERT: C 347 ASN cc_start: 0.8089 (m-40) cc_final: 0.7571 (p0) REVERT: C 412 PHE cc_start: 0.8323 (t80) cc_final: 0.7823 (t80) REVERT: D 155 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7886 (tm-30) REVERT: D 261 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7408 (tm-30) REVERT: D 270 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.7882 (mp10) REVERT: E 11 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.8234 (mmp-170) REVERT: E 125 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8335 (mtpp) REVERT: E 221 GLU cc_start: 0.7298 (mp0) cc_final: 0.7097 (mp0) REVERT: E 234 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8435 (m110) REVERT: E 353 LYS cc_start: 0.7893 (tttt) cc_final: 0.7615 (tttt) REVERT: E 368 LYS cc_start: 0.8524 (ptpt) cc_final: 0.7998 (tptm) REVERT: E 376 LEU cc_start: 0.8347 (mp) cc_final: 0.7985 (pt) REVERT: F 290 ASN cc_start: 0.7876 (m-40) cc_final: 0.7536 (m110) REVERT: F 332 PHE cc_start: 0.8138 (m-10) cc_final: 0.7544 (m-10) REVERT: F 354 MET cc_start: 0.7664 (mmt) cc_final: 0.7298 (mmp) REVERT: F 358 LYS cc_start: 0.8227 (pmmt) cc_final: 0.7647 (tptt) REVERT: F 396 GLU cc_start: 0.7913 (tp30) cc_final: 0.7360 (tp30) REVERT: I 240 ARG cc_start: 0.8546 (mtm-85) cc_final: 0.8268 (mtm110) REVERT: I 423 GLN cc_start: 0.8610 (tt0) cc_final: 0.8226 (tt0) REVERT: I 426 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8248 (mtmt) REVERT: I 454 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: I 484 ARG cc_start: 0.7726 (mtt90) cc_final: 0.7519 (mpt90) outliers start: 89 outliers final: 44 residues processed: 338 average time/residue: 1.5942 time to fit residues: 607.3301 Evaluate side-chains 304 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 253 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 551 GLU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 327 ASN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 500 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 262 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 ASN ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24276 Z= 0.270 Angle : 0.540 13.569 33153 Z= 0.289 Chirality : 0.041 0.160 3781 Planarity : 0.004 0.054 3861 Dihedral : 18.172 84.076 3974 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.31 % Allowed : 21.94 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.16), residues: 2616 helix: 1.21 (0.14), residues: 1443 sheet: 0.26 (0.31), residues: 256 loop : -0.53 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 494 HIS 0.004 0.001 HIS A 629 PHE 0.022 0.001 PHE I 186 TYR 0.015 0.001 TYR C 483 ARG 0.014 0.001 ARG F 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 257 time to evaluate : 2.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8655 (mmpt) REVERT: A 411 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8608 (mmtt) REVERT: A 420 GLU cc_start: 0.7186 (mp0) cc_final: 0.6701 (mp0) REVERT: A 678 ARG cc_start: 0.8062 (mtm180) cc_final: 0.7791 (ttp80) REVERT: A 786 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8731 (tp) REVERT: A 813 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8640 (ttpp) REVERT: B 260 ARG cc_start: 0.6552 (ptp-110) cc_final: 0.6301 (ptp90) REVERT: C 46 SER cc_start: 0.9284 (m) cc_final: 0.9001 (p) REVERT: C 62 HIS cc_start: 0.8494 (OUTLIER) cc_final: 0.8231 (m170) REVERT: C 331 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7828 (tp-100) REVERT: C 412 PHE cc_start: 0.8276 (t80) cc_final: 0.7772 (t80) REVERT: D 155 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7962 (tm-30) REVERT: D 261 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: D 270 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: E 11 ARG cc_start: 0.9345 (OUTLIER) cc_final: 0.8252 (mmp-170) REVERT: E 125 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8373 (mtpp) REVERT: E 221 GLU cc_start: 0.7404 (mp0) cc_final: 0.7197 (mp0) REVERT: E 234 ASN cc_start: 0.8765 (m-40) cc_final: 0.8473 (m110) REVERT: E 368 LYS cc_start: 0.8561 (ptpt) cc_final: 0.7990 (tptm) REVERT: E 376 LEU cc_start: 0.8340 (mp) cc_final: 0.7935 (pt) REVERT: F 285 ILE cc_start: 0.8369 (mp) cc_final: 0.8165 (mm) REVERT: F 287 ARG cc_start: 0.8718 (ttm-80) cc_final: 0.8498 (ttm110) REVERT: F 290 ASN cc_start: 0.7917 (m-40) cc_final: 0.7554 (m110) REVERT: F 332 PHE cc_start: 0.8423 (m-10) cc_final: 0.7894 (m-80) REVERT: F 348 SER cc_start: 0.7955 (m) cc_final: 0.7586 (p) REVERT: F 354 MET cc_start: 0.7677 (mmt) cc_final: 0.7371 (mmp) REVERT: F 368 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6828 (mm) REVERT: F 376 GLU cc_start: 0.7912 (mp0) cc_final: 0.7661 (mp0) REVERT: F 386 TYR cc_start: 0.7481 (m-10) cc_final: 0.7054 (m-10) REVERT: F 396 GLU cc_start: 0.7900 (tp30) cc_final: 0.7417 (tp30) REVERT: I 244 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7409 (mt-10) REVERT: I 387 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8728 (tt) REVERT: I 390 ILE cc_start: 0.9421 (OUTLIER) cc_final: 0.9156 (mm) REVERT: I 423 GLN cc_start: 0.8635 (tt0) cc_final: 0.8239 (tt0) REVERT: I 426 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8306 (mtmt) REVERT: I 435 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7323 (mt-10) REVERT: I 454 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7621 (mp10) outliers start: 106 outliers final: 57 residues processed: 342 average time/residue: 1.4787 time to fit residues: 575.2148 Evaluate side-chains 315 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 245 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 62 HIS Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 500 ASP Chi-restraints excluded: chain I residue 503 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 218 optimal weight: 0.2980 chunk 149 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 195 optimal weight: 0.0050 chunk 108 optimal weight: 10.0000 chunk 224 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 134 optimal weight: 0.4980 chunk 235 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN I 90 ASN ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24276 Z= 0.199 Angle : 0.505 12.342 33153 Z= 0.272 Chirality : 0.039 0.155 3781 Planarity : 0.003 0.054 3861 Dihedral : 17.975 82.160 3974 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.23 % Allowed : 22.15 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.98 (0.17), residues: 2616 helix: 1.43 (0.14), residues: 1444 sheet: 0.33 (0.31), residues: 256 loop : -0.43 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 539 HIS 0.004 0.001 HIS C 69 PHE 0.028 0.001 PHE F 345 TYR 0.020 0.001 TYR A 580 ARG 0.014 0.000 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 262 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8662 (mmpt) REVERT: A 411 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8642 (mmtt) REVERT: A 420 GLU cc_start: 0.7101 (mp0) cc_final: 0.6681 (mp0) REVERT: A 678 ARG cc_start: 0.8058 (mtm180) cc_final: 0.7797 (ttp80) REVERT: B 242 THR cc_start: 0.7751 (p) cc_final: 0.7515 (p) REVERT: B 260 ARG cc_start: 0.6499 (ptp-110) cc_final: 0.6268 (ptp90) REVERT: C 46 SER cc_start: 0.9225 (m) cc_final: 0.8952 (p) REVERT: C 62 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.8199 (m170) REVERT: C 331 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7838 (tp-100) REVERT: C 412 PHE cc_start: 0.8247 (t80) cc_final: 0.7713 (t80) REVERT: D 155 GLN cc_start: 0.8258 (tm-30) cc_final: 0.8017 (tm-30) REVERT: D 261 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: D 270 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: E 11 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8222 (mmp-170) REVERT: E 125 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8367 (mtpp) REVERT: E 234 ASN cc_start: 0.8667 (m-40) cc_final: 0.8392 (m110) REVERT: E 282 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8976 (mm) REVERT: E 368 LYS cc_start: 0.8562 (ptpt) cc_final: 0.8032 (tptm) REVERT: E 376 LEU cc_start: 0.8319 (mp) cc_final: 0.7927 (pt) REVERT: F 285 ILE cc_start: 0.8397 (mp) cc_final: 0.8144 (mm) REVERT: F 290 ASN cc_start: 0.7957 (m-40) cc_final: 0.7601 (m110) REVERT: F 293 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7459 (tm-30) REVERT: F 297 GLU cc_start: 0.8151 (mp0) cc_final: 0.7781 (pm20) REVERT: F 332 PHE cc_start: 0.8440 (m-10) cc_final: 0.8114 (m-80) REVERT: F 354 MET cc_start: 0.7811 (mmt) cc_final: 0.7393 (mmp) REVERT: F 358 LYS cc_start: 0.8262 (pmmt) cc_final: 0.7704 (tptt) REVERT: F 368 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6748 (mm) REVERT: F 376 GLU cc_start: 0.8048 (mp0) cc_final: 0.7716 (mp0) REVERT: F 386 TYR cc_start: 0.7433 (m-10) cc_final: 0.7061 (m-10) REVERT: F 396 GLU cc_start: 0.7824 (tp30) cc_final: 0.7360 (tp30) REVERT: I 57 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7938 (mtm180) REVERT: I 154 TRP cc_start: 0.7374 (m100) cc_final: 0.7127 (m100) REVERT: I 244 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7401 (mt-10) REVERT: I 390 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9151 (mm) REVERT: I 423 GLN cc_start: 0.8650 (tt0) cc_final: 0.8250 (tt0) REVERT: I 426 LYS cc_start: 0.8692 (mmmt) cc_final: 0.8350 (mtmt) REVERT: I 435 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7359 (mt-10) REVERT: I 454 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7556 (mp10) outliers start: 104 outliers final: 54 residues processed: 344 average time/residue: 1.5079 time to fit residues: 587.5120 Evaluate side-chains 316 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 250 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 62 HIS Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 459 LEU Chi-restraints excluded: chain I residue 503 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 218 optimal weight: 9.9990 chunk 121 optimal weight: 20.0000 chunk 21 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN I 90 ASN ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24276 Z= 0.216 Angle : 0.517 11.611 33153 Z= 0.276 Chirality : 0.040 0.169 3781 Planarity : 0.003 0.058 3861 Dihedral : 17.917 82.466 3970 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 4.27 % Allowed : 22.31 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.08 (0.17), residues: 2616 helix: 1.52 (0.14), residues: 1444 sheet: 0.34 (0.31), residues: 256 loop : -0.39 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 539 HIS 0.003 0.001 HIS C 69 PHE 0.013 0.001 PHE C 408 TYR 0.014 0.001 TYR A 580 ARG 0.014 0.000 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 259 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8653 (mmpt) REVERT: A 411 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8645 (mmtt) REVERT: A 420 GLU cc_start: 0.7248 (mp0) cc_final: 0.6816 (mp0) REVERT: A 678 ARG cc_start: 0.8054 (mtm180) cc_final: 0.7727 (ttp80) REVERT: A 813 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8720 (ttpp) REVERT: A 914 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6862 (pp) REVERT: B 242 THR cc_start: 0.7780 (p) cc_final: 0.7514 (p) REVERT: B 260 ARG cc_start: 0.6551 (ptp-110) cc_final: 0.6325 (ptp90) REVERT: C 46 SER cc_start: 0.9270 (m) cc_final: 0.8998 (p) REVERT: C 48 LYS cc_start: 0.8574 (tttt) cc_final: 0.7932 (tttt) REVERT: C 331 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7830 (tp-100) REVERT: C 347 ASN cc_start: 0.8136 (m110) cc_final: 0.7636 (p0) REVERT: C 412 PHE cc_start: 0.8238 (t80) cc_final: 0.7696 (t80) REVERT: D 155 GLN cc_start: 0.8270 (tm-30) cc_final: 0.8045 (tm-30) REVERT: D 261 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: D 270 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.7869 (mp10) REVERT: E 11 ARG cc_start: 0.9322 (OUTLIER) cc_final: 0.8225 (mmp-170) REVERT: E 125 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8367 (mtpp) REVERT: E 234 ASN cc_start: 0.8725 (m-40) cc_final: 0.8454 (m110) REVERT: E 282 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8973 (mm) REVERT: E 291 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7252 (pp) REVERT: E 376 LEU cc_start: 0.8307 (mp) cc_final: 0.7888 (pt) REVERT: F 284 GLU cc_start: 0.7230 (tp30) cc_final: 0.6453 (tp30) REVERT: F 290 ASN cc_start: 0.7967 (m-40) cc_final: 0.7625 (m110) REVERT: F 293 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7346 (tm-30) REVERT: F 297 GLU cc_start: 0.8194 (mp0) cc_final: 0.7913 (pm20) REVERT: F 312 ARG cc_start: 0.8568 (ptt180) cc_final: 0.8109 (ptt90) REVERT: F 332 PHE cc_start: 0.8588 (m-10) cc_final: 0.8313 (m-80) REVERT: F 354 MET cc_start: 0.7773 (mmt) cc_final: 0.7368 (mmp) REVERT: F 358 LYS cc_start: 0.8237 (pmmt) cc_final: 0.7707 (tptt) REVERT: F 368 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6849 (mm) REVERT: F 376 GLU cc_start: 0.8089 (mp0) cc_final: 0.7783 (mp0) REVERT: F 386 TYR cc_start: 0.7492 (m-10) cc_final: 0.7129 (m-10) REVERT: F 396 GLU cc_start: 0.7821 (tp30) cc_final: 0.7402 (tp30) REVERT: I 57 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7935 (mtm180) REVERT: I 154 TRP cc_start: 0.7387 (m100) cc_final: 0.7118 (m100) REVERT: I 244 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7466 (mt-10) REVERT: I 387 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8733 (tt) REVERT: I 423 GLN cc_start: 0.8654 (tt0) cc_final: 0.8267 (tt0) REVERT: I 426 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8373 (ttmt) REVERT: I 435 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7456 (mt-10) REVERT: I 454 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: I 457 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7627 (mt-10) outliers start: 105 outliers final: 55 residues processed: 340 average time/residue: 1.5598 time to fit residues: 602.1783 Evaluate side-chains 312 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 242 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain D residue 500 ASP Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 226 ASP Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 500 ASP Chi-restraints excluded: chain I residue 503 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 221 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN I 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 24276 Z= 0.395 Angle : 0.595 12.368 33153 Z= 0.316 Chirality : 0.044 0.177 3781 Planarity : 0.004 0.063 3861 Dihedral : 18.241 82.645 3970 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.31 % Allowed : 22.55 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.17), residues: 2616 helix: 1.32 (0.14), residues: 1450 sheet: 0.22 (0.31), residues: 257 loop : -0.41 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 494 HIS 0.005 0.001 HIS A 629 PHE 0.025 0.002 PHE F 345 TYR 0.017 0.002 TYR C 483 ARG 0.014 0.001 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 244 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8643 (mmpt) REVERT: A 411 LYS cc_start: 0.8937 (mmtt) cc_final: 0.8624 (mmtt) REVERT: A 678 ARG cc_start: 0.8014 (mtm180) cc_final: 0.7777 (ttp80) REVERT: A 914 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6868 (pp) REVERT: B 260 ARG cc_start: 0.6748 (ptp-110) cc_final: 0.6516 (ptp90) REVERT: C 46 SER cc_start: 0.9277 (m) cc_final: 0.8993 (p) REVERT: C 48 LYS cc_start: 0.8532 (tttt) cc_final: 0.7940 (tttt) REVERT: C 331 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7841 (tp-100) REVERT: C 347 ASN cc_start: 0.8266 (m110) cc_final: 0.7755 (p0) REVERT: C 412 PHE cc_start: 0.8240 (t80) cc_final: 0.7728 (t80) REVERT: D 155 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8053 (tm-30) REVERT: D 270 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: E 11 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8467 (mmp-170) REVERT: E 125 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8408 (mtpp) REVERT: E 230 ASP cc_start: 0.7753 (t0) cc_final: 0.7336 (t0) REVERT: E 234 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8332 (m-40) REVERT: E 282 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9016 (mm) REVERT: E 291 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7485 (pp) REVERT: E 353 LYS cc_start: 0.8139 (tttt) cc_final: 0.7877 (tttt) REVERT: F 290 ASN cc_start: 0.7846 (m-40) cc_final: 0.7501 (m110) REVERT: F 291 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: F 293 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7418 (tm-30) REVERT: F 297 GLU cc_start: 0.8188 (mp0) cc_final: 0.7862 (pm20) REVERT: F 301 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7666 (mppt) REVERT: F 332 PHE cc_start: 0.8442 (m-10) cc_final: 0.7800 (m-80) REVERT: F 348 SER cc_start: 0.7940 (m) cc_final: 0.7603 (p) REVERT: F 354 MET cc_start: 0.7769 (mmt) cc_final: 0.7379 (mmp) REVERT: F 358 LYS cc_start: 0.8221 (pmmt) cc_final: 0.7720 (tptt) REVERT: F 368 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7020 (mm) REVERT: F 371 GLU cc_start: 0.7855 (pt0) cc_final: 0.7491 (pt0) REVERT: F 376 GLU cc_start: 0.8155 (mp0) cc_final: 0.7821 (mp0) REVERT: F 396 GLU cc_start: 0.7977 (tp30) cc_final: 0.7514 (tp30) REVERT: I 57 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.7932 (mtm180) REVERT: I 244 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7432 (mt-10) REVERT: I 387 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8682 (tt) REVERT: I 390 ILE cc_start: 0.9468 (OUTLIER) cc_final: 0.9208 (mm) REVERT: I 423 GLN cc_start: 0.8685 (tt0) cc_final: 0.8339 (tt0) REVERT: I 426 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8392 (mtmt) REVERT: I 435 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7528 (mt-10) REVERT: I 454 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: I 457 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7537 (mt-10) outliers start: 106 outliers final: 52 residues processed: 326 average time/residue: 1.5694 time to fit residues: 583.0802 Evaluate side-chains 307 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 238 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 500 ASP Chi-restraints excluded: chain I residue 503 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 162 optimal weight: 0.4980 chunk 104 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN I 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24276 Z= 0.212 Angle : 0.532 11.580 33153 Z= 0.284 Chirality : 0.040 0.172 3781 Planarity : 0.003 0.059 3861 Dihedral : 17.968 82.012 3970 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.41 % Allowed : 23.81 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.17), residues: 2616 helix: 1.52 (0.14), residues: 1444 sheet: 0.26 (0.31), residues: 257 loop : -0.32 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 539 HIS 0.004 0.001 HIS C 69 PHE 0.017 0.001 PHE E 232 TYR 0.014 0.001 TYR A 580 ARG 0.014 0.001 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 251 time to evaluate : 3.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8666 (mmpt) REVERT: A 411 LYS cc_start: 0.8951 (mmtt) cc_final: 0.8646 (mmtt) REVERT: A 420 GLU cc_start: 0.7091 (mp0) cc_final: 0.6672 (mp0) REVERT: A 678 ARG cc_start: 0.8061 (mtm180) cc_final: 0.7769 (ttp80) REVERT: A 690 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7578 (tm-30) REVERT: A 914 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6857 (pp) REVERT: B 242 THR cc_start: 0.7834 (p) cc_final: 0.7528 (p) REVERT: B 260 ARG cc_start: 0.6611 (ptp-110) cc_final: 0.6308 (ptp90) REVERT: C 46 SER cc_start: 0.9267 (m) cc_final: 0.9007 (p) REVERT: C 62 HIS cc_start: 0.8470 (OUTLIER) cc_final: 0.8186 (m170) REVERT: C 331 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7811 (tp-100) REVERT: C 391 PHE cc_start: 0.8195 (t80) cc_final: 0.7961 (t80) REVERT: C 412 PHE cc_start: 0.8224 (t80) cc_final: 0.7694 (t80) REVERT: D 141 THR cc_start: 0.9457 (OUTLIER) cc_final: 0.9147 (p) REVERT: D 155 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8059 (tm-30) REVERT: D 270 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7854 (mp10) REVERT: E 11 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.8197 (mmp-170) REVERT: E 230 ASP cc_start: 0.7725 (t0) cc_final: 0.7322 (t0) REVERT: E 234 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8348 (m-40) REVERT: E 282 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8999 (mm) REVERT: E 291 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7396 (pp) REVERT: F 290 ASN cc_start: 0.7855 (m-40) cc_final: 0.7444 (m110) REVERT: F 291 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: F 332 PHE cc_start: 0.8418 (m-10) cc_final: 0.7807 (m-80) REVERT: F 348 SER cc_start: 0.7954 (m) cc_final: 0.7595 (p) REVERT: F 354 MET cc_start: 0.7794 (mmt) cc_final: 0.7434 (mmp) REVERT: F 358 LYS cc_start: 0.8150 (pmmt) cc_final: 0.7673 (tptt) REVERT: F 364 GLU cc_start: 0.7241 (pp20) cc_final: 0.6935 (tm-30) REVERT: F 368 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6957 (mm) REVERT: F 371 GLU cc_start: 0.7806 (pt0) cc_final: 0.7440 (pt0) REVERT: F 376 GLU cc_start: 0.8185 (mp0) cc_final: 0.7934 (mp0) REVERT: F 386 TYR cc_start: 0.7478 (m-10) cc_final: 0.7252 (m-10) REVERT: F 392 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8640 (pp) REVERT: F 396 GLU cc_start: 0.7869 (tp30) cc_final: 0.7448 (tp30) REVERT: I 57 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7945 (mtm180) REVERT: I 244 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7443 (mt-10) REVERT: I 390 ILE cc_start: 0.9419 (OUTLIER) cc_final: 0.9154 (mm) REVERT: I 423 GLN cc_start: 0.8678 (tt0) cc_final: 0.8314 (tt0) REVERT: I 426 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8393 (mtmt) REVERT: I 435 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7565 (mt-10) REVERT: I 454 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: I 457 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7597 (mt-10) outliers start: 84 outliers final: 47 residues processed: 319 average time/residue: 1.4867 time to fit residues: 539.2113 Evaluate side-chains 301 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 236 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain C residue 62 HIS Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 459 LEU Chi-restraints excluded: chain I residue 503 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 238 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 244 optimal weight: 0.0170 chunk 147 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 243 optimal weight: 20.0000 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN I 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24276 Z= 0.309 Angle : 0.572 11.353 33153 Z= 0.305 Chirality : 0.042 0.175 3781 Planarity : 0.004 0.055 3861 Dihedral : 18.052 81.871 3969 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.33 % Allowed : 24.06 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.17), residues: 2616 helix: 1.44 (0.14), residues: 1451 sheet: 0.23 (0.31), residues: 256 loop : -0.32 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 539 HIS 0.004 0.001 HIS A 629 PHE 0.026 0.001 PHE F 345 TYR 0.015 0.001 TYR C 483 ARG 0.012 0.001 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 228 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8662 (mmpt) REVERT: A 411 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8642 (mmtt) REVERT: A 420 GLU cc_start: 0.7194 (mp0) cc_final: 0.6810 (mp0) REVERT: A 678 ARG cc_start: 0.8018 (mtm180) cc_final: 0.7733 (ttp80) REVERT: A 690 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: A 914 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6933 (pp) REVERT: B 260 ARG cc_start: 0.6633 (ptp-110) cc_final: 0.6330 (ptp90) REVERT: C 46 SER cc_start: 0.9282 (m) cc_final: 0.9017 (p) REVERT: C 62 HIS cc_start: 0.8498 (OUTLIER) cc_final: 0.8229 (m170) REVERT: C 331 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7822 (tp-100) REVERT: C 412 PHE cc_start: 0.8231 (t80) cc_final: 0.7705 (t80) REVERT: D 141 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9161 (p) REVERT: D 155 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8061 (tm-30) REVERT: D 270 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: E 11 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.8367 (mmp-170) REVERT: E 282 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8991 (mm) REVERT: E 291 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7371 (pp) REVERT: E 353 LYS cc_start: 0.8147 (tttt) cc_final: 0.7918 (tttt) REVERT: F 290 ASN cc_start: 0.7748 (m-40) cc_final: 0.7408 (m110) REVERT: F 291 ASP cc_start: 0.8825 (OUTLIER) cc_final: 0.8321 (m-30) REVERT: F 301 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7648 (mppt) REVERT: F 326 ASN cc_start: 0.8125 (m-40) cc_final: 0.7915 (m110) REVERT: F 329 PHE cc_start: 0.8868 (m-80) cc_final: 0.7867 (m-80) REVERT: F 348 SER cc_start: 0.7967 (m) cc_final: 0.7621 (p) REVERT: F 358 LYS cc_start: 0.8158 (pmmt) cc_final: 0.7692 (tptt) REVERT: F 368 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7012 (mm) REVERT: F 371 GLU cc_start: 0.7888 (pt0) cc_final: 0.7507 (pt0) REVERT: F 376 GLU cc_start: 0.8199 (mp0) cc_final: 0.7863 (mp0) REVERT: F 386 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.7288 (m-10) REVERT: F 392 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8654 (pp) REVERT: F 396 GLU cc_start: 0.7917 (tp30) cc_final: 0.7488 (tp30) REVERT: I 57 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7934 (mtm180) REVERT: I 244 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7487 (mt-10) REVERT: I 387 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8740 (tt) REVERT: I 390 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9201 (mm) REVERT: I 423 GLN cc_start: 0.8689 (tt0) cc_final: 0.8334 (tt0) REVERT: I 426 LYS cc_start: 0.8874 (mmmt) cc_final: 0.8435 (mtmt) REVERT: I 435 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7559 (mt-10) REVERT: I 454 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: I 457 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7620 (mt-10) outliers start: 82 outliers final: 49 residues processed: 293 average time/residue: 1.5371 time to fit residues: 514.8062 Evaluate side-chains 299 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 230 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain C residue 62 HIS Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 291 ASP Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 386 TYR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 503 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 160 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 249 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 774 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24276 Z= 0.187 Angle : 0.534 10.929 33153 Z= 0.284 Chirality : 0.040 0.178 3781 Planarity : 0.003 0.052 3861 Dihedral : 17.847 83.335 3969 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.76 % Allowed : 24.71 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.17), residues: 2616 helix: 1.60 (0.14), residues: 1447 sheet: 0.30 (0.32), residues: 257 loop : -0.25 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 539 HIS 0.004 0.001 HIS C 69 PHE 0.017 0.001 PHE C 408 TYR 0.012 0.001 TYR A 580 ARG 0.014 0.000 ARG F 287 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 241 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8656 (mmpt) REVERT: A 411 LYS cc_start: 0.8965 (mmtt) cc_final: 0.8683 (mmtt) REVERT: A 420 GLU cc_start: 0.7107 (mp0) cc_final: 0.6897 (mp0) REVERT: A 678 ARG cc_start: 0.8051 (mtm180) cc_final: 0.7773 (ttp80) REVERT: A 690 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: A 914 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6856 (pp) REVERT: B 242 THR cc_start: 0.7854 (p) cc_final: 0.7525 (p) REVERT: B 260 ARG cc_start: 0.6558 (ptp-110) cc_final: 0.6260 (ptp90) REVERT: C 46 SER cc_start: 0.9285 (m) cc_final: 0.9024 (p) REVERT: C 62 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.8164 (m170) REVERT: C 331 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7816 (tp-100) REVERT: C 412 PHE cc_start: 0.8226 (t80) cc_final: 0.7692 (t80) REVERT: D 141 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9159 (p) REVERT: D 155 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8069 (tm-30) REVERT: D 270 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: E 11 ARG cc_start: 0.9311 (OUTLIER) cc_final: 0.8188 (mmp-170) REVERT: E 282 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8981 (mm) REVERT: E 291 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7330 (pp) REVERT: F 287 ARG cc_start: 0.8896 (ttm110) cc_final: 0.8620 (ttm-80) REVERT: F 290 ASN cc_start: 0.7840 (m-40) cc_final: 0.7551 (m110) REVERT: F 301 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7664 (mppt) REVERT: F 326 ASN cc_start: 0.8154 (m-40) cc_final: 0.7936 (m110) REVERT: F 329 PHE cc_start: 0.8819 (m-80) cc_final: 0.7914 (m-80) REVERT: F 348 SER cc_start: 0.7949 (m) cc_final: 0.7585 (p) REVERT: F 354 MET cc_start: 0.7778 (mmt) cc_final: 0.7430 (mmp) REVERT: F 358 LYS cc_start: 0.8099 (pmmt) cc_final: 0.7675 (tptt) REVERT: F 364 GLU cc_start: 0.7220 (pp20) cc_final: 0.6896 (tm-30) REVERT: F 368 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6910 (mm) REVERT: F 371 GLU cc_start: 0.7841 (pt0) cc_final: 0.7467 (pt0) REVERT: F 376 GLU cc_start: 0.8202 (mp0) cc_final: 0.7602 (mp0) REVERT: F 386 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.7328 (m-10) REVERT: F 392 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8569 (pp) REVERT: F 396 GLU cc_start: 0.7874 (tp30) cc_final: 0.7461 (tp30) REVERT: I 57 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7937 (mtm180) REVERT: I 244 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7443 (mt-10) REVERT: I 423 GLN cc_start: 0.8674 (tt0) cc_final: 0.8344 (tt0) REVERT: I 426 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8423 (mtmt) REVERT: I 435 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7584 (mt-10) REVERT: I 454 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7457 (mp10) REVERT: I 457 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7574 (mt-10) outliers start: 68 outliers final: 42 residues processed: 295 average time/residue: 1.5987 time to fit residues: 533.0812 Evaluate side-chains 292 residues out of total 2461 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 233 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 690 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 270 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 62 HIS Chi-restraints excluded: chain C residue 193 ARG Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain E residue 11 ARG Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 339 SER Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 293 GLU Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 386 TYR Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 57 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 388 ASN Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 503 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 171 optimal weight: 0.8980 chunk 229 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 198 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 774 HIS ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.108442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.075587 restraints weight = 41935.704| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.24 r_work: 0.2852 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24276 Z= 0.221 Angle : 0.544 10.696 33153 Z= 0.290 Chirality : 0.040 0.199 3781 Planarity : 0.004 0.058 3861 Dihedral : 17.840 84.225 3967 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.76 % Allowed : 24.66 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.23 (0.17), residues: 2616 helix: 1.61 (0.14), residues: 1446 sheet: 0.30 (0.32), residues: 256 loop : -0.23 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 539 HIS 0.004 0.001 HIS E 467 PHE 0.028 0.001 PHE F 345 TYR 0.013 0.001 TYR C 483 ARG 0.013 0.001 ARG F 287 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9846.66 seconds wall clock time: 175 minutes 9.99 seconds (10509.99 seconds total)