Starting phenix.real_space_refine on Sun Sep 13 13:51:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eby_28002/09_2026/8eby_28002.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eby_28002/09_2026/8eby_28002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eby_28002/09_2026/8eby_28002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eby_28002/09_2026/8eby_28002.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8eby_28002/09_2026/8eby_28002.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eby_28002/09_2026/8eby_28002.cif" model { file = "/net/cci-nas-00/data/ceres_data/8eby_28002/09_2026/8eby_28002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eby_28002/09_2026/8eby_28002.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 6 6.06 5 P 45 5.49 5 S 147 5.16 5 C 14972 2.51 5 N 4102 2.21 5 O 4433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23709 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4882 Classifications: {'peptide': 604} Link IDs: {'CIS': 2, 'PTRANS': 24, 'TRANS': 577} Chain breaks: 2 Chain: "B" Number of atoms: 5457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5457 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 29, 'TRANS': 647} Chain breaks: 1 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1547 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 183} Chain breaks: 1 Chain: "D" Number of atoms: 3483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3483 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 412} Chain breaks: 1 Chain: "E" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2989 Classifications: {'peptide': 380} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 361} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2034 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 1 Chain: "G" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "H" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 409 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "K" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1450 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 166} Chain: "L" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 474 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "M" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 448 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5825 SG CYS B 116 53.297 37.029 41.202 1.00263.29 S ATOM 6134 SG CYS B 155 49.513 33.668 36.833 1.00300.18 S ATOM 5965 SG CYS B 134 51.622 39.585 35.448 1.00303.96 S ATOM 6423 SG CYS B 190 47.149 38.769 39.239 1.00271.00 S ATOM 18036 SG CYS E 345 38.051 62.356 131.419 1.00122.93 S ATOM 18058 SG CYS E 348 40.150 65.336 132.500 1.00116.67 S ATOM 18215 SG CYS E 368 38.606 65.341 129.030 1.00122.84 S ATOM 18236 SG CYS E 371 41.399 62.925 129.836 1.00118.26 S ATOM 18156 SG CYS E 360 36.552 51.504 125.996 1.00129.98 S ATOM 18174 SG CYS E 363 36.939 51.444 129.785 1.00135.09 S ATOM 18323 SG CYS E 382 39.645 52.947 127.641 1.00115.61 S ATOM 18340 SG CYS E 385 39.138 49.194 127.559 1.00119.48 S ATOM 17600 SG CYS E 291 75.688 37.349 121.894 1.00127.66 S ATOM 17622 SG CYS E 294 79.187 35.810 121.632 1.00140.91 S ATOM 17711 SG CYS E 305 78.141 38.296 119.053 1.00128.50 S ATOM 17734 SG CYS E 308 76.426 34.920 119.139 1.00140.97 S ATOM 20236 SG CYS F 268 56.176 37.648 111.865 1.00 96.74 S ATOM 20255 SG CYS F 271 53.681 39.644 113.945 1.00102.67 S ATOM 20340 SG CYS F 282 53.412 35.892 113.821 1.00125.77 S ATOM 20360 SG CYS F 285 52.562 37.945 110.734 1.00134.39 S ATOM 20128 SG CYS F 255 57.007 34.170 124.147 1.00120.27 S ATOM 20145 SG CYS F 257 54.346 31.472 123.794 1.00127.38 S ATOM 20294 SG CYS F 276 58.058 30.496 124.364 1.00121.49 S ATOM 21356 SG CYS K 105 47.369 99.660 21.740 1.00248.15 S ATOM 21380 SG CYS K 108 46.759 99.169 18.020 1.00257.96 S ATOM 21528 SG CYS K 126 49.369 97.058 19.858 1.00238.28 S ATOM 21550 SG CYS K 129 49.984 100.744 19.158 1.00238.81 S Time building chain proxies: 4.78, per 1000 atoms: 0.20 Number of scatterers: 23709 At special positions: 0 Unit cell: (119.52, 155.625, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 S 147 16.00 P 45 15.00 O 4433 8.00 N 4102 7.00 C 14972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 B1000 " pdb="FE4 SF4 B1000 " - pdb=" SG CYS B 190 " pdb="FE3 SF4 B1000 " - pdb=" SG CYS B 134 " pdb="FE1 SF4 B1000 " - pdb=" SG CYS B 116 " pdb="FE2 SF4 B1000 " - pdb=" SG CYS B 155 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN E 401 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 371 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 368 " pdb=" ZN E 402 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 382 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 360 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 363 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 271 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 282 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 285 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " pdb=" ZN F 402 " pdb="ZN ZN F 402 " - pdb=" NE2 HIS F 258 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 255 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 257 " pdb="ZN ZN F 402 " - pdb=" SG CYS F 276 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 126 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 129 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 108 " Number of angles added : 33 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5390 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 24 sheets defined 52.3% alpha, 10.7% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 2.66 Creating SS restraints... Processing helix chain 'A' and resid 92 through 104 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 132 through 143 Processing helix chain 'A' and resid 152 through 162 removed outlier: 4.096A pdb=" N SER A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 190 removed outlier: 4.370A pdb=" N ILE A 185 " --> pdb=" O HIS A 181 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLN A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN A 190 " --> pdb=" O GLN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 196 removed outlier: 3.597A pdb=" N ARG A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 196 " --> pdb=" O PRO A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 196' Processing helix chain 'A' and resid 273 through 275 No H-bonds generated for 'chain 'A' and resid 273 through 275' Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.859A pdb=" N ILE A 285 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N HIS A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 328 Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 369 through 382 Processing helix chain 'A' and resid 420 through 431 Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 451 through 458 removed outlier: 4.228A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.624A pdb=" N LEU A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A 481 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 499 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.881A pdb=" N ARG A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 536 Processing helix chain 'A' and resid 537 through 554 Processing helix chain 'A' and resid 564 through 574 removed outlier: 4.122A pdb=" N GLU A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 598 removed outlier: 4.100A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N HIS A 598 " --> pdb=" O GLN A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 642 Processing helix chain 'A' and resid 667 through 677 removed outlier: 3.997A pdb=" N ALA A 671 " --> pdb=" O THR A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 684 Processing helix chain 'A' and resid 705 through 718 removed outlier: 3.753A pdb=" N GLN A 709 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 35 Processing helix chain 'B' and resid 47 through 63 removed outlier: 3.531A pdb=" N SER B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 99 Processing helix chain 'B' and resid 129 through 138 Processing helix chain 'B' and resid 139 through 146 Processing helix chain 'B' and resid 156 through 165 removed outlier: 4.650A pdb=" N ALA B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 209 through 214 removed outlier: 3.597A pdb=" N ASP B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 removed outlier: 3.871A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.573A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 271 removed outlier: 3.994A pdb=" N GLU B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 335 removed outlier: 3.693A pdb=" N GLY B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG B 335 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 346 removed outlier: 4.221A pdb=" N TYR B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG B 343 " --> pdb=" O TYR B 339 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 344 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 345 " --> pdb=" O LYS B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 4.022A pdb=" N SER B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.834A pdb=" N ARG B 373 " --> pdb=" O ARG B 369 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 369 through 374' Processing helix chain 'B' and resid 374 through 380 removed outlier: 4.012A pdb=" N ARG B 380 " --> pdb=" O ALA B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 387 removed outlier: 3.730A pdb=" N THR B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 Processing helix chain 'B' and resid 440 through 449 Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 466 through 471 Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.570A pdb=" N ARG B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 529 removed outlier: 3.695A pdb=" N ALA B 529 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 555 Processing helix chain 'B' and resid 557 through 565 removed outlier: 3.735A pdb=" N ASN B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 590 removed outlier: 3.663A pdb=" N ASN B 590 " --> pdb=" O GLU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 608 removed outlier: 4.176A pdb=" N GLU B 606 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 644 Processing helix chain 'B' and resid 647 through 665 Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.819A pdb=" N GLU B 699 " --> pdb=" O ARG B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 725 Processing helix chain 'C' and resid 112 through 121 removed outlier: 3.546A pdb=" N MET C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 138 through 147 removed outlier: 3.589A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG C 146 " --> pdb=" O PHE C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 413 removed outlier: 3.859A pdb=" N ALA C 413 " --> pdb=" O GLN C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 422 removed outlier: 3.654A pdb=" N VAL C 421 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU C 422 " --> pdb=" O THR C 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 418 through 422' Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 454 through 479 removed outlier: 3.503A pdb=" N GLU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 516 removed outlier: 3.793A pdb=" N GLU C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Proline residue: C 507 - end of helix Processing helix chain 'C' and resid 520 through 547 removed outlier: 3.823A pdb=" N HIS C 524 " --> pdb=" O ASN C 520 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 25 removed outlier: 3.510A pdb=" N GLY D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 37 through 47 Processing helix chain 'D' and resid 49 through 59 removed outlier: 3.545A pdb=" N ASN D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 62 No H-bonds generated for 'chain 'D' and resid 60 through 62' Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 79 through 94 Processing helix chain 'D' and resid 111 through 123 Processing helix chain 'D' and resid 144 through 165 Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 197 through 206 Processing helix chain 'D' and resid 207 through 223 Processing helix chain 'D' and resid 224 through 226 No H-bonds generated for 'chain 'D' and resid 224 through 226' Processing helix chain 'D' and resid 229 through 242 Processing helix chain 'D' and resid 255 through 269 Processing helix chain 'D' and resid 284 through 290 Processing helix chain 'D' and resid 321 through 331 removed outlier: 3.509A pdb=" N ILE D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 357 Processing helix chain 'D' and resid 360 through 371 Processing helix chain 'D' and resid 373 through 379 Processing helix chain 'D' and resid 384 through 399 removed outlier: 4.145A pdb=" N ARG D 398 " --> pdb=" O TRP D 394 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASP D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 429 Processing helix chain 'D' and resid 444 through 462 removed outlier: 4.524A pdb=" N SER D 449 " --> pdb=" O PRO D 445 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 removed outlier: 3.553A pdb=" N ILE E 21 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 22 " --> pdb=" O TRP E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 42 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 79 through 99 Processing helix chain 'E' and resid 123 through 135 removed outlier: 3.888A pdb=" N HIS E 127 " --> pdb=" O ASN E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 157 Processing helix chain 'E' and resid 181 through 193 removed outlier: 4.015A pdb=" N LEU E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 216 Processing helix chain 'E' and resid 224 through 237 removed outlier: 3.743A pdb=" N SER E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 removed outlier: 3.681A pdb=" N ASP E 277 " --> pdb=" O MET E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 removed outlier: 3.546A pdb=" N LEU E 318 " --> pdb=" O SER E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 326 removed outlier: 4.187A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 378 Processing helix chain 'E' and resid 382 through 387 removed outlier: 3.782A pdb=" N HIS E 387 " --> pdb=" O PRO E 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'F' and resid 33 through 52 removed outlier: 3.965A pdb=" N ASN F 52 " --> pdb=" O HIS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 121 Processing helix chain 'F' and resid 132 through 151 removed outlier: 3.576A pdb=" N GLU F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 200 through 211 Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'F' and resid 234 through 241 removed outlier: 3.958A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 288 Processing helix chain 'G' and resid 13 through 27 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 49 through 64 removed outlier: 3.559A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 890 through 902 removed outlier: 3.771A pdb=" N ALA H 902 " --> pdb=" O ARG H 898 " (cutoff:3.500A) Processing helix chain 'H' and resid 908 through 915 Processing helix chain 'H' and resid 923 through 934 removed outlier: 3.630A pdb=" N LYS H 927 " --> pdb=" O THR H 923 " (cutoff:3.500A) Processing helix chain 'H' and resid 935 through 939 Processing helix chain 'K' and resid 115 through 122 Processing helix chain 'K' and resid 141 through 149 Processing helix chain 'K' and resid 151 through 157 Processing helix chain 'K' and resid 183 through 195 Processing helix chain 'K' and resid 199 through 232 removed outlier: 4.078A pdb=" N LEU K 226 " --> pdb=" O LYS K 222 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG K 228 " --> pdb=" O LYS K 224 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ALA K 229 " --> pdb=" O GLU K 225 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL K 230 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG K 231 " --> pdb=" O ARG K 227 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.815A pdb=" N ARG D 337 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL D 343 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG D 337 " --> pdb=" O MET D 341 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.670A pdb=" N GLU A 115 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 105 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 171 Processing sheet with id=AA4, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 391 removed outlier: 6.546A pdb=" N CYS A 390 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N THR A 409 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N SER A 408 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU A 362 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ASP A 441 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 364 " --> pdb=" O ASP A 441 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLY A 336 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR A 467 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE A 338 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL A 337 " --> pdb=" O LYS A 487 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 580 removed outlier: 6.401A pdb=" N ILE A 558 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE A 607 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL A 560 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE A 559 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE A 626 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 561 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU A 623 " --> pdb=" O TYR A 660 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU A 662 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN A 625 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N SER A 664 " --> pdb=" O GLN A 625 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 663 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 690 " --> pdb=" O GLU A 509 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 511 " --> pdb=" O ILE A 690 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 5 Processing sheet with id=AA8, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.806A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE B 455 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 231 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N THR B 457 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N PHE B 233 " --> pdb=" O THR B 457 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU B 70 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 107 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 250 through 251 Processing sheet with id=AB1, first strand: chain 'B' and resid 490 through 495 removed outlier: 3.696A pdb=" N CYS B 491 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N MET B 677 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 618 " --> pdb=" O VAL B 678 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ALA B 680 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET B 620 " --> pdb=" O ALA B 680 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 535 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N SER B 598 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA B 537 " --> pdb=" O SER B 598 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 67 removed outlier: 3.627A pdb=" N ILE D 109 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 185 through 186 Processing sheet with id=AB4, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AB5, first strand: chain 'D' and resid 431 through 435 removed outlier: 6.639A pdb=" N VAL D 442 " --> pdb=" O VAL D 432 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLU D 434 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU D 440 " --> pdb=" O GLU D 434 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN G 36 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 113 through 121 removed outlier: 6.683A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N GLU E 119 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ILE E 104 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N HIS E 60 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LEU E 168 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N TYR E 62 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE E 170 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL E 64 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 303 through 304 removed outlier: 4.094A pdb=" N THR E 311 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 257 through 258 removed outlier: 3.509A pdb=" N GLY E 288 " --> pdb=" O THR E 258 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 270 through 271 removed outlier: 3.809A pdb=" N SER E 270 " --> pdb=" O THR E 285 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR E 285 " --> pdb=" O SER E 270 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'E' and resid 332 through 335 Processing sheet with id=AC2, first strand: chain 'F' and resid 67 through 69 removed outlier: 7.984A pdb=" N LYS F 56 " --> pdb=" O GLU F 7 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN F 9 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA F 58 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU F 11 " --> pdb=" O ALA F 58 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE F 60 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE F 13 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER F 62 " --> pdb=" O ILE F 13 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL F 15 " --> pdb=" O SER F 62 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 8 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 190 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 253 through 254 Processing sheet with id=AC4, first strand: chain 'K' and resid 103 through 104 Processing sheet with id=AC5, first strand: chain 'K' and resid 138 through 140 Processing sheet with id=AC6, first strand: chain 'K' and resid 250 through 251 1053 hydrogen bonds defined for protein. 3048 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10205 1.43 - 1.64: 13862 1.64 - 1.86: 216 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 24295 Sorted by residual: bond pdb=" C3' DC L 22 " pdb=" C2' DC L 22 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 7.99e+00 bond pdb=" C3' DG M 49 " pdb=" C2' DG M 49 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.17e+00 bond pdb=" C3' DC L 10 " pdb=" C2' DC L 10 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.84e+00 bond pdb=" C3' DC M 45 " pdb=" C2' DC M 45 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.67e+00 bond pdb=" C1' DT L 17 " pdb=" N1 DT L 17 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.42e+00 ... (remaining 24290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 32527 1.62 - 3.24: 437 3.24 - 4.86: 59 4.86 - 6.48: 9 6.48 - 8.10: 3 Bond angle restraints: 33035 Sorted by residual: angle pdb=" N3 DT L 17 " pdb=" C4 DT L 17 " pdb=" O4 DT L 17 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT M 41 " pdb=" C4 DT M 41 " pdb=" O4 DT M 41 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT L 14 " pdb=" C4 DT L 14 " pdb=" O4 DT L 14 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT L 4 " pdb=" C4 DT L 4 " pdb=" O4 DT L 4 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT L 7 " pdb=" C4 DT L 7 " pdb=" O4 DT L 7 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 33030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.42: 14191 28.42 - 56.85: 393 56.85 - 85.27: 25 85.27 - 113.70: 1 113.70 - 142.12: 1 Dihedral angle restraints: 14611 sinusoidal: 6297 harmonic: 8314 Sorted by residual: dihedral pdb=" CA ASP A 70 " pdb=" C ASP A 70 " pdb=" N HIS A 71 " pdb=" CA HIS A 71 " ideal model delta harmonic sigma weight residual 0.00 -22.24 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" C4' DA L 9 " pdb=" C3' DA L 9 " pdb=" O3' DA L 9 " pdb=" P DC L 10 " ideal model delta sinusoidal sigma weight residual 220.00 77.88 142.12 1 3.50e+01 8.16e-04 1.40e+01 dihedral pdb=" CA ASP A 81 " pdb=" C ASP A 81 " pdb=" N GLY A 82 " pdb=" CA GLY A 82 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 14608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2264 0.027 - 0.054: 902 0.054 - 0.081: 280 0.081 - 0.108: 206 0.108 - 0.135: 44 Chirality restraints: 3696 Sorted by residual: chirality pdb=" CB VAL C 453 " pdb=" CA VAL C 453 " pdb=" CG1 VAL C 453 " pdb=" CG2 VAL C 453 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CB VAL A 92 " pdb=" CA VAL A 92 " pdb=" CG1 VAL A 92 " pdb=" CG2 VAL A 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE B 535 " pdb=" N ILE B 535 " pdb=" C ILE B 535 " pdb=" CB ILE B 535 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 3693 not shown) Planarity restraints: 4058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO A 583 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 353 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 354 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 354 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 354 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 373 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO D 374 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 374 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 374 " 0.019 5.00e-02 4.00e+02 ... (remaining 4055 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 487 2.69 - 3.25: 23295 3.25 - 3.80: 37739 3.80 - 4.35: 48778 4.35 - 4.90: 79113 Nonbonded interactions: 189412 Sorted by model distance: nonbonded pdb=" O ILE H 899 " pdb=" OG SER H 903 " model vdw 2.142 3.040 nonbonded pdb=" O PHE A 378 " pdb=" OG SER A 382 " model vdw 2.184 3.040 nonbonded pdb=" O LEU B 382 " pdb=" OG1 THR B 385 " model vdw 2.225 3.040 nonbonded pdb=" OG SER E 243 " pdb=" O ALA F 288 " model vdw 2.231 3.040 nonbonded pdb=" O LEU E 30 " pdb=" OG1 THR E 33 " model vdw 2.239 3.040 ... (remaining 189407 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 group one per residue 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: 1.800 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 28.030 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 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 : 0.002 0.037 24323 Z= 0.168 Angle : 0.512 12.728 33080 Z= 0.321 Chirality : 0.039 0.135 3696 Planarity : 0.003 0.059 4058 Dihedral : 11.969 142.123 9221 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.65 % Rotamer: Outliers : 2.23 % Allowed : 5.90 % Favored : 91.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2804 helix: 1.97 (0.15), residues: 1316 sheet: 0.45 (0.29), residues: 360 loop : -0.98 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 676 TYR 0.012 0.001 TYR A 534 PHE 0.010 0.001 PHE A 482 TRP 0.012 0.001 TRP A 511 HIS 0.004 0.000 HIS B 729 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.17 (24295) covalent geometry : angle 0.49335 / 0.32 (33035) hydrogen bonds : bond 0.16640 / 10.83 ( 1106) hydrogen bonds : angle 5.66740 / 4.06 ( 3154) metal coordination : bond 0.00339 / 0.21 ( 28) metal coordination : angle 3.72588 / 1.91 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 900 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7349 (ptt) cc_final: 0.7143 (ptt) REVERT: A 68 LYS cc_start: 0.6400 (mtmt) cc_final: 0.5743 (tttm) REVERT: A 94 LYS cc_start: 0.7609 (ptpt) cc_final: 0.6960 (ptpt) REVERT: A 98 ASP cc_start: 0.7477 (m-30) cc_final: 0.7160 (m-30) REVERT: A 138 GLU cc_start: 0.7499 (pt0) cc_final: 0.7238 (tp30) REVERT: A 163 TYR cc_start: 0.7720 (t80) cc_final: 0.7483 (t80) REVERT: A 171 LYS cc_start: 0.7775 (tttp) cc_final: 0.7216 (tttp) REVERT: A 172 HIS cc_start: 0.7801 (m170) cc_final: 0.7404 (m90) REVERT: A 174 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.6665 (mtp-110) REVERT: A 175 TYR cc_start: 0.8247 (m-80) cc_final: 0.7917 (m-10) REVERT: A 178 GLU cc_start: 0.6119 (tm-30) cc_final: 0.5700 (tm-30) REVERT: A 191 ASP cc_start: 0.7174 (t0) cc_final: 0.6708 (t0) REVERT: A 272 VAL cc_start: 0.8466 (m) cc_final: 0.8174 (m) REVERT: A 273 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7158 (mmtm) REVERT: A 276 MET cc_start: 0.7391 (ttm) cc_final: 0.6928 (ttm) REVERT: A 278 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6934 (tm-30) REVERT: A 287 LEU cc_start: 0.8479 (mt) cc_final: 0.8244 (mm) REVERT: A 299 ASN cc_start: 0.7481 (p0) cc_final: 0.6945 (p0) REVERT: A 332 ARG cc_start: 0.8059 (mpp80) cc_final: 0.7096 (ptp90) REVERT: A 347 SER cc_start: 0.8577 (m) cc_final: 0.7753 (t) REVERT: A 359 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8392 (mmtt) REVERT: A 373 GLN cc_start: 0.7675 (tp40) cc_final: 0.7423 (tp40) REVERT: A 375 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7703 (ttpt) REVERT: A 418 LYS cc_start: 0.7561 (tmmt) cc_final: 0.7057 (tmmt) REVERT: A 419 ARG cc_start: 0.8105 (ttm170) cc_final: 0.7666 (tpp80) REVERT: A 425 ARG cc_start: 0.7198 (mtt-85) cc_final: 0.6875 (mtt-85) REVERT: A 457 ILE cc_start: 0.7885 (tt) cc_final: 0.7631 (tt) REVERT: A 463 LYS cc_start: 0.8671 (mttt) cc_final: 0.8333 (mttp) REVERT: A 470 LEU cc_start: 0.8748 (tp) cc_final: 0.8407 (tp) REVERT: A 476 LYS cc_start: 0.8194 (mttt) cc_final: 0.7551 (mmmm) REVERT: A 478 VAL cc_start: 0.8105 (t) cc_final: 0.7837 (m) REVERT: A 487 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8296 (mtpp) REVERT: A 490 GLU cc_start: 0.7007 (tp30) cc_final: 0.6562 (tp30) REVERT: A 504 LYS cc_start: 0.8491 (ttpt) cc_final: 0.7937 (pttt) REVERT: A 510 VAL cc_start: 0.7790 (OUTLIER) cc_final: 0.7514 (p) REVERT: A 525 ILE cc_start: 0.8194 (tp) cc_final: 0.7844 (tp) REVERT: A 526 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7400 (tppt) REVERT: A 556 ASP cc_start: 0.7244 (m-30) cc_final: 0.6949 (m-30) REVERT: A 564 ASN cc_start: 0.8160 (t0) cc_final: 0.7592 (t0) REVERT: A 570 GLU cc_start: 0.6936 (pm20) cc_final: 0.6569 (pm20) REVERT: A 579 TYR cc_start: 0.7535 (p90) cc_final: 0.7088 (p90) REVERT: A 609 LYS cc_start: 0.8135 (tttt) cc_final: 0.7878 (ttpp) REVERT: A 632 SER cc_start: 0.8131 (p) cc_final: 0.7868 (p) REVERT: A 644 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8089 (pp) REVERT: A 659 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7362 (p90) REVERT: A 668 GLN cc_start: 0.7372 (mt0) cc_final: 0.7168 (mt0) REVERT: A 669 GLU cc_start: 0.7469 (tt0) cc_final: 0.7146 (tt0) REVERT: A 675 LYS cc_start: 0.8345 (ptmt) cc_final: 0.8016 (ttpt) REVERT: A 677 GLN cc_start: 0.7759 (mt0) cc_final: 0.7319 (mt0) REVERT: A 682 ASP cc_start: 0.6849 (m-30) cc_final: 0.6642 (m-30) REVERT: A 683 GLN cc_start: 0.7591 (mm-40) cc_final: 0.6932 (mm-40) REVERT: A 688 LYS cc_start: 0.8160 (tttt) cc_final: 0.7856 (ttmt) REVERT: A 703 PHE cc_start: 0.8042 (m-10) cc_final: 0.7533 (m-80) REVERT: A 715 LYS cc_start: 0.8436 (ptmt) cc_final: 0.8037 (ptmm) REVERT: B 40 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7519 (mm) REVERT: B 91 LEU cc_start: 0.7981 (mm) cc_final: 0.7613 (mm) REVERT: B 158 TYR cc_start: 0.7431 (t80) cc_final: 0.6930 (t80) REVERT: B 235 GLU cc_start: 0.7540 (tp30) cc_final: 0.7239 (tp30) REVERT: B 243 CYS cc_start: 0.8369 (m) cc_final: 0.7924 (m) REVERT: B 445 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7101 (mmtt) REVERT: B 455 ILE cc_start: 0.7467 (mm) cc_final: 0.7263 (mm) REVERT: B 487 ARG cc_start: 0.7213 (ptt-90) cc_final: 0.6589 (ptt-90) REVERT: B 512 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7175 (mm-30) REVERT: B 518 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7763 (mtm110) REVERT: B 533 ASP cc_start: 0.7335 (p0) cc_final: 0.6910 (p0) REVERT: B 570 GLU cc_start: 0.5912 (tm-30) cc_final: 0.4944 (tm-30) REVERT: B 586 GLU cc_start: 0.7443 (pp20) cc_final: 0.7169 (pp20) REVERT: B 634 LYS cc_start: 0.6746 (ptpp) cc_final: 0.6390 (mtmm) REVERT: B 638 GLU cc_start: 0.6893 (mm-30) cc_final: 0.6229 (mm-30) REVERT: B 641 ARG cc_start: 0.7255 (ttm-80) cc_final: 0.6409 (mtm-85) REVERT: B 642 ASP cc_start: 0.6555 (p0) cc_final: 0.6294 (p0) REVERT: B 648 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6566 (tm-30) REVERT: B 662 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7763 (pp30) REVERT: B 668 ILE cc_start: 0.8227 (mm) cc_final: 0.7913 (mm) REVERT: B 669 ARG cc_start: 0.6513 (mpt90) cc_final: 0.6197 (mpt90) REVERT: B 681 ASP cc_start: 0.7711 (t0) cc_final: 0.7452 (t0) REVERT: B 686 ARG cc_start: 0.7049 (ttm-80) cc_final: 0.6616 (mmm-85) REVERT: B 692 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7884 (mmtm) REVERT: B 707 ASN cc_start: 0.7419 (t0) cc_final: 0.7064 (t0) REVERT: B 709 THR cc_start: 0.8157 (p) cc_final: 0.7639 (t) REVERT: B 712 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6066 (pt0) REVERT: B 719 TYR cc_start: 0.8064 (t80) cc_final: 0.7824 (t80) REVERT: B 724 MET cc_start: 0.6534 (mmm) cc_final: 0.6059 (mmm) REVERT: C 405 GLN cc_start: 0.7913 (mt0) cc_final: 0.7542 (mt0) REVERT: C 414 TYR cc_start: 0.7154 (t80) cc_final: 0.6882 (t80) REVERT: C 442 GLN cc_start: 0.5033 (OUTLIER) cc_final: 0.3754 (pp30) REVERT: C 473 ARG cc_start: 0.7472 (tmt170) cc_final: 0.7242 (ttt180) REVERT: C 475 PHE cc_start: 0.7509 (t80) cc_final: 0.7033 (t80) REVERT: C 498 GLU cc_start: 0.8700 (mt-10) cc_final: 0.8388 (mp0) REVERT: C 506 CYS cc_start: 0.6405 (t) cc_final: 0.6200 (m) REVERT: C 517 LEU cc_start: 0.4877 (OUTLIER) cc_final: 0.4128 (mm) REVERT: C 524 HIS cc_start: 0.8098 (t-90) cc_final: 0.7873 (t-170) REVERT: C 528 MET cc_start: 0.8960 (mtp) cc_final: 0.8521 (mtm) REVERT: D 20 GLN cc_start: 0.8728 (mt0) cc_final: 0.8407 (mp10) REVERT: D 34 LEU cc_start: 0.8637 (mt) cc_final: 0.8261 (mt) REVERT: D 50 SER cc_start: 0.8419 (m) cc_final: 0.7711 (t) REVERT: D 119 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7796 (mmm-85) REVERT: D 120 ILE cc_start: 0.7900 (mt) cc_final: 0.7626 (mm) REVERT: D 173 GLN cc_start: 0.8720 (tt0) cc_final: 0.8401 (pp30) REVERT: D 174 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7973 (p0) REVERT: D 179 LEU cc_start: 0.8482 (mt) cc_final: 0.7909 (mm) REVERT: D 205 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7276 (mm) REVERT: D 218 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7126 (tp-100) REVERT: D 219 TYR cc_start: 0.7927 (t80) cc_final: 0.7174 (t80) REVERT: D 228 MET cc_start: 0.4654 (mtm) cc_final: 0.4044 (mtm) REVERT: D 243 SER cc_start: 0.7656 (m) cc_final: 0.6972 (p) REVERT: D 244 THR cc_start: 0.8057 (m) cc_final: 0.7849 (t) REVERT: D 254 MET cc_start: 0.6830 (mtt) cc_final: 0.5915 (mtp) REVERT: D 258 LEU cc_start: 0.8250 (mt) cc_final: 0.7880 (tp) REVERT: D 261 PHE cc_start: 0.7964 (t80) cc_final: 0.7663 (t80) REVERT: D 263 GLN cc_start: 0.8411 (mm-40) cc_final: 0.7875 (mm-40) REVERT: D 267 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8118 (mt-10) REVERT: D 268 PHE cc_start: 0.7893 (m-10) cc_final: 0.7556 (m-10) REVERT: D 276 ARG cc_start: 0.7350 (ttt90) cc_final: 0.6788 (ttt90) REVERT: D 284 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8187 (p) REVERT: D 345 GLN cc_start: 0.8127 (tt0) cc_final: 0.7887 (tt0) REVERT: D 362 GLN cc_start: 0.8135 (tp40) cc_final: 0.7832 (tp40) REVERT: D 369 ARG cc_start: 0.7137 (ttm170) cc_final: 0.6918 (ttm170) REVERT: D 371 ARG cc_start: 0.7607 (mmt180) cc_final: 0.7268 (mpt180) REVERT: D 395 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7090 (tm-30) REVERT: D 397 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6970 (mm-30) REVERT: D 433 PHE cc_start: 0.7842 (t80) cc_final: 0.6997 (t80) REVERT: D 439 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7449 (mtp85) REVERT: E 12 GLU cc_start: 0.7721 (pt0) cc_final: 0.7290 (pt0) REVERT: E 16 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6360 (mm-30) REVERT: E 36 ASP cc_start: 0.7756 (t0) cc_final: 0.7556 (t0) REVERT: E 70 THR cc_start: 0.8226 (p) cc_final: 0.7702 (t) REVERT: E 72 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7378 (mm-30) REVERT: E 73 ASP cc_start: 0.6919 (t0) cc_final: 0.5333 (t0) REVERT: E 75 ASP cc_start: 0.7232 (m-30) cc_final: 0.6306 (m-30) REVERT: E 79 ASN cc_start: 0.7743 (p0) cc_final: 0.7451 (p0) REVERT: E 80 ARG cc_start: 0.7729 (mtt180) cc_final: 0.6695 (mtt180) REVERT: E 89 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6414 (mt-10) REVERT: E 96 PHE cc_start: 0.7341 (m-80) cc_final: 0.7052 (m-80) REVERT: E 101 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8104 (pt) REVERT: E 112 LYS cc_start: 0.7783 (mtmt) cc_final: 0.7345 (mttp) REVERT: E 125 ARG cc_start: 0.7367 (mtt180) cc_final: 0.7161 (mtt180) REVERT: E 132 LYS cc_start: 0.8547 (mttt) cc_final: 0.8234 (mttt) REVERT: E 139 CYS cc_start: 0.7316 (m) cc_final: 0.7074 (m) REVERT: E 153 MET cc_start: 0.7022 (ttp) cc_final: 0.6661 (ttm) REVERT: E 154 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7199 (tm-30) REVERT: E 157 LYS cc_start: 0.8098 (tttt) cc_final: 0.7743 (tttt) REVERT: E 166 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6495 (mt-10) REVERT: E 174 LEU cc_start: 0.8671 (mt) cc_final: 0.8303 (mp) REVERT: E 177 CYS cc_start: 0.7473 (m) cc_final: 0.6652 (m) REVERT: E 181 ASN cc_start: 0.8191 (t0) cc_final: 0.7681 (t0) REVERT: E 184 ASP cc_start: 0.6948 (m-30) cc_final: 0.6738 (m-30) REVERT: E 187 LYS cc_start: 0.7762 (mttt) cc_final: 0.7535 (mttt) REVERT: E 190 LYS cc_start: 0.8012 (tptt) cc_final: 0.7738 (tptt) REVERT: E 193 LYS cc_start: 0.8254 (mttt) cc_final: 0.8023 (mttt) REVERT: E 202 SER cc_start: 0.8074 (m) cc_final: 0.7755 (p) REVERT: E 289 TYR cc_start: 0.7980 (m-80) cc_final: 0.7280 (m-80) REVERT: E 299 CYS cc_start: 0.7739 (m) cc_final: 0.7524 (m) REVERT: E 333 GLU cc_start: 0.7916 (tt0) cc_final: 0.7657 (tt0) REVERT: E 353 LYS cc_start: 0.8291 (mttt) cc_final: 0.7687 (mttt) REVERT: E 366 VAL cc_start: 0.8490 (m) cc_final: 0.8226 (m) REVERT: F 16 ASP cc_start: 0.7876 (t0) cc_final: 0.7326 (t0) REVERT: F 34 LEU cc_start: 0.7165 (tp) cc_final: 0.6881 (tt) REVERT: F 39 ASP cc_start: 0.7767 (m-30) cc_final: 0.7118 (m-30) REVERT: F 42 MET cc_start: 0.7774 (mtm) cc_final: 0.7442 (mtt) REVERT: F 56 LYS cc_start: 0.7863 (mmtt) cc_final: 0.7601 (mmtt) REVERT: F 60 ILE cc_start: 0.8564 (mt) cc_final: 0.8199 (tt) REVERT: F 105 THR cc_start: 0.7938 (m) cc_final: 0.7667 (p) REVERT: F 109 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7409 (mt-10) REVERT: F 116 LYS cc_start: 0.7814 (mttt) cc_final: 0.7451 (mmmm) REVERT: F 139 LYS cc_start: 0.8364 (mttt) cc_final: 0.8061 (mtpp) REVERT: F 149 LYS cc_start: 0.7675 (mttt) cc_final: 0.7315 (mttt) REVERT: F 158 LYS cc_start: 0.8270 (mttt) cc_final: 0.7689 (mttt) REVERT: F 172 LEU cc_start: 0.8219 (mt) cc_final: 0.7958 (mm) REVERT: F 205 GLN cc_start: 0.8153 (mt0) cc_final: 0.7948 (mt0) REVERT: F 224 LEU cc_start: 0.8443 (tp) cc_final: 0.7934 (tp) REVERT: F 226 TYR cc_start: 0.8211 (m-80) cc_final: 0.7916 (m-80) REVERT: F 249 VAL cc_start: 0.7794 (t) cc_final: 0.7501 (p) REVERT: F 252 ARG cc_start: 0.7827 (mtm180) cc_final: 0.7308 (ptp90) REVERT: F 266 TYR cc_start: 0.7813 (m-80) cc_final: 0.7059 (m-80) REVERT: F 267 VAL cc_start: 0.8482 (t) cc_final: 0.8206 (m) REVERT: F 278 PHE cc_start: 0.7548 (t80) cc_final: 0.7222 (t80) REVERT: G 8 VAL cc_start: 0.8460 (t) cc_final: 0.8120 (m) REVERT: G 9 LEU cc_start: 0.8112 (tt) cc_final: 0.7829 (tp) REVERT: G 12 CYS cc_start: 0.8529 (p) cc_final: 0.7701 (p) REVERT: G 16 MET cc_start: 0.8078 (mmt) cc_final: 0.7275 (mmm) REVERT: G 43 VAL cc_start: 0.8052 (m) cc_final: 0.7484 (p) REVERT: G 66 PHE cc_start: 0.8449 (t80) cc_final: 0.7920 (t80) REVERT: H 926 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6288 (tp30) REVERT: K 150 LEU cc_start: 0.8119 (mt) cc_final: 0.7657 (mt) REVERT: K 187 VAL cc_start: 0.8520 (t) cc_final: 0.8258 (m) REVERT: K 188 LYS cc_start: 0.8028 (tttt) cc_final: 0.7759 (tttt) REVERT: K 204 LYS cc_start: 0.8046 (ptpp) cc_final: 0.7594 (pttm) REVERT: K 211 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7779 (ttm-80) REVERT: K 222 LYS cc_start: 0.8105 (pttm) cc_final: 0.7892 (pttp) REVERT: K 263 MET cc_start: 0.5585 (mmm) cc_final: 0.5211 (mmm) outliers start: 56 outliers final: 18 residues processed: 941 average time/residue: 0.1824 time to fit residues: 254.7805 Evaluate side-chains 785 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 755 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS A 499 ASN B 238 ASN B 241 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 ASN ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 HIS D 363 GLN D 458 GLN E 74 GLN E 349 GLN ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 185 GLN F 248 HIS K 146 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.158128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128948 restraints weight = 40911.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132850 restraints weight = 19760.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.135395 restraints weight = 12157.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.137004 restraints weight = 8789.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138045 restraints weight = 7150.719| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24323 Z= 0.157 Angle : 0.636 13.053 33080 Z= 0.320 Chirality : 0.042 0.174 3696 Planarity : 0.005 0.074 4058 Dihedral : 13.152 146.276 3631 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.71 % Allowed : 14.47 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2804 helix: 1.57 (0.15), residues: 1347 sheet: 0.27 (0.28), residues: 365 loop : -1.02 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 94 TYR 0.026 0.002 TYR K 116 PHE 0.019 0.002 PHE A 541 TRP 0.020 0.001 TRP E 11 HIS 0.024 0.001 HIS D 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (24295) covalent geometry : angle 0.61461 / 0.32 (33035) hydrogen bonds : bond 0.04512 / 3.01 ( 1106) hydrogen bonds : angle 4.78975 / 3.41 ( 3154) metal coordination : bond 0.00719 / 0.39 ( 28) metal coordination : angle 4.48541 / 2.35 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 782 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7714 (mp10) REVERT: A 68 LYS cc_start: 0.6193 (mtmt) cc_final: 0.5764 (tttm) REVERT: A 98 ASP cc_start: 0.7201 (m-30) cc_final: 0.6949 (m-30) REVERT: A 157 LYS cc_start: 0.8163 (ptmm) cc_final: 0.7802 (ttpp) REVERT: A 158 LEU cc_start: 0.8231 (mt) cc_final: 0.8027 (mt) REVERT: A 163 TYR cc_start: 0.7786 (t80) cc_final: 0.7479 (t80) REVERT: A 167 LYS cc_start: 0.7821 (mttp) cc_final: 0.7403 (mtpp) REVERT: A 168 LEU cc_start: 0.8275 (tt) cc_final: 0.7949 (tp) REVERT: A 174 ARG cc_start: 0.7718 (mmm-85) cc_final: 0.7225 (ttm110) REVERT: A 176 PHE cc_start: 0.8125 (m-80) cc_final: 0.7504 (m-80) REVERT: A 272 VAL cc_start: 0.8338 (m) cc_final: 0.8105 (p) REVERT: A 273 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7763 (ttpt) REVERT: A 282 LYS cc_start: 0.8483 (tttt) cc_final: 0.8128 (ttmm) REVERT: A 299 ASN cc_start: 0.6939 (p0) cc_final: 0.6419 (p0) REVERT: A 310 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8086 (pt) REVERT: A 347 SER cc_start: 0.8461 (m) cc_final: 0.8007 (p) REVERT: A 372 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6700 (tp30) REVERT: A 373 GLN cc_start: 0.7747 (tp40) cc_final: 0.7540 (tp40) REVERT: A 375 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7881 (tttm) REVERT: A 392 PHE cc_start: 0.7519 (t80) cc_final: 0.7162 (t80) REVERT: A 418 LYS cc_start: 0.7470 (tmmt) cc_final: 0.7095 (tmmt) REVERT: A 419 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7418 (tpp80) REVERT: A 424 GLU cc_start: 0.7253 (tp30) cc_final: 0.7043 (mm-30) REVERT: A 457 ILE cc_start: 0.8053 (tt) cc_final: 0.7846 (tt) REVERT: A 463 LYS cc_start: 0.8709 (mttt) cc_final: 0.8302 (mttp) REVERT: A 470 LEU cc_start: 0.8785 (tp) cc_final: 0.8111 (tp) REVERT: A 476 LYS cc_start: 0.8212 (mttt) cc_final: 0.7662 (mttm) REVERT: A 478 VAL cc_start: 0.8333 (t) cc_final: 0.8079 (m) REVERT: A 504 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8301 (ptmt) REVERT: A 510 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7598 (p) REVERT: A 518 PHE cc_start: 0.7568 (m-80) cc_final: 0.7354 (m-10) REVERT: A 525 ILE cc_start: 0.8353 (tp) cc_final: 0.8099 (tp) REVERT: A 554 ARG cc_start: 0.7429 (ttm-80) cc_final: 0.7185 (ttp80) REVERT: A 556 ASP cc_start: 0.7369 (m-30) cc_final: 0.7052 (m-30) REVERT: A 564 ASN cc_start: 0.8396 (t0) cc_final: 0.7754 (t0) REVERT: A 570 GLU cc_start: 0.6881 (pm20) cc_final: 0.6489 (pm20) REVERT: A 579 TYR cc_start: 0.7526 (p90) cc_final: 0.6906 (p90) REVERT: A 632 SER cc_start: 0.7903 (p) cc_final: 0.7596 (p) REVERT: A 642 ARG cc_start: 0.7239 (mtp85) cc_final: 0.7021 (mtp85) REVERT: A 644 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8202 (pp) REVERT: A 659 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7447 (p90) REVERT: A 670 MET cc_start: 0.8118 (mmm) cc_final: 0.7675 (mmm) REVERT: A 677 GLN cc_start: 0.7740 (mt0) cc_final: 0.7350 (mt0) REVERT: A 678 ARG cc_start: 0.7300 (ptt180) cc_final: 0.7044 (ptt180) REVERT: A 682 ASP cc_start: 0.6862 (m-30) cc_final: 0.6606 (m-30) REVERT: A 683 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7163 (mm-40) REVERT: A 688 LYS cc_start: 0.8259 (tttt) cc_final: 0.7853 (ttmt) REVERT: A 715 LYS cc_start: 0.8156 (ptmt) cc_final: 0.7952 (ptmm) REVERT: B 42 MET cc_start: 0.7105 (mtp) cc_final: 0.6567 (mtp) REVERT: B 48 LYS cc_start: 0.7638 (ttpp) cc_final: 0.7026 (mtpp) REVERT: B 91 LEU cc_start: 0.7931 (mm) cc_final: 0.7644 (mm) REVERT: B 158 TYR cc_start: 0.7146 (t80) cc_final: 0.6756 (t80) REVERT: B 243 CYS cc_start: 0.8219 (m) cc_final: 0.7764 (m) REVERT: B 393 ASP cc_start: 0.7640 (m-30) cc_final: 0.7436 (m-30) REVERT: B 414 PHE cc_start: 0.6812 (m-80) cc_final: 0.6440 (m-80) REVERT: B 445 LYS cc_start: 0.7697 (mmtt) cc_final: 0.7183 (mmtt) REVERT: B 455 ILE cc_start: 0.7601 (mm) cc_final: 0.7383 (mm) REVERT: B 466 ILE cc_start: 0.7527 (tt) cc_final: 0.7084 (tp) REVERT: B 469 LYS cc_start: 0.7671 (ptpp) cc_final: 0.7365 (ptpp) REVERT: B 507 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7438 (mttm) REVERT: B 512 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6919 (mm-30) REVERT: B 533 ASP cc_start: 0.7153 (p0) cc_final: 0.6800 (p0) REVERT: B 559 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: B 586 GLU cc_start: 0.7081 (pp20) cc_final: 0.6769 (pp20) REVERT: B 589 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6374 (mm-30) REVERT: B 620 MET cc_start: 0.7657 (mmm) cc_final: 0.7038 (mmm) REVERT: B 638 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6178 (mm-30) REVERT: B 641 ARG cc_start: 0.7489 (ttm-80) cc_final: 0.6825 (mtm-85) REVERT: B 662 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7677 (pp30) REVERT: B 668 ILE cc_start: 0.8151 (mm) cc_final: 0.7811 (mm) REVERT: B 681 ASP cc_start: 0.7905 (t0) cc_final: 0.7631 (t0) REVERT: B 719 TYR cc_start: 0.8131 (t80) cc_final: 0.7828 (t80) REVERT: C 442 GLN cc_start: 0.4766 (OUTLIER) cc_final: 0.3728 (pp30) REVERT: C 475 PHE cc_start: 0.6857 (t80) cc_final: 0.6546 (t80) REVERT: C 501 GLN cc_start: 0.8129 (tp40) cc_final: 0.7692 (tp40) REVERT: C 528 MET cc_start: 0.8575 (mtp) cc_final: 0.8242 (mtm) REVERT: D 50 SER cc_start: 0.8432 (m) cc_final: 0.7905 (t) REVERT: D 81 LYS cc_start: 0.8619 (tttt) cc_final: 0.8108 (tttm) REVERT: D 215 PHE cc_start: 0.8256 (t80) cc_final: 0.7643 (t80) REVERT: D 218 GLN cc_start: 0.7583 (mm-40) cc_final: 0.7136 (tm-30) REVERT: D 219 TYR cc_start: 0.7621 (t80) cc_final: 0.7379 (t80) REVERT: D 243 SER cc_start: 0.7826 (m) cc_final: 0.7432 (p) REVERT: D 254 MET cc_start: 0.6156 (mtt) cc_final: 0.5497 (mtp) REVERT: D 258 LEU cc_start: 0.8083 (mt) cc_final: 0.7732 (tp) REVERT: D 260 ASN cc_start: 0.7486 (t0) cc_final: 0.6554 (t0) REVERT: D 261 PHE cc_start: 0.7948 (t80) cc_final: 0.7320 (t80) REVERT: D 263 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7832 (mm-40) REVERT: D 276 ARG cc_start: 0.6883 (ttt90) cc_final: 0.6433 (ttt90) REVERT: D 284 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8329 (p) REVERT: D 362 GLN cc_start: 0.8193 (tp40) cc_final: 0.7879 (tp40) REVERT: D 395 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6969 (tm-30) REVERT: D 397 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6915 (mm-30) REVERT: D 433 PHE cc_start: 0.7365 (t80) cc_final: 0.6662 (t80) REVERT: E 16 GLU cc_start: 0.6429 (mm-30) cc_final: 0.6107 (mm-30) REVERT: E 70 THR cc_start: 0.8261 (p) cc_final: 0.7893 (t) REVERT: E 72 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7138 (mm-30) REVERT: E 73 ASP cc_start: 0.7195 (t0) cc_final: 0.5803 (t0) REVERT: E 75 ASP cc_start: 0.7224 (m-30) cc_final: 0.6623 (m-30) REVERT: E 80 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7089 (mtt180) REVERT: E 89 GLU cc_start: 0.6407 (mt-10) cc_final: 0.6146 (mt-10) REVERT: E 96 PHE cc_start: 0.7520 (m-80) cc_final: 0.7218 (m-80) REVERT: E 101 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7944 (pt) REVERT: E 112 LYS cc_start: 0.7849 (mtmt) cc_final: 0.7548 (mttt) REVERT: E 125 ARG cc_start: 0.7060 (mtt180) cc_final: 0.6844 (mtt180) REVERT: E 132 LYS cc_start: 0.8479 (mttt) cc_final: 0.8232 (mttt) REVERT: E 154 GLN cc_start: 0.7297 (tm-30) cc_final: 0.7059 (tm-30) REVERT: E 159 MET cc_start: 0.7351 (mmm) cc_final: 0.7084 (mmm) REVERT: E 166 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6692 (mt-10) REVERT: E 174 LEU cc_start: 0.8624 (mt) cc_final: 0.8384 (mp) REVERT: E 177 CYS cc_start: 0.7475 (m) cc_final: 0.6708 (m) REVERT: E 181 ASN cc_start: 0.8058 (t0) cc_final: 0.7721 (t0) REVERT: E 184 ASP cc_start: 0.6710 (m-30) cc_final: 0.6371 (m-30) REVERT: E 193 LYS cc_start: 0.8245 (mttt) cc_final: 0.7578 (ttmm) REVERT: E 273 MET cc_start: 0.6275 (mmm) cc_final: 0.5998 (mmm) REVERT: E 299 CYS cc_start: 0.7676 (m) cc_final: 0.7396 (m) REVERT: E 322 TYR cc_start: 0.8224 (m-10) cc_final: 0.7698 (m-80) REVERT: E 333 GLU cc_start: 0.7746 (tt0) cc_final: 0.7474 (tt0) REVERT: E 353 LYS cc_start: 0.8119 (mttt) cc_final: 0.7594 (mttt) REVERT: F 16 ASP cc_start: 0.7826 (t0) cc_final: 0.7453 (t0) REVERT: F 55 ASN cc_start: 0.7840 (m-40) cc_final: 0.7317 (m110) REVERT: F 60 ILE cc_start: 0.8635 (mt) cc_final: 0.8365 (tt) REVERT: F 103 LEU cc_start: 0.8121 (mt) cc_final: 0.7755 (mt) REVERT: F 105 THR cc_start: 0.8281 (m) cc_final: 0.8036 (p) REVERT: F 113 GLU cc_start: 0.7486 (tt0) cc_final: 0.7234 (tt0) REVERT: F 116 LYS cc_start: 0.8214 (mttt) cc_final: 0.7824 (mmmm) REVERT: F 139 LYS cc_start: 0.8632 (mttt) cc_final: 0.8333 (mtpp) REVERT: F 149 LYS cc_start: 0.7965 (mttt) cc_final: 0.7708 (mttt) REVERT: F 150 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6933 (mt-10) REVERT: F 172 LEU cc_start: 0.8190 (mt) cc_final: 0.7981 (mm) REVERT: F 224 LEU cc_start: 0.8544 (tp) cc_final: 0.8269 (tp) REVERT: F 226 TYR cc_start: 0.8004 (m-80) cc_final: 0.7637 (m-80) REVERT: F 229 TRP cc_start: 0.8257 (t60) cc_final: 0.8052 (t60) REVERT: F 249 VAL cc_start: 0.8058 (t) cc_final: 0.7765 (p) REVERT: G 9 LEU cc_start: 0.8360 (tt) cc_final: 0.8123 (tp) REVERT: G 12 CYS cc_start: 0.8411 (p) cc_final: 0.7757 (p) REVERT: G 16 MET cc_start: 0.8171 (mmt) cc_final: 0.7317 (mmm) REVERT: G 43 VAL cc_start: 0.8540 (m) cc_final: 0.8024 (p) REVERT: G 66 PHE cc_start: 0.8467 (t80) cc_final: 0.8004 (t80) REVERT: H 926 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6100 (tp30) REVERT: K 188 LYS cc_start: 0.8135 (tttt) cc_final: 0.7833 (tttt) REVERT: K 212 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6965 (mp0) outliers start: 93 outliers final: 52 residues processed: 839 average time/residue: 0.1754 time to fit residues: 219.6924 Evaluate side-chains 794 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 731 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 514 ILE Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 712 GLU Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 271 GLU Chi-restraints excluded: chain K residue 273 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 59 optimal weight: 0.3980 chunk 139 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 238 optimal weight: 0.6980 chunk 188 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 555 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN D 117 ASN D 141 HIS D 263 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN F 25 GLN F 48 HIS F 204 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.155747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126969 restraints weight = 40879.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.130849 restraints weight = 19669.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.133353 restraints weight = 12036.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134963 restraints weight = 8709.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135955 restraints weight = 7042.400| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24323 Z= 0.157 Angle : 0.625 13.181 33080 Z= 0.313 Chirality : 0.042 0.167 3696 Planarity : 0.004 0.066 4058 Dihedral : 13.160 146.792 3622 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 4.07 % Allowed : 17.38 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.16), residues: 2804 helix: 1.36 (0.15), residues: 1343 sheet: 0.19 (0.28), residues: 364 loop : -1.07 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 94 TYR 0.020 0.001 TYR A 534 PHE 0.026 0.002 PHE A 703 TRP 0.013 0.001 TRP D 55 HIS 0.020 0.001 HIS C 474 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (24295) covalent geometry : angle 0.60452 / 0.31 (33035) hydrogen bonds : bond 0.04153 / 2.76 ( 1106) hydrogen bonds : angle 4.57457 / 3.25 ( 3154) metal coordination : bond 0.00595 / 0.35 ( 28) metal coordination : angle 4.33942 / 2.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 752 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.7933 (m-80) cc_final: 0.7553 (m-80) REVERT: A 65 MET cc_start: 0.7035 (ptt) cc_final: 0.6825 (ptt) REVERT: A 68 LYS cc_start: 0.6234 (mtmt) cc_final: 0.5761 (tttm) REVERT: A 94 LYS cc_start: 0.7661 (ptpt) cc_final: 0.7038 (ptpt) REVERT: A 98 ASP cc_start: 0.7360 (m-30) cc_final: 0.7139 (m-30) REVERT: A 100 LEU cc_start: 0.8524 (mt) cc_final: 0.8319 (mm) REVERT: A 117 LYS cc_start: 0.7893 (tttt) cc_final: 0.7693 (tttt) REVERT: A 146 THR cc_start: 0.7389 (p) cc_final: 0.7076 (p) REVERT: A 157 LYS cc_start: 0.8184 (ptmm) cc_final: 0.7802 (ttpp) REVERT: A 158 LEU cc_start: 0.8301 (mt) cc_final: 0.8090 (mt) REVERT: A 163 TYR cc_start: 0.7844 (t80) cc_final: 0.7476 (t80) REVERT: A 171 LYS cc_start: 0.8009 (tttp) cc_final: 0.7724 (tttp) REVERT: A 174 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7117 (ttm110) REVERT: A 176 PHE cc_start: 0.8084 (m-80) cc_final: 0.7376 (m-10) REVERT: A 273 LYS cc_start: 0.8053 (ttmt) cc_final: 0.7808 (ttpt) REVERT: A 282 LYS cc_start: 0.8541 (tttt) cc_final: 0.8086 (ttmm) REVERT: A 287 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8087 (mm) REVERT: A 288 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7216 (mp0) REVERT: A 299 ASN cc_start: 0.7065 (p0) cc_final: 0.6555 (p0) REVERT: A 310 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8161 (pt) REVERT: A 330 ASN cc_start: 0.7486 (p0) cc_final: 0.7270 (p0) REVERT: A 332 ARG cc_start: 0.7951 (mpp80) cc_final: 0.7563 (mtp85) REVERT: A 347 SER cc_start: 0.8468 (m) cc_final: 0.8013 (p) REVERT: A 372 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6671 (tp30) REVERT: A 375 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7932 (tttm) REVERT: A 418 LYS cc_start: 0.7433 (tmmt) cc_final: 0.7050 (tmmt) REVERT: A 419 ARG cc_start: 0.7791 (ttm170) cc_final: 0.7451 (tpp80) REVERT: A 457 ILE cc_start: 0.8065 (tt) cc_final: 0.7819 (tt) REVERT: A 463 LYS cc_start: 0.8693 (mttt) cc_final: 0.8389 (mttp) REVERT: A 470 LEU cc_start: 0.8762 (tp) cc_final: 0.8365 (tp) REVERT: A 476 LYS cc_start: 0.8097 (mttt) cc_final: 0.7665 (mttm) REVERT: A 478 VAL cc_start: 0.8381 (t) cc_final: 0.8136 (m) REVERT: A 504 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8294 (ptmt) REVERT: A 510 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7590 (p) REVERT: A 520 ARG cc_start: 0.7559 (mmm160) cc_final: 0.6793 (tpt-90) REVERT: A 525 ILE cc_start: 0.8334 (tp) cc_final: 0.8051 (tp) REVERT: A 526 LYS cc_start: 0.7648 (tppt) cc_final: 0.7346 (tppt) REVERT: A 537 ASN cc_start: 0.8301 (t0) cc_final: 0.8004 (t0) REVERT: A 555 ASN cc_start: 0.7877 (p0) cc_final: 0.7642 (p0) REVERT: A 556 ASP cc_start: 0.7435 (m-30) cc_final: 0.7114 (m-30) REVERT: A 564 ASN cc_start: 0.8427 (t0) cc_final: 0.7746 (t0) REVERT: A 570 GLU cc_start: 0.6915 (pm20) cc_final: 0.6522 (pm20) REVERT: A 579 TYR cc_start: 0.7529 (p90) cc_final: 0.6905 (p90) REVERT: A 588 GLU cc_start: 0.7049 (tp30) cc_final: 0.6439 (tp30) REVERT: A 590 MET cc_start: 0.7695 (tpp) cc_final: 0.7455 (tpt) REVERT: A 632 SER cc_start: 0.7965 (p) cc_final: 0.7646 (p) REVERT: A 644 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8172 (pp) REVERT: A 659 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7287 (p90) REVERT: A 670 MET cc_start: 0.8058 (mmm) cc_final: 0.7820 (mmm) REVERT: A 677 GLN cc_start: 0.7635 (mt0) cc_final: 0.7309 (mt0) REVERT: A 678 ARG cc_start: 0.7211 (ptt180) cc_final: 0.6956 (ptt180) REVERT: A 682 ASP cc_start: 0.6874 (m-30) cc_final: 0.6650 (m-30) REVERT: A 683 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7180 (mm-40) REVERT: A 688 LYS cc_start: 0.8293 (tttt) cc_final: 0.7874 (ttmt) REVERT: A 703 PHE cc_start: 0.8036 (m-80) cc_final: 0.7627 (m-80) REVERT: B 1 MET cc_start: 0.7205 (ppp) cc_final: 0.6993 (ppp) REVERT: B 40 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7947 (mt) REVERT: B 42 MET cc_start: 0.7124 (mtp) cc_final: 0.6622 (mtp) REVERT: B 48 LYS cc_start: 0.7686 (ttpp) cc_final: 0.6935 (mtpp) REVERT: B 91 LEU cc_start: 0.7898 (mm) cc_final: 0.7592 (mm) REVERT: B 158 TYR cc_start: 0.7176 (t80) cc_final: 0.6815 (t80) REVERT: B 243 CYS cc_start: 0.8249 (m) cc_final: 0.7836 (m) REVERT: B 352 GLU cc_start: 0.7122 (mp0) cc_final: 0.6893 (mp0) REVERT: B 414 PHE cc_start: 0.7013 (m-80) cc_final: 0.6497 (m-80) REVERT: B 438 MET cc_start: 0.7593 (mtm) cc_final: 0.7370 (mtm) REVERT: B 445 LYS cc_start: 0.7727 (mmtt) cc_final: 0.7240 (mmtt) REVERT: B 455 ILE cc_start: 0.7770 (mm) cc_final: 0.7496 (mm) REVERT: B 466 ILE cc_start: 0.7624 (tt) cc_final: 0.7287 (tp) REVERT: B 469 LYS cc_start: 0.7783 (ptpp) cc_final: 0.7503 (ptpp) REVERT: B 512 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6824 (mm-30) REVERT: B 533 ASP cc_start: 0.7030 (p0) cc_final: 0.6685 (p0) REVERT: B 570 GLU cc_start: 0.5726 (tm-30) cc_final: 0.5103 (tm-30) REVERT: B 586 GLU cc_start: 0.7102 (pp20) cc_final: 0.6757 (pp20) REVERT: B 589 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6361 (mm-30) REVERT: B 620 MET cc_start: 0.7738 (mmm) cc_final: 0.7098 (mmm) REVERT: B 638 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6211 (mm-30) REVERT: B 639 TYR cc_start: 0.7435 (t80) cc_final: 0.7169 (t80) REVERT: B 641 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.6987 (mtm-85) REVERT: B 662 GLN cc_start: 0.7967 (tm-30) cc_final: 0.7637 (pp30) REVERT: B 681 ASP cc_start: 0.7899 (t0) cc_final: 0.7683 (t0) REVERT: B 719 TYR cc_start: 0.8152 (t80) cc_final: 0.7891 (t80) REVERT: B 724 MET cc_start: 0.7570 (mmm) cc_final: 0.7031 (mmm) REVERT: C 442 GLN cc_start: 0.4630 (OUTLIER) cc_final: 0.4167 (pp30) REVERT: C 475 PHE cc_start: 0.6974 (t80) cc_final: 0.6624 (t80) REVERT: C 501 GLN cc_start: 0.8089 (tp40) cc_final: 0.7873 (tp40) REVERT: D 20 GLN cc_start: 0.8336 (mp10) cc_final: 0.7958 (mp10) REVERT: D 47 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7406 (mm-30) REVERT: D 50 SER cc_start: 0.8142 (m) cc_final: 0.7744 (t) REVERT: D 174 ASP cc_start: 0.7617 (p0) cc_final: 0.7255 (p0) REVERT: D 185 MET cc_start: 0.6484 (mpp) cc_final: 0.6249 (mpp) REVERT: D 218 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7103 (tm-30) REVERT: D 219 TYR cc_start: 0.7692 (t80) cc_final: 0.7464 (t80) REVERT: D 233 ILE cc_start: 0.8239 (mt) cc_final: 0.8012 (mm) REVERT: D 243 SER cc_start: 0.7852 (m) cc_final: 0.7488 (p) REVERT: D 254 MET cc_start: 0.6243 (mtt) cc_final: 0.5403 (mtp) REVERT: D 258 LEU cc_start: 0.8183 (mt) cc_final: 0.7902 (tp) REVERT: D 260 ASN cc_start: 0.7498 (t0) cc_final: 0.6980 (t0) REVERT: D 261 PHE cc_start: 0.8017 (t80) cc_final: 0.7471 (t80) REVERT: D 263 GLN cc_start: 0.8156 (mm110) cc_final: 0.7802 (mm-40) REVERT: D 276 ARG cc_start: 0.6858 (ttt90) cc_final: 0.6451 (ttt90) REVERT: D 284 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8325 (p) REVERT: D 362 GLN cc_start: 0.8171 (tp40) cc_final: 0.7868 (tp40) REVERT: D 395 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6955 (tm-30) REVERT: D 397 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6904 (mm-30) REVERT: D 426 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7929 (tpp80) REVERT: D 433 PHE cc_start: 0.6832 (t80) cc_final: 0.6336 (t80) REVERT: E 70 THR cc_start: 0.8254 (p) cc_final: 0.7859 (t) REVERT: E 73 ASP cc_start: 0.7234 (t0) cc_final: 0.5739 (t0) REVERT: E 75 ASP cc_start: 0.7249 (m-30) cc_final: 0.6621 (m-30) REVERT: E 80 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7053 (mtt180) REVERT: E 89 GLU cc_start: 0.6290 (mt-10) cc_final: 0.6036 (mt-10) REVERT: E 96 PHE cc_start: 0.7524 (m-80) cc_final: 0.7199 (m-80) REVERT: E 103 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7656 (mt0) REVERT: E 112 LYS cc_start: 0.7870 (mtmt) cc_final: 0.7480 (mttm) REVERT: E 116 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8002 (ttmm) REVERT: E 125 ARG cc_start: 0.7120 (mtt180) cc_final: 0.6843 (mtt180) REVERT: E 132 LYS cc_start: 0.8503 (mttt) cc_final: 0.8246 (mttt) REVERT: E 153 MET cc_start: 0.6892 (ttp) cc_final: 0.6558 (ttm) REVERT: E 154 GLN cc_start: 0.7325 (tm-30) cc_final: 0.6989 (tm-30) REVERT: E 159 MET cc_start: 0.7539 (mmm) cc_final: 0.7273 (mmm) REVERT: E 166 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6699 (mt-10) REVERT: E 174 LEU cc_start: 0.8643 (mt) cc_final: 0.8202 (mp) REVERT: E 181 ASN cc_start: 0.8129 (t0) cc_final: 0.7796 (t0) REVERT: E 184 ASP cc_start: 0.6767 (m-30) cc_final: 0.6441 (m-30) REVERT: E 193 LYS cc_start: 0.8274 (mttt) cc_final: 0.7702 (ttmm) REVERT: E 202 SER cc_start: 0.8141 (m) cc_final: 0.7649 (p) REVERT: E 273 MET cc_start: 0.6367 (mmm) cc_final: 0.6109 (mmm) REVERT: E 322 TYR cc_start: 0.8032 (m-10) cc_final: 0.7670 (m-80) REVERT: E 333 GLU cc_start: 0.7734 (tt0) cc_final: 0.7453 (tt0) REVERT: E 353 LYS cc_start: 0.8153 (mttt) cc_final: 0.7644 (mttt) REVERT: F 16 ASP cc_start: 0.7816 (t0) cc_final: 0.7421 (t0) REVERT: F 60 ILE cc_start: 0.8665 (mt) cc_final: 0.8371 (tt) REVERT: F 103 LEU cc_start: 0.7969 (mt) cc_final: 0.7758 (mt) REVERT: F 116 LYS cc_start: 0.8282 (mttt) cc_final: 0.7907 (mmmm) REVERT: F 139 LYS cc_start: 0.8620 (mttt) cc_final: 0.8312 (mtpp) REVERT: F 150 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6969 (mt-10) REVERT: F 158 LYS cc_start: 0.8348 (mttt) cc_final: 0.7965 (mttt) REVERT: F 165 LYS cc_start: 0.8165 (tptm) cc_final: 0.7963 (tptm) REVERT: F 187 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: F 216 LYS cc_start: 0.8391 (tttt) cc_final: 0.8109 (tttt) REVERT: F 224 LEU cc_start: 0.8593 (tp) cc_final: 0.8321 (tp) REVERT: F 249 VAL cc_start: 0.8123 (t) cc_final: 0.7866 (p) REVERT: G 16 MET cc_start: 0.8186 (mmt) cc_final: 0.7519 (mmm) REVERT: G 66 PHE cc_start: 0.8491 (t80) cc_final: 0.8003 (t80) REVERT: H 926 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6096 (tp30) REVERT: K 188 LYS cc_start: 0.8168 (tttt) cc_final: 0.7772 (tttt) REVERT: K 212 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7460 (tp30) REVERT: K 215 LYS cc_start: 0.8092 (ptpp) cc_final: 0.7844 (ptpp) REVERT: K 222 LYS cc_start: 0.8541 (pttp) cc_final: 0.8114 (ptpp) outliers start: 102 outliers final: 54 residues processed: 804 average time/residue: 0.1774 time to fit residues: 213.4285 Evaluate side-chains 795 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 728 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 271 GLU Chi-restraints excluded: chain K residue 273 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 129 optimal weight: 50.0000 chunk 159 optimal weight: 0.7980 chunk 283 optimal weight: 4.9990 chunk 206 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 173 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 537 ASN A 668 GLN B 210 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.152995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.124122 restraints weight = 40669.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128072 restraints weight = 19516.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130573 restraints weight = 11865.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.132165 restraints weight = 8542.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133102 restraints weight = 6921.073| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 24323 Z= 0.194 Angle : 0.670 13.575 33080 Z= 0.336 Chirality : 0.044 0.184 3696 Planarity : 0.004 0.067 4058 Dihedral : 13.369 148.287 3617 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 4.94 % Allowed : 18.49 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 2804 helix: 1.20 (0.15), residues: 1351 sheet: -0.05 (0.27), residues: 371 loop : -1.11 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 213 TYR 0.018 0.002 TYR K 116 PHE 0.023 0.002 PHE D 22 TRP 0.037 0.002 TRP D 55 HIS 0.023 0.001 HIS D 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (24295) covalent geometry : angle 0.64723 / 0.34 (33035) hydrogen bonds : bond 0.04173 / 2.78 ( 1106) hydrogen bonds : angle 4.52521 / 3.20 ( 3154) metal coordination : bond 0.00733 / 0.46 ( 28) metal coordination : angle 4.69159 / 2.48 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 762 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6789 (ptt) REVERT: A 68 LYS cc_start: 0.6313 (mtmt) cc_final: 0.5767 (tttm) REVERT: A 94 LYS cc_start: 0.7741 (ptpt) cc_final: 0.7144 (ptpt) REVERT: A 98 ASP cc_start: 0.7407 (m-30) cc_final: 0.7203 (m-30) REVERT: A 100 LEU cc_start: 0.8560 (mt) cc_final: 0.8354 (mm) REVERT: A 146 THR cc_start: 0.7436 (p) cc_final: 0.6991 (p) REVERT: A 157 LYS cc_start: 0.8290 (ptmm) cc_final: 0.7877 (ttpp) REVERT: A 158 LEU cc_start: 0.8385 (mt) cc_final: 0.8112 (mt) REVERT: A 162 SER cc_start: 0.8238 (p) cc_final: 0.7939 (p) REVERT: A 163 TYR cc_start: 0.7836 (t80) cc_final: 0.7504 (t80) REVERT: A 169 VAL cc_start: 0.8617 (p) cc_final: 0.8159 (m) REVERT: A 173 ASN cc_start: 0.7812 (m-40) cc_final: 0.7456 (m-40) REVERT: A 174 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7500 (tpp80) REVERT: A 273 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7810 (ttpt) REVERT: A 279 GLU cc_start: 0.7661 (mp0) cc_final: 0.7363 (mp0) REVERT: A 282 LYS cc_start: 0.8535 (tttt) cc_final: 0.8111 (ttmm) REVERT: A 287 LEU cc_start: 0.8704 (mm) cc_final: 0.8167 (mm) REVERT: A 288 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7240 (mp0) REVERT: A 299 ASN cc_start: 0.7263 (p0) cc_final: 0.6826 (p0) REVERT: A 310 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8028 (pt) REVERT: A 321 GLU cc_start: 0.6529 (tm-30) cc_final: 0.6310 (tm-30) REVERT: A 332 ARG cc_start: 0.8018 (mpp80) cc_final: 0.7619 (mtp85) REVERT: A 347 SER cc_start: 0.8535 (m) cc_final: 0.7706 (t) REVERT: A 375 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7926 (tttm) REVERT: A 418 LYS cc_start: 0.7652 (tmmt) cc_final: 0.7303 (tmmt) REVERT: A 419 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7528 (tpp80) REVERT: A 424 GLU cc_start: 0.7418 (mm-30) cc_final: 0.7031 (mm-30) REVERT: A 453 ARG cc_start: 0.7209 (ptm160) cc_final: 0.6721 (ptp-170) REVERT: A 457 ILE cc_start: 0.8122 (tt) cc_final: 0.7922 (tt) REVERT: A 470 LEU cc_start: 0.8789 (tp) cc_final: 0.8363 (tp) REVERT: A 476 LYS cc_start: 0.8125 (mttt) cc_final: 0.7690 (mttm) REVERT: A 478 VAL cc_start: 0.8512 (t) cc_final: 0.8285 (m) REVERT: A 504 LYS cc_start: 0.8598 (ttpt) cc_final: 0.8398 (ttmt) REVERT: A 520 ARG cc_start: 0.7485 (mmm160) cc_final: 0.6740 (tpt-90) REVERT: A 525 ILE cc_start: 0.8345 (tp) cc_final: 0.8039 (tp) REVERT: A 526 LYS cc_start: 0.7559 (tppt) cc_final: 0.5868 (tppt) REVERT: A 556 ASP cc_start: 0.7388 (m-30) cc_final: 0.7111 (m-30) REVERT: A 564 ASN cc_start: 0.8316 (t0) cc_final: 0.8099 (t0) REVERT: A 570 GLU cc_start: 0.7039 (pm20) cc_final: 0.6653 (pm20) REVERT: A 579 TYR cc_start: 0.7543 (p90) cc_final: 0.6886 (p90) REVERT: A 588 GLU cc_start: 0.7060 (tp30) cc_final: 0.6413 (tp30) REVERT: A 632 SER cc_start: 0.8090 (p) cc_final: 0.7774 (p) REVERT: A 644 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8243 (pp) REVERT: A 659 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7085 (p90) REVERT: A 670 MET cc_start: 0.8074 (mmm) cc_final: 0.7810 (mmm) REVERT: A 677 GLN cc_start: 0.7668 (mt0) cc_final: 0.7389 (mt0) REVERT: A 682 ASP cc_start: 0.6954 (m-30) cc_final: 0.6698 (m-30) REVERT: A 688 LYS cc_start: 0.8348 (tttt) cc_final: 0.7872 (ttmt) REVERT: A 692 LYS cc_start: 0.7569 (tppp) cc_final: 0.7238 (tptt) REVERT: A 703 PHE cc_start: 0.8182 (m-80) cc_final: 0.7274 (m-80) REVERT: A 712 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7768 (mt) REVERT: B 40 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8235 (mt) REVERT: B 42 MET cc_start: 0.7232 (mtp) cc_final: 0.6973 (mtp) REVERT: B 48 LYS cc_start: 0.7827 (ttpp) cc_final: 0.7379 (ttpp) REVERT: B 75 ARG cc_start: 0.7331 (ttp80) cc_final: 0.7061 (ttp80) REVERT: B 91 LEU cc_start: 0.7886 (mm) cc_final: 0.7572 (mm) REVERT: B 122 THR cc_start: 0.6392 (OUTLIER) cc_final: 0.6175 (p) REVERT: B 158 TYR cc_start: 0.7237 (t80) cc_final: 0.6827 (t80) REVERT: B 230 VAL cc_start: 0.8043 (t) cc_final: 0.7821 (p) REVERT: B 233 PHE cc_start: 0.8080 (m-10) cc_final: 0.7715 (m-80) REVERT: B 243 CYS cc_start: 0.8400 (m) cc_final: 0.8096 (m) REVERT: B 352 GLU cc_start: 0.7221 (mp0) cc_final: 0.6970 (mp0) REVERT: B 416 ILE cc_start: 0.7245 (OUTLIER) cc_final: 0.6861 (mp) REVERT: B 445 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7608 (mmtt) REVERT: B 455 ILE cc_start: 0.8047 (mm) cc_final: 0.7700 (mm) REVERT: B 469 LYS cc_start: 0.7902 (ptpp) cc_final: 0.7667 (ptpt) REVERT: B 533 ASP cc_start: 0.6888 (p0) cc_final: 0.6436 (p0) REVERT: B 570 GLU cc_start: 0.6025 (tm-30) cc_final: 0.5367 (tm-30) REVERT: B 586 GLU cc_start: 0.7246 (pp20) cc_final: 0.6828 (pp20) REVERT: B 589 GLU cc_start: 0.6853 (mm-30) cc_final: 0.6472 (mm-30) REVERT: B 613 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7249 (p90) REVERT: B 638 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6817 (mm-30) REVERT: B 639 TYR cc_start: 0.7532 (t80) cc_final: 0.7250 (t80) REVERT: B 641 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7267 (mtm-85) REVERT: B 662 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7642 (pp30) REVERT: B 669 ARG cc_start: 0.6187 (mpt90) cc_final: 0.5758 (mpt90) REVERT: B 681 ASP cc_start: 0.7891 (t0) cc_final: 0.7661 (t0) REVERT: B 724 MET cc_start: 0.7698 (mmm) cc_final: 0.7419 (tpp) REVERT: C 411 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6885 (tpp) REVERT: C 441 MET cc_start: 0.7320 (mmm) cc_final: 0.6811 (mmt) REVERT: C 442 GLN cc_start: 0.4585 (OUTLIER) cc_final: 0.4108 (pp30) REVERT: C 475 PHE cc_start: 0.7160 (t80) cc_final: 0.6770 (t80) REVERT: C 501 GLN cc_start: 0.8076 (tp40) cc_final: 0.7681 (tp40) REVERT: C 524 HIS cc_start: 0.7828 (t-170) cc_final: 0.7306 (t-170) REVERT: C 528 MET cc_start: 0.8640 (mtp) cc_final: 0.8242 (mtm) REVERT: D 20 GLN cc_start: 0.8301 (mp10) cc_final: 0.7974 (mp10) REVERT: D 22 PHE cc_start: 0.8356 (t80) cc_final: 0.8100 (t80) REVERT: D 47 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7357 (mm-30) REVERT: D 50 SER cc_start: 0.7841 (m) cc_final: 0.7093 (p) REVERT: D 218 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7312 (tm-30) REVERT: D 219 TYR cc_start: 0.7705 (t80) cc_final: 0.7466 (t80) REVERT: D 233 ILE cc_start: 0.8424 (mt) cc_final: 0.8146 (mm) REVERT: D 243 SER cc_start: 0.7944 (m) cc_final: 0.7606 (p) REVERT: D 254 MET cc_start: 0.6348 (mtt) cc_final: 0.5609 (mtp) REVERT: D 258 LEU cc_start: 0.8271 (mt) cc_final: 0.7940 (tp) REVERT: D 260 ASN cc_start: 0.7498 (t0) cc_final: 0.7015 (t0) REVERT: D 261 PHE cc_start: 0.8161 (t80) cc_final: 0.7819 (t80) REVERT: D 263 GLN cc_start: 0.8319 (mm110) cc_final: 0.7718 (tp40) REVERT: D 267 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7177 (mp0) REVERT: D 268 PHE cc_start: 0.8060 (m-10) cc_final: 0.7832 (m-10) REVERT: D 276 ARG cc_start: 0.6881 (ttt90) cc_final: 0.6619 (ttt90) REVERT: D 284 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8352 (p) REVERT: D 313 TYR cc_start: 0.8290 (m-80) cc_final: 0.7955 (m-80) REVERT: D 362 GLN cc_start: 0.8068 (tp40) cc_final: 0.7769 (tp40) REVERT: D 395 GLU cc_start: 0.7391 (tm-30) cc_final: 0.7142 (tm-30) REVERT: D 397 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6935 (mm-30) REVERT: D 433 PHE cc_start: 0.6846 (t80) cc_final: 0.6446 (t80) REVERT: D 439 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7709 (mtp85) REVERT: E 70 THR cc_start: 0.8209 (p) cc_final: 0.7777 (t) REVERT: E 73 ASP cc_start: 0.7232 (t0) cc_final: 0.5656 (t0) REVERT: E 75 ASP cc_start: 0.7213 (m-30) cc_final: 0.6577 (m-30) REVERT: E 80 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7033 (mtt180) REVERT: E 96 PHE cc_start: 0.7562 (m-80) cc_final: 0.7171 (m-80) REVERT: E 103 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: E 112 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7609 (mttm) REVERT: E 125 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6872 (mtt180) REVERT: E 132 LYS cc_start: 0.8470 (mttt) cc_final: 0.8254 (mttt) REVERT: E 153 MET cc_start: 0.7019 (ttp) cc_final: 0.6802 (ttt) REVERT: E 154 GLN cc_start: 0.7366 (tm-30) cc_final: 0.6969 (tm-30) REVERT: E 159 MET cc_start: 0.7770 (mmm) cc_final: 0.7521 (mmm) REVERT: E 166 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6685 (mt-10) REVERT: E 174 LEU cc_start: 0.8726 (mt) cc_final: 0.8523 (mp) REVERT: E 181 ASN cc_start: 0.8102 (t0) cc_final: 0.7797 (t0) REVERT: E 184 ASP cc_start: 0.6878 (m-30) cc_final: 0.6413 (m-30) REVERT: E 193 LYS cc_start: 0.8355 (mttt) cc_final: 0.8078 (mttt) REVERT: E 322 TYR cc_start: 0.8138 (m-10) cc_final: 0.7824 (m-80) REVERT: E 333 GLU cc_start: 0.7719 (tt0) cc_final: 0.7440 (tt0) REVERT: E 353 LYS cc_start: 0.8208 (mttt) cc_final: 0.7728 (mttt) REVERT: E 366 VAL cc_start: 0.8573 (OUTLIER) cc_final: 0.8326 (m) REVERT: F 16 ASP cc_start: 0.7746 (t0) cc_final: 0.7279 (t0) REVERT: F 60 ILE cc_start: 0.8693 (mt) cc_final: 0.8406 (tt) REVERT: F 116 LYS cc_start: 0.8292 (mttt) cc_final: 0.7925 (mmmm) REVERT: F 131 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8162 (p) REVERT: F 139 LYS cc_start: 0.8667 (mttt) cc_final: 0.8361 (mtpp) REVERT: F 158 LYS cc_start: 0.8378 (mttt) cc_final: 0.8002 (mttt) REVERT: F 187 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: F 204 GLN cc_start: 0.8592 (mt0) cc_final: 0.8375 (mt0) REVERT: F 213 LEU cc_start: 0.8317 (tp) cc_final: 0.7973 (tt) REVERT: F 216 LYS cc_start: 0.8388 (tttt) cc_final: 0.8064 (ttpp) REVERT: F 224 LEU cc_start: 0.8661 (tp) cc_final: 0.8390 (tp) REVERT: F 237 GLN cc_start: 0.7135 (mt0) cc_final: 0.6774 (mt0) REVERT: F 249 VAL cc_start: 0.8246 (t) cc_final: 0.7938 (p) REVERT: F 252 ARG cc_start: 0.8094 (ptp-110) cc_final: 0.7736 (mtm110) REVERT: G 4 VAL cc_start: 0.2156 (OUTLIER) cc_final: 0.1157 (m) REVERT: G 16 MET cc_start: 0.8315 (mmt) cc_final: 0.7602 (mmm) REVERT: H 926 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6115 (tp30) REVERT: K 167 LYS cc_start: 0.8577 (tttt) cc_final: 0.8330 (ttmt) REVERT: K 188 LYS cc_start: 0.8210 (tttt) cc_final: 0.7968 (tttt) REVERT: K 215 LYS cc_start: 0.7985 (ptpp) cc_final: 0.7748 (ptpp) outliers start: 124 outliers final: 76 residues processed: 825 average time/residue: 0.1768 time to fit residues: 216.9614 Evaluate side-chains 833 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 739 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 526 GLU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 423 SER Chi-restraints excluded: chain C residue 435 SER Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 273 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 167 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 555 ASN B 700 HIS ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN F 48 HIS F 205 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.151333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122627 restraints weight = 40340.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126468 restraints weight = 19401.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128948 restraints weight = 11894.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.130533 restraints weight = 8598.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131612 restraints weight = 6925.407| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24323 Z= 0.197 Angle : 0.677 13.964 33080 Z= 0.338 Chirality : 0.044 0.203 3696 Planarity : 0.004 0.046 4058 Dihedral : 13.367 151.042 3612 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.10 % Favored : 94.86 % Rotamer: Outliers : 5.06 % Allowed : 19.33 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2804 helix: 1.12 (0.14), residues: 1352 sheet: -0.23 (0.27), residues: 373 loop : -1.13 (0.19), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 143 TYR 0.029 0.002 TYR A 581 PHE 0.023 0.002 PHE D 272 TRP 0.055 0.002 TRP D 55 HIS 0.025 0.001 HIS D 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (24295) covalent geometry : angle 0.65189 / 0.34 (33035) hydrogen bonds : bond 0.04088 / 2.73 ( 1106) hydrogen bonds : angle 4.51161 / 3.18 ( 3154) metal coordination : bond 0.00819 / 0.50 ( 28) metal coordination : angle 5.02404 / 2.70 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 765 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8149 (m-80) cc_final: 0.7778 (m-80) REVERT: A 65 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6801 (ptt) REVERT: A 68 LYS cc_start: 0.6330 (mtmt) cc_final: 0.5768 (tttm) REVERT: A 94 LYS cc_start: 0.7777 (ptpt) cc_final: 0.7303 (ptpt) REVERT: A 98 ASP cc_start: 0.7422 (m-30) cc_final: 0.7211 (m-30) REVERT: A 100 LEU cc_start: 0.8556 (mt) cc_final: 0.8346 (mm) REVERT: A 146 THR cc_start: 0.7559 (p) cc_final: 0.7145 (p) REVERT: A 157 LYS cc_start: 0.8329 (ptmm) cc_final: 0.7917 (ttpp) REVERT: A 158 LEU cc_start: 0.8428 (mt) cc_final: 0.8207 (mt) REVERT: A 162 SER cc_start: 0.8296 (p) cc_final: 0.7996 (p) REVERT: A 163 TYR cc_start: 0.7865 (t80) cc_final: 0.7497 (t80) REVERT: A 173 ASN cc_start: 0.7813 (m-40) cc_final: 0.7441 (m-40) REVERT: A 174 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7542 (tpp80) REVERT: A 271 GLU cc_start: 0.6288 (pp20) cc_final: 0.5658 (tm-30) REVERT: A 273 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7720 (ttpt) REVERT: A 275 GLU cc_start: 0.7714 (pm20) cc_final: 0.7454 (pm20) REVERT: A 282 LYS cc_start: 0.8526 (tttt) cc_final: 0.8076 (ttmm) REVERT: A 287 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.7959 (mt) REVERT: A 288 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7273 (mp0) REVERT: A 299 ASN cc_start: 0.7387 (p0) cc_final: 0.6896 (p0) REVERT: A 310 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8286 (pt) REVERT: A 332 ARG cc_start: 0.8013 (mpp80) cc_final: 0.7723 (mtp85) REVERT: A 334 ARG cc_start: 0.6953 (ptp90) cc_final: 0.6612 (ptp90) REVERT: A 347 SER cc_start: 0.8559 (m) cc_final: 0.7774 (t) REVERT: A 375 LYS cc_start: 0.8341 (ttpt) cc_final: 0.8007 (ttpp) REVERT: A 392 PHE cc_start: 0.7481 (t80) cc_final: 0.6927 (t80) REVERT: A 418 LYS cc_start: 0.7727 (tmmt) cc_final: 0.7399 (tmmt) REVERT: A 419 ARG cc_start: 0.7744 (ttm170) cc_final: 0.7124 (tpp80) REVERT: A 424 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7153 (mm-30) REVERT: A 457 ILE cc_start: 0.8227 (tt) cc_final: 0.7922 (tt) REVERT: A 470 LEU cc_start: 0.8792 (tp) cc_final: 0.8327 (tp) REVERT: A 476 LYS cc_start: 0.8191 (mttt) cc_final: 0.7754 (mttm) REVERT: A 478 VAL cc_start: 0.8533 (t) cc_final: 0.8308 (m) REVERT: A 504 LYS cc_start: 0.8574 (ttpt) cc_final: 0.8370 (ttmt) REVERT: A 520 ARG cc_start: 0.7493 (mmm160) cc_final: 0.6559 (tpt90) REVERT: A 525 ILE cc_start: 0.8403 (tp) cc_final: 0.8128 (tp) REVERT: A 526 LYS cc_start: 0.7505 (tppt) cc_final: 0.7210 (tppt) REVERT: A 556 ASP cc_start: 0.7436 (m-30) cc_final: 0.7133 (m-30) REVERT: A 570 GLU cc_start: 0.7102 (pm20) cc_final: 0.6616 (pm20) REVERT: A 579 TYR cc_start: 0.7474 (p90) cc_final: 0.6945 (p90) REVERT: A 590 MET cc_start: 0.7766 (tpp) cc_final: 0.7517 (tpt) REVERT: A 632 SER cc_start: 0.8086 (p) cc_final: 0.7740 (p) REVERT: A 642 ARG cc_start: 0.7406 (mtp85) cc_final: 0.7169 (mmt90) REVERT: A 644 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8259 (pp) REVERT: A 659 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7156 (p90) REVERT: A 670 MET cc_start: 0.8092 (mmm) cc_final: 0.7840 (mmm) REVERT: A 677 GLN cc_start: 0.7679 (mt0) cc_final: 0.7398 (mt0) REVERT: A 682 ASP cc_start: 0.6929 (m-30) cc_final: 0.6727 (m-30) REVERT: A 683 GLN cc_start: 0.7697 (tp40) cc_final: 0.7278 (mm-40) REVERT: A 688 LYS cc_start: 0.8445 (tttt) cc_final: 0.7983 (ttmt) REVERT: A 692 LYS cc_start: 0.7702 (tppp) cc_final: 0.7429 (tptt) REVERT: A 696 MET cc_start: 0.7334 (mmm) cc_final: 0.6738 (tmm) REVERT: A 703 PHE cc_start: 0.8237 (m-80) cc_final: 0.7744 (m-80) REVERT: B 40 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8303 (mt) REVERT: B 42 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6948 (mtp) REVERT: B 75 ARG cc_start: 0.7393 (ttp80) cc_final: 0.7173 (ttp80) REVERT: B 91 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7600 (mm) REVERT: B 158 TYR cc_start: 0.7262 (t80) cc_final: 0.6847 (t80) REVERT: B 233 PHE cc_start: 0.8130 (m-10) cc_final: 0.7846 (m-80) REVERT: B 243 CYS cc_start: 0.8420 (m) cc_final: 0.8165 (m) REVERT: B 352 GLU cc_start: 0.7260 (mp0) cc_final: 0.6896 (mp0) REVERT: B 384 HIS cc_start: 0.5159 (OUTLIER) cc_final: 0.4736 (p-80) REVERT: B 414 PHE cc_start: 0.7062 (m-80) cc_final: 0.6832 (m-80) REVERT: B 416 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.6983 (pt) REVERT: B 438 MET cc_start: 0.7694 (mtm) cc_final: 0.7417 (mtm) REVERT: B 445 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7702 (mmtt) REVERT: B 455 ILE cc_start: 0.8076 (mm) cc_final: 0.7742 (mm) REVERT: B 533 ASP cc_start: 0.6783 (p0) cc_final: 0.6339 (p0) REVERT: B 570 GLU cc_start: 0.6134 (tm-30) cc_final: 0.5495 (tm-30) REVERT: B 585 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7429 (tp40) REVERT: B 586 GLU cc_start: 0.7246 (pp20) cc_final: 0.6876 (pp20) REVERT: B 589 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6486 (mm-30) REVERT: B 612 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.7266 (p-80) REVERT: B 613 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7228 (p90) REVERT: B 641 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7403 (mtm-85) REVERT: B 662 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7606 (pp30) REVERT: B 681 ASP cc_start: 0.7910 (t0) cc_final: 0.7689 (t0) REVERT: B 686 ARG cc_start: 0.7382 (tpp80) cc_final: 0.7034 (tpp80) REVERT: B 724 MET cc_start: 0.7715 (mmm) cc_final: 0.7134 (tpp) REVERT: C 411 MET cc_start: 0.7195 (OUTLIER) cc_final: 0.6925 (tpp) REVERT: C 442 GLN cc_start: 0.4543 (OUTLIER) cc_final: 0.4090 (pp30) REVERT: C 475 PHE cc_start: 0.7100 (t80) cc_final: 0.6736 (t80) REVERT: C 501 GLN cc_start: 0.8062 (tp40) cc_final: 0.7672 (tp40) REVERT: D 20 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: D 33 ARG cc_start: 0.7686 (mmm-85) cc_final: 0.7481 (mtm-85) REVERT: D 47 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7363 (mm-30) REVERT: D 50 SER cc_start: 0.7776 (m) cc_final: 0.6971 (p) REVERT: D 78 GLU cc_start: 0.6867 (pt0) cc_final: 0.6666 (pt0) REVERT: D 216 MET cc_start: 0.7851 (mmm) cc_final: 0.7645 (mmm) REVERT: D 218 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7306 (tm-30) REVERT: D 233 ILE cc_start: 0.8453 (mt) cc_final: 0.8182 (mm) REVERT: D 243 SER cc_start: 0.7961 (m) cc_final: 0.7678 (p) REVERT: D 254 MET cc_start: 0.6431 (mtt) cc_final: 0.5716 (mtp) REVERT: D 258 LEU cc_start: 0.8282 (mt) cc_final: 0.7974 (tp) REVERT: D 260 ASN cc_start: 0.7546 (t0) cc_final: 0.7060 (t0) REVERT: D 261 PHE cc_start: 0.8206 (t80) cc_final: 0.7943 (t80) REVERT: D 284 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8442 (p) REVERT: D 313 TYR cc_start: 0.8297 (m-80) cc_final: 0.7946 (m-80) REVERT: D 362 GLN cc_start: 0.8077 (tp40) cc_final: 0.7733 (tp40) REVERT: D 395 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7147 (tm-30) REVERT: D 397 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6944 (mm-30) REVERT: D 398 ARG cc_start: 0.7232 (ttt90) cc_final: 0.6913 (mtt90) REVERT: D 433 PHE cc_start: 0.6880 (t80) cc_final: 0.6453 (t80) REVERT: D 439 ARG cc_start: 0.7951 (mtp85) cc_final: 0.7622 (mtp85) REVERT: E 70 THR cc_start: 0.8187 (p) cc_final: 0.7793 (t) REVERT: E 73 ASP cc_start: 0.7286 (t0) cc_final: 0.5662 (t0) REVERT: E 75 ASP cc_start: 0.7227 (m-30) cc_final: 0.6589 (m-30) REVERT: E 80 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7048 (mtt180) REVERT: E 96 PHE cc_start: 0.7586 (m-80) cc_final: 0.7262 (m-80) REVERT: E 103 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: E 112 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7568 (mmtp) REVERT: E 119 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7154 (tm-30) REVERT: E 125 ARG cc_start: 0.7196 (mtt180) cc_final: 0.6853 (mtt180) REVERT: E 154 GLN cc_start: 0.7375 (tm-30) cc_final: 0.6910 (tm-30) REVERT: E 159 MET cc_start: 0.7845 (mmm) cc_final: 0.7608 (mmm) REVERT: E 166 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6854 (mt-10) REVERT: E 174 LEU cc_start: 0.8756 (mt) cc_final: 0.8548 (mp) REVERT: E 181 ASN cc_start: 0.8099 (t0) cc_final: 0.7829 (t0) REVERT: E 184 ASP cc_start: 0.6921 (m-30) cc_final: 0.6528 (m-30) REVERT: E 193 LYS cc_start: 0.8379 (mttt) cc_final: 0.8090 (mttt) REVERT: E 251 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.7847 (mtp180) REVERT: E 322 TYR cc_start: 0.8110 (m-10) cc_final: 0.7789 (m-80) REVERT: E 333 GLU cc_start: 0.7712 (tt0) cc_final: 0.7453 (tt0) REVERT: E 353 LYS cc_start: 0.8210 (mttt) cc_final: 0.7748 (mttt) REVERT: F 16 ASP cc_start: 0.7749 (t0) cc_final: 0.7315 (t0) REVERT: F 34 LEU cc_start: 0.8250 (tp) cc_final: 0.7969 (tt) REVERT: F 60 ILE cc_start: 0.8715 (mt) cc_final: 0.8397 (tt) REVERT: F 105 THR cc_start: 0.8357 (p) cc_final: 0.8120 (t) REVERT: F 116 LYS cc_start: 0.8275 (mttt) cc_final: 0.7942 (mmmm) REVERT: F 139 LYS cc_start: 0.8686 (mttt) cc_final: 0.8382 (mtpp) REVERT: F 158 LYS cc_start: 0.8380 (mttt) cc_final: 0.8014 (mttt) REVERT: F 187 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7994 (mp10) REVERT: F 204 GLN cc_start: 0.8625 (mt0) cc_final: 0.8423 (mt0) REVERT: F 213 LEU cc_start: 0.8413 (tp) cc_final: 0.8083 (tt) REVERT: F 216 LYS cc_start: 0.8397 (tttt) cc_final: 0.8085 (ttpp) REVERT: F 224 LEU cc_start: 0.8661 (tp) cc_final: 0.8417 (tp) REVERT: F 237 GLN cc_start: 0.7216 (mt0) cc_final: 0.6796 (mt0) REVERT: F 248 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7429 (p90) REVERT: F 249 VAL cc_start: 0.8314 (t) cc_final: 0.7959 (p) REVERT: F 252 ARG cc_start: 0.8153 (ptp-110) cc_final: 0.7739 (mtm110) REVERT: G 16 MET cc_start: 0.8323 (mmt) cc_final: 0.7472 (mmm) REVERT: H 926 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6115 (tp30) REVERT: K 163 LYS cc_start: 0.8113 (mttt) cc_final: 0.7884 (mttt) REVERT: K 167 LYS cc_start: 0.8646 (tttt) cc_final: 0.8392 (ttmt) REVERT: K 188 LYS cc_start: 0.8226 (tttt) cc_final: 0.8023 (tttt) REVERT: K 205 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7241 (mm-30) REVERT: K 222 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8219 (ptpp) outliers start: 127 outliers final: 84 residues processed: 820 average time/residue: 0.1851 time to fit residues: 225.5896 Evaluate side-chains 852 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 746 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 457 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 304 GLU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 222 LYS Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 273 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 97 optimal weight: 0.0570 chunk 60 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 225 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 264 optimal weight: 0.6980 chunk 260 optimal weight: 0.5980 chunk 241 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 555 ASN B 37 HIS B 649 ASN D 340 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS F 205 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.152587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123938 restraints weight = 40927.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.127818 restraints weight = 19464.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130351 restraints weight = 11846.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131936 restraints weight = 8493.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.132952 restraints weight = 6847.378| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 24323 Z= 0.138 Angle : 0.669 14.774 33080 Z= 0.327 Chirality : 0.043 0.209 3696 Planarity : 0.004 0.055 4058 Dihedral : 13.352 153.183 3612 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 4.70 % Allowed : 20.69 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.16), residues: 2804 helix: 1.12 (0.14), residues: 1360 sheet: -0.19 (0.27), residues: 370 loop : -1.17 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 298 TYR 0.023 0.001 TYR K 116 PHE 0.023 0.001 PHE D 272 TRP 0.056 0.002 TRP D 55 HIS 0.018 0.001 HIS D 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (24295) covalent geometry : angle 0.64362 / 0.33 (33035) hydrogen bonds : bond 0.03780 / 2.52 ( 1106) hydrogen bonds : angle 4.42078 / 3.12 ( 3154) metal coordination : bond 0.00572 / 0.34 ( 28) metal coordination : angle 4.96697 / 2.64 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 760 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 TYR cc_start: 0.8134 (m-80) cc_final: 0.7774 (m-80) REVERT: A 65 MET cc_start: 0.6978 (OUTLIER) cc_final: 0.6776 (ptt) REVERT: A 68 LYS cc_start: 0.6133 (mtmt) cc_final: 0.5730 (tttm) REVERT: A 146 THR cc_start: 0.7507 (p) cc_final: 0.7147 (p) REVERT: A 157 LYS cc_start: 0.8320 (ptmm) cc_final: 0.7907 (ttpp) REVERT: A 158 LEU cc_start: 0.8388 (mt) cc_final: 0.8132 (mt) REVERT: A 162 SER cc_start: 0.8281 (p) cc_final: 0.7977 (p) REVERT: A 163 TYR cc_start: 0.7851 (t80) cc_final: 0.7491 (t80) REVERT: A 171 LYS cc_start: 0.8145 (tppt) cc_final: 0.7818 (mppt) REVERT: A 173 ASN cc_start: 0.7825 (m-40) cc_final: 0.7556 (m-40) REVERT: A 174 ARG cc_start: 0.7727 (mmm-85) cc_final: 0.7477 (tpp80) REVERT: A 273 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7587 (tppp) REVERT: A 282 LYS cc_start: 0.8511 (tttt) cc_final: 0.8058 (ttmm) REVERT: A 287 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.7989 (mt) REVERT: A 288 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7209 (mp0) REVERT: A 294 GLU cc_start: 0.6941 (tp30) cc_final: 0.6428 (tp30) REVERT: A 299 ASN cc_start: 0.7331 (p0) cc_final: 0.6783 (p0) REVERT: A 310 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8303 (pt) REVERT: A 321 GLU cc_start: 0.6663 (tm-30) cc_final: 0.6407 (tm-30) REVERT: A 332 ARG cc_start: 0.8042 (mpp80) cc_final: 0.7431 (mtp85) REVERT: A 347 SER cc_start: 0.8537 (m) cc_final: 0.7756 (t) REVERT: A 375 LYS cc_start: 0.8339 (ttpt) cc_final: 0.7985 (ttpp) REVERT: A 392 PHE cc_start: 0.7571 (t80) cc_final: 0.7003 (t80) REVERT: A 418 LYS cc_start: 0.7640 (tmmt) cc_final: 0.7326 (tmmt) REVERT: A 419 ARG cc_start: 0.7412 (ttm170) cc_final: 0.7087 (tpp80) REVERT: A 424 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7216 (mm-30) REVERT: A 427 MET cc_start: 0.7766 (mtm) cc_final: 0.7440 (mtm) REVERT: A 457 ILE cc_start: 0.8176 (tt) cc_final: 0.7897 (tt) REVERT: A 470 LEU cc_start: 0.8798 (tp) cc_final: 0.8467 (tp) REVERT: A 476 LYS cc_start: 0.8189 (mttt) cc_final: 0.7754 (mttm) REVERT: A 478 VAL cc_start: 0.8554 (t) cc_final: 0.8266 (m) REVERT: A 504 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8335 (ttmt) REVERT: A 525 ILE cc_start: 0.8443 (tp) cc_final: 0.8156 (tp) REVERT: A 526 LYS cc_start: 0.7516 (tppt) cc_final: 0.7104 (tppt) REVERT: A 556 ASP cc_start: 0.7314 (m-30) cc_final: 0.6980 (m-30) REVERT: A 570 GLU cc_start: 0.7099 (pm20) cc_final: 0.6790 (pm20) REVERT: A 579 TYR cc_start: 0.7449 (p90) cc_final: 0.7007 (p90) REVERT: A 588 GLU cc_start: 0.7015 (tp30) cc_final: 0.6722 (tp30) REVERT: A 590 MET cc_start: 0.7816 (tpp) cc_final: 0.7572 (tpt) REVERT: A 632 SER cc_start: 0.8077 (p) cc_final: 0.7739 (p) REVERT: A 642 ARG cc_start: 0.7375 (mtp85) cc_final: 0.6687 (mmt180) REVERT: A 659 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7058 (p90) REVERT: A 677 GLN cc_start: 0.7654 (mt0) cc_final: 0.7384 (mt0) REVERT: A 678 ARG cc_start: 0.7425 (ptt180) cc_final: 0.7050 (ptt180) REVERT: A 682 ASP cc_start: 0.6882 (m-30) cc_final: 0.6671 (m-30) REVERT: A 683 GLN cc_start: 0.7690 (tp40) cc_final: 0.7269 (mm-40) REVERT: A 688 LYS cc_start: 0.8368 (tttt) cc_final: 0.7982 (ttmt) REVERT: A 692 LYS cc_start: 0.7684 (tppp) cc_final: 0.7474 (tptm) REVERT: A 696 MET cc_start: 0.7306 (mmm) cc_final: 0.6736 (tmm) REVERT: A 703 PHE cc_start: 0.8208 (m-80) cc_final: 0.7305 (m-80) REVERT: A 712 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7797 (mt) REVERT: B 27 GLU cc_start: 0.6634 (pp20) cc_final: 0.6082 (pp20) REVERT: B 40 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 48 LYS cc_start: 0.8036 (ttpp) cc_final: 0.7521 (ttpp) REVERT: B 55 LEU cc_start: 0.7742 (tt) cc_final: 0.7354 (tp) REVERT: B 91 LEU cc_start: 0.7916 (mm) cc_final: 0.7602 (mm) REVERT: B 113 LYS cc_start: 0.7943 (ttpp) cc_final: 0.7578 (ttmm) REVERT: B 122 THR cc_start: 0.6443 (OUTLIER) cc_final: 0.6069 (p) REVERT: B 158 TYR cc_start: 0.7248 (t80) cc_final: 0.6831 (t80) REVERT: B 233 PHE cc_start: 0.8123 (m-10) cc_final: 0.7846 (m-80) REVERT: B 243 CYS cc_start: 0.8431 (m) cc_final: 0.8186 (m) REVERT: B 352 GLU cc_start: 0.7190 (mp0) cc_final: 0.6796 (mp0) REVERT: B 384 HIS cc_start: 0.5139 (OUTLIER) cc_final: 0.4718 (p-80) REVERT: B 414 PHE cc_start: 0.7147 (m-80) cc_final: 0.6767 (m-80) REVERT: B 416 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.7010 (pt) REVERT: B 438 MET cc_start: 0.7783 (mtm) cc_final: 0.7535 (mtm) REVERT: B 445 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7723 (mmtt) REVERT: B 455 ILE cc_start: 0.8080 (mm) cc_final: 0.7752 (mm) REVERT: B 518 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7722 (mtm110) REVERT: B 533 ASP cc_start: 0.6723 (p0) cc_final: 0.6505 (p0) REVERT: B 570 GLU cc_start: 0.6281 (tm-30) cc_final: 0.5710 (tm-30) REVERT: B 585 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7518 (tp40) REVERT: B 586 GLU cc_start: 0.7202 (pp20) cc_final: 0.6818 (pp20) REVERT: B 589 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6430 (mm-30) REVERT: B 613 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7429 (p90) REVERT: B 641 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7438 (mtm-85) REVERT: B 662 GLN cc_start: 0.7845 (tm-30) cc_final: 0.7591 (pp30) REVERT: B 688 ASP cc_start: 0.7872 (p0) cc_final: 0.7625 (p0) REVERT: B 724 MET cc_start: 0.7745 (mmm) cc_final: 0.7124 (tpp) REVERT: C 411 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6896 (tpp) REVERT: C 442 GLN cc_start: 0.4638 (OUTLIER) cc_final: 0.4081 (pp30) REVERT: C 475 PHE cc_start: 0.7045 (t80) cc_final: 0.6663 (t80) REVERT: C 493 MET cc_start: 0.7507 (tpp) cc_final: 0.7283 (mpp) REVERT: C 501 GLN cc_start: 0.8060 (tp40) cc_final: 0.7684 (tp40) REVERT: D 35 TYR cc_start: 0.8501 (m-10) cc_final: 0.8275 (m-80) REVERT: D 140 LYS cc_start: 0.6956 (pttp) cc_final: 0.6438 (mmtt) REVERT: D 216 MET cc_start: 0.7807 (mmm) cc_final: 0.7503 (mmm) REVERT: D 218 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7322 (tm-30) REVERT: D 233 ILE cc_start: 0.8444 (mt) cc_final: 0.8169 (mm) REVERT: D 243 SER cc_start: 0.7977 (m) cc_final: 0.7728 (p) REVERT: D 254 MET cc_start: 0.6390 (mtt) cc_final: 0.5726 (mtp) REVERT: D 258 LEU cc_start: 0.8265 (mt) cc_final: 0.7934 (tp) REVERT: D 260 ASN cc_start: 0.7490 (t0) cc_final: 0.7055 (t0) REVERT: D 261 PHE cc_start: 0.8182 (t80) cc_final: 0.7944 (t80) REVERT: D 268 PHE cc_start: 0.8055 (m-10) cc_final: 0.7802 (m-10) REVERT: D 281 TYR cc_start: 0.7543 (p90) cc_final: 0.7009 (p90) REVERT: D 284 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8461 (p) REVERT: D 313 TYR cc_start: 0.8261 (m-80) cc_final: 0.7944 (m-80) REVERT: D 316 TYR cc_start: 0.8386 (m-80) cc_final: 0.8061 (m-10) REVERT: D 318 TYR cc_start: 0.7860 (m-10) cc_final: 0.7617 (m-80) REVERT: D 341 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6641 (ttt) REVERT: D 362 GLN cc_start: 0.8049 (tp40) cc_final: 0.7685 (tp40) REVERT: D 378 LYS cc_start: 0.8069 (mttt) cc_final: 0.7800 (mttt) REVERT: D 395 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7108 (tm-30) REVERT: D 397 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6924 (mm-30) REVERT: D 398 ARG cc_start: 0.7253 (ttt90) cc_final: 0.6869 (mtt90) REVERT: D 433 PHE cc_start: 0.6831 (t80) cc_final: 0.6468 (t80) REVERT: D 439 ARG cc_start: 0.7952 (mtp85) cc_final: 0.7618 (mtp85) REVERT: E 16 GLU cc_start: 0.6512 (mm-30) cc_final: 0.6158 (mm-30) REVERT: E 70 THR cc_start: 0.8172 (p) cc_final: 0.7733 (t) REVERT: E 73 ASP cc_start: 0.7248 (t0) cc_final: 0.5565 (t0) REVERT: E 75 ASP cc_start: 0.7203 (m-30) cc_final: 0.6558 (m-30) REVERT: E 80 ARG cc_start: 0.8150 (mtt180) cc_final: 0.7005 (mtt180) REVERT: E 96 PHE cc_start: 0.7554 (m-80) cc_final: 0.7272 (m-80) REVERT: E 103 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: E 112 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7561 (mmtp) REVERT: E 119 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7273 (tm-30) REVERT: E 125 ARG cc_start: 0.7156 (mtt180) cc_final: 0.6833 (mtt180) REVERT: E 132 LYS cc_start: 0.8601 (mttt) cc_final: 0.8387 (mmtt) REVERT: E 154 GLN cc_start: 0.7344 (tm-30) cc_final: 0.6850 (tm-30) REVERT: E 159 MET cc_start: 0.7847 (mmm) cc_final: 0.7601 (mmm) REVERT: E 166 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6831 (mt-10) REVERT: E 181 ASN cc_start: 0.8102 (t0) cc_final: 0.7841 (t0) REVERT: E 184 ASP cc_start: 0.6917 (m-30) cc_final: 0.6651 (m-30) REVERT: E 193 LYS cc_start: 0.8369 (mttt) cc_final: 0.8081 (mttt) REVERT: E 237 SER cc_start: 0.8209 (m) cc_final: 0.7949 (t) REVERT: E 322 TYR cc_start: 0.8096 (m-10) cc_final: 0.7787 (m-80) REVERT: E 333 GLU cc_start: 0.7661 (tt0) cc_final: 0.7439 (tt0) REVERT: E 353 LYS cc_start: 0.8180 (mttt) cc_final: 0.7714 (mttt) REVERT: F 16 ASP cc_start: 0.7699 (t0) cc_final: 0.7210 (t0) REVERT: F 34 LEU cc_start: 0.8155 (tp) cc_final: 0.7895 (tt) REVERT: F 60 ILE cc_start: 0.8713 (mt) cc_final: 0.8406 (tt) REVERT: F 68 ARG cc_start: 0.8332 (tpp80) cc_final: 0.8039 (tpp-160) REVERT: F 116 LYS cc_start: 0.8266 (mttt) cc_final: 0.7882 (mmmm) REVERT: F 139 LYS cc_start: 0.8626 (mttt) cc_final: 0.8352 (mtpp) REVERT: F 158 LYS cc_start: 0.8363 (mttt) cc_final: 0.8000 (mttt) REVERT: F 187 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7931 (mp10) REVERT: F 213 LEU cc_start: 0.8471 (tp) cc_final: 0.8092 (tt) REVERT: F 216 LYS cc_start: 0.8389 (tttt) cc_final: 0.8070 (ttpp) REVERT: F 224 LEU cc_start: 0.8673 (tp) cc_final: 0.8411 (tp) REVERT: F 248 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7420 (p90) REVERT: F 249 VAL cc_start: 0.8273 (t) cc_final: 0.7984 (p) REVERT: F 252 ARG cc_start: 0.8127 (ptp-110) cc_final: 0.7753 (mtm110) REVERT: G 16 MET cc_start: 0.8240 (mmt) cc_final: 0.7579 (mmm) REVERT: H 926 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6126 (tp30) REVERT: K 163 LYS cc_start: 0.8142 (mttt) cc_final: 0.7932 (mttt) REVERT: K 167 LYS cc_start: 0.8574 (tttt) cc_final: 0.8315 (ttmt) REVERT: K 188 LYS cc_start: 0.8204 (tttt) cc_final: 0.7983 (tttt) REVERT: K 205 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7210 (mm-30) REVERT: K 259 LYS cc_start: 0.6738 (mmtm) cc_final: 0.6099 (mmtm) outliers start: 118 outliers final: 81 residues processed: 818 average time/residue: 0.1786 time to fit residues: 217.9296 Evaluate side-chains 854 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 754 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 273 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 220 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 278 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 HIS A 555 ASN B 37 HIS B 499 ASN C 537 HIS ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS K 266 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.150843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.122250 restraints weight = 40521.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.126116 restraints weight = 19328.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128643 restraints weight = 11731.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130196 restraints weight = 8435.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130979 restraints weight = 6844.229| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24323 Z= 0.184 Angle : 0.702 14.648 33080 Z= 0.346 Chirality : 0.044 0.220 3696 Planarity : 0.004 0.054 4058 Dihedral : 13.390 153.069 3610 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 4.70 % Allowed : 21.60 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.16), residues: 2804 helix: 1.05 (0.14), residues: 1359 sheet: -0.22 (0.27), residues: 369 loop : -1.19 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 211 TYR 0.019 0.001 TYR A 534 PHE 0.022 0.002 PHE A 659 TRP 0.071 0.002 TRP D 55 HIS 0.023 0.001 HIS D 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (24295) covalent geometry : angle 0.67656 / 0.35 (33035) hydrogen bonds : bond 0.03941 / 2.64 ( 1106) hydrogen bonds : angle 4.48574 / 3.16 ( 3154) metal coordination : bond 0.01016 / 0.62 ( 28) metal coordination : angle 5.12928 / 2.76 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 756 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8248 (mttt) cc_final: 0.7956 (mmmt) REVERT: A 61 TYR cc_start: 0.8170 (m-80) cc_final: 0.7807 (m-80) REVERT: A 65 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6204 (ptt) REVERT: A 68 LYS cc_start: 0.6195 (mtmt) cc_final: 0.5770 (tttm) REVERT: A 117 LYS cc_start: 0.7962 (tppt) cc_final: 0.7735 (tppt) REVERT: A 146 THR cc_start: 0.7563 (p) cc_final: 0.6316 (t) REVERT: A 157 LYS cc_start: 0.8363 (ptmm) cc_final: 0.7891 (ttpp) REVERT: A 158 LEU cc_start: 0.8351 (mt) cc_final: 0.8125 (mt) REVERT: A 162 SER cc_start: 0.8329 (p) cc_final: 0.7977 (p) REVERT: A 163 TYR cc_start: 0.7854 (t80) cc_final: 0.7526 (t80) REVERT: A 166 VAL cc_start: 0.8713 (t) cc_final: 0.8432 (p) REVERT: A 167 LYS cc_start: 0.7846 (mtpp) cc_final: 0.7371 (ttmm) REVERT: A 171 LYS cc_start: 0.8195 (tppt) cc_final: 0.7918 (mmtm) REVERT: A 273 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7971 (ttpt) REVERT: A 282 LYS cc_start: 0.8523 (tttt) cc_final: 0.8091 (ttmm) REVERT: A 287 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8044 (mt) REVERT: A 288 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7243 (mp0) REVERT: A 294 GLU cc_start: 0.6984 (tp30) cc_final: 0.6504 (tp30) REVERT: A 298 ARG cc_start: 0.7741 (mmm160) cc_final: 0.7422 (mmm160) REVERT: A 299 ASN cc_start: 0.7509 (p0) cc_final: 0.6944 (p0) REVERT: A 310 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8284 (pt) REVERT: A 332 ARG cc_start: 0.8006 (mpp80) cc_final: 0.7455 (mtp85) REVERT: A 347 SER cc_start: 0.8567 (m) cc_final: 0.7806 (t) REVERT: A 375 LYS cc_start: 0.8368 (ttpt) cc_final: 0.7996 (tttm) REVERT: A 391 ARG cc_start: 0.7052 (mtm-85) cc_final: 0.6783 (mtm-85) REVERT: A 418 LYS cc_start: 0.7717 (tmmt) cc_final: 0.7454 (tmmt) REVERT: A 424 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 434 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7197 (mm-30) REVERT: A 457 ILE cc_start: 0.8207 (tt) cc_final: 0.7931 (tt) REVERT: A 470 LEU cc_start: 0.8802 (tp) cc_final: 0.8474 (tp) REVERT: A 476 LYS cc_start: 0.8191 (mttt) cc_final: 0.7766 (mttm) REVERT: A 478 VAL cc_start: 0.8529 (t) cc_final: 0.8306 (m) REVERT: A 504 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8329 (ttmt) REVERT: A 514 MET cc_start: 0.7922 (tpp) cc_final: 0.7452 (tpp) REVERT: A 525 ILE cc_start: 0.8465 (tp) cc_final: 0.8174 (tp) REVERT: A 526 LYS cc_start: 0.7530 (tppt) cc_final: 0.7244 (tppt) REVERT: A 537 ASN cc_start: 0.8122 (t0) cc_final: 0.7016 (t0) REVERT: A 556 ASP cc_start: 0.7330 (m-30) cc_final: 0.7026 (m-30) REVERT: A 570 GLU cc_start: 0.7143 (pm20) cc_final: 0.6825 (pm20) REVERT: A 579 TYR cc_start: 0.7427 (p90) cc_final: 0.7054 (p90) REVERT: A 632 SER cc_start: 0.8099 (p) cc_final: 0.7748 (p) REVERT: A 642 ARG cc_start: 0.7466 (mtp85) cc_final: 0.6921 (mmt180) REVERT: A 659 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.6867 (p90) REVERT: A 670 MET cc_start: 0.8223 (mmm) cc_final: 0.7935 (mmm) REVERT: A 677 GLN cc_start: 0.7646 (mt0) cc_final: 0.7396 (mt0) REVERT: A 682 ASP cc_start: 0.6857 (m-30) cc_final: 0.6596 (m-30) REVERT: A 688 LYS cc_start: 0.8465 (tttt) cc_final: 0.8061 (ttmt) REVERT: A 692 LYS cc_start: 0.7769 (tppp) cc_final: 0.7556 (tptm) REVERT: A 696 MET cc_start: 0.7347 (mmm) cc_final: 0.6727 (tmm) REVERT: A 703 PHE cc_start: 0.8187 (m-80) cc_final: 0.7274 (m-80) REVERT: A 712 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7804 (mt) REVERT: B 27 GLU cc_start: 0.6647 (pp20) cc_final: 0.6176 (pp20) REVERT: B 48 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7721 (mtpp) REVERT: B 91 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7574 (mm) REVERT: B 113 LYS cc_start: 0.8131 (ttpp) cc_final: 0.7744 (ttmm) REVERT: B 122 THR cc_start: 0.6629 (OUTLIER) cc_final: 0.6258 (p) REVERT: B 158 TYR cc_start: 0.7300 (t80) cc_final: 0.6864 (t80) REVERT: B 243 CYS cc_start: 0.8461 (m) cc_final: 0.8228 (m) REVERT: B 384 HIS cc_start: 0.5120 (OUTLIER) cc_final: 0.4720 (p-80) REVERT: B 414 PHE cc_start: 0.7170 (m-80) cc_final: 0.6753 (m-80) REVERT: B 416 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7042 (pt) REVERT: B 445 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7870 (mmtt) REVERT: B 455 ILE cc_start: 0.8115 (mm) cc_final: 0.7785 (mm) REVERT: B 518 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7714 (mtm110) REVERT: B 570 GLU cc_start: 0.6364 (tm-30) cc_final: 0.5758 (tm-30) REVERT: B 586 GLU cc_start: 0.7200 (pp20) cc_final: 0.6850 (pp20) REVERT: B 589 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6488 (mm-30) REVERT: B 604 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8245 (t) REVERT: B 613 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7431 (p90) REVERT: B 641 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7474 (mtm-85) REVERT: B 662 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7589 (pp30) REVERT: B 681 ASP cc_start: 0.7944 (t0) cc_final: 0.7717 (t0) REVERT: B 724 MET cc_start: 0.7752 (mmm) cc_final: 0.7273 (mmm) REVERT: C 411 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6944 (tpp) REVERT: C 442 GLN cc_start: 0.4695 (OUTLIER) cc_final: 0.4143 (pp30) REVERT: C 475 PHE cc_start: 0.7144 (t80) cc_final: 0.6722 (t80) REVERT: C 493 MET cc_start: 0.7539 (tpp) cc_final: 0.7324 (mpp) REVERT: C 501 GLN cc_start: 0.8055 (tp40) cc_final: 0.7658 (tp40) REVERT: D 35 TYR cc_start: 0.8531 (m-10) cc_final: 0.8224 (m-80) REVERT: D 47 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7590 (mm-30) REVERT: D 150 LYS cc_start: 0.7493 (tttt) cc_final: 0.7201 (tttt) REVERT: D 155 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.7629 (mmm-85) REVERT: D 178 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8415 (pp) REVERT: D 216 MET cc_start: 0.7831 (mmm) cc_final: 0.7523 (mmm) REVERT: D 218 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7309 (tm-30) REVERT: D 219 TYR cc_start: 0.7898 (t80) cc_final: 0.7639 (t80) REVERT: D 233 ILE cc_start: 0.8476 (mt) cc_final: 0.8166 (mm) REVERT: D 243 SER cc_start: 0.8045 (m) cc_final: 0.7828 (p) REVERT: D 254 MET cc_start: 0.6436 (mtt) cc_final: 0.5736 (mtp) REVERT: D 258 LEU cc_start: 0.8182 (mt) cc_final: 0.7868 (tp) REVERT: D 260 ASN cc_start: 0.7557 (t0) cc_final: 0.7125 (t0) REVERT: D 261 PHE cc_start: 0.8202 (t80) cc_final: 0.7919 (t80) REVERT: D 268 PHE cc_start: 0.8080 (m-10) cc_final: 0.7873 (m-80) REVERT: D 281 TYR cc_start: 0.7674 (p90) cc_final: 0.7191 (p90) REVERT: D 284 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8527 (p) REVERT: D 313 TYR cc_start: 0.8277 (m-80) cc_final: 0.7972 (m-80) REVERT: D 316 TYR cc_start: 0.8416 (m-80) cc_final: 0.8061 (m-10) REVERT: D 318 TYR cc_start: 0.7834 (m-10) cc_final: 0.7602 (m-80) REVERT: D 341 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6459 (ttt) REVERT: D 362 GLN cc_start: 0.8045 (tp40) cc_final: 0.7437 (tp40) REVERT: D 378 LYS cc_start: 0.8089 (mttt) cc_final: 0.7805 (mttt) REVERT: D 395 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7122 (tm-30) REVERT: D 397 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6958 (mm-30) REVERT: D 398 ARG cc_start: 0.7268 (ttt90) cc_final: 0.6889 (mtt90) REVERT: D 433 PHE cc_start: 0.6941 (t80) cc_final: 0.6549 (t80) REVERT: D 439 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7650 (mtp85) REVERT: E 16 GLU cc_start: 0.6635 (mm-30) cc_final: 0.6334 (mm-30) REVERT: E 70 THR cc_start: 0.8191 (p) cc_final: 0.7768 (t) REVERT: E 73 ASP cc_start: 0.7282 (t0) cc_final: 0.5927 (t0) REVERT: E 75 ASP cc_start: 0.7209 (m-30) cc_final: 0.6618 (m-30) REVERT: E 80 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7253 (mtt180) REVERT: E 96 PHE cc_start: 0.7693 (m-80) cc_final: 0.7393 (m-80) REVERT: E 103 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: E 112 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7673 (mmtp) REVERT: E 119 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7375 (tm-30) REVERT: E 125 ARG cc_start: 0.7177 (mtt180) cc_final: 0.6844 (mtt180) REVERT: E 132 LYS cc_start: 0.8605 (mttt) cc_final: 0.8381 (mmtt) REVERT: E 154 GLN cc_start: 0.7355 (tm-30) cc_final: 0.6894 (tm-30) REVERT: E 159 MET cc_start: 0.7912 (mmm) cc_final: 0.7641 (mmm) REVERT: E 166 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6950 (mt-10) REVERT: E 181 ASN cc_start: 0.8062 (t0) cc_final: 0.7848 (t0) REVERT: E 184 ASP cc_start: 0.6732 (m-30) cc_final: 0.6421 (m-30) REVERT: E 193 LYS cc_start: 0.8386 (mttt) cc_final: 0.8083 (mttt) REVERT: E 237 SER cc_start: 0.8263 (m) cc_final: 0.8046 (t) REVERT: E 322 TYR cc_start: 0.8121 (m-10) cc_final: 0.7758 (m-80) REVERT: E 333 GLU cc_start: 0.7642 (tt0) cc_final: 0.7415 (tt0) REVERT: E 353 LYS cc_start: 0.8056 (mttt) cc_final: 0.7587 (mttt) REVERT: F 16 ASP cc_start: 0.7720 (t0) cc_final: 0.7240 (t0) REVERT: F 28 LYS cc_start: 0.8100 (ttpt) cc_final: 0.7820 (ttpt) REVERT: F 34 LEU cc_start: 0.8226 (tp) cc_final: 0.7954 (tt) REVERT: F 60 ILE cc_start: 0.8718 (mt) cc_final: 0.8427 (tt) REVERT: F 116 LYS cc_start: 0.8286 (mttt) cc_final: 0.7889 (mmmm) REVERT: F 139 LYS cc_start: 0.8622 (mttt) cc_final: 0.8356 (mtpp) REVERT: F 158 LYS cc_start: 0.8276 (mttt) cc_final: 0.7933 (mttt) REVERT: F 200 SER cc_start: 0.8337 (t) cc_final: 0.7780 (p) REVERT: F 213 LEU cc_start: 0.8468 (tp) cc_final: 0.8105 (tt) REVERT: F 216 LYS cc_start: 0.8390 (tttt) cc_final: 0.8099 (ttpp) REVERT: F 224 LEU cc_start: 0.8698 (tp) cc_final: 0.8422 (tp) REVERT: F 240 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7508 (mt0) REVERT: F 248 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7393 (p90) REVERT: F 249 VAL cc_start: 0.8312 (t) cc_final: 0.8042 (p) REVERT: G 16 MET cc_start: 0.8248 (mmt) cc_final: 0.7621 (mmm) REVERT: H 926 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6151 (tp30) REVERT: K 163 LYS cc_start: 0.8156 (mttt) cc_final: 0.7950 (mttt) REVERT: K 167 LYS cc_start: 0.8656 (tttt) cc_final: 0.8399 (ttmt) REVERT: K 188 LYS cc_start: 0.8230 (tttt) cc_final: 0.8021 (tttt) REVERT: K 205 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7268 (mm-30) REVERT: K 259 LYS cc_start: 0.6496 (mmtm) cc_final: 0.6105 (mptt) outliers start: 118 outliers final: 83 residues processed: 813 average time/residue: 0.1769 time to fit residues: 214.6792 Evaluate side-chains 847 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 745 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 273 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 208 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 124 optimal weight: 0.1980 chunk 144 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 227 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 ASN A 555 ASN B 37 HIS B 499 ASN B 519 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN F 48 HIS F 205 GLN ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 210 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.118777 restraints weight = 40649.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.122661 restraints weight = 19425.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.125095 restraints weight = 11841.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.126682 restraints weight = 8553.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127695 restraints weight = 6923.697| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24323 Z= 0.189 Angle : 0.729 15.008 33080 Z= 0.358 Chirality : 0.044 0.232 3696 Planarity : 0.004 0.057 4058 Dihedral : 13.476 154.007 3608 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer: Outliers : 5.50 % Allowed : 21.36 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2804 helix: 0.96 (0.14), residues: 1362 sheet: -0.33 (0.27), residues: 369 loop : -1.20 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 166 TYR 0.022 0.002 TYR F 266 PHE 0.023 0.002 PHE A 659 TRP 0.091 0.002 TRP D 55 HIS 0.013 0.001 HIS D 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (24295) covalent geometry : angle 0.70303 / 0.36 (33035) hydrogen bonds : bond 0.04020 / 2.69 ( 1106) hydrogen bonds : angle 4.51347 / 3.17 ( 3154) metal coordination : bond 0.01122 / 0.69 ( 28) metal coordination : angle 5.29159 / 2.87 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 765 time to evaluate : 0.839 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 59 LYS cc_start: 0.8328 (mttt) cc_final: 0.8085 (mmmt) REVERT: A 61 TYR cc_start: 0.8228 (m-80) cc_final: 0.7918 (m-80) REVERT: A 65 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6161 (ptt) REVERT: A 68 LYS cc_start: 0.6259 (mtmt) cc_final: 0.5810 (tttm) REVERT: A 146 THR cc_start: 0.7555 (p) cc_final: 0.6368 (t) REVERT: A 157 LYS cc_start: 0.8353 (ptmm) cc_final: 0.8011 (ttpp) REVERT: A 162 SER cc_start: 0.8244 (p) cc_final: 0.7906 (p) REVERT: A 163 TYR cc_start: 0.7842 (t80) cc_final: 0.7530 (t80) REVERT: A 166 VAL cc_start: 0.8746 (t) cc_final: 0.8425 (p) REVERT: A 167 LYS cc_start: 0.7728 (mtpp) cc_final: 0.7458 (ttmm) REVERT: A 270 PHE cc_start: 0.8211 (p90) cc_final: 0.7372 (p90) REVERT: A 273 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7641 (ttpp) REVERT: A 282 LYS cc_start: 0.8491 (tttt) cc_final: 0.8100 (ttmm) REVERT: A 287 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8054 (mt) REVERT: A 288 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7211 (mp0) REVERT: A 294 GLU cc_start: 0.6964 (tp30) cc_final: 0.6511 (tp30) REVERT: A 298 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7420 (mmm160) REVERT: A 299 ASN cc_start: 0.7634 (p0) cc_final: 0.7066 (p0) REVERT: A 310 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8313 (pt) REVERT: A 332 ARG cc_start: 0.8029 (mpp80) cc_final: 0.7469 (mtp85) REVERT: A 347 SER cc_start: 0.8580 (m) cc_final: 0.7836 (t) REVERT: A 375 LYS cc_start: 0.8391 (ttpt) cc_final: 0.8020 (tttm) REVERT: A 389 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7161 (tt) REVERT: A 391 ARG cc_start: 0.7111 (mtm-85) cc_final: 0.6798 (mtm-85) REVERT: A 418 LYS cc_start: 0.7769 (tmmt) cc_final: 0.7421 (tmmt) REVERT: A 424 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7344 (mm-30) REVERT: A 457 ILE cc_start: 0.8222 (tt) cc_final: 0.7945 (tt) REVERT: A 470 LEU cc_start: 0.8789 (tp) cc_final: 0.8431 (tp) REVERT: A 476 LYS cc_start: 0.8193 (mttt) cc_final: 0.7775 (mttm) REVERT: A 504 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8304 (ttmt) REVERT: A 505 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8067 (m) REVERT: A 514 MET cc_start: 0.7874 (tpp) cc_final: 0.7410 (tpp) REVERT: A 525 ILE cc_start: 0.8489 (tp) cc_final: 0.8150 (tp) REVERT: A 526 LYS cc_start: 0.7432 (tppt) cc_final: 0.7192 (tppt) REVERT: A 537 ASN cc_start: 0.8122 (t0) cc_final: 0.6907 (t0) REVERT: A 556 ASP cc_start: 0.7333 (m-30) cc_final: 0.6987 (m-30) REVERT: A 570 GLU cc_start: 0.7171 (pm20) cc_final: 0.6848 (pm20) REVERT: A 579 TYR cc_start: 0.7413 (p90) cc_final: 0.7052 (p90) REVERT: A 632 SER cc_start: 0.8096 (p) cc_final: 0.7755 (p) REVERT: A 642 ARG cc_start: 0.7520 (mtp85) cc_final: 0.6941 (mmt180) REVERT: A 659 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.6792 (p90) REVERT: A 670 MET cc_start: 0.8213 (mmm) cc_final: 0.7982 (mmm) REVERT: A 677 GLN cc_start: 0.7634 (mt0) cc_final: 0.7382 (mt0) REVERT: A 682 ASP cc_start: 0.6843 (m-30) cc_final: 0.6603 (m-30) REVERT: A 683 GLN cc_start: 0.7657 (tp40) cc_final: 0.7315 (mm-40) REVERT: A 688 LYS cc_start: 0.8450 (tttt) cc_final: 0.7962 (ttmt) REVERT: A 696 MET cc_start: 0.7319 (mmm) cc_final: 0.6763 (tmm) REVERT: A 703 PHE cc_start: 0.8198 (m-80) cc_final: 0.7344 (m-80) REVERT: A 712 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7843 (mt) REVERT: B 42 MET cc_start: 0.7277 (mtm) cc_final: 0.6991 (mtm) REVERT: B 91 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7612 (mm) REVERT: B 113 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7799 (ttmm) REVERT: B 122 THR cc_start: 0.6643 (OUTLIER) cc_final: 0.6286 (p) REVERT: B 158 TYR cc_start: 0.7290 (t80) cc_final: 0.6896 (t80) REVERT: B 185 ARG cc_start: 0.6261 (ptp-110) cc_final: 0.5967 (ptp90) REVERT: B 243 CYS cc_start: 0.8466 (m) cc_final: 0.8240 (m) REVERT: B 384 HIS cc_start: 0.5163 (OUTLIER) cc_final: 0.4715 (p-80) REVERT: B 414 PHE cc_start: 0.7147 (m-80) cc_final: 0.6630 (m-80) REVERT: B 416 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7107 (pt) REVERT: B 445 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7970 (mmtt) REVERT: B 455 ILE cc_start: 0.8174 (mm) cc_final: 0.7868 (mm) REVERT: B 487 ARG cc_start: 0.7215 (ptt-90) cc_final: 0.7014 (ptt180) REVERT: B 499 ASN cc_start: 0.7867 (m-40) cc_final: 0.7561 (m110) REVERT: B 518 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7737 (mtm110) REVERT: B 533 ASP cc_start: 0.6823 (p0) cc_final: 0.6424 (p0) REVERT: B 570 GLU cc_start: 0.6378 (tm-30) cc_final: 0.5740 (tm-30) REVERT: B 585 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7592 (tp40) REVERT: B 586 GLU cc_start: 0.7173 (pp20) cc_final: 0.6820 (pp20) REVERT: B 589 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6526 (mm-30) REVERT: B 604 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8315 (t) REVERT: B 613 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7192 (p90) REVERT: B 641 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7396 (mtm-85) REVERT: B 649 ASN cc_start: 0.7234 (m110) cc_final: 0.6907 (m110) REVERT: B 662 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7579 (pp30) REVERT: B 712 GLU cc_start: 0.6736 (pt0) cc_final: 0.6126 (pt0) REVERT: B 724 MET cc_start: 0.7793 (mmm) cc_final: 0.7280 (tmm) REVERT: C 408 ARG cc_start: 0.8248 (tpp80) cc_final: 0.8020 (tpp80) REVERT: C 411 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6922 (tpp) REVERT: C 442 GLN cc_start: 0.4682 (OUTLIER) cc_final: 0.4081 (pp30) REVERT: C 475 PHE cc_start: 0.7075 (t80) cc_final: 0.6668 (t80) REVERT: C 493 MET cc_start: 0.7561 (tpp) cc_final: 0.7354 (mpp) REVERT: C 501 GLN cc_start: 0.8077 (tp40) cc_final: 0.7666 (tp40) REVERT: C 524 HIS cc_start: 0.7889 (t-170) cc_final: 0.7628 (t-170) REVERT: D 35 TYR cc_start: 0.8527 (m-10) cc_final: 0.8165 (m-80) REVERT: D 47 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7533 (mm-30) REVERT: D 63 GLU cc_start: 0.7102 (mp0) cc_final: 0.6855 (mp0) REVERT: D 140 LYS cc_start: 0.6686 (pttm) cc_final: 0.6407 (mmtm) REVERT: D 150 LYS cc_start: 0.7555 (tttt) cc_final: 0.7288 (tttt) REVERT: D 178 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8356 (pp) REVERT: D 201 PHE cc_start: 0.8544 (m-80) cc_final: 0.8251 (m-80) REVERT: D 218 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7316 (tm-30) REVERT: D 233 ILE cc_start: 0.8484 (mt) cc_final: 0.8175 (mm) REVERT: D 258 LEU cc_start: 0.8204 (mt) cc_final: 0.7981 (tp) REVERT: D 260 ASN cc_start: 0.7653 (t0) cc_final: 0.7104 (t0) REVERT: D 261 PHE cc_start: 0.8198 (t80) cc_final: 0.7878 (t80) REVERT: D 281 TYR cc_start: 0.7683 (p90) cc_final: 0.7224 (p90) REVERT: D 284 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8521 (p) REVERT: D 313 TYR cc_start: 0.8272 (m-80) cc_final: 0.7944 (m-80) REVERT: D 316 TYR cc_start: 0.8411 (m-80) cc_final: 0.8060 (m-10) REVERT: D 318 TYR cc_start: 0.7839 (m-10) cc_final: 0.7570 (m-80) REVERT: D 341 MET cc_start: 0.6961 (ttt) cc_final: 0.6742 (ttt) REVERT: D 362 GLN cc_start: 0.8025 (tp40) cc_final: 0.7728 (tp40) REVERT: D 378 LYS cc_start: 0.8102 (mttt) cc_final: 0.7814 (mttt) REVERT: D 395 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7095 (tm-30) REVERT: D 398 ARG cc_start: 0.7315 (ttt90) cc_final: 0.6901 (mtt90) REVERT: D 433 PHE cc_start: 0.6974 (t80) cc_final: 0.6553 (t80) REVERT: D 439 ARG cc_start: 0.7959 (mtp85) cc_final: 0.7678 (mtp85) REVERT: E 16 GLU cc_start: 0.6554 (mm-30) cc_final: 0.6285 (mm-30) REVERT: E 31 LYS cc_start: 0.8250 (ptmt) cc_final: 0.8044 (ptmt) REVERT: E 70 THR cc_start: 0.8176 (p) cc_final: 0.7763 (t) REVERT: E 73 ASP cc_start: 0.7355 (t0) cc_final: 0.6190 (t0) REVERT: E 75 ASP cc_start: 0.7203 (m-30) cc_final: 0.6628 (m-30) REVERT: E 80 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7252 (mtt180) REVERT: E 96 PHE cc_start: 0.7728 (m-80) cc_final: 0.7450 (m-80) REVERT: E 103 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: E 112 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7718 (mmtp) REVERT: E 119 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7344 (tm-30) REVERT: E 125 ARG cc_start: 0.7169 (mtt180) cc_final: 0.6838 (mtt180) REVERT: E 132 LYS cc_start: 0.8609 (mttt) cc_final: 0.8394 (mmtt) REVERT: E 154 GLN cc_start: 0.7321 (tm-30) cc_final: 0.6832 (tm-30) REVERT: E 159 MET cc_start: 0.7924 (mmm) cc_final: 0.7672 (mmm) REVERT: E 184 ASP cc_start: 0.6723 (m-30) cc_final: 0.6413 (m-30) REVERT: E 193 LYS cc_start: 0.8423 (mttt) cc_final: 0.7763 (ttmm) REVERT: E 237 SER cc_start: 0.8383 (m) cc_final: 0.8152 (t) REVERT: E 256 GLN cc_start: 0.7614 (mt0) cc_final: 0.7355 (mt0) REVERT: E 322 TYR cc_start: 0.8128 (m-10) cc_final: 0.7795 (m-80) REVERT: E 333 GLU cc_start: 0.7641 (tt0) cc_final: 0.7404 (tt0) REVERT: E 353 LYS cc_start: 0.8091 (mttt) cc_final: 0.7648 (mttt) REVERT: F 16 ASP cc_start: 0.7707 (t0) cc_final: 0.7198 (t0) REVERT: F 28 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7876 (ttpt) REVERT: F 34 LEU cc_start: 0.8282 (tp) cc_final: 0.7995 (tt) REVERT: F 60 ILE cc_start: 0.8720 (mt) cc_final: 0.8413 (tt) REVERT: F 67 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8592 (p) REVERT: F 68 ARG cc_start: 0.8364 (tpp80) cc_final: 0.8112 (tpp80) REVERT: F 116 LYS cc_start: 0.8242 (mttt) cc_final: 0.7860 (mmmm) REVERT: F 158 LYS cc_start: 0.8289 (mttt) cc_final: 0.7892 (mttt) REVERT: F 200 SER cc_start: 0.8282 (t) cc_final: 0.7781 (p) REVERT: F 213 LEU cc_start: 0.8508 (tp) cc_final: 0.8142 (tt) REVERT: F 216 LYS cc_start: 0.8384 (tttt) cc_final: 0.8096 (ttpp) REVERT: F 224 LEU cc_start: 0.8721 (tp) cc_final: 0.8457 (tp) REVERT: F 240 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7465 (mt0) REVERT: F 248 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7467 (p90) REVERT: F 249 VAL cc_start: 0.8318 (t) cc_final: 0.8054 (p) REVERT: F 252 ARG cc_start: 0.8222 (ptp-110) cc_final: 0.7830 (mtp-110) REVERT: G 16 MET cc_start: 0.8240 (mmt) cc_final: 0.7653 (mmm) REVERT: H 926 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6137 (tp30) REVERT: K 163 LYS cc_start: 0.8160 (mttt) cc_final: 0.7940 (mttt) REVERT: K 167 LYS cc_start: 0.8726 (tttt) cc_final: 0.8474 (ttmt) REVERT: K 188 LYS cc_start: 0.8274 (tttt) cc_final: 0.8071 (tttt) REVERT: K 205 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7303 (mm-30) REVERT: K 259 LYS cc_start: 0.6605 (mmtm) cc_final: 0.6139 (mptt) outliers start: 138 outliers final: 95 residues processed: 828 average time/residue: 0.1757 time to fit residues: 217.1216 Evaluate side-chains 867 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 750 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 512 CYS Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 273 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 196 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 277 optimal weight: 0.9990 chunk 278 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 ASN A 461 HIS A 555 ASN B 37 HIS D 161 HIS ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS ** F 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.146946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118389 restraints weight = 40770.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122261 restraints weight = 19422.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.124684 restraints weight = 11801.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.126290 restraints weight = 8481.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127308 restraints weight = 6872.334| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24323 Z= 0.181 Angle : 0.746 21.129 33080 Z= 0.365 Chirality : 0.045 0.230 3696 Planarity : 0.005 0.066 4058 Dihedral : 13.501 154.374 3608 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 5.02 % Allowed : 22.24 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2804 helix: 0.93 (0.14), residues: 1366 sheet: -0.37 (0.27), residues: 358 loop : -1.22 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 317 TYR 0.022 0.002 TYR F 266 PHE 0.034 0.002 PHE B 12 TRP 0.060 0.002 TRP D 55 HIS 0.016 0.001 HIS C 524 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (24295) covalent geometry : angle 0.71915 / 0.36 (33035) hydrogen bonds : bond 0.03969 / 2.67 ( 1106) hydrogen bonds : angle 4.53750 / 3.19 ( 3154) metal coordination : bond 0.01074 / 0.66 ( 28) metal coordination : angle 5.46961 / 2.96 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 760 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8341 (mttt) cc_final: 0.8082 (mmmt) REVERT: A 65 MET cc_start: 0.7013 (OUTLIER) cc_final: 0.6190 (ptt) REVERT: A 68 LYS cc_start: 0.6241 (mtmt) cc_final: 0.5808 (tttm) REVERT: A 146 THR cc_start: 0.7533 (p) cc_final: 0.6535 (t) REVERT: A 157 LYS cc_start: 0.8328 (ptmm) cc_final: 0.8004 (ttpp) REVERT: A 162 SER cc_start: 0.8263 (p) cc_final: 0.7911 (p) REVERT: A 163 TYR cc_start: 0.7874 (t80) cc_final: 0.7535 (t80) REVERT: A 166 VAL cc_start: 0.8725 (t) cc_final: 0.8424 (p) REVERT: A 270 PHE cc_start: 0.8233 (p90) cc_final: 0.7380 (p90) REVERT: A 273 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8035 (ttpt) REVERT: A 282 LYS cc_start: 0.8532 (tttt) cc_final: 0.8119 (ttmm) REVERT: A 287 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8071 (mt) REVERT: A 288 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7220 (mp0) REVERT: A 294 GLU cc_start: 0.7028 (tp30) cc_final: 0.6524 (tp30) REVERT: A 298 ARG cc_start: 0.7752 (mmm160) cc_final: 0.7437 (mmm160) REVERT: A 299 ASN cc_start: 0.7773 (p0) cc_final: 0.7103 (p0) REVERT: A 310 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8340 (pt) REVERT: A 332 ARG cc_start: 0.8016 (mpp80) cc_final: 0.7449 (mtp85) REVERT: A 347 SER cc_start: 0.8575 (m) cc_final: 0.7839 (t) REVERT: A 375 LYS cc_start: 0.8287 (ttpt) cc_final: 0.7938 (tttm) REVERT: A 389 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7245 (tt) REVERT: A 391 ARG cc_start: 0.7233 (mtm-85) cc_final: 0.7013 (mtm-85) REVERT: A 418 LYS cc_start: 0.7787 (tmmt) cc_final: 0.7420 (tmmt) REVERT: A 419 ARG cc_start: 0.7700 (ttm110) cc_final: 0.7099 (tpp80) REVERT: A 424 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 457 ILE cc_start: 0.8215 (tt) cc_final: 0.7932 (tt) REVERT: A 470 LEU cc_start: 0.8829 (tp) cc_final: 0.8440 (tp) REVERT: A 476 LYS cc_start: 0.8270 (mttt) cc_final: 0.7833 (mttm) REVERT: A 504 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8292 (ttmt) REVERT: A 505 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8069 (m) REVERT: A 514 MET cc_start: 0.7854 (tpp) cc_final: 0.7393 (tpp) REVERT: A 525 ILE cc_start: 0.8438 (tp) cc_final: 0.8123 (tp) REVERT: A 526 LYS cc_start: 0.7425 (tppt) cc_final: 0.7185 (tppt) REVERT: A 537 ASN cc_start: 0.8109 (t0) cc_final: 0.6849 (t0) REVERT: A 542 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8211 (mtp-110) REVERT: A 556 ASP cc_start: 0.7335 (m-30) cc_final: 0.7014 (m-30) REVERT: A 570 GLU cc_start: 0.7197 (pm20) cc_final: 0.6883 (pm20) REVERT: A 579 TYR cc_start: 0.7394 (p90) cc_final: 0.7140 (p90) REVERT: A 632 SER cc_start: 0.8092 (p) cc_final: 0.7745 (p) REVERT: A 642 ARG cc_start: 0.7519 (mtp85) cc_final: 0.7157 (mmt-90) REVERT: A 658 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7536 (p90) REVERT: A 659 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.6674 (p90) REVERT: A 670 MET cc_start: 0.8155 (mmm) cc_final: 0.7924 (mmm) REVERT: A 677 GLN cc_start: 0.7603 (mt0) cc_final: 0.7366 (mt0) REVERT: A 682 ASP cc_start: 0.6880 (m-30) cc_final: 0.6603 (m-30) REVERT: A 683 GLN cc_start: 0.7647 (tp40) cc_final: 0.7289 (mm-40) REVERT: A 688 LYS cc_start: 0.8457 (tttt) cc_final: 0.7977 (ttmt) REVERT: A 692 LYS cc_start: 0.7843 (tptm) cc_final: 0.7394 (tptt) REVERT: A 696 MET cc_start: 0.7315 (mmm) cc_final: 0.6600 (tmm) REVERT: A 703 PHE cc_start: 0.8275 (m-80) cc_final: 0.7430 (m-80) REVERT: A 712 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7837 (mt) REVERT: B 42 MET cc_start: 0.7210 (mtm) cc_final: 0.6988 (mtm) REVERT: B 85 GLU cc_start: 0.7417 (pp20) cc_final: 0.7179 (pp20) REVERT: B 91 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7565 (mm) REVERT: B 113 LYS cc_start: 0.8273 (ttpp) cc_final: 0.7887 (ttmm) REVERT: B 122 THR cc_start: 0.6756 (OUTLIER) cc_final: 0.6405 (p) REVERT: B 158 TYR cc_start: 0.7256 (t80) cc_final: 0.6892 (t80) REVERT: B 243 CYS cc_start: 0.8511 (m) cc_final: 0.8291 (m) REVERT: B 384 HIS cc_start: 0.5117 (OUTLIER) cc_final: 0.4679 (p-80) REVERT: B 414 PHE cc_start: 0.7196 (m-80) cc_final: 0.6553 (m-80) REVERT: B 416 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7187 (pt) REVERT: B 439 ASP cc_start: 0.7006 (p0) cc_final: 0.6738 (p0) REVERT: B 455 ILE cc_start: 0.8170 (mm) cc_final: 0.7753 (mm) REVERT: B 518 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7665 (ttp80) REVERT: B 533 ASP cc_start: 0.6853 (p0) cc_final: 0.6651 (p0) REVERT: B 570 GLU cc_start: 0.6424 (tm-30) cc_final: 0.5786 (tm-30) REVERT: B 585 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7587 (tp40) REVERT: B 586 GLU cc_start: 0.7110 (pp20) cc_final: 0.6788 (pp20) REVERT: B 589 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6546 (mm-30) REVERT: B 613 HIS cc_start: 0.7858 (OUTLIER) cc_final: 0.7288 (p90) REVERT: B 620 MET cc_start: 0.7797 (mmm) cc_final: 0.7102 (mmm) REVERT: B 641 ARG cc_start: 0.8000 (ttm-80) cc_final: 0.7437 (mtm-85) REVERT: B 649 ASN cc_start: 0.7236 (m110) cc_final: 0.6901 (m110) REVERT: B 677 MET cc_start: 0.7010 (mtp) cc_final: 0.6777 (mtm) REVERT: B 681 ASP cc_start: 0.7960 (t0) cc_final: 0.7757 (t0) REVERT: B 686 ARG cc_start: 0.7392 (tpp80) cc_final: 0.7160 (tpp80) REVERT: B 724 MET cc_start: 0.7828 (mmm) cc_final: 0.7147 (tmm) REVERT: C 408 ARG cc_start: 0.8258 (tpp80) cc_final: 0.8032 (tpp80) REVERT: C 411 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6942 (tpp) REVERT: C 442 GLN cc_start: 0.4656 (OUTLIER) cc_final: 0.4104 (pp30) REVERT: C 475 PHE cc_start: 0.7100 (t80) cc_final: 0.6649 (t80) REVERT: C 493 MET cc_start: 0.7585 (tpp) cc_final: 0.7357 (mpp) REVERT: C 501 GLN cc_start: 0.8142 (tp40) cc_final: 0.7753 (tp40) REVERT: D 35 TYR cc_start: 0.8521 (m-10) cc_final: 0.8126 (m-80) REVERT: D 47 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7540 (mm-30) REVERT: D 150 LYS cc_start: 0.7578 (tttt) cc_final: 0.7315 (tttt) REVERT: D 178 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8198 (tp) REVERT: D 201 PHE cc_start: 0.8583 (m-80) cc_final: 0.8258 (m-80) REVERT: D 212 LEU cc_start: 0.8903 (tp) cc_final: 0.8532 (mt) REVERT: D 218 GLN cc_start: 0.7620 (mm-40) cc_final: 0.7311 (tm-30) REVERT: D 233 ILE cc_start: 0.8445 (mt) cc_final: 0.8167 (mm) REVERT: D 254 MET cc_start: 0.6377 (mtt) cc_final: 0.5806 (mtt) REVERT: D 258 LEU cc_start: 0.8194 (mt) cc_final: 0.7971 (tp) REVERT: D 260 ASN cc_start: 0.7546 (t0) cc_final: 0.7122 (t0) REVERT: D 261 PHE cc_start: 0.8166 (t80) cc_final: 0.7901 (t80) REVERT: D 281 TYR cc_start: 0.7692 (p90) cc_final: 0.7295 (p90) REVERT: D 313 TYR cc_start: 0.8276 (m-80) cc_final: 0.7955 (m-80) REVERT: D 316 TYR cc_start: 0.8398 (m-80) cc_final: 0.8055 (m-10) REVERT: D 318 TYR cc_start: 0.7821 (m-10) cc_final: 0.7551 (m-80) REVERT: D 362 GLN cc_start: 0.8007 (tp40) cc_final: 0.7713 (tp40) REVERT: D 378 LYS cc_start: 0.8103 (mttt) cc_final: 0.7816 (mttt) REVERT: D 395 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7082 (tm-30) REVERT: D 398 ARG cc_start: 0.7313 (ttt90) cc_final: 0.6896 (mtt90) REVERT: D 433 PHE cc_start: 0.6950 (t80) cc_final: 0.6484 (t80) REVERT: D 439 ARG cc_start: 0.7959 (mtp85) cc_final: 0.7677 (mtp85) REVERT: E 16 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6296 (mm-30) REVERT: E 31 LYS cc_start: 0.8207 (ptmt) cc_final: 0.7984 (ptmt) REVERT: E 70 THR cc_start: 0.8175 (p) cc_final: 0.7756 (t) REVERT: E 73 ASP cc_start: 0.7360 (t0) cc_final: 0.6189 (t0) REVERT: E 75 ASP cc_start: 0.7210 (m-30) cc_final: 0.6640 (m-30) REVERT: E 80 ARG cc_start: 0.8182 (mtt180) cc_final: 0.7240 (mtt180) REVERT: E 96 PHE cc_start: 0.7725 (m-80) cc_final: 0.7434 (m-80) REVERT: E 103 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7651 (mt0) REVERT: E 112 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7750 (mmtp) REVERT: E 119 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7364 (tm-30) REVERT: E 125 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6844 (mtt180) REVERT: E 154 GLN cc_start: 0.7313 (tm-30) cc_final: 0.6771 (tm-30) REVERT: E 159 MET cc_start: 0.7903 (mmm) cc_final: 0.7678 (mmm) REVERT: E 193 LYS cc_start: 0.8419 (mttt) cc_final: 0.8110 (mttt) REVERT: E 237 SER cc_start: 0.8411 (m) cc_final: 0.8203 (t) REVERT: E 256 GLN cc_start: 0.7616 (mt0) cc_final: 0.7324 (mt0) REVERT: E 322 TYR cc_start: 0.8152 (m-10) cc_final: 0.7787 (m-80) REVERT: E 333 GLU cc_start: 0.7642 (tt0) cc_final: 0.7406 (tt0) REVERT: E 353 LYS cc_start: 0.8082 (mttt) cc_final: 0.7644 (mttt) REVERT: F 16 ASP cc_start: 0.7714 (t0) cc_final: 0.7208 (t0) REVERT: F 28 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7900 (ttpt) REVERT: F 34 LEU cc_start: 0.8292 (tp) cc_final: 0.8001 (tt) REVERT: F 60 ILE cc_start: 0.8740 (mt) cc_final: 0.8446 (tt) REVERT: F 68 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8105 (tpp80) REVERT: F 116 LYS cc_start: 0.8240 (mttt) cc_final: 0.7913 (mmmm) REVERT: F 139 LYS cc_start: 0.8640 (mttt) cc_final: 0.8386 (mtpp) REVERT: F 213 LEU cc_start: 0.8536 (tp) cc_final: 0.8144 (tt) REVERT: F 216 LYS cc_start: 0.8379 (tttt) cc_final: 0.8094 (ttpp) REVERT: F 224 LEU cc_start: 0.8747 (tp) cc_final: 0.8495 (tp) REVERT: F 240 GLN cc_start: 0.7844 (mm-40) cc_final: 0.7429 (mt0) REVERT: F 248 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7525 (p90) REVERT: F 249 VAL cc_start: 0.8357 (t) cc_final: 0.8087 (p) REVERT: G 16 MET cc_start: 0.8235 (mmt) cc_final: 0.7624 (mmm) REVERT: H 926 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6142 (tp30) REVERT: K 167 LYS cc_start: 0.8713 (tttt) cc_final: 0.8439 (ttmt) REVERT: K 205 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7307 (mm-30) REVERT: K 259 LYS cc_start: 0.6630 (mmtm) cc_final: 0.6157 (mptt) REVERT: K 263 MET cc_start: 0.4781 (mmm) cc_final: 0.4577 (mmm) outliers start: 126 outliers final: 93 residues processed: 813 average time/residue: 0.1754 time to fit residues: 212.3487 Evaluate side-chains 865 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 752 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 603 LYS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 54 GLN Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 227 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 276 optimal weight: 10.0000 chunk 103 optimal weight: 0.3980 chunk 227 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 129 optimal weight: 40.0000 chunk 148 optimal weight: 0.7980 chunk 184 optimal weight: 5.9990 chunk 206 optimal weight: 0.7980 chunk 240 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 273 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 ASN A 555 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 499 ASN B 649 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS F 205 GLN F 237 GLN ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.146200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.117666 restraints weight = 40507.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.121547 restraints weight = 19297.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123975 restraints weight = 11709.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125578 restraints weight = 8403.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.126550 restraints weight = 6798.281| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 24323 Z= 0.191 Angle : 0.758 15.096 33080 Z= 0.373 Chirality : 0.045 0.245 3696 Planarity : 0.004 0.057 4058 Dihedral : 13.545 154.473 3607 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 4.50 % Allowed : 22.92 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2804 helix: 0.95 (0.14), residues: 1350 sheet: -0.40 (0.28), residues: 330 loop : -1.19 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 155 TYR 0.015 0.002 TYR A 534 PHE 0.024 0.002 PHE A 659 TRP 0.021 0.002 TRP D 213 HIS 0.015 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (24295) covalent geometry : angle 0.73245 / 0.37 (33035) hydrogen bonds : bond 0.04050 / 2.70 ( 1106) hydrogen bonds : angle 4.56805 / 3.21 ( 3154) metal coordination : bond 0.00704 / 0.44 ( 28) metal coordination : angle 5.35149 / 2.89 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5608 Ramachandran restraints generated. 2804 Oldfield, 0 Emsley, 2804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 767 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8290 (mttt) cc_final: 0.8022 (mmmt) REVERT: A 61 TYR cc_start: 0.8207 (m-10) cc_final: 0.7756 (m-80) REVERT: A 65 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6277 (ptt) REVERT: A 68 LYS cc_start: 0.6315 (mtmt) cc_final: 0.5881 (tttm) REVERT: A 146 THR cc_start: 0.7563 (p) cc_final: 0.6550 (t) REVERT: A 157 LYS cc_start: 0.8372 (ptmm) cc_final: 0.8032 (ttpp) REVERT: A 162 SER cc_start: 0.8270 (p) cc_final: 0.7926 (p) REVERT: A 163 TYR cc_start: 0.7897 (t80) cc_final: 0.7562 (t80) REVERT: A 166 VAL cc_start: 0.8753 (t) cc_final: 0.8460 (p) REVERT: A 167 LYS cc_start: 0.8089 (ttmm) cc_final: 0.7496 (ttmm) REVERT: A 273 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8078 (ttpt) REVERT: A 282 LYS cc_start: 0.8539 (tttt) cc_final: 0.8123 (ttmm) REVERT: A 287 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8112 (mt) REVERT: A 288 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7247 (mp0) REVERT: A 294 GLU cc_start: 0.7035 (tp30) cc_final: 0.6521 (tp30) REVERT: A 298 ARG cc_start: 0.7777 (mmm160) cc_final: 0.7443 (mmm160) REVERT: A 299 ASN cc_start: 0.7667 (p0) cc_final: 0.7081 (p0) REVERT: A 310 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8346 (pt) REVERT: A 332 ARG cc_start: 0.8043 (mpp80) cc_final: 0.7386 (mtp85) REVERT: A 347 SER cc_start: 0.8587 (m) cc_final: 0.7848 (t) REVERT: A 375 LYS cc_start: 0.8335 (ttpt) cc_final: 0.7905 (tttm) REVERT: A 379 LYS cc_start: 0.8341 (mmtt) cc_final: 0.8127 (mmtt) REVERT: A 391 ARG cc_start: 0.7262 (mtm-85) cc_final: 0.7059 (mtm-85) REVERT: A 418 LYS cc_start: 0.7732 (tmmt) cc_final: 0.7424 (tmmt) REVERT: A 419 ARG cc_start: 0.7683 (ttm110) cc_final: 0.7208 (tpp80) REVERT: A 424 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 457 ILE cc_start: 0.8300 (tt) cc_final: 0.7983 (tt) REVERT: A 470 LEU cc_start: 0.8828 (tp) cc_final: 0.8416 (tp) REVERT: A 476 LYS cc_start: 0.8259 (mttt) cc_final: 0.7504 (mttm) REVERT: A 504 LYS cc_start: 0.8612 (ttpt) cc_final: 0.8277 (ttmt) REVERT: A 505 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8067 (m) REVERT: A 514 MET cc_start: 0.7852 (tpp) cc_final: 0.7377 (tpp) REVERT: A 520 ARG cc_start: 0.7479 (mmm160) cc_final: 0.7170 (mmm-85) REVERT: A 525 ILE cc_start: 0.8417 (tp) cc_final: 0.8097 (tp) REVERT: A 526 LYS cc_start: 0.7363 (tppt) cc_final: 0.7057 (tppt) REVERT: A 537 ASN cc_start: 0.8101 (t0) cc_final: 0.6799 (t0) REVERT: A 556 ASP cc_start: 0.7269 (m-30) cc_final: 0.6911 (m-30) REVERT: A 569 LYS cc_start: 0.8042 (mmmt) cc_final: 0.7433 (mmmt) REVERT: A 570 GLU cc_start: 0.7217 (pm20) cc_final: 0.6909 (pm20) REVERT: A 579 TYR cc_start: 0.7385 (p90) cc_final: 0.6958 (p90) REVERT: A 588 GLU cc_start: 0.7163 (tp30) cc_final: 0.6637 (tp30) REVERT: A 632 SER cc_start: 0.8105 (p) cc_final: 0.7771 (p) REVERT: A 642 ARG cc_start: 0.7537 (mtp85) cc_final: 0.7151 (mmt-90) REVERT: A 658 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7487 (p90) REVERT: A 659 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.6627 (p90) REVERT: A 677 GLN cc_start: 0.7602 (mt0) cc_final: 0.7348 (mt0) REVERT: A 682 ASP cc_start: 0.6889 (m-30) cc_final: 0.6586 (m-30) REVERT: A 683 GLN cc_start: 0.7653 (tp40) cc_final: 0.7093 (mm-40) REVERT: A 688 LYS cc_start: 0.8449 (tttt) cc_final: 0.7956 (ttmt) REVERT: A 692 LYS cc_start: 0.7905 (tptm) cc_final: 0.7447 (tptt) REVERT: A 696 MET cc_start: 0.7346 (mmm) cc_final: 0.6898 (tmm) REVERT: A 703 PHE cc_start: 0.8315 (m-80) cc_final: 0.7632 (m-80) REVERT: A 712 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7896 (mt) REVERT: B 63 TYR cc_start: 0.8083 (m-80) cc_final: 0.7818 (m-80) REVERT: B 91 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7623 (mm) REVERT: B 113 LYS cc_start: 0.8348 (ttpp) cc_final: 0.7999 (ttmm) REVERT: B 122 THR cc_start: 0.6797 (OUTLIER) cc_final: 0.6427 (p) REVERT: B 158 TYR cc_start: 0.7263 (t80) cc_final: 0.6853 (t80) REVERT: B 185 ARG cc_start: 0.6256 (ptp-110) cc_final: 0.5992 (ptp90) REVERT: B 243 CYS cc_start: 0.8556 (m) cc_final: 0.8336 (m) REVERT: B 384 HIS cc_start: 0.5120 (OUTLIER) cc_final: 0.4684 (p-80) REVERT: B 414 PHE cc_start: 0.7211 (m-80) cc_final: 0.6633 (m-80) REVERT: B 416 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7242 (mt) REVERT: B 439 ASP cc_start: 0.7195 (p0) cc_final: 0.6861 (p0) REVERT: B 455 ILE cc_start: 0.8230 (mm) cc_final: 0.7816 (mm) REVERT: B 472 ASP cc_start: 0.6960 (m-30) cc_final: 0.6701 (m-30) REVERT: B 507 LYS cc_start: 0.8428 (mttt) cc_final: 0.8072 (mttm) REVERT: B 518 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7713 (mtm110) REVERT: B 570 GLU cc_start: 0.6520 (tm-30) cc_final: 0.5886 (tm-30) REVERT: B 585 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7595 (tp40) REVERT: B 586 GLU cc_start: 0.7098 (pp20) cc_final: 0.6721 (pp20) REVERT: B 589 GLU cc_start: 0.6985 (mm-30) cc_final: 0.6593 (mm-30) REVERT: B 613 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7306 (p90) REVERT: B 620 MET cc_start: 0.7782 (mmm) cc_final: 0.7092 (mmm) REVERT: B 641 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7471 (mtm-85) REVERT: B 649 ASN cc_start: 0.7189 (m-40) cc_final: 0.6907 (m-40) REVERT: B 677 MET cc_start: 0.7024 (mtp) cc_final: 0.6793 (mtm) REVERT: B 681 ASP cc_start: 0.7978 (t0) cc_final: 0.7730 (t0) REVERT: B 724 MET cc_start: 0.7872 (mmm) cc_final: 0.7316 (mmm) REVERT: C 411 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.7008 (tpp) REVERT: C 442 GLN cc_start: 0.4660 (OUTLIER) cc_final: 0.4087 (pp30) REVERT: C 475 PHE cc_start: 0.7090 (t80) cc_final: 0.6675 (t80) REVERT: C 493 MET cc_start: 0.7586 (tpp) cc_final: 0.7378 (mpp) REVERT: C 501 GLN cc_start: 0.8124 (tp40) cc_final: 0.7732 (tp40) REVERT: D 35 TYR cc_start: 0.8568 (m-10) cc_final: 0.8150 (m-80) REVERT: D 40 THR cc_start: 0.7689 (p) cc_final: 0.7475 (p) REVERT: D 47 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7564 (mm-30) REVERT: D 150 LYS cc_start: 0.7608 (tttt) cc_final: 0.7338 (tttt) REVERT: D 201 PHE cc_start: 0.8645 (m-80) cc_final: 0.8295 (m-80) REVERT: D 212 LEU cc_start: 0.8876 (tp) cc_final: 0.8633 (mt) REVERT: D 213 TRP cc_start: 0.7001 (t-100) cc_final: 0.6784 (m100) REVERT: D 218 GLN cc_start: 0.7630 (mm-40) cc_final: 0.7359 (tm-30) REVERT: D 233 ILE cc_start: 0.8432 (mt) cc_final: 0.8114 (mm) REVERT: D 254 MET cc_start: 0.6408 (mtt) cc_final: 0.5807 (mtt) REVERT: D 258 LEU cc_start: 0.8117 (mt) cc_final: 0.7910 (tp) REVERT: D 260 ASN cc_start: 0.7647 (t0) cc_final: 0.7240 (t0) REVERT: D 261 PHE cc_start: 0.8178 (t80) cc_final: 0.7931 (t80) REVERT: D 275 LYS cc_start: 0.7459 (mttp) cc_final: 0.7196 (mttp) REVERT: D 313 TYR cc_start: 0.8284 (m-80) cc_final: 0.7884 (m-80) REVERT: D 316 TYR cc_start: 0.8402 (m-80) cc_final: 0.8002 (m-10) REVERT: D 318 TYR cc_start: 0.7830 (m-10) cc_final: 0.7541 (m-80) REVERT: D 362 GLN cc_start: 0.7996 (tp40) cc_final: 0.7692 (tp40) REVERT: D 378 LYS cc_start: 0.8120 (mttt) cc_final: 0.7831 (mttt) REVERT: D 398 ARG cc_start: 0.7332 (ttt90) cc_final: 0.6895 (mtt90) REVERT: D 433 PHE cc_start: 0.6949 (t80) cc_final: 0.6508 (t80) REVERT: D 439 ARG cc_start: 0.7982 (mtp85) cc_final: 0.7707 (mtp85) REVERT: E 16 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6392 (mm-30) REVERT: E 31 LYS cc_start: 0.8163 (ptmt) cc_final: 0.7907 (ptmt) REVERT: E 70 THR cc_start: 0.8178 (p) cc_final: 0.7753 (t) REVERT: E 73 ASP cc_start: 0.7391 (t0) cc_final: 0.6206 (t0) REVERT: E 75 ASP cc_start: 0.7220 (m-30) cc_final: 0.6662 (m-30) REVERT: E 80 ARG cc_start: 0.8192 (mtt180) cc_final: 0.7265 (mtt180) REVERT: E 96 PHE cc_start: 0.7729 (m-80) cc_final: 0.7445 (m-80) REVERT: E 103 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7675 (mt0) REVERT: E 112 LYS cc_start: 0.8098 (mtmt) cc_final: 0.7778 (mmtp) REVERT: E 125 ARG cc_start: 0.6925 (mtt180) cc_final: 0.6419 (mtt180) REVERT: E 154 GLN cc_start: 0.7353 (tm-30) cc_final: 0.6794 (tm-30) REVERT: E 193 LYS cc_start: 0.8442 (mttt) cc_final: 0.7799 (ttmm) REVERT: E 237 SER cc_start: 0.8456 (m) cc_final: 0.8225 (t) REVERT: E 256 GLN cc_start: 0.7530 (mt0) cc_final: 0.7302 (mt0) REVERT: E 300 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6668 (mt-10) REVERT: E 322 TYR cc_start: 0.8212 (m-10) cc_final: 0.7852 (m-80) REVERT: E 353 LYS cc_start: 0.8002 (mttt) cc_final: 0.7586 (mttt) REVERT: F 16 ASP cc_start: 0.7748 (t0) cc_final: 0.7261 (t0) REVERT: F 28 LYS cc_start: 0.8177 (ttpt) cc_final: 0.7796 (ttpt) REVERT: F 34 LEU cc_start: 0.8334 (tp) cc_final: 0.8023 (tt) REVERT: F 60 ILE cc_start: 0.8743 (mt) cc_final: 0.8419 (tt) REVERT: F 67 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8485 (p) REVERT: F 68 ARG cc_start: 0.8373 (tpp80) cc_final: 0.8097 (tpp80) REVERT: F 116 LYS cc_start: 0.8278 (mttt) cc_final: 0.7923 (mmmm) REVERT: F 213 LEU cc_start: 0.8531 (tp) cc_final: 0.8144 (tt) REVERT: F 216 LYS cc_start: 0.8379 (tttt) cc_final: 0.8094 (ttpp) REVERT: F 224 LEU cc_start: 0.8767 (tp) cc_final: 0.8516 (tp) REVERT: F 237 GLN cc_start: 0.7255 (mt0) cc_final: 0.6920 (mt0) REVERT: F 240 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7497 (mt0) REVERT: F 248 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7578 (p90) REVERT: F 249 VAL cc_start: 0.8394 (t) cc_final: 0.8086 (p) REVERT: G 16 MET cc_start: 0.8234 (mmt) cc_final: 0.7768 (mmm) REVERT: G 54 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: G 59 GLU cc_start: 0.7596 (tt0) cc_final: 0.7269 (tt0) REVERT: G 61 MET cc_start: 0.8100 (mmm) cc_final: 0.7734 (mmm) REVERT: H 926 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6064 (tp30) REVERT: K 167 LYS cc_start: 0.8713 (tttt) cc_final: 0.8439 (ttmt) REVERT: K 205 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7313 (mm-30) REVERT: K 259 LYS cc_start: 0.6706 (mmtm) cc_final: 0.6195 (mptt) REVERT: K 263 MET cc_start: 0.4846 (mmm) cc_final: 0.4605 (mmm) outliers start: 113 outliers final: 84 residues processed: 821 average time/residue: 0.1731 time to fit residues: 212.2226 Evaluate side-chains 864 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 760 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 GLN Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 403 CYS Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 450 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 487 LYS Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 564 ASN Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 187 GLN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 54 GLN Chi-restraints excluded: chain H residue 900 LEU Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 146 GLN Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 227 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 42 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 233 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 160 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 30.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 ASN A 555 ASN A 564 ASN B 37 HIS ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN E 356 HIS ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.145385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.116884 restraints weight = 40491.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120762 restraints weight = 19335.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.123122 restraints weight = 11725.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.124795 restraints weight = 8469.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.125827 restraints weight = 6794.753| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 24323 Z= 0.202 Angle : 0.773 15.396 33080 Z= 0.383 Chirality : 0.045 0.248 3696 Planarity : 0.005 0.048 4058 Dihedral : 13.597 154.645 3607 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.42 % Favored : 94.54 % Rotamer: Outliers : 4.62 % Allowed : 23.79 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.16), residues: 2804 helix: 0.91 (0.14), residues: 1349 sheet: -0.39 (0.27), residues: 346 loop : -1.27 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 155 TYR 0.025 0.002 TYR D 281 PHE 0.027 0.002 PHE A 659 TRP 0.019 0.002 TRP D 213 HIS 0.012 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (24295) covalent geometry : angle 0.74691 / 0.38 (33035) hydrogen bonds : bond 0.04105 / 2.73 ( 1106) hydrogen bonds : angle 4.57676 / 3.20 ( 3154) metal coordination : bond 0.00996 / 0.62 ( 28) metal coordination : angle 5.44211 / 2.96 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5069.77 seconds wall clock time: 87 minutes 55.00 seconds (5275.00 seconds total)