Starting phenix.real_space_refine on Fri Jun 20 10:37:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tji_25926/06_2025/7tji_25926.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tji_25926/06_2025/7tji_25926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tji_25926/06_2025/7tji_25926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tji_25926/06_2025/7tji_25926.map" model { file = "/net/cci-nas-00/data/ceres_data/7tji_25926/06_2025/7tji_25926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tji_25926/06_2025/7tji_25926.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 93 5.49 5 Mg 4 5.21 5 S 96 5.16 5 C 14944 2.51 5 N 3949 2.21 5 O 4680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23766 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3885 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 475} Chain breaks: 4 Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2066 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 11, 'TRANS': 237} Chain breaks: 1 Chain: "C" Number of atoms: 4497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4497 Classifications: {'peptide': 543} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 528} Chain breaks: 5 Chain: "D" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3543 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 421} Chain breaks: 3 Chain: "E" Number of atoms: 3562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3562 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 3 Chain: "F" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1300 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "G" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 40} Chain: "H" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 846 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2995 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 14, 'TRANS': 361} Chain breaks: 7 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Chain: "G" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 14.28, per 1000 atoms: 0.60 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: 5.79 Conformation dependent library (CDL) restraints added in 2.9 seconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5190 Finding SS restraints... 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: 8.43 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: 9.74 Time building geometry restraints manager: 7.04 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: 32407 2.53 - 5.06: 604 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=" C PRO I 252 " pdb=" N THR I 253 " pdb=" CA THR I 253 " ideal model delta sigma weight residual 122.61 130.33 -7.72 1.56e+00 4.11e-01 2.45e+01 angle pdb=" CB LYS C 48 " pdb=" CG LYS C 48 " pdb=" CD LYS C 48 " ideal model delta sigma weight residual 111.30 122.57 -11.27 2.30e+00 1.89e-01 2.40e+01 ... (remaining 33148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11928 17.84 - 35.69: 1753 35.69 - 53.53: 708 53.53 - 71.38: 183 71.38 - 89.22: 44 Dihedral angle restraints: 14616 sinusoidal: 6675 harmonic: 7941 Sorted by residual: dihedral pdb=" CA VAL E 8 " pdb=" C VAL E 8 " pdb=" N ALA E 9 " pdb=" CA ALA E 9 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA PHE B 475 " pdb=" C PHE B 475 " pdb=" N VAL B 476 " pdb=" CA VAL B 476 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA ILE D 516 " pdb=" C ILE D 516 " pdb=" N ILE D 517 " pdb=" CA ILE D 517 " ideal model delta harmonic sigma weight residual 180.00 157.25 22.75 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 14613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3170 0.068 - 0.136: 557 0.136 - 0.205: 43 0.205 - 0.273: 10 0.273 - 0.341: 1 Chirality restraints: 3781 Sorted by residual: chirality pdb=" CA PRO I 314 " pdb=" N PRO I 314 " pdb=" C PRO I 314 " pdb=" CB PRO I 314 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL F 369 " pdb=" CA VAL F 369 " pdb=" CG1 VAL F 369 " pdb=" CG2 VAL F 369 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA TRP C 494 " pdb=" N TRP C 494 " pdb=" C TRP C 494 " pdb=" CB TRP C 494 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3778 not shown) Planarity restraints: 3861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 313 " 0.067 5.00e-02 4.00e+02 9.69e-02 1.50e+01 pdb=" N PRO I 314 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO I 314 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO I 314 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 450 " 0.014 2.00e-02 2.50e+03 2.14e-02 1.14e+01 pdb=" CG TRP E 450 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP E 450 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP E 450 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 450 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP E 450 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 450 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 450 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 450 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP E 450 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 509 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO I 510 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO I 510 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO I 510 " 0.044 5.00e-02 4.00e+02 ... (remaining 3858 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 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: 1.140 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: 0.030 Extract box with map and model: 0.890 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 61.540 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 24276 Z= 0.262 Angle : 0.899 12.645 33153 Z= 0.500 Chirality : 0.052 0.341 3781 Planarity : 0.007 0.097 3861 Dihedral : 20.303 89.220 9426 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.52 % Allowed : 21.50 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.14), residues: 2616 helix: -0.85 (0.12), residues: 1421 sheet: -0.10 (0.30), residues: 258 loop : -1.12 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP E 450 HIS 0.009 0.001 HIS C 22 PHE 0.024 0.002 PHE E 239 TYR 0.030 0.003 TYR I 389 ARG 0.022 0.001 ARG E 272 Details of bonding type rmsd hydrogen bonds : bond 0.15939 ( 1181) hydrogen bonds : angle 6.23554 ( 3295) covalent geometry : bond 0.00528 (24276) covalent geometry : angle 0.89858 (33153) *********************** 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 : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 LYS cc_start: 0.8664 (mmtt) cc_final: 0.8324 (mmtt) REVERT: A 889 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9172 (pp) REVERT: B 291 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8465 (mt0) REVERT: C 46 SER cc_start: 0.9280 (m) cc_final: 0.8952 (p) REVERT: C 395 PHE cc_start: 0.6817 (m-80) cc_final: 0.6379 (m-10) REVERT: C 414 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8128 (tp30) REVERT: C 568 GLU cc_start: 0.8750 (tt0) cc_final: 0.8346 (tm-30) REVERT: E 221 GLU cc_start: 0.7296 (mp0) cc_final: 0.6982 (mp0) REVERT: E 234 ASN cc_start: 0.8684 (m-40) cc_final: 0.8381 (m110) REVERT: E 368 LYS cc_start: 0.8430 (ptpt) cc_final: 0.7992 (tptm) REVERT: E 376 LEU cc_start: 0.8390 (mp) cc_final: 0.8165 (pt) REVERT: E 431 LYS cc_start: 0.8859 (mptt) cc_final: 0.8640 (mptt) REVERT: F 293 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7669 (tm-30) REVERT: F 309 ASN cc_start: 0.7501 (m-40) cc_final: 0.7132 (m-40) REVERT: F 329 PHE cc_start: 0.8494 (m-80) cc_final: 0.7764 (m-80) REVERT: F 332 PHE cc_start: 0.8284 (m-80) cc_final: 0.8022 (m-10) REVERT: F 354 MET cc_start: 0.7692 (mmt) cc_final: 0.7401 (mmp) REVERT: F 370 LYS cc_start: 0.7929 (tptm) cc_final: 0.7633 (tppt) REVERT: F 386 TYR cc_start: 0.7744 (m-10) cc_final: 0.7331 (m-10) REVERT: F 392 ILE cc_start: 0.8602 (pt) cc_final: 0.8283 (pp) REVERT: I 173 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8457 (mt) REVERT: I 240 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8177 (mtm110) REVERT: I 244 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7241 (mt-10) outliers start: 62 outliers final: 32 residues processed: 495 average time/residue: 1.8029 time to fit residues: 1004.0825 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 : 2.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 775 ILE Chi-restraints excluded: chain A residue 835 VAL Chi-restraints excluded: chain A residue 889 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 442 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 454 HIS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain I residue 164 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 238 SER Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain I residue 310 ILE Chi-restraints excluded: chain I residue 331 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 6.9990 chunk 206 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 139 optimal weight: 8.9990 chunk 110 optimal weight: 0.0980 chunk 213 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 530 ASN B 425 HIS B 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 284 GLN I 289 GLN I 411 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.107841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.073515 restraints weight = 41837.092| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.18 r_work: 0.2832 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 24276 Z= 0.247 Angle : 0.628 8.086 33153 Z= 0.338 Chirality : 0.044 0.169 3781 Planarity : 0.005 0.060 3861 Dihedral : 18.578 89.680 4012 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.06 % Allowed : 21.29 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2616 helix: 0.59 (0.13), residues: 1446 sheet: 0.09 (0.30), residues: 257 loop : -0.80 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 450 HIS 0.007 0.001 HIS C 405 PHE 0.025 0.002 PHE I 511 TYR 0.020 0.002 TYR C 483 ARG 0.006 0.001 ARG E 344 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 1181) hydrogen bonds : angle 4.34820 ( 3295) covalent geometry : bond 0.00581 (24276) covalent geometry : angle 0.62792 (33153) *********************** 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 376 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 276 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 ARG cc_start: 0.8110 (mtm180) cc_final: 0.7764 (ttp80) REVERT: B 260 ARG cc_start: 0.6921 (ptp-110) cc_final: 0.6564 (ptp90) REVERT: B 288 ARG cc_start: 0.8961 (ttt-90) cc_final: 0.8682 (tpp-160) REVERT: C 46 SER cc_start: 0.9365 (m) cc_final: 0.9033 (p) REVERT: C 48 LYS cc_start: 0.8624 (tmtt) cc_final: 0.8294 (tttt) REVERT: C 347 ASN cc_start: 0.7794 (m110) cc_final: 0.7140 (p0) REVERT: C 412 PHE cc_start: 0.8452 (t80) cc_final: 0.8052 (t80) REVERT: C 555 ASN cc_start: 0.9001 (t0) cc_final: 0.8667 (t0) REVERT: D 270 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: E 221 GLU cc_start: 0.7352 (mp0) cc_final: 0.7064 (mp0) REVERT: E 234 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8454 (m110) REVERT: E 354 THR cc_start: 0.8949 (p) cc_final: 0.8730 (t) REVERT: E 360 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7038 (mtp180) REVERT: E 368 LYS cc_start: 0.8444 (ptpt) cc_final: 0.7973 (tptm) REVERT: E 431 LYS cc_start: 0.9046 (mptt) cc_final: 0.8839 (mptt) REVERT: F 290 ASN cc_start: 0.7609 (m-40) cc_final: 0.7299 (m110) REVERT: F 293 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7818 (tm-30) REVERT: F 344 HIS cc_start: 0.8068 (m-70) cc_final: 0.7832 (m-70) REVERT: F 376 GLU cc_start: 0.8128 (mp0) cc_final: 0.7835 (mp0) REVERT: F 396 GLU cc_start: 0.8070 (tp30) cc_final: 0.7777 (tp30) REVERT: I 173 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8770 (mt) REVERT: I 201 ASN cc_start: 0.7951 (p0) cc_final: 0.7710 (p0) REVERT: I 228 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8791 (mm) REVERT: I 240 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8146 (mtt90) REVERT: I 244 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7755 (mt-10) REVERT: I 327 ASN cc_start: 0.8240 (p0) cc_final: 0.7611 (t0) REVERT: I 404 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7673 (mmt90) REVERT: I 423 GLN cc_start: 0.8681 (tt0) cc_final: 0.8339 (tt0) REVERT: I 426 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8172 (mtmt) REVERT: I 457 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8599 (mt-10) outliers start: 100 outliers final: 33 residues processed: 356 average time/residue: 1.7497 time to fit residues: 702.2594 Evaluate side-chains 291 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 253 time to evaluate : 2.685 ------------------------------------------------------------------------------- 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 264 SER 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 310 THR 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 512 ASP Chi-restraints excluded: chain C residue 564 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 436 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 367 LYS Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 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 331 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 132 optimal weight: 1.9990 chunk 252 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 268 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 774 HIS B 261 HIS D 58 GLN D 76 GLN D 489 ASN I 411 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.110698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.077002 restraints weight = 41428.715| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.26 r_work: 0.2898 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24276 Z= 0.132 Angle : 0.540 13.551 33153 Z= 0.292 Chirality : 0.040 0.161 3781 Planarity : 0.004 0.051 3861 Dihedral : 18.185 85.533 3981 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.45 % Allowed : 22.19 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2616 helix: 1.21 (0.14), residues: 1456 sheet: 0.10 (0.31), residues: 256 loop : -0.60 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 494 HIS 0.005 0.001 HIS E 467 PHE 0.024 0.001 PHE F 345 TYR 0.014 0.001 TYR I 85 ARG 0.010 0.001 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.03649 ( 1181) hydrogen bonds : angle 3.99512 ( 3295) covalent geometry : bond 0.00304 (24276) covalent geometry : angle 0.53958 (33153) *********************** 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 360 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 275 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7554 (mp0) cc_final: 0.6967 (mp0) REVERT: A 678 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7859 (ttp80) REVERT: B 260 ARG cc_start: 0.6952 (ptp-110) cc_final: 0.6625 (ptp90) REVERT: B 288 ARG cc_start: 0.8906 (ttt-90) cc_final: 0.8698 (tpp-160) REVERT: C 46 SER cc_start: 0.9342 (m) cc_final: 0.9049 (p) REVERT: C 62 HIS cc_start: 0.8791 (OUTLIER) cc_final: 0.8528 (m170) REVERT: C 412 PHE cc_start: 0.8408 (t80) cc_final: 0.7910 (t80) REVERT: C 555 ASN cc_start: 0.8945 (t0) cc_final: 0.8586 (t0) REVERT: D 141 THR cc_start: 0.9518 (OUTLIER) cc_final: 0.9190 (p) REVERT: D 155 GLN cc_start: 0.8488 (tm-30) cc_final: 0.8122 (tm-30) REVERT: D 209 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7661 (mmmm) REVERT: D 261 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8214 (tm-30) REVERT: D 270 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8175 (mp10) REVERT: E 221 GLU cc_start: 0.7438 (mp0) cc_final: 0.7117 (mp0) REVERT: E 234 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8424 (m110) REVERT: E 353 LYS cc_start: 0.7833 (tttt) cc_final: 0.7448 (tttt) REVERT: E 354 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8636 (t) REVERT: E 368 LYS cc_start: 0.8497 (ptpt) cc_final: 0.7951 (tptm) REVERT: F 290 ASN cc_start: 0.7682 (m-40) cc_final: 0.7333 (m110) REVERT: F 332 PHE cc_start: 0.8284 (m-10) cc_final: 0.7600 (m-10) REVERT: F 354 MET cc_start: 0.7604 (mmt) cc_final: 0.7213 (mmp) REVERT: F 358 LYS cc_start: 0.8130 (pmmt) cc_final: 0.7531 (tptt) REVERT: F 376 GLU cc_start: 0.8296 (mp0) cc_final: 0.7789 (mp0) REVERT: F 396 GLU cc_start: 0.8315 (tp30) cc_final: 0.7749 (tp30) REVERT: I 240 ARG cc_start: 0.8454 (mtm-85) cc_final: 0.8113 (mtt90) REVERT: I 244 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7815 (mt-10) REVERT: I 267 MET cc_start: 0.7010 (ttp) cc_final: 0.6748 (ptm) REVERT: I 327 ASN cc_start: 0.8318 (p0) cc_final: 0.7804 (t0) REVERT: I 346 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8510 (mt-10) REVERT: I 423 GLN cc_start: 0.8573 (tt0) cc_final: 0.8234 (tt0) REVERT: I 426 LYS cc_start: 0.8610 (mmmt) cc_final: 0.8180 (mtmt) REVERT: I 454 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: I 495 MET cc_start: 0.7922 (mmm) cc_final: 0.7683 (mmm) outliers start: 85 outliers final: 33 residues processed: 336 average time/residue: 1.7504 time to fit residues: 661.1213 Evaluate side-chains 281 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 2.632 ------------------------------------------------------------------------------- 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 856 ASN Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 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 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 D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 209 LYS 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 138 LEU Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 321 CYS Chi-restraints excluded: chain F residue 341 ARG Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 202 MET Chi-restraints excluded: chain I residue 225 MET Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 454 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 93 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 145 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 263 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 774 HIS ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.106591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.072254 restraints weight = 42375.101| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.19 r_work: 0.2805 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24276 Z= 0.256 Angle : 0.606 13.284 33153 Z= 0.325 Chirality : 0.044 0.167 3781 Planarity : 0.004 0.058 3861 Dihedral : 18.329 85.116 3973 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.70 % Allowed : 21.94 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.16), residues: 2616 helix: 1.34 (0.14), residues: 1459 sheet: 0.13 (0.31), residues: 247 loop : -0.53 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 539 HIS 0.006 0.001 HIS E 467 PHE 0.022 0.002 PHE I 186 TYR 0.019 0.002 TYR C 483 ARG 0.011 0.001 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 1181) hydrogen bonds : angle 4.07233 ( 3295) covalent geometry : bond 0.00604 (24276) covalent geometry : angle 0.60601 (33153) *********************** 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 337 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 246 time to evaluate : 2.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LYS cc_start: 0.9114 (mppt) cc_final: 0.8911 (mtpp) REVERT: A 678 ARG cc_start: 0.8143 (mtm180) cc_final: 0.7807 (ttp80) REVERT: A 813 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8872 (ttpp) REVERT: A 912 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8173 (ptp90) REVERT: B 260 ARG cc_start: 0.7022 (ptp-110) cc_final: 0.6723 (ptp90) REVERT: C 46 SER cc_start: 0.9355 (m) cc_final: 0.9064 (p) REVERT: C 412 PHE cc_start: 0.8372 (t80) cc_final: 0.7842 (t80) REVERT: D 155 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 209 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7644 (mmmm) REVERT: D 261 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: D 270 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8185 (mp10) REVERT: E 221 GLU cc_start: 0.7483 (mp0) cc_final: 0.7242 (mp0) REVERT: E 234 ASN cc_start: 0.8701 (m-40) cc_final: 0.8420 (m110) REVERT: E 353 LYS cc_start: 0.7942 (tttt) cc_final: 0.7624 (tttt) REVERT: E 368 LYS cc_start: 0.8576 (ptpt) cc_final: 0.7929 (tptm) REVERT: F 290 ASN cc_start: 0.7733 (m-40) cc_final: 0.7371 (m110) REVERT: F 301 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7449 (mppt) REVERT: F 348 SER cc_start: 0.7512 (m) cc_final: 0.7209 (p) REVERT: F 354 MET cc_start: 0.7647 (mmt) cc_final: 0.7243 (mmp) REVERT: F 368 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6664 (mm) REVERT: F 376 GLU cc_start: 0.8344 (mp0) cc_final: 0.7775 (mp0) REVERT: F 386 TYR cc_start: 0.7672 (m-10) cc_final: 0.7176 (m-10) REVERT: F 396 GLU cc_start: 0.8374 (tp30) cc_final: 0.7639 (tp30) REVERT: I 240 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.7631 (mtt90) REVERT: I 244 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7845 (mp0) REVERT: I 327 ASN cc_start: 0.8303 (p0) cc_final: 0.7717 (t0) REVERT: I 346 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8523 (mt-10) REVERT: I 390 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9238 (mm) REVERT: I 423 GLN cc_start: 0.8706 (tt0) cc_final: 0.8351 (tt0) REVERT: I 426 LYS cc_start: 0.8683 (mmmt) cc_final: 0.8250 (mtmt) REVERT: I 454 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7299 (mt0) REVERT: I 457 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8102 (mt-10) outliers start: 91 outliers final: 39 residues processed: 316 average time/residue: 1.6142 time to fit residues: 574.6524 Evaluate side-chains 283 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 235 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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 255 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 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 431 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 585 MET Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 261 GLU Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain D residue 280 ASN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 301 LYS 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 393 ARG Chi-restraints excluded: chain F residue 400 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 188 SER Chi-restraints excluded: chain I residue 302 GLN Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 390 ILE Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 459 LEU Chi-restraints excluded: chain I residue 500 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 271 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 127 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN I 90 ASN I 190 GLN ** I 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 411 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.109328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.075262 restraints weight = 41679.396| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.17 r_work: 0.2883 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24276 Z= 0.126 Angle : 0.524 12.378 33153 Z= 0.283 Chirality : 0.040 0.159 3781 Planarity : 0.003 0.051 3861 Dihedral : 18.032 87.327 3973 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.09 % Allowed : 22.39 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.17), residues: 2616 helix: 1.66 (0.14), residues: 1451 sheet: 0.09 (0.31), residues: 256 loop : -0.36 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 539 HIS 0.009 0.001 HIS E 467 PHE 0.026 0.001 PHE F 345 TYR 0.020 0.001 TYR A 580 ARG 0.016 0.001 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 1181) hydrogen bonds : angle 3.86981 ( 3295) covalent geometry : bond 0.00288 (24276) covalent geometry : angle 0.52370 (33153) *********************** 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 332 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 256 time to evaluate : 2.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7593 (mp0) cc_final: 0.7055 (mp0) REVERT: A 678 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7877 (ttp80) REVERT: A 914 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7039 (pp) REVERT: B 260 ARG cc_start: 0.6874 (ptp-110) cc_final: 0.6608 (ptp90) REVERT: B 291 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8623 (mt0) REVERT: C 46 SER cc_start: 0.9311 (m) cc_final: 0.9023 (p) REVERT: C 48 LYS cc_start: 0.8771 (tttt) cc_final: 0.8337 (tttt) REVERT: C 62 HIS cc_start: 0.8795 (OUTLIER) cc_final: 0.8538 (m170) REVERT: C 347 ASN cc_start: 0.8030 (m-40) cc_final: 0.7377 (p0) REVERT: C 399 GLU cc_start: 0.8747 (mp0) cc_final: 0.8544 (tm-30) REVERT: C 412 PHE cc_start: 0.8390 (t80) cc_final: 0.7851 (t80) REVERT: C 600 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7752 (mm-40) REVERT: D 141 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9223 (p) REVERT: D 155 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8215 (tm-30) REVERT: D 209 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7732 (mmmm) REVERT: E 234 ASN cc_start: 0.8721 (m-40) cc_final: 0.8454 (m110) REVERT: E 368 LYS cc_start: 0.8581 (ptpt) cc_final: 0.8001 (tptm) REVERT: F 290 ASN cc_start: 0.7802 (m-40) cc_final: 0.7473 (m110) REVERT: F 301 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7553 (mppt) REVERT: F 332 PHE cc_start: 0.8775 (m-80) cc_final: 0.8111 (m-80) REVERT: F 348 SER cc_start: 0.7600 (m) cc_final: 0.7285 (p) REVERT: F 354 MET cc_start: 0.7786 (mmt) cc_final: 0.7438 (mmp) REVERT: F 358 LYS cc_start: 0.8115 (pmmt) cc_final: 0.7571 (tptt) REVERT: F 368 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6680 (mm) REVERT: F 376 GLU cc_start: 0.8445 (mp0) cc_final: 0.7963 (mp0) REVERT: F 386 TYR cc_start: 0.7663 (m-10) cc_final: 0.7210 (m-10) REVERT: F 396 GLU cc_start: 0.8322 (tp30) cc_final: 0.7629 (tp30) REVERT: I 154 TRP cc_start: 0.7527 (m100) cc_final: 0.7220 (m100) REVERT: I 240 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.7691 (mtt90) REVERT: I 244 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7839 (mp0) REVERT: I 309 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8876 (p) REVERT: I 327 ASN cc_start: 0.8237 (p0) cc_final: 0.7705 (t0) REVERT: I 346 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8435 (mt-10) REVERT: I 390 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9248 (mm) REVERT: I 423 GLN cc_start: 0.8668 (tt0) cc_final: 0.8284 (tt0) REVERT: I 426 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8336 (mtmt) REVERT: I 434 ASP cc_start: 0.7905 (m-30) cc_final: 0.7601 (m-30) REVERT: I 454 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7239 (mt0) REVERT: I 457 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8058 (mt-10) outliers start: 76 outliers final: 28 residues processed: 319 average time/residue: 1.5225 time to fit residues: 550.4512 Evaluate side-chains 280 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 2.985 ------------------------------------------------------------------------------- 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 A residue 914 LEU 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 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 D residue 119 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 416 GLU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 301 LYS 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 F residue 400 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 390 ILE Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU 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 71 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** I 204 HIS ** 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 = 0.3563 r_free = 0.3563 target = 0.106678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.072391 restraints weight = 41810.687| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.17 r_work: 0.2825 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 24276 Z= 0.254 Angle : 0.596 11.580 33153 Z= 0.319 Chirality : 0.044 0.166 3781 Planarity : 0.004 0.056 3861 Dihedral : 18.197 84.293 3969 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.29 % Allowed : 22.67 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2616 helix: 1.55 (0.14), residues: 1462 sheet: 0.13 (0.31), residues: 247 loop : -0.43 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 539 HIS 0.007 0.001 HIS E 467 PHE 0.018 0.002 PHE D 363 TYR 0.017 0.002 TYR C 483 ARG 0.014 0.001 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.04239 ( 1181) hydrogen bonds : angle 3.98974 ( 3295) covalent geometry : bond 0.00601 (24276) covalent geometry : angle 0.59576 (33153) *********************** 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 327 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 246 time to evaluate : 2.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.7352 (tt0) cc_final: 0.7068 (tm-30) REVERT: A 420 GLU cc_start: 0.7750 (mp0) cc_final: 0.7259 (mp0) REVERT: A 678 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7852 (ttp80) REVERT: A 813 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8841 (ttpp) REVERT: A 914 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7178 (pp) REVERT: B 260 ARG cc_start: 0.7118 (ptp-110) cc_final: 0.6852 (ptp90) REVERT: C 46 SER cc_start: 0.9314 (m) cc_final: 0.9031 (p) REVERT: C 62 HIS cc_start: 0.8846 (OUTLIER) cc_final: 0.8592 (m170) REVERT: C 412 PHE cc_start: 0.8394 (t80) cc_final: 0.7858 (t80) REVERT: D 141 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9201 (p) REVERT: D 155 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8238 (tm-30) REVERT: D 209 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7745 (mmmm) REVERT: D 270 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8181 (mp10) REVERT: E 230 ASP cc_start: 0.7877 (t0) cc_final: 0.7412 (t0) REVERT: E 234 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8371 (m-40) REVERT: F 290 ASN cc_start: 0.7696 (m-40) cc_final: 0.7373 (m110) REVERT: F 301 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7581 (mppt) REVERT: F 312 ARG cc_start: 0.8524 (ptt180) cc_final: 0.8091 (ptt90) REVERT: F 332 PHE cc_start: 0.8686 (m-80) cc_final: 0.8479 (m-80) REVERT: F 348 SER cc_start: 0.7585 (m) cc_final: 0.7275 (p) REVERT: F 368 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6883 (mm) REVERT: F 376 GLU cc_start: 0.8446 (mp0) cc_final: 0.8034 (mp0) REVERT: F 386 TYR cc_start: 0.7669 (m-10) cc_final: 0.7283 (m-10) REVERT: F 396 GLU cc_start: 0.8388 (tp30) cc_final: 0.7713 (tp30) REVERT: I 240 ARG cc_start: 0.8464 (mtm-85) cc_final: 0.7708 (mtt90) REVERT: I 244 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7852 (mp0) REVERT: I 309 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8873 (p) REVERT: I 346 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8488 (mt-10) REVERT: I 390 ILE cc_start: 0.9510 (OUTLIER) cc_final: 0.9270 (mm) REVERT: I 423 GLN cc_start: 0.8727 (tt0) cc_final: 0.8344 (tt0) REVERT: I 426 LYS cc_start: 0.8846 (mmmt) cc_final: 0.8310 (mtpt) REVERT: I 454 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: I 457 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.7973 (mt-10) outliers start: 81 outliers final: 37 residues processed: 307 average time/residue: 1.6371 time to fit residues: 566.8092 Evaluate side-chains 281 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL 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 255 THR Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 419 LYS Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 62 HIS Chi-restraints excluded: chain C residue 247 ILE Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 533 MET Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 301 LYS 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 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 169 SER 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 390 ILE Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 459 LEU Chi-restraints excluded: chain I residue 500 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 260 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 218 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 208 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 629 HIS A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.074377 restraints weight = 41901.092| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.13 r_work: 0.2854 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24276 Z= 0.152 Angle : 0.548 10.745 33153 Z= 0.295 Chirality : 0.041 0.294 3781 Planarity : 0.003 0.064 3861 Dihedral : 18.032 86.016 3969 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.93 % Allowed : 23.24 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.17), residues: 2616 helix: 1.71 (0.14), residues: 1456 sheet: 0.12 (0.32), residues: 244 loop : -0.34 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 539 HIS 0.008 0.001 HIS E 467 PHE 0.027 0.001 PHE F 345 TYR 0.018 0.001 TYR E 330 ARG 0.014 0.000 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 1181) hydrogen bonds : angle 3.87912 ( 3295) covalent geometry : bond 0.00355 (24276) covalent geometry : angle 0.54820 (33153) *********************** 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 314 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 242 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 GLN cc_start: 0.7236 (tt0) cc_final: 0.7029 (tm-30) REVERT: A 420 GLU cc_start: 0.7673 (mp0) cc_final: 0.7180 (mp0) REVERT: A 678 ARG cc_start: 0.8133 (mtm180) cc_final: 0.7885 (ttp80) REVERT: A 914 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7138 (pp) REVERT: B 260 ARG cc_start: 0.6971 (ptp-110) cc_final: 0.6607 (ptp90) REVERT: C 46 SER cc_start: 0.9361 (m) cc_final: 0.9075 (p) REVERT: C 62 HIS cc_start: 0.8807 (OUTLIER) cc_final: 0.8539 (m170) REVERT: C 399 GLU cc_start: 0.8778 (mp0) cc_final: 0.8546 (tm-30) REVERT: C 412 PHE cc_start: 0.8395 (t80) cc_final: 0.7856 (t80) REVERT: D 141 THR cc_start: 0.9511 (OUTLIER) cc_final: 0.9239 (p) REVERT: D 155 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8220 (tm-30) REVERT: D 209 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7705 (mmmm) REVERT: D 270 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8130 (mp10) REVERT: E 230 ASP cc_start: 0.7830 (t0) cc_final: 0.7369 (OUTLIER) REVERT: E 234 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8382 (m-40) REVERT: E 238 ASN cc_start: 0.8937 (m110) cc_final: 0.8519 (t0) REVERT: F 290 ASN cc_start: 0.7685 (m-40) cc_final: 0.7371 (m110) REVERT: F 293 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7463 (tm-30) REVERT: F 301 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7581 (mppt) REVERT: F 348 SER cc_start: 0.7689 (m) cc_final: 0.7376 (p) REVERT: F 358 LYS cc_start: 0.8039 (pmmt) cc_final: 0.7555 (tptt) REVERT: F 368 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6842 (mm) REVERT: F 376 GLU cc_start: 0.8479 (mp0) cc_final: 0.7939 (mp0) REVERT: F 386 TYR cc_start: 0.7685 (m-10) cc_final: 0.7287 (m-10) REVERT: F 396 GLU cc_start: 0.8375 (tp30) cc_final: 0.7723 (tp30) REVERT: I 154 TRP cc_start: 0.7478 (m100) cc_final: 0.7188 (m100) REVERT: I 240 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.7662 (mtt90) REVERT: I 244 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7845 (mp0) REVERT: I 309 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8864 (p) REVERT: I 346 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8445 (mt-10) REVERT: I 390 ILE cc_start: 0.9476 (OUTLIER) cc_final: 0.9265 (mm) REVERT: I 423 GLN cc_start: 0.8704 (tt0) cc_final: 0.8310 (tt0) REVERT: I 426 LYS cc_start: 0.8842 (mmmt) cc_final: 0.8290 (mtpt) REVERT: I 454 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7249 (mt0) REVERT: I 457 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7986 (mt-10) outliers start: 72 outliers final: 34 residues processed: 301 average time/residue: 1.5203 time to fit residues: 518.6672 Evaluate side-chains 283 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 2.497 ------------------------------------------------------------------------------- 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 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 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 119 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 209 LYS 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 138 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 CYS Chi-restraints excluded: chain F residue 301 LYS Chi-restraints excluded: chain F residue 362 VAL Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 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 390 ILE Chi-restraints excluded: chain I residue 444 ILE Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 459 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 185 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 213 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 211 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN I 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.107491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.073371 restraints weight = 41616.758| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.15 r_work: 0.2844 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24276 Z= 0.184 Angle : 0.562 9.843 33153 Z= 0.302 Chirality : 0.042 0.241 3781 Planarity : 0.004 0.066 3861 Dihedral : 18.044 85.867 3969 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.97 % Allowed : 23.49 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2616 helix: 1.73 (0.14), residues: 1457 sheet: 0.13 (0.32), residues: 244 loop : -0.29 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 539 HIS 0.005 0.001 HIS E 467 PHE 0.017 0.001 PHE C 408 TYR 0.015 0.001 TYR C 483 ARG 0.016 0.001 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 1181) hydrogen bonds : angle 3.88701 ( 3295) covalent geometry : bond 0.00433 (24276) covalent geometry : angle 0.56175 (33153) *********************** 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 317 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 244 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7680 (mp0) cc_final: 0.7204 (mp0) REVERT: A 678 ARG cc_start: 0.8103 (mtm180) cc_final: 0.7836 (ttp80) REVERT: A 914 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7203 (pp) REVERT: B 260 ARG cc_start: 0.6991 (ptp-110) cc_final: 0.6638 (ptp90) REVERT: B 291 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8672 (mt0) REVERT: C 46 SER cc_start: 0.9323 (m) cc_final: 0.9047 (p) REVERT: C 62 HIS cc_start: 0.8818 (OUTLIER) cc_final: 0.8555 (m170) REVERT: C 331 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8196 (tp-100) REVERT: C 336 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8510 (p) REVERT: C 412 PHE cc_start: 0.8375 (t80) cc_final: 0.7818 (t80) REVERT: D 141 THR cc_start: 0.9523 (OUTLIER) cc_final: 0.9288 (p) REVERT: D 155 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8246 (tm-30) REVERT: D 209 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7737 (mmmm) REVERT: D 261 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8203 (tm-30) REVERT: D 270 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: E 106 PHE cc_start: 0.9386 (OUTLIER) cc_final: 0.8841 (p90) REVERT: E 230 ASP cc_start: 0.7894 (t0) cc_final: 0.7421 (t0) REVERT: E 234 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8328 (m-40) REVERT: E 238 ASN cc_start: 0.8940 (m110) cc_final: 0.8527 (t0) REVERT: F 290 ASN cc_start: 0.7556 (m-40) cc_final: 0.7234 (m110) REVERT: F 293 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7500 (tm-30) REVERT: F 312 ARG cc_start: 0.8562 (ptt180) cc_final: 0.8115 (ptt90) REVERT: F 348 SER cc_start: 0.7732 (m) cc_final: 0.7416 (p) REVERT: F 358 LYS cc_start: 0.8054 (pmmt) cc_final: 0.7587 (tptt) REVERT: F 368 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7010 (mm) REVERT: F 371 GLU cc_start: 0.7888 (pt0) cc_final: 0.7642 (pt0) REVERT: F 376 GLU cc_start: 0.8546 (mp0) cc_final: 0.8085 (mp0) REVERT: F 386 TYR cc_start: 0.7698 (m-10) cc_final: 0.7315 (m-10) REVERT: F 396 GLU cc_start: 0.8388 (tp30) cc_final: 0.7768 (tp30) REVERT: I 154 TRP cc_start: 0.7488 (m100) cc_final: 0.7196 (m100) REVERT: I 240 ARG cc_start: 0.8426 (mtm-85) cc_final: 0.7693 (mtt90) REVERT: I 244 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7848 (mp0) REVERT: I 309 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8844 (p) REVERT: I 346 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8447 (mt-10) REVERT: I 390 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9262 (mm) REVERT: I 423 GLN cc_start: 0.8725 (tt0) cc_final: 0.8333 (tt0) REVERT: I 426 LYS cc_start: 0.8862 (mmmt) cc_final: 0.8382 (mtmt) REVERT: I 454 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7164 (mt0) REVERT: I 457 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.7945 (mt-10) outliers start: 73 outliers final: 37 residues processed: 302 average time/residue: 1.6200 time to fit residues: 554.6465 Evaluate side-chains 283 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL 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 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 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 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 119 LEU 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 209 LYS 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 106 PHE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 415 LYS 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 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 390 ILE Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 459 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 8.9990 chunk 111 optimal weight: 0.0010 chunk 228 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 48 optimal weight: 0.3980 chunk 256 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 overall best weight: 1.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN E 123 GLN F 326 ASN I 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.108355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.074352 restraints weight = 41716.914| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.16 r_work: 0.2867 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24276 Z= 0.150 Angle : 0.554 12.392 33153 Z= 0.297 Chirality : 0.041 0.232 3781 Planarity : 0.003 0.069 3861 Dihedral : 17.936 87.361 3969 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.52 % Allowed : 24.01 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2616 helix: 1.81 (0.14), residues: 1453 sheet: 0.13 (0.32), residues: 244 loop : -0.26 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 539 HIS 0.004 0.001 HIS C 69 PHE 0.029 0.001 PHE F 345 TYR 0.013 0.001 TYR E 330 ARG 0.016 0.000 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 1181) hydrogen bonds : angle 3.83826 ( 3295) covalent geometry : bond 0.00349 (24276) covalent geometry : angle 0.55389 (33153) *********************** 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 300 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 238 time to evaluate : 2.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7665 (mp0) cc_final: 0.7261 (mp0) REVERT: A 678 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7906 (ttp80) REVERT: A 914 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7183 (pp) REVERT: B 260 ARG cc_start: 0.6997 (ptp-110) cc_final: 0.6655 (ptp90) REVERT: C 46 SER cc_start: 0.9316 (m) cc_final: 0.9038 (p) REVERT: C 62 HIS cc_start: 0.8805 (OUTLIER) cc_final: 0.8539 (m170) REVERT: C 331 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8192 (tp-100) REVERT: C 336 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8500 (p) REVERT: C 412 PHE cc_start: 0.8382 (t80) cc_final: 0.7823 (t80) REVERT: D 141 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9305 (p) REVERT: D 155 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8253 (tm-30) REVERT: D 209 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.7615 (tppp) REVERT: D 261 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: D 270 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: E 106 PHE cc_start: 0.9369 (OUTLIER) cc_final: 0.8827 (p90) REVERT: E 230 ASP cc_start: 0.7877 (t0) cc_final: 0.7393 (OUTLIER) REVERT: E 234 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8398 (m-40) REVERT: E 238 ASN cc_start: 0.8933 (m110) cc_final: 0.8537 (t0) REVERT: F 290 ASN cc_start: 0.7489 (m-40) cc_final: 0.7114 (m110) REVERT: F 293 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7567 (tm-30) REVERT: F 329 PHE cc_start: 0.8812 (m-80) cc_final: 0.7861 (m-80) REVERT: F 348 SER cc_start: 0.7740 (m) cc_final: 0.7469 (p) REVERT: F 354 MET cc_start: 0.7705 (mmt) cc_final: 0.7246 (mmp) REVERT: F 358 LYS cc_start: 0.8011 (pmmt) cc_final: 0.7598 (tptt) REVERT: F 368 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6937 (mm) REVERT: F 371 GLU cc_start: 0.7925 (pt0) cc_final: 0.7668 (pt0) REVERT: F 376 GLU cc_start: 0.8553 (mp0) cc_final: 0.8048 (mp0) REVERT: F 386 TYR cc_start: 0.7715 (m-10) cc_final: 0.7355 (m-10) REVERT: F 396 GLU cc_start: 0.8355 (tp30) cc_final: 0.7752 (tp30) REVERT: I 154 TRP cc_start: 0.7514 (m100) cc_final: 0.7248 (m100) REVERT: I 240 ARG cc_start: 0.8415 (mtm-85) cc_final: 0.7688 (mtt90) REVERT: I 244 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7854 (mp0) REVERT: I 309 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8858 (p) REVERT: I 346 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8431 (mt-10) REVERT: I 390 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9272 (mm) REVERT: I 423 GLN cc_start: 0.8702 (tt0) cc_final: 0.8311 (tt0) REVERT: I 426 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8392 (mtmt) REVERT: I 454 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7206 (mt0) REVERT: I 457 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8018 (mt-10) outliers start: 62 outliers final: 34 residues processed: 290 average time/residue: 1.5502 time to fit residues: 509.7228 Evaluate side-chains 279 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 231 time to evaluate : 2.671 ------------------------------------------------------------------------------- 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 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 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 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 119 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 209 LYS 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 106 PHE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 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 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 169 SER 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 390 ILE Chi-restraints excluded: chain I residue 453 LEU Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU Chi-restraints excluded: chain I residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 ASN I 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.109440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.076288 restraints weight = 41959.861| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.10 r_work: 0.2879 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24276 Z= 0.137 Angle : 0.550 9.817 33153 Z= 0.295 Chirality : 0.040 0.220 3781 Planarity : 0.003 0.073 3861 Dihedral : 17.853 88.914 3967 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.40 % Allowed : 24.06 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.17), residues: 2616 helix: 1.88 (0.14), residues: 1451 sheet: 0.15 (0.32), residues: 244 loop : -0.17 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 539 HIS 0.004 0.001 HIS C 69 PHE 0.020 0.001 PHE C 408 TYR 0.015 0.001 TYR I 105 ARG 0.017 0.001 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 1181) hydrogen bonds : angle 3.79741 ( 3295) covalent geometry : bond 0.00318 (24276) covalent geometry : angle 0.54995 (33153) ********************** 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 301 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 2.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 GLU cc_start: 0.7683 (mp0) cc_final: 0.7227 (mp0) REVERT: A 678 ARG cc_start: 0.8085 (mtm180) cc_final: 0.7836 (ttp80) REVERT: A 914 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7147 (pp) REVERT: B 260 ARG cc_start: 0.6988 (ptp-110) cc_final: 0.6636 (ptp90) REVERT: C 46 SER cc_start: 0.9339 (m) cc_final: 0.9037 (p) REVERT: C 62 HIS cc_start: 0.8779 (OUTLIER) cc_final: 0.8508 (m170) REVERT: C 336 VAL cc_start: 0.8772 (OUTLIER) cc_final: 0.8487 (p) REVERT: C 412 PHE cc_start: 0.8375 (t80) cc_final: 0.7818 (t80) REVERT: D 141 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9298 (p) REVERT: D 155 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8226 (tm-30) REVERT: D 209 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7549 (tppp) REVERT: D 261 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8171 (tm-30) REVERT: D 270 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: E 106 PHE cc_start: 0.9354 (OUTLIER) cc_final: 0.8764 (p90) REVERT: E 230 ASP cc_start: 0.7861 (t0) cc_final: 0.7396 (OUTLIER) REVERT: E 234 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8337 (m-40) REVERT: E 238 ASN cc_start: 0.8934 (m110) cc_final: 0.8514 (t0) REVERT: F 290 ASN cc_start: 0.7483 (m-40) cc_final: 0.7077 (m110) REVERT: F 293 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7574 (tm-30) REVERT: F 336 ARG cc_start: 0.7759 (mtp180) cc_final: 0.6883 (mpp80) REVERT: F 348 SER cc_start: 0.7655 (m) cc_final: 0.7375 (p) REVERT: F 354 MET cc_start: 0.7704 (mmt) cc_final: 0.7219 (mmp) REVERT: F 358 LYS cc_start: 0.8003 (pmmt) cc_final: 0.7599 (tptt) REVERT: F 368 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.6908 (mm) REVERT: F 376 GLU cc_start: 0.8559 (mp0) cc_final: 0.8047 (mp0) REVERT: F 386 TYR cc_start: 0.7728 (m-10) cc_final: 0.7352 (m-10) REVERT: F 396 GLU cc_start: 0.8336 (tp30) cc_final: 0.7741 (tp30) REVERT: I 154 TRP cc_start: 0.7454 (m100) cc_final: 0.7213 (m100) REVERT: I 240 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.7721 (mtt90) REVERT: I 244 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7842 (mp0) REVERT: I 309 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8839 (p) REVERT: I 346 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8460 (mt-10) REVERT: I 390 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9256 (mm) REVERT: I 423 GLN cc_start: 0.8693 (tt0) cc_final: 0.8316 (tt0) REVERT: I 426 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8383 (mtmt) REVERT: I 434 ASP cc_start: 0.7982 (m-30) cc_final: 0.7713 (m-30) REVERT: I 454 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7147 (mt0) REVERT: I 457 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.7982 (mt-10) outliers start: 59 outliers final: 32 residues processed: 288 average time/residue: 1.5705 time to fit residues: 511.2415 Evaluate side-chains 274 residues out of total 2461 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 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 336 VAL 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 119 LEU Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 209 LYS 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 106 PHE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 441 ILE Chi-restraints excluded: chain F residue 289 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 393 ARG Chi-restraints excluded: chain I residue 89 MET Chi-restraints excluded: chain I residue 169 SER 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 390 ILE Chi-restraints excluded: chain I residue 454 GLN Chi-restraints excluded: chain I residue 457 GLU 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 27 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 502 GLN A 774 HIS ** C 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 GLN F 326 ASN I 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.109098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075544 restraints weight = 41747.111| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.12 r_work: 0.2874 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24276 Z= 0.147 Angle : 0.562 12.958 33153 Z= 0.300 Chirality : 0.041 0.212 3781 Planarity : 0.003 0.075 3861 Dihedral : 17.838 89.052 3966 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.36 % Allowed : 24.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.17), residues: 2616 helix: 1.88 (0.14), residues: 1452 sheet: 0.17 (0.32), residues: 244 loop : -0.14 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 539 HIS 0.004 0.001 HIS C 69 PHE 0.028 0.001 PHE F 345 TYR 0.015 0.001 TYR C 449 ARG 0.017 0.000 ARG E 216 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 1181) hydrogen bonds : angle 3.80054 ( 3295) covalent geometry : bond 0.00345 (24276) covalent geometry : angle 0.56177 (33153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21720.37 seconds wall clock time: 375 minutes 5.54 seconds (22505.54 seconds total)