Starting phenix.real_space_refine on Sat Jul 4 21:35:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tji_25926/07_2026/7tji_25926.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tji_25926/07_2026/7tji_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 { model { file = "/net/cci-nas-00/data/ceres_data/7tji_25926/07_2026/7tji_25926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tji_25926/07_2026/7tji_25926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tji_25926/07_2026/7tji_25926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tji_25926/07_2026/7tji_25926.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tji_25926/07_2026/7tji_25926.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tji_25926/07_2026/7tji_25926.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 4.69, per 1000 atoms: 0.20 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 944.6 milliseconds 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... Secondary structure from input PDB file: 145 helices and 14 sheets defined 61.6% alpha, 8.0% beta 41 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.359A pdb=" N GLY A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 397 " --> pdb=" O PHE A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 421 through 430 removed outlier: 4.216A pdb=" N LYS A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL A 426 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 469 Processing helix chain 'A' and resid 484 through 502 removed outlier: 3.522A pdb=" N GLN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 522 through 534 removed outlier: 3.652A pdb=" N GLU A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 554 through 558 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 576 through 586 removed outlier: 3.928A pdb=" N THR A 586 " --> pdb=" O PHE A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 610 through 618 Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 702 through 726 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 774 through 784 removed outlier: 3.658A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 796 removed outlier: 4.533A pdb=" N THR A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 815 Processing helix chain 'A' and resid 822 through 836 Processing helix chain 'A' and resid 839 through 852 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 865 through 876 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.636A pdb=" N GLU A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.590A pdb=" N ARG B 250 " --> pdb=" O TYR B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'B' and resid 262 through 266 removed outlier: 3.746A pdb=" N MET B 265 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 266 " --> pdb=" O MET B 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 262 through 266' Processing helix chain 'B' and resid 270 through 284 removed outlier: 3.829A pdb=" N PHE B 274 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 275 " --> pdb=" O ARG B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 298 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 333 through 342 Processing helix chain 'B' and resid 371 through 384 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 434 through 447 removed outlier: 4.027A pdb=" N ILE B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 466 through 474 Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.661A pdb=" N PHE B 492 " --> pdb=" O GLU B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'C' and resid 50 through 93 removed outlier: 4.000A pdb=" N GLN C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 158 Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 190 through 196 Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 212 through 225 removed outlier: 3.785A pdb=" N SER C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 229 removed outlier: 3.502A pdb=" N TYR C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 229' Processing helix chain 'C' and resid 244 through 249 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 276 through 288 Processing helix chain 'C' and resid 295 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 313 through 332 Processing helix chain 'C' and resid 333 through 345 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) removed outlier: 3.940A pdb=" N ASP C 339 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Proline residue: C 340 - end of helix 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) removed outlier: 3.723A pdb=" N PHE C 345 " --> pdb=" O ASN C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 355 Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 389 through 395 removed outlier: 3.755A pdb=" N PHE C 395 " --> pdb=" O PHE C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 416 Processing helix chain 'C' and resid 423 through 434 Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 449 through 454 Processing helix chain 'C' and resid 462 through 465 removed outlier: 3.611A pdb=" N LEU C 465 " --> pdb=" O PHE C 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 462 through 465' Processing helix chain 'C' and resid 473 through 479 Processing helix chain 'C' and resid 482 through 494 Processing helix chain 'C' and resid 510 through 517 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) Processing helix chain 'C' and resid 519 through 531 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 548 Processing helix chain 'C' and resid 549 through 559 removed outlier: 3.675A pdb=" N ILE C 553 " --> pdb=" O PRO C 549 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 554 " --> pdb=" O LYS C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 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 574 through 595 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'D' and resid 75 through 91 Processing helix chain 'D' and resid 107 through 121 removed outlier: 3.705A pdb=" N GLN D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 158 removed outlier: 3.955A pdb=" N ASN D 144 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 189 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 228 through 240 Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.653A pdb=" N TYR D 259 " --> pdb=" O ASN D 255 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 255 through 260' Processing helix chain 'D' and resid 261 through 268 Processing helix chain 'D' and resid 280 through 293 removed outlier: 3.770A pdb=" N MET D 284 " --> pdb=" O ASN D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 315 Processing helix chain 'D' and resid 318 through 331 Processing helix chain 'D' and resid 333 through 347 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 350 through 361 Processing helix chain 'D' and resid 361 through 372 removed outlier: 3.508A pdb=" N ASP D 365 " --> pdb=" O CYS D 361 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 372 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 381 removed outlier: 3.531A pdb=" N GLN D 381 " --> pdb=" O THR D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 401 Processing helix chain 'D' and resid 407 through 424 Processing helix chain 'D' and resid 452 through 466 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 480 through 489 Processing helix chain 'D' and resid 492 through 496 removed outlier: 3.656A pdb=" N MET D 496 " --> pdb=" O GLN D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 509 through 517 removed outlier: 3.645A pdb=" N ILE D 516 " --> pdb=" O GLU D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.092A pdb=" N GLN D 528 " --> pdb=" O SER D 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 22 Processing helix chain 'E' and resid 25 through 29 removed outlier: 3.540A pdb=" N ILE E 28 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 29 " --> pdb=" O PRO E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 25 through 29' Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 63 through 68 removed outlier: 3.912A pdb=" N LEU E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 68 " --> pdb=" O PRO E 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 68' Processing helix chain 'E' and resid 69 through 89 removed outlier: 3.786A pdb=" N GLN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 104 through 117 Processing helix chain 'E' and resid 135 through 138 removed outlier: 3.513A pdb=" N LEU E 138 " --> pdb=" O PHE E 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 144 through 152 removed outlier: 3.927A pdb=" N LYS E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 156 removed outlier: 3.525A pdb=" N LEU E 156 " --> pdb=" O ASN E 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 156' Processing helix chain 'E' and resid 172 through 178 Processing helix chain 'E' and resid 179 through 183 Processing helix chain 'E' and resid 193 through 211 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) removed outlier: 3.886A pdb=" N GLU E 211 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 221 removed outlier: 3.704A pdb=" N ARG E 216 " --> pdb=" O ASP E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 252 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 254 through 271 Proline residue: E 267 - end of helix Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 289 through 293 removed outlier: 3.639A pdb=" N LEU E 293 " --> pdb=" O LYS E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 341 Processing helix chain 'E' and resid 342 through 349 removed outlier: 5.038A pdb=" N ALA E 347 " --> pdb=" O ARG E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 376 Processing helix chain 'E' and resid 382 through 394 Processing helix chain 'E' and resid 417 through 430 Processing helix chain 'E' and resid 455 through 466 Processing helix chain 'F' and resid 281 through 292 removed outlier: 3.846A pdb=" N ILE F 285 " --> pdb=" O THR F 281 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE F 292 " --> pdb=" O LEU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 309 removed outlier: 3.783A pdb=" N ASN F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 332 removed outlier: 3.642A pdb=" N LEU F 319 " --> pdb=" O CYS F 315 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE F 332 " --> pdb=" O THR F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 339 Processing helix chain 'F' and resid 340 through 352 removed outlier: 4.150A pdb=" N HIS F 344 " --> pdb=" O PRO F 340 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 371 removed outlier: 3.941A pdb=" N ILE F 363 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU F 371 " --> pdb=" O LYS F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 376 through 387 Processing helix chain 'F' and resid 393 through 403 removed outlier: 4.423A pdb=" N PHE F 399 " --> pdb=" O ASP F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 426 Processing helix chain 'I' and resid 54 through 62 Processing helix chain 'I' and resid 81 through 99 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 113 through 125 Processing helix chain 'I' and resid 177 through 179 No H-bonds generated for 'chain 'I' and resid 177 through 179' Processing helix chain 'I' and resid 180 through 189 removed outlier: 3.530A pdb=" N SER I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 210 removed outlier: 3.987A pdb=" N LEU I 205 " --> pdb=" O ASN I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 229 Processing helix chain 'I' and resid 234 through 239 removed outlier: 4.300A pdb=" N VAL I 239 " --> pdb=" O GLU I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 249 Processing helix chain 'I' and resid 292 through 305 Processing helix chain 'I' and resid 313 through 325 Processing helix chain 'I' and resid 330 through 349 removed outlier: 3.614A pdb=" N LEU I 334 " --> pdb=" O ASP I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 397 removed outlier: 3.874A pdb=" N ILE I 390 " --> pdb=" O GLY I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 409 Processing helix chain 'I' and resid 411 through 428 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) removed outlier: 3.625A pdb=" N ASN I 428 " --> pdb=" O SER I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 446 removed outlier: 3.682A pdb=" N THR I 445 " --> pdb=" O ILE I 441 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS I 446 " --> pdb=" O LYS I 442 " (cutoff:3.500A) Processing helix chain 'I' and resid 454 through 468 Processing helix chain 'I' and resid 494 through 504 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) removed outlier: 3.957A pdb=" N LYS I 504 " --> pdb=" O ASP I 500 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 512 removed outlier: 3.603A pdb=" N LEU I 512 " --> pdb=" O LYS I 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 412 Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 514 removed outlier: 6.346A pdb=" N LEU A 509 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU A 564 " --> pdb=" O LEU A 509 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 511 " --> pdb=" O LEU A 564 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP A 566 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 513 " --> pdb=" O ASP A 566 " (cutoff:3.500A) 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) Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 659 removed outlier: 8.246A pdb=" N GLN A 771 " --> pdb=" O LYS A 679 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG A 681 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL A 773 " --> pdb=" O ARG A 681 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ARG A 683 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 820 through 821 Processing sheet with id=AA5, 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: 6.055A pdb=" N LEU B 314 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 124 through 131 removed outlier: 6.524A pdb=" N TYR C 125 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL C 202 " --> pdb=" O TYR C 125 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL C 127 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ASN C 204 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE C 129 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASN C 103 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N PHE C 238 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 105 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE C 240 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU C 107 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 293 through 294 removed outlier: 6.651A pdb=" N ASN C 293 " --> pdb=" O LEU C 468 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 534 through 536 Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 133 removed outlier: 6.473A pdb=" N ILE D 128 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE D 215 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE D 130 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ASP D 217 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU D 132 " --> pdb=" O ASP D 217 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 62 removed outlier: 4.406A pdb=" N HIS E 58 " --> pdb=" O CYS E 127 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU E 33 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N MET E 170 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU E 35 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N VAL E 187 " --> pdb=" O ASN E 32 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE E 34 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE E 189 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN E 36 " --> pdb=" O PHE E 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 433 through 435 Processing sheet with id=AB4, first strand: chain 'I' and resid 152 through 155 removed outlier: 3.558A pdb=" N VAL I 165 " --> pdb=" O SER I 153 " (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: 6.903A pdb=" N SER I 103 " --> pdb=" O GLN I 284 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ILE I 286 " --> pdb=" O SER I 103 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR I 105 " --> pdb=" O ILE I 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 471 through 477 1089 hydrogen bonds defined for protein. 3111 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: 3.98 Time building geometry restraints manager: 2.02 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: 0.00 - 2.53: 32342 2.53 - 5.06: 669 5.06 - 7.59: 105 7.59 - 10.12: 28 10.12 - 12.64: 9 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=" O4' DG H 44 " pdb=" C1' DG H 44 " pdb=" N9 DG H 44 " ideal model delta sigma weight residual 108.00 111.67 -3.67 7.00e-01 2.04e+00 2.75e+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 ... (remaining 33148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 11856 17.68 - 35.35: 1730 35.35 - 53.03: 682 53.03 - 70.71: 182 70.71 - 88.38: 42 Dihedral angle restraints: 14492 sinusoidal: 6551 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 14489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3147 0.068 - 0.136: 580 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: 188 2.56 - 3.14: 17119 3.14 - 3.73: 39739 3.73 - 4.31: 55719 4.31 - 4.90: 87613 Nonbonded interactions: 200378 Sorted by model distance: nonbonded pdb=" NH1 ARG I 406 " pdb=" O GLY I 469 " model vdw 1.974 3.120 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 200373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.910 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 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 : 0.006 0.086 24276 Z= 0.339 Angle : 0.921 12.645 33153 Z= 0.562 Chirality : 0.053 0.341 3781 Planarity : 0.007 0.097 3861 Dihedral : 20.000 88.384 9302 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (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 ARG 0.022 0.001 ARG E 272 TYR 0.030 0.003 TYR I 389 PHE 0.024 0.002 PHE E 239 TRP 0.051 0.003 TRP E 450 HIS 0.009 0.001 HIS C 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.34 (24276) covalent geometry : angle 0.92057 / 0.56 (33153) hydrogen bonds : bond 0.15939 / 10.16 ( 1181) hydrogen bonds : angle 6.23554 / 4.35 ( 3295) *********************** 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 to be fit. rotamer outliers: 62 poor density : 443 time to evaluate : 0.670 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: 0.7182 time to fit residues: 399.5954 Evaluate side-chains 295 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 197 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 GLN B 425 HIS B 474 ASN C 463 GLN D 120 GLN D 350 ASN E 422 GLN F 326 ASN F 407 GLN I 206 GLN I 232 ASN I 289 GLN I 411 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.110933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.076513 restraints weight = 41731.498| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.20 r_work: 0.2885 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 24276 Z= 0.170 Angle : 0.623 10.022 33153 Z= 0.338 Chirality : 0.044 0.213 3781 Planarity : 0.005 0.055 3861 Dihedral : 18.253 108.233 3888 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.82 % Allowed : 21.94 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2616 helix: 0.54 (0.13), residues: 1436 sheet: 0.10 (0.31), residues: 247 loop : -0.87 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 287 TYR 0.018 0.001 TYR C 483 PHE 0.022 0.001 PHE I 511 TRP 0.019 0.002 TRP C 494 HIS 0.007 0.001 HIS C 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (24276) covalent geometry : angle 0.62329 / 0.34 (33153) hydrogen bonds : bond 0.04684 / 3.04 ( 1181) hydrogen bonds : angle 4.50385 / 3.15 ( 3295) *********************** 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 378 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 284 time to evaluate : 0.817 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: 0.9195 (OUTLIER) cc_final: 0.8821 (mmtt) REVERT: A 411 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8292 (mmtt) REVERT: B 288 ARG cc_start: 0.8915 (ttt-90) cc_final: 0.8669 (tpp-160) REVERT: C 46 SER cc_start: 0.9359 (m) cc_final: 0.9002 (p) REVERT: C 347 ASN cc_start: 0.7799 (m110) cc_final: 0.7124 (p0) REVERT: C 412 PHE cc_start: 0.8426 (t80) cc_final: 0.8161 (t80) REVERT: C 414 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8513 (tp30) REVERT: D 236 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8958 (m-30) REVERT: D 261 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: D 270 GLN cc_start: 0.9268 (OUTLIER) cc_final: 0.8269 (mp10) REVERT: E 87 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9097 (p) REVERT: E 221 GLU cc_start: 0.7371 (mp0) cc_final: 0.7101 (mp0) REVERT: E 234 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8338 (m110) REVERT: E 360 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6737 (mtp180) REVERT: E 368 LYS cc_start: 0.8396 (ptpt) cc_final: 0.8003 (tptm) REVERT: E 376 LEU cc_start: 0.8282 (mp) cc_final: 0.7864 (pt) REVERT: F 285 ILE cc_start: 0.8226 (mm) cc_final: 0.7963 (tp) REVERT: F 290 ASN cc_start: 0.7738 (m-40) cc_final: 0.7479 (m-40) REVERT: F 293 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7830 (tm-30) REVERT: F 344 HIS cc_start: 0.8074 (m-70) cc_final: 0.7820 (m-70) REVERT: F 354 MET cc_start: 0.7705 (mmt) cc_final: 0.7338 (mmp) REVERT: F 376 GLU cc_start: 0.7826 (mp0) cc_final: 0.7574 (mp0) REVERT: F 393 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6594 (ttp80) REVERT: I 173 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8617 (mt) REVERT: I 201 ASN cc_start: 0.7746 (p0) cc_final: 0.7410 (p0) REVERT: I 228 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8607 (mm) REVERT: I 240 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8124 (mtt90) REVERT: I 244 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7663 (mt-10) REVERT: I 327 ASN cc_start: 0.8214 (p0) cc_final: 0.7629 (t0) REVERT: I 423 GLN cc_start: 0.8484 (tt0) cc_final: 0.8176 (tt0) outliers start: 94 outliers final: 31 residues processed: 358 average time/residue: 0.7077 time to fit residues: 286.6401 Evaluate side-chains 296 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 255 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 432 SER 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 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 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 495 VAL 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 608 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 362 VAL 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 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 238 SER Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 331 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 128 optimal weight: 2.9990 chunk 212 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 184 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 264 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 502 GLN A 530 ASN A 556 ASN D 58 GLN D 76 GLN I 411 ASN I 454 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.110648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076706 restraints weight = 41829.707| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.35 r_work: 0.2868 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24276 Z= 0.142 Angle : 0.572 17.449 33153 Z= 0.306 Chirality : 0.042 0.188 3781 Planarity : 0.004 0.065 3861 Dihedral : 18.089 84.083 3863 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.94 % Allowed : 21.37 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2616 helix: 1.12 (0.14), residues: 1438 sheet: 0.06 (0.31), residues: 246 loop : -0.68 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 216 TYR 0.016 0.001 TYR C 483 PHE 0.019 0.001 PHE F 345 TRP 0.017 0.001 TRP C 494 HIS 0.004 0.001 HIS A 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (24276) covalent geometry : angle 0.57198 / 0.31 (33153) hydrogen bonds : bond 0.04038 / 2.63 ( 1181) hydrogen bonds : angle 4.16950 / 2.92 ( 3295) *********************** 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 370 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 273 time to evaluate : 0.862 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: 0.8789 (mmtt) cc_final: 0.8327 (mmtt) REVERT: A 420 GLU cc_start: 0.7451 (mp0) cc_final: 0.6886 (mp0) REVERT: B 260 ARG cc_start: 0.6549 (ptp-110) cc_final: 0.6186 (ptp90) REVERT: B 288 ARG cc_start: 0.8963 (ttt-90) cc_final: 0.8687 (tpp-160) REVERT: C 46 SER cc_start: 0.9361 (m) cc_final: 0.9036 (p) REVERT: C 331 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8234 (tp-100) REVERT: C 412 PHE cc_start: 0.8454 (t80) cc_final: 0.8057 (t80) REVERT: C 512 ASP cc_start: 0.7961 (p0) cc_final: 0.7679 (p0) REVERT: C 555 ASN cc_start: 0.8981 (t0) cc_final: 0.8611 (t0) REVERT: D 155 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 189 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.7995 (t0) REVERT: D 261 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8188 (tm-30) REVERT: D 270 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: E 87 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9063 (p) REVERT: E 125 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8349 (mtpp) REVERT: E 221 GLU cc_start: 0.7436 (mp0) cc_final: 0.7184 (mp0) REVERT: E 234 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8328 (m110) REVERT: E 360 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6831 (mtp180) REVERT: E 367 LYS cc_start: 0.8602 (tmmm) cc_final: 0.8365 (tmmm) REVERT: E 368 LYS cc_start: 0.8407 (ptpt) cc_final: 0.7940 (tptm) REVERT: E 437 MET cc_start: 0.7707 (tpp) cc_final: 0.7496 (tpp) REVERT: F 279 LYS cc_start: 0.7269 (mmpt) cc_final: 0.7059 (mmpt) REVERT: F 290 ASN cc_start: 0.7691 (m-40) cc_final: 0.7344 (m110) REVERT: F 293 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7809 (tm-30) REVERT: F 332 PHE cc_start: 0.8199 (m-10) cc_final: 0.7622 (m-10) REVERT: F 341 ARG cc_start: 0.7904 (tmt170) cc_final: 0.7597 (mmm160) REVERT: F 344 HIS cc_start: 0.7976 (m-70) cc_final: 0.7563 (m-70) REVERT: F 354 MET cc_start: 0.7681 (mmt) cc_final: 0.7294 (mmp) REVERT: F 368 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6504 (mm) REVERT: F 376 GLU cc_start: 0.8047 (mp0) cc_final: 0.7575 (mp0) REVERT: F 386 TYR cc_start: 0.7721 (m-10) cc_final: 0.7297 (m-10) REVERT: F 408 THR cc_start: 0.8574 (OUTLIER) cc_final: 0.8347 (t) REVERT: I 173 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8639 (mt) REVERT: I 225 MET cc_start: 0.9027 (mtp) cc_final: 0.8810 (mtp) REVERT: I 228 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8673 (mm) REVERT: I 240 ARG cc_start: 0.8509 (mtm-85) cc_final: 0.8018 (mtt90) REVERT: I 244 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7719 (mt-10) REVERT: I 327 ASN cc_start: 0.8241 (p0) cc_final: 0.7728 (t0) REVERT: I 387 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8908 (tt) REVERT: I 404 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7856 (mmt90) REVERT: I 423 GLN cc_start: 0.8512 (tt0) cc_final: 0.8200 (tt0) outliers start: 97 outliers final: 28 residues processed: 349 average time/residue: 0.7915 time to fit residues: 310.6299 Evaluate side-chains 292 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 251 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 495 VAL 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 435 LYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 189 ASP 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 69 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 436 THR 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 393 ARG Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 238 SER Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 177 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 113 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 196 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 261 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 284 GLN I 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.109501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.075200 restraints weight = 41680.947| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.18 r_work: 0.2865 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9085 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 24276 Z= 0.163 Angle : 0.562 13.586 33153 Z= 0.301 Chirality : 0.042 0.191 3781 Planarity : 0.004 0.060 3861 Dihedral : 18.037 86.115 3853 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.17 % Allowed : 22.35 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.16), residues: 2616 helix: 1.35 (0.14), residues: 1444 sheet: 0.02 (0.30), residues: 256 loop : -0.56 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 216 TYR 0.016 0.001 TYR C 483 PHE 0.023 0.001 PHE I 186 TRP 0.016 0.001 TRP C 494 HIS 0.005 0.001 HIS E 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (24276) covalent geometry : angle 0.56211 / 0.30 (33153) hydrogen bonds : bond 0.03930 / 2.55 ( 1181) hydrogen bonds : angle 4.05910 / 2.84 ( 3295) *********************** 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 342 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 264 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8483 (mmtt) REVERT: A 786 LEU cc_start: 0.9013 (tp) cc_final: 0.8807 (tp) REVERT: B 242 THR cc_start: 0.7848 (p) cc_final: 0.7606 (p) REVERT: B 260 ARG cc_start: 0.6713 (ptp-110) cc_final: 0.6405 (ptp90) REVERT: B 288 ARG cc_start: 0.8918 (ttt-90) cc_final: 0.8716 (tpp-160) REVERT: C 46 SER cc_start: 0.9371 (m) cc_final: 0.9055 (p) REVERT: C 80 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: C 412 PHE cc_start: 0.8441 (t80) cc_final: 0.8048 (t80) REVERT: C 512 ASP cc_start: 0.7926 (p0) cc_final: 0.7641 (p0) REVERT: C 555 ASN cc_start: 0.8971 (t0) cc_final: 0.8584 (t0) REVERT: C 600 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7801 (mm-40) REVERT: D 155 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8121 (tm-30) REVERT: D 270 GLN cc_start: 0.9231 (OUTLIER) cc_final: 0.8215 (mp10) REVERT: E 125 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8375 (mtpp) REVERT: E 221 GLU cc_start: 0.7493 (mp0) cc_final: 0.7183 (mp0) REVERT: E 234 ASN cc_start: 0.8726 (m-40) cc_final: 0.8440 (m110) REVERT: E 360 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6927 (mtp180) REVERT: E 367 LYS cc_start: 0.8625 (tmmm) cc_final: 0.8390 (tmmm) REVERT: E 368 LYS cc_start: 0.8392 (ptpt) cc_final: 0.7923 (tptm) REVERT: E 376 LEU cc_start: 0.8223 (mp) cc_final: 0.7799 (pt) REVERT: F 285 ILE cc_start: 0.8291 (mp) cc_final: 0.8088 (mm) REVERT: F 290 ASN cc_start: 0.7722 (m-40) cc_final: 0.7368 (m110) REVERT: F 297 GLU cc_start: 0.8217 (mp0) cc_final: 0.7956 (pm20) REVERT: F 332 PHE cc_start: 0.8458 (m-10) cc_final: 0.7985 (m-10) REVERT: F 354 MET cc_start: 0.7707 (mmt) cc_final: 0.7330 (mmp) REVERT: F 358 LYS cc_start: 0.8165 (pmmt) cc_final: 0.7538 (tptt) REVERT: F 368 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.6496 (mm) REVERT: F 386 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7280 (m-10) REVERT: F 396 GLU cc_start: 0.8333 (tp30) cc_final: 0.7702 (tp30) REVERT: I 67 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7459 (mm-30) REVERT: I 173 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8709 (mt) REVERT: I 225 MET cc_start: 0.8988 (mtp) cc_final: 0.8785 (mtp) REVERT: I 228 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8767 (mm) REVERT: I 240 ARG cc_start: 0.8478 (mtm-85) cc_final: 0.8102 (mtt90) REVERT: I 244 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7852 (mt-10) REVERT: I 309 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8827 (p) REVERT: I 327 ASN cc_start: 0.8252 (p0) cc_final: 0.7735 (t0) REVERT: I 346 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8482 (mt-10) REVERT: I 423 GLN cc_start: 0.8512 (tt0) cc_final: 0.8189 (tt0) outliers start: 78 outliers final: 37 residues processed: 326 average time/residue: 0.7454 time to fit residues: 275.3138 Evaluate side-chains 286 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 253 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 377 LYS 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 495 VAL Chi-restraints excluded: chain C residue 80 GLU 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 402 ILE 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 C residue 608 VAL 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 416 GLU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 360 ARG 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 341 ARG 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 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 387 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 77 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 162 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 411 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075273 restraints weight = 41699.596| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.25 r_work: 0.2846 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24276 Z= 0.184 Angle : 0.576 14.450 33153 Z= 0.306 Chirality : 0.043 0.190 3781 Planarity : 0.004 0.084 3861 Dihedral : 18.054 88.482 3852 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.41 % Allowed : 22.27 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2616 helix: 1.47 (0.14), residues: 1449 sheet: 0.03 (0.31), residues: 256 loop : -0.50 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 193 TYR 0.017 0.001 TYR C 483 PHE 0.022 0.001 PHE F 332 TRP 0.014 0.001 TRP C 494 HIS 0.005 0.001 HIS E 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (24276) covalent geometry : angle 0.57567 / 0.31 (33153) hydrogen bonds : bond 0.03975 / 2.58 ( 1181) hydrogen bonds : angle 4.01643 / 2.81 ( 3295) *********************** 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 336 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 252 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8483 (mmtt) REVERT: A 420 GLU cc_start: 0.7606 (mp0) cc_final: 0.7077 (mp0) REVERT: B 242 THR cc_start: 0.7929 (p) cc_final: 0.7630 (p) REVERT: B 260 ARG cc_start: 0.6903 (ptp-110) cc_final: 0.6599 (ptp90) REVERT: B 288 ARG cc_start: 0.8960 (ttt-90) cc_final: 0.8719 (tpp-160) REVERT: C 46 SER cc_start: 0.9372 (m) cc_final: 0.9064 (p) REVERT: C 62 HIS cc_start: 0.8819 (OUTLIER) cc_final: 0.8589 (m170) REVERT: C 331 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8217 (tp-100) REVERT: C 412 PHE cc_start: 0.8415 (t80) cc_final: 0.7975 (t80) REVERT: C 512 ASP cc_start: 0.7955 (p0) cc_final: 0.7674 (p0) REVERT: C 555 ASN cc_start: 0.8956 (t0) cc_final: 0.8546 (t0) REVERT: D 155 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8147 (tm-30) REVERT: D 261 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: D 270 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: E 221 GLU cc_start: 0.7557 (mp0) cc_final: 0.7325 (mp0) REVERT: E 234 ASN cc_start: 0.8696 (m-40) cc_final: 0.8411 (m110) REVERT: E 282 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8910 (mm) REVERT: E 360 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6958 (mtp180) REVERT: E 367 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8421 (tmmm) REVERT: E 368 LYS cc_start: 0.8476 (ptpt) cc_final: 0.7964 (tptm) REVERT: E 376 LEU cc_start: 0.8194 (mp) cc_final: 0.7741 (pt) REVERT: F 285 ILE cc_start: 0.8327 (mp) cc_final: 0.8118 (mm) REVERT: F 290 ASN cc_start: 0.7767 (m-40) cc_final: 0.7409 (m110) REVERT: F 332 PHE cc_start: 0.8447 (m-10) cc_final: 0.7996 (m-80) REVERT: F 335 ARG cc_start: 0.7464 (ttp-170) cc_final: 0.7169 (ttp-170) REVERT: F 354 MET cc_start: 0.7790 (mmt) cc_final: 0.7392 (mmp) REVERT: F 358 LYS cc_start: 0.8171 (pmmt) cc_final: 0.7584 (tptt) REVERT: F 367 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8086 (mmmm) REVERT: F 368 LEU cc_start: 0.6997 (OUTLIER) cc_final: 0.6449 (mm) REVERT: F 376 GLU cc_start: 0.8220 (mp0) cc_final: 0.7648 (mp0) REVERT: F 386 TYR cc_start: 0.7696 (OUTLIER) cc_final: 0.7270 (m-10) REVERT: F 396 GLU cc_start: 0.8394 (tp30) cc_final: 0.7784 (tp30) REVERT: I 173 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8744 (mt) REVERT: I 240 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8077 (mtt90) REVERT: I 244 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7827 (mt-10) REVERT: I 327 ASN cc_start: 0.8308 (p0) cc_final: 0.7837 (t0) REVERT: I 346 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8551 (mt-10) REVERT: I 423 GLN cc_start: 0.8540 (tt0) cc_final: 0.8196 (tt0) REVERT: I 457 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8674 (mp0) REVERT: I 500 ASP cc_start: 0.8533 (m-30) cc_final: 0.8241 (m-30) outliers start: 84 outliers final: 38 residues processed: 318 average time/residue: 0.7488 time to fit residues: 269.6019 Evaluate side-chains 289 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 240 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 785 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 253 VAL 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 495 VAL Chi-restraints excluded: chain C residue 62 HIS 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 402 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 585 MET 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 E residue 69 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 436 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 341 ARG 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 386 TYR Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 53 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 91 optimal weight: 0.0770 chunk 229 optimal weight: 20.0000 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 HIS ** C 600 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.107910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.073353 restraints weight = 42101.327| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.21 r_work: 0.2831 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 24276 Z= 0.200 Angle : 0.580 13.655 33153 Z= 0.309 Chirality : 0.043 0.191 3781 Planarity : 0.004 0.069 3861 Dihedral : 18.056 89.897 3851 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.58 % Allowed : 22.47 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2616 helix: 1.54 (0.14), residues: 1450 sheet: 0.09 (0.31), residues: 256 loop : -0.45 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 216 TYR 0.017 0.001 TYR C 483 PHE 0.017 0.001 PHE I 186 TRP 0.013 0.001 TRP A 539 HIS 0.006 0.001 HIS E 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (24276) covalent geometry : angle 0.58026 / 0.31 (33153) hydrogen bonds : bond 0.04024 / 2.61 ( 1181) hydrogen bonds : angle 3.99980 / 2.80 ( 3295) *********************** 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 331 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 243 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8527 (mmtt) REVERT: A 420 GLU cc_start: 0.7645 (mp0) cc_final: 0.7197 (mp0) REVERT: A 681 ARG cc_start: 0.8251 (ttm110) cc_final: 0.8040 (ttm-80) REVERT: A 813 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.8915 (ttpp) REVERT: B 260 ARG cc_start: 0.6962 (ptp-110) cc_final: 0.6668 (ptp90) REVERT: B 288 ARG cc_start: 0.8956 (ttt-90) cc_final: 0.8717 (tpp-160) REVERT: C 46 SER cc_start: 0.9341 (m) cc_final: 0.9044 (p) REVERT: C 331 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8234 (tp-100) REVERT: C 412 PHE cc_start: 0.8405 (t80) cc_final: 0.7961 (t80) REVERT: C 512 ASP cc_start: 0.7948 (p0) cc_final: 0.7686 (p0) REVERT: C 555 ASN cc_start: 0.8934 (t0) cc_final: 0.8536 (t0) REVERT: D 155 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8171 (tm-30) REVERT: D 261 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: D 270 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: E 125 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8445 (mtpp) REVERT: E 221 GLU cc_start: 0.7514 (mp0) cc_final: 0.7231 (mp0) REVERT: E 234 ASN cc_start: 0.8760 (m-40) cc_final: 0.8481 (m110) REVERT: E 291 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7238 (pp) REVERT: E 353 LYS cc_start: 0.7820 (tttt) cc_final: 0.7389 (tttt) REVERT: E 360 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.7019 (mtp180) REVERT: E 367 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8381 (tmmm) REVERT: E 368 LYS cc_start: 0.8527 (ptpt) cc_final: 0.7910 (tptm) REVERT: E 376 LEU cc_start: 0.8231 (mp) cc_final: 0.7754 (pt) REVERT: F 285 ILE cc_start: 0.8358 (mp) cc_final: 0.8113 (mm) REVERT: F 290 ASN cc_start: 0.7781 (m-40) cc_final: 0.7427 (m110) REVERT: F 297 GLU cc_start: 0.8223 (mp0) cc_final: 0.7952 (pm20) REVERT: F 332 PHE cc_start: 0.8518 (m-10) cc_final: 0.8017 (m-80) REVERT: F 335 ARG cc_start: 0.7525 (ttp-170) cc_final: 0.7180 (ttp-170) REVERT: F 354 MET cc_start: 0.7796 (mmt) cc_final: 0.7396 (mmp) REVERT: F 358 LYS cc_start: 0.8179 (pmmt) cc_final: 0.7612 (tptt) REVERT: F 367 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8137 (mmmm) REVERT: F 368 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6548 (mm) REVERT: F 376 GLU cc_start: 0.8282 (mp0) cc_final: 0.7738 (mp0) REVERT: F 386 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.7276 (m-10) REVERT: F 396 GLU cc_start: 0.8356 (tp30) cc_final: 0.7805 (tp30) REVERT: I 173 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8789 (mt) REVERT: I 240 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8137 (mtt90) REVERT: I 244 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7862 (mt-10) REVERT: I 309 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8864 (p) REVERT: I 327 ASN cc_start: 0.8318 (p0) cc_final: 0.7829 (t0) REVERT: I 346 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8535 (mt-10) REVERT: I 423 GLN cc_start: 0.8577 (tt0) cc_final: 0.8219 (tt0) REVERT: I 435 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8059 (mt-10) outliers start: 88 outliers final: 41 residues processed: 314 average time/residue: 0.7457 time to fit residues: 265.4162 Evaluate side-chains 292 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 237 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 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 813 LYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 291 GLN 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 495 VAL 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 533 MET 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 416 GLU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 436 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 386 TYR Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain I residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 237 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 230 optimal weight: 40.0000 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 7 optimal weight: 0.6980 chunk 224 optimal weight: 0.9980 chunk 122 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 ASN ** I 201 ASN ** 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 = 0.3589 r_free = 0.3589 target = 0.108414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.074035 restraints weight = 41578.429| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.18 r_work: 0.2859 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9127 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 24276 Z= 0.165 Angle : 0.569 15.902 33153 Z= 0.302 Chirality : 0.042 0.178 3781 Planarity : 0.004 0.075 3861 Dihedral : 18.027 89.282 3851 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.13 % Allowed : 23.28 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2616 helix: 1.60 (0.14), residues: 1460 sheet: 0.14 (0.32), residues: 247 loop : -0.42 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 216 TYR 0.015 0.001 TYR C 483 PHE 0.025 0.001 PHE F 345 TRP 0.013 0.001 TRP A 539 HIS 0.006 0.001 HIS E 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (24276) covalent geometry : angle 0.56912 / 0.30 (33153) hydrogen bonds : bond 0.03820 / 2.49 ( 1181) hydrogen bonds : angle 3.94582 / 2.76 ( 3295) *********************** 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 327 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 250 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8557 (mmtt) REVERT: A 420 GLU cc_start: 0.7714 (mp0) cc_final: 0.7160 (mp0) REVERT: A 813 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8853 (ttpp) REVERT: B 260 ARG cc_start: 0.7004 (ptp-110) cc_final: 0.6735 (ptp90) REVERT: B 288 ARG cc_start: 0.8937 (ttt-90) cc_final: 0.8716 (tpp-160) REVERT: C 46 SER cc_start: 0.9335 (m) cc_final: 0.9043 (p) REVERT: C 62 HIS cc_start: 0.8798 (OUTLIER) cc_final: 0.8540 (m170) REVERT: C 331 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8251 (tp-100) REVERT: C 412 PHE cc_start: 0.8365 (t80) cc_final: 0.7888 (t80) REVERT: C 512 ASP cc_start: 0.7922 (p0) cc_final: 0.7633 (p0) REVERT: C 555 ASN cc_start: 0.8890 (t0) cc_final: 0.8515 (t0) REVERT: C 592 GLU cc_start: 0.8971 (tt0) cc_final: 0.8709 (tt0) REVERT: D 141 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9202 (p) REVERT: D 155 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8245 (tm-30) REVERT: D 261 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: D 270 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: E 125 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8451 (mtpp) REVERT: E 221 GLU cc_start: 0.7571 (mp0) cc_final: 0.7356 (mp0) REVERT: E 234 ASN cc_start: 0.8782 (m-40) cc_final: 0.8515 (m110) REVERT: E 282 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8966 (mm) REVERT: E 291 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7337 (pp) REVERT: E 353 LYS cc_start: 0.7885 (tttt) cc_final: 0.7494 (tttt) REVERT: E 360 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6895 (mtp180) REVERT: E 367 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8394 (tmmm) REVERT: E 368 LYS cc_start: 0.8532 (ptpt) cc_final: 0.7913 (tptm) REVERT: E 376 LEU cc_start: 0.8280 (mp) cc_final: 0.7822 (pt) REVERT: F 283 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8354 (mm-30) REVERT: F 290 ASN cc_start: 0.7824 (m-40) cc_final: 0.7460 (m110) REVERT: F 297 GLU cc_start: 0.8183 (mp0) cc_final: 0.7823 (pm20) REVERT: F 329 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8065 (m-80) REVERT: F 332 PHE cc_start: 0.8556 (m-10) cc_final: 0.8009 (m-80) REVERT: F 335 ARG cc_start: 0.7540 (ttp-170) cc_final: 0.7219 (ttp-170) REVERT: F 354 MET cc_start: 0.7839 (mmt) cc_final: 0.7460 (mmp) REVERT: F 358 LYS cc_start: 0.8171 (pmmt) cc_final: 0.7621 (tptt) REVERT: F 376 GLU cc_start: 0.8319 (mp0) cc_final: 0.7796 (mp0) REVERT: F 386 TYR cc_start: 0.7687 (OUTLIER) cc_final: 0.7251 (m-10) REVERT: F 396 GLU cc_start: 0.8382 (tp30) cc_final: 0.7749 (tp30) REVERT: F 400 ARG cc_start: 0.9030 (mtm180) cc_final: 0.8719 (mtp85) REVERT: I 173 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8836 (mt) REVERT: I 240 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8105 (mtt90) REVERT: I 244 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7849 (mt-10) REVERT: I 309 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8855 (p) REVERT: I 327 ASN cc_start: 0.8222 (p0) cc_final: 0.7733 (t0) REVERT: I 346 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8484 (mt-10) REVERT: I 423 GLN cc_start: 0.8634 (tt0) cc_final: 0.8253 (tt0) REVERT: I 435 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8082 (mt-10) REVERT: I 457 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8647 (mp0) outliers start: 77 outliers final: 44 residues processed: 310 average time/residue: 0.7725 time to fit residues: 270.0671 Evaluate side-chains 292 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 233 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 813 LYS 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 264 SER Chi-restraints excluded: chain B residue 291 GLN 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 495 VAL Chi-restraints excluded: chain C residue 62 HIS 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 475 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 608 VAL 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 69 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 LYS 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 326 ILE Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 436 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 329 PHE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 386 TYR Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 459 LEU Chi-restraints excluded: chain I residue 500 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 110 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 230 optimal weight: 40.0000 chunk 104 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 153 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 258 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN ** I 201 ASN ** 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 = 0.3567 r_free = 0.3567 target = 0.106872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.073643 restraints weight = 41748.752| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.25 r_work: 0.2822 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9142 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 24276 Z= 0.247 Angle : 0.615 16.099 33153 Z= 0.326 Chirality : 0.045 0.196 3781 Planarity : 0.004 0.075 3861 Dihedral : 18.071 88.094 3851 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.05 % Allowed : 23.65 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2616 helix: 1.55 (0.14), residues: 1460 sheet: 0.15 (0.32), residues: 247 loop : -0.41 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 216 TYR 0.017 0.002 TYR C 483 PHE 0.018 0.002 PHE D 363 TRP 0.012 0.002 TRP A 539 HIS 0.008 0.001 HIS E 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.25 (24276) covalent geometry : angle 0.61549 / 0.33 (33153) hydrogen bonds : bond 0.04281 / 2.77 ( 1181) hydrogen bonds : angle 4.02974 / 2.81 ( 3295) *********************** 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 311 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 236 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8524 (mmtt) REVERT: A 574 LYS cc_start: 0.9223 (mmmt) cc_final: 0.8988 (mmmm) REVERT: A 813 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8854 (ttpp) REVERT: B 260 ARG cc_start: 0.7070 (ptp-110) cc_final: 0.6799 (ptp90) REVERT: B 291 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8664 (mt0) REVERT: C 46 SER cc_start: 0.9356 (m) cc_final: 0.9064 (p) REVERT: C 331 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8216 (tp-100) REVERT: C 412 PHE cc_start: 0.8386 (t80) cc_final: 0.7931 (t80) REVERT: C 592 GLU cc_start: 0.9020 (tt0) cc_final: 0.8756 (tt0) REVERT: D 155 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8249 (tm-30) REVERT: D 261 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: D 270 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: E 125 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8463 (mtpp) REVERT: E 234 ASN cc_start: 0.8783 (m-40) cc_final: 0.8506 (m110) REVERT: E 282 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9020 (mm) REVERT: E 291 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7359 (pp) REVERT: E 353 LYS cc_start: 0.7907 (tttt) cc_final: 0.7521 (tttt) REVERT: E 360 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7060 (mtp180) REVERT: E 367 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8371 (tmmm) REVERT: E 368 LYS cc_start: 0.8584 (ptpt) cc_final: 0.7905 (tptm) REVERT: F 290 ASN cc_start: 0.7701 (m-40) cc_final: 0.7368 (m110) REVERT: F 297 GLU cc_start: 0.8270 (mp0) cc_final: 0.7998 (pm20) REVERT: F 332 PHE cc_start: 0.8589 (m-10) cc_final: 0.8208 (m-80) REVERT: F 335 ARG cc_start: 0.7564 (ttp-170) cc_final: 0.7212 (ttp-170) REVERT: F 354 MET cc_start: 0.7784 (mmt) cc_final: 0.7406 (mmp) REVERT: F 358 LYS cc_start: 0.8117 (pmmt) cc_final: 0.7584 (tptt) REVERT: F 368 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6653 (mm) REVERT: F 376 GLU cc_start: 0.8353 (mp0) cc_final: 0.7895 (mp0) REVERT: F 385 ARG cc_start: 0.8559 (ttp-110) cc_final: 0.8313 (ttp-110) REVERT: F 396 GLU cc_start: 0.8432 (tp30) cc_final: 0.7902 (tp30) REVERT: I 173 ILE cc_start: 0.9341 (OUTLIER) cc_final: 0.8835 (mt) REVERT: I 240 ARG cc_start: 0.8469 (mtm-85) cc_final: 0.8125 (mtt90) REVERT: I 244 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7862 (mt-10) REVERT: I 309 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8850 (p) REVERT: I 327 ASN cc_start: 0.8267 (p0) cc_final: 0.7717 (t0) REVERT: I 346 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8529 (mt-10) REVERT: I 423 GLN cc_start: 0.8661 (tt0) cc_final: 0.8288 (tt0) REVERT: I 435 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: I 457 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8554 (mp0) outliers start: 75 outliers final: 37 residues processed: 297 average time/residue: 0.6952 time to fit residues: 233.3555 Evaluate side-chains 284 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 813 LYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 291 GLN 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 495 VAL Chi-restraints excluded: chain C residue 247 ILE 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 501 LEU Chi-restraints excluded: chain C residue 608 VAL 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 E residue 69 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 238 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 354 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 367 LYS Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain I residue 459 LEU Chi-restraints excluded: chain I residue 500 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 84 optimal weight: 3.9990 chunk 216 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 265 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN ** I 201 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.107345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.073248 restraints weight = 41786.791| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 2.14 r_work: 0.2839 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9134 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24276 Z= 0.210 Angle : 0.604 16.603 33153 Z= 0.321 Chirality : 0.044 0.296 3781 Planarity : 0.004 0.075 3861 Dihedral : 18.071 87.685 3851 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.76 % Allowed : 23.89 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2616 helix: 1.62 (0.14), residues: 1455 sheet: 0.15 (0.32), residues: 247 loop : -0.32 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 216 TYR 0.019 0.001 TYR E 330 PHE 0.027 0.001 PHE F 345 TRP 0.013 0.002 TRP A 539 HIS 0.011 0.001 HIS E 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (24276) covalent geometry : angle 0.60366 / 0.32 (33153) hydrogen bonds : bond 0.04076 / 2.65 ( 1181) hydrogen bonds : angle 4.00243 / 2.80 ( 3295) *********************** 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 313 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 245 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8529 (mmtt) REVERT: A 420 GLU cc_start: 0.7657 (mp0) cc_final: 0.7161 (mp0) REVERT: A 574 LYS cc_start: 0.9223 (mmmt) cc_final: 0.9005 (mmmm) REVERT: A 678 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7679 (ttp80) REVERT: A 813 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8854 (ttpp) REVERT: A 912 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8208 (ptp90) REVERT: A 914 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.7107 (pp) REVERT: B 260 ARG cc_start: 0.7058 (ptp-110) cc_final: 0.6793 (ptp90) REVERT: C 46 SER cc_start: 0.9348 (m) cc_final: 0.9051 (p) REVERT: C 62 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8603 (m170) REVERT: C 331 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8204 (tp-100) REVERT: C 412 PHE cc_start: 0.8396 (t80) cc_final: 0.7929 (t80) REVERT: C 592 GLU cc_start: 0.8991 (tt0) cc_final: 0.8730 (tt0) REVERT: D 141 THR cc_start: 0.9529 (OUTLIER) cc_final: 0.9207 (p) REVERT: D 155 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8249 (tm-30) REVERT: D 261 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8181 (tm-30) REVERT: D 270 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: E 125 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8420 (mtpp) REVERT: E 221 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7339 (mp0) REVERT: E 291 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7396 (pp) REVERT: E 353 LYS cc_start: 0.7922 (tttt) cc_final: 0.7573 (tttt) REVERT: E 360 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7145 (mtp180) REVERT: E 368 LYS cc_start: 0.8502 (ptpt) cc_final: 0.7859 (tptm) REVERT: F 290 ASN cc_start: 0.7817 (m-40) cc_final: 0.7477 (m110) REVERT: F 312 ARG cc_start: 0.8523 (ptt180) cc_final: 0.8022 (ptt90) REVERT: F 332 PHE cc_start: 0.8588 (m-10) cc_final: 0.8122 (m-80) REVERT: F 335 ARG cc_start: 0.7554 (ttp-170) cc_final: 0.7198 (ttp-170) REVERT: F 348 SER cc_start: 0.7624 (m) cc_final: 0.7318 (p) REVERT: F 358 LYS cc_start: 0.8098 (pmmt) cc_final: 0.7588 (tptt) REVERT: F 368 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6735 (mm) REVERT: F 376 GLU cc_start: 0.8372 (mp0) cc_final: 0.7951 (mp0) REVERT: F 386 TYR cc_start: 0.7666 (m-80) cc_final: 0.7333 (m-10) REVERT: F 396 GLU cc_start: 0.8354 (tp30) cc_final: 0.7612 (tp30) REVERT: F 400 ARG cc_start: 0.9027 (mtm180) cc_final: 0.8667 (mtp85) REVERT: I 173 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8810 (mt) REVERT: I 240 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.7616 (mtt90) REVERT: I 244 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7814 (mp0) REVERT: I 309 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8858 (p) REVERT: I 346 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8503 (mt-10) REVERT: I 423 GLN cc_start: 0.8657 (tt0) cc_final: 0.8286 (tt0) REVERT: I 435 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8179 (mt-10) outliers start: 68 outliers final: 38 residues processed: 298 average time/residue: 0.6918 time to fit residues: 232.5998 Evaluate side-chains 285 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 785 THR Chi-restraints excluded: chain A residue 813 LYS Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 912 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL 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 495 VAL Chi-restraints excluded: chain C residue 62 HIS 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 475 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain C residue 608 VAL 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 E residue 69 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain I residue 459 LEU Chi-restraints excluded: chain I residue 500 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 202 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 239 optimal weight: 0.0570 chunk 37 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 229 optimal weight: 20.0000 chunk 220 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN F 326 ASN ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075559 restraints weight = 41871.687| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.31 r_work: 0.2852 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9108 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 24276 Z= 0.129 Angle : 0.574 15.719 33153 Z= 0.306 Chirality : 0.041 0.289 3781 Planarity : 0.004 0.075 3861 Dihedral : 17.996 88.774 3851 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.28 % Allowed : 24.50 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.17), residues: 2616 helix: 1.74 (0.14), residues: 1454 sheet: 0.16 (0.32), residues: 247 loop : -0.26 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 216 TYR 0.017 0.001 TYR E 330 PHE 0.012 0.001 PHE D 363 TRP 0.016 0.001 TRP A 539 HIS 0.007 0.001 HIS E 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (24276) covalent geometry : angle 0.57352 / 0.31 (33153) hydrogen bonds : bond 0.03572 / 2.34 ( 1181) hydrogen bonds : angle 3.91158 / 2.74 ( 3295) ********************** 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 293 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8519 (mmtt) REVERT: A 420 GLU cc_start: 0.7554 (mp0) cc_final: 0.7091 (mp0) REVERT: A 678 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7670 (ttp80) REVERT: A 914 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7054 (pp) REVERT: B 260 ARG cc_start: 0.6912 (ptp-110) cc_final: 0.6525 (ptp90) REVERT: C 46 SER cc_start: 0.9349 (m) cc_final: 0.9052 (p) REVERT: C 62 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.8534 (m170) REVERT: C 331 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8187 (tp-100) REVERT: C 412 PHE cc_start: 0.8402 (t80) cc_final: 0.7946 (t80) REVERT: C 512 ASP cc_start: 0.8114 (p0) cc_final: 0.7819 (m-30) REVERT: C 592 GLU cc_start: 0.8971 (tt0) cc_final: 0.8709 (tt0) REVERT: D 141 THR cc_start: 0.9512 (OUTLIER) cc_final: 0.9219 (p) REVERT: D 155 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8233 (tm-30) REVERT: D 261 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8160 (tm-30) REVERT: D 270 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: E 125 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8358 (mtpp) REVERT: E 291 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7290 (pp) REVERT: E 353 LYS cc_start: 0.7877 (tttt) cc_final: 0.7506 (tttt) REVERT: E 360 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6821 (mtp180) REVERT: E 368 LYS cc_start: 0.8507 (ptpt) cc_final: 0.7888 (tptm) REVERT: F 290 ASN cc_start: 0.7745 (m-40) cc_final: 0.7411 (m110) REVERT: F 294 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7148 (mt) REVERT: F 332 PHE cc_start: 0.8585 (m-10) cc_final: 0.8133 (m-80) REVERT: F 335 ARG cc_start: 0.7495 (ttp-170) cc_final: 0.7124 (ttp-170) REVERT: F 354 MET cc_start: 0.7819 (mmt) cc_final: 0.7457 (mmp) REVERT: F 358 LYS cc_start: 0.8096 (pmmt) cc_final: 0.7621 (tptt) REVERT: F 368 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6663 (mm) REVERT: F 376 GLU cc_start: 0.8386 (mp0) cc_final: 0.7859 (mp0) REVERT: F 386 TYR cc_start: 0.7673 (m-80) cc_final: 0.7390 (m-10) REVERT: F 396 GLU cc_start: 0.8349 (tp30) cc_final: 0.7724 (tp30) REVERT: I 240 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.7589 (mtt90) REVERT: I 244 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7822 (mp0) REVERT: I 309 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8862 (p) REVERT: I 346 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8503 (mt-10) REVERT: I 423 GLN cc_start: 0.8658 (tt0) cc_final: 0.8274 (tt0) REVERT: I 435 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8093 (mt-10) REVERT: I 457 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8613 (mp0) outliers start: 56 outliers final: 32 residues processed: 286 average time/residue: 0.7164 time to fit residues: 231.9533 Evaluate side-chains 280 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 236 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 62 HIS 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 585 MET Chi-restraints excluded: chain C residue 608 VAL 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 E residue 69 SER Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 204 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 245 optimal weight: 9.9990 chunk 263 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 169 optimal weight: 0.5980 chunk 240 optimal weight: 8.9990 chunk 186 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 249 optimal weight: 5.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 774 HIS C 470 ASN ** C 600 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.108979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.074994 restraints weight = 41600.064| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.16 r_work: 0.2861 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 24276 Z= 0.139 Angle : 0.563 12.495 33153 Z= 0.304 Chirality : 0.042 0.290 3781 Planarity : 0.004 0.076 3861 Dihedral : 17.914 89.421 3847 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.36 % Allowed : 24.50 % Favored : 73.14 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.17), residues: 2616 helix: 1.79 (0.14), residues: 1454 sheet: 0.22 (0.32), residues: 247 loop : -0.24 (0.21), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 216 TYR 0.016 0.001 TYR A 580 PHE 0.027 0.001 PHE F 345 TRP 0.017 0.001 TRP C 494 HIS 0.010 0.001 HIS E 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (24276) covalent geometry : angle 0.56322 / 0.30 (33153) hydrogen bonds : bond 0.03556 / 2.33 ( 1181) hydrogen bonds : angle 3.87733 / 2.71 ( 3295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10434.12 seconds wall clock time: 178 minutes 6.19 seconds (10686.19 seconds total)