Starting phenix.real_space_refine on Fri Jun 20 13:35:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eby_28002/06_2025/8eby_28002.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eby_28002/06_2025/8eby_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_28002/06_2025/8eby_28002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eby_28002/06_2025/8eby_28002.map" model { file = "/net/cci-nas-00/data/ceres_data/8eby_28002/06_2025/8eby_28002.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eby_28002/06_2025/8eby_28002.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.14, per 1000 atoms: 0.55 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: 6.22 Conformation dependent library (CDL) restraints added in 2.8 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: 8.44 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: 9.60 Time building geometry restraints manager: 7.18 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=" C PRO B 354 " pdb=" N PRO B 355 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.36e+00 bond pdb=" N LYS H 917 " pdb=" CA LYS H 917 " ideal model delta sigma weight residual 1.459 1.470 -0.012 1.16e-02 7.43e+03 1.02e+00 bond pdb=" CA VAL C 453 " pdb=" CB VAL C 453 " ideal model delta sigma weight residual 1.537 1.549 -0.012 1.29e-02 6.01e+03 8.70e-01 bond pdb=" C3' DA L 16 " pdb=" O3' DA L 16 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.60e-01 bond pdb=" N PRO A 304 " pdb=" CA PRO A 304 " ideal model delta sigma weight residual 1.469 1.480 -0.011 1.28e-02 6.10e+03 7.61e-01 ... (remaining 24290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 32611 1.62 - 3.24: 356 3.24 - 4.86: 56 4.86 - 6.48: 9 6.48 - 8.10: 3 Bond angle restraints: 33035 Sorted by residual: angle pdb=" N GLN H 906 " pdb=" CA GLN H 906 " pdb=" C GLN H 906 " ideal model delta sigma weight residual 114.62 110.61 4.01 1.14e+00 7.69e-01 1.24e+01 angle pdb=" C LYS H 917 " pdb=" CA LYS H 917 " pdb=" CB LYS H 917 " ideal model delta sigma weight residual 110.92 115.78 -4.86 1.59e+00 3.96e-01 9.36e+00 angle pdb=" CA GLN K 197 " pdb=" C GLN K 197 " pdb=" N GLU K 198 " ideal model delta sigma weight residual 118.15 113.06 5.09 1.80e+00 3.09e-01 7.98e+00 angle pdb=" C LEU H 916 " pdb=" N LYS H 917 " pdb=" CA LYS H 917 " ideal model delta sigma weight residual 120.79 124.67 -3.88 1.39e+00 5.18e-01 7.79e+00 angle pdb=" C ASP B 423 " pdb=" N ARG B 424 " pdb=" CA ARG B 424 " ideal model delta sigma weight residual 121.54 126.73 -5.19 1.91e+00 2.74e-01 7.39e+00 ... (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: 2339 0.027 - 0.054: 871 0.054 - 0.081: 255 0.081 - 0.108: 190 0.108 - 0.135: 41 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.210 Process input model: 68.580 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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= 0.104 Angle : 0.491 12.728 33080 Z= 0.274 Chirality : 0.037 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 : 8.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (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 TRP 0.012 0.001 TRP A 511 HIS 0.004 0.000 HIS B 729 PHE 0.010 0.001 PHE A 482 TYR 0.012 0.001 TYR A 534 ARG 0.003 0.000 ARG A 676 Details of bonding type rmsd hydrogen bonds : bond 0.16640 ( 1106) hydrogen bonds : angle 5.66740 ( 3154) metal coordination : bond 0.00339 ( 28) metal coordination : angle 3.72588 ( 45) covalent geometry : bond 0.00205 (24295) covalent geometry : angle 0.47154 (33035) *********************** 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 : 2.502 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: 0.6959 (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: 0.7405 (m90) REVERT: A 174 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.6669 (mtp-110) REVERT: A 175 TYR cc_start: 0.8247 (m-80) cc_final: 0.7918 (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: 0.6707 (t0) REVERT: A 271 GLU cc_start: 0.6259 (pp20) cc_final: 0.6025 (pp20) REVERT: A 272 VAL cc_start: 0.8466 (m) cc_final: 0.8241 (m) REVERT: A 273 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7163 (mmtm) REVERT: A 276 MET cc_start: 0.7391 (ttm) cc_final: 0.6931 (ttm) REVERT: A 278 GLU cc_start: 0.7404 (tm-30) cc_final: 0.6935 (tm-30) REVERT: A 287 LEU cc_start: 0.8478 (mt) cc_final: 0.8243 (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: 0.7754 (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: 0.7702 (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: 0.7667 (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: 0.7630 (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: 0.8406 (tp) REVERT: A 476 LYS cc_start: 0.8194 (mttt) cc_final: 0.7552 (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: 0.7512 (p) REVERT: A 525 ILE cc_start: 0.8194 (tp) cc_final: 0.7843 (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: 0.7591 (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: 0.7087 (p90) REVERT: A 609 LYS cc_start: 0.8135 (tttt) cc_final: 0.7873 (ttpp) REVERT: A 632 SER cc_start: 0.8131 (p) cc_final: 0.7869 (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: 0.7147 (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: 0.7318 (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: 0.7534 (m-80) REVERT: A 715 LYS cc_start: 0.8436 (ptmt) cc_final: 0.8034 (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: 0.7238 (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: 0.7264 (mm) REVERT: B 487 ARG cc_start: 0.7213 (ptt-90) cc_final: 0.6590 (ptt-90) REVERT: B 512 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 518 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7764 (mtm110) REVERT: B 533 ASP cc_start: 0.7335 (p0) cc_final: 0.6911 (p0) REVERT: B 570 GLU cc_start: 0.5913 (tm-30) cc_final: 0.4943 (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: 0.6391 (mtmm) REVERT: B 638 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6229 (mm-30) REVERT: B 641 ARG cc_start: 0.7255 (ttm-80) cc_final: 0.6408 (mtm-85) REVERT: B 642 ASP cc_start: 0.6555 (p0) cc_final: 0.6295 (p0) REVERT: B 648 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6571 (tm-30) REVERT: B 662 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7765 (pp30) REVERT: B 668 ILE cc_start: 0.8227 (mm) cc_final: 0.7914 (mm) REVERT: B 669 ARG cc_start: 0.6513 (mpt90) cc_final: 0.6198 (mpt90) REVERT: B 681 ASP cc_start: 0.7711 (t0) cc_final: 0.7449 (t0) REVERT: B 692 LYS cc_start: 0.8099 (mmmt) cc_final: 0.7889 (mmtm) REVERT: B 707 ASN cc_start: 0.7419 (t0) cc_final: 0.7065 (t0) REVERT: B 709 THR cc_start: 0.8157 (p) cc_final: 0.7640 (t) REVERT: B 712 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.6067 (pt0) REVERT: B 719 TYR cc_start: 0.8064 (t80) cc_final: 0.7825 (t80) REVERT: B 724 MET cc_start: 0.6534 (mmm) cc_final: 0.6058 (mmm) REVERT: C 405 GLN cc_start: 0.7913 (mt0) cc_final: 0.7546 (mt0) REVERT: C 414 TYR cc_start: 0.7154 (t80) cc_final: 0.6877 (t80) REVERT: C 442 GLN cc_start: 0.5033 (OUTLIER) cc_final: 0.3736 (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: 0.6199 (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: 0.8260 (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: 0.7985 (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: 0.4653 (mtm) cc_final: 0.4043 (mtm) REVERT: D 243 SER cc_start: 0.7656 (m) cc_final: 0.6973 (p) REVERT: D 244 THR cc_start: 0.8057 (m) cc_final: 0.7850 (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: 0.6787 (ttt90) REVERT: D 284 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8186 (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: 0.7269 (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: 0.6971 (mm-30) REVERT: D 433 PHE cc_start: 0.7842 (t80) cc_final: 0.6996 (t80) REVERT: D 439 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7448 (mtp85) REVERT: E 12 GLU cc_start: 0.7721 (pt0) cc_final: 0.7289 (pt0) REVERT: E 16 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6361 (mm-30) REVERT: E 36 ASP cc_start: 0.7756 (t0) cc_final: 0.7555 (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: 0.5332 (t0) REVERT: E 75 ASP cc_start: 0.7232 (m-30) cc_final: 0.6305 (m-30) REVERT: E 79 ASN cc_start: 0.7743 (p0) cc_final: 0.7452 (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: 0.6413 (mt-10) REVERT: E 96 PHE cc_start: 0.7341 (m-80) cc_final: 0.7053 (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: 0.7344 (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: 0.7075 (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: 0.8302 (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: 0.6739 (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: 0.7756 (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: 0.7327 (t0) REVERT: F 34 LEU cc_start: 0.7165 (tp) cc_final: 0.6880 (tt) REVERT: F 39 ASP cc_start: 0.7767 (m-30) cc_final: 0.7119 (m-30) REVERT: F 42 MET cc_start: 0.7775 (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: 0.7668 (p) REVERT: F 109 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7407 (mt-10) REVERT: F 116 LYS cc_start: 0.7814 (mttt) cc_final: 0.7525 (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: 0.7314 (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: 0.7933 (tp) REVERT: F 226 TYR cc_start: 0.8211 (m-80) cc_final: 0.7917 (m-80) REVERT: F 249 VAL cc_start: 0.7794 (t) cc_final: 0.7502 (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: 0.7827 (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: 0.7271 (mmm) REVERT: G 43 VAL cc_start: 0.8052 (m) cc_final: 0.7491 (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: 0.6289 (tp30) REVERT: K 150 LEU cc_start: 0.8119 (mt) cc_final: 0.7658 (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: 0.7744 (pttm) REVERT: K 211 ARG cc_start: 0.8347 (ttm110) cc_final: 0.8069 (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: 0.5212 (mmm) outliers start: 56 outliers final: 18 residues processed: 941 average time/residue: 0.4159 time to fit residues: 569.8275 Evaluate side-chains 788 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 758 time to evaluate : 2.518 ------------------------------------------------------------------------------- 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 239 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 145 optimal weight: 0.2980 chunk 115 optimal weight: 0.7980 chunk 222 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 165 optimal weight: 1.9990 chunk 257 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 HIS B 238 ASN B 241 ASN B 560 ASN B 700 HIS ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 HIS D 363 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 349 GLN F 25 GLN ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 185 GLN ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.153637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124484 restraints weight = 40464.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128370 restraints weight = 19280.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130879 restraints weight = 11808.608| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24323 Z= 0.224 Angle : 0.682 13.051 33080 Z= 0.341 Chirality : 0.045 0.218 3696 Planarity : 0.005 0.072 4058 Dihedral : 13.338 142.805 3631 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.22 % Allowed : 14.07 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.16), residues: 2804 helix: 1.31 (0.14), residues: 1351 sheet: 0.17 (0.27), residues: 368 loop : -1.08 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 511 HIS 0.025 0.002 HIS D 424 PHE 0.028 0.002 PHE A 659 TYR 0.025 0.002 TYR A 534 ARG 0.009 0.001 ARG D 94 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 1106) hydrogen bonds : angle 4.65174 ( 3154) metal coordination : bond 0.00877 ( 28) metal coordination : angle 5.18182 ( 45) covalent geometry : bond 0.00487 (24295) covalent geometry : angle 0.65518 (33035) *********************** 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 912 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 806 time to evaluate : 2.506 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: A 64 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7799 (mm110) REVERT: A 68 LYS cc_start: 0.6381 (mtmt) cc_final: 0.5887 (tttm) REVERT: A 94 LYS cc_start: 0.7762 (ptpt) cc_final: 0.7155 (ptpt) REVERT: A 100 LEU cc_start: 0.8543 (mt) cc_final: 0.8318 (mm) REVERT: A 117 LYS cc_start: 0.7885 (tttt) cc_final: 0.7674 (tttt) REVERT: A 157 LYS cc_start: 0.8243 (ptmm) cc_final: 0.7860 (ttpp) REVERT: A 158 LEU cc_start: 0.8296 (mt) cc_final: 0.8005 (mt) REVERT: A 162 SER cc_start: 0.8126 (p) cc_final: 0.7879 (p) REVERT: A 163 TYR cc_start: 0.7842 (t80) cc_final: 0.7550 (t80) REVERT: A 167 LYS cc_start: 0.7956 (mttp) cc_final: 0.7158 (ttpp) REVERT: A 169 VAL cc_start: 0.8672 (p) cc_final: 0.8390 (m) REVERT: A 173 ASN cc_start: 0.7831 (m-40) cc_final: 0.7275 (m-40) REVERT: A 174 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7252 (ttm110) REVERT: A 176 PHE cc_start: 0.8224 (m-80) cc_final: 0.7514 (m-10) REVERT: A 273 LYS cc_start: 0.8313 (ttmt) cc_final: 0.8052 (ttmm) REVERT: A 282 LYS cc_start: 0.8518 (tttt) cc_final: 0.8168 (ttmm) REVERT: A 287 LEU cc_start: 0.8510 (mt) cc_final: 0.7265 (mt) REVERT: A 288 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7382 (mp0) REVERT: A 294 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6538 (tp30) REVERT: A 299 ASN cc_start: 0.7365 (p0) cc_final: 0.6827 (p0) REVERT: A 310 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8231 (pt) REVERT: A 332 ARG cc_start: 0.8102 (mpp80) cc_final: 0.7424 (mtp85) REVERT: A 347 SER cc_start: 0.8503 (m) cc_final: 0.7674 (t) REVERT: A 372 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6734 (tp30) REVERT: A 373 GLN cc_start: 0.7828 (tp40) cc_final: 0.7620 (tp40) REVERT: A 375 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7954 (tttm) REVERT: A 392 PHE cc_start: 0.7559 (t80) cc_final: 0.7180 (t80) REVERT: A 418 LYS cc_start: 0.7771 (tmmt) cc_final: 0.7491 (tmmt) REVERT: A 419 ARG cc_start: 0.8086 (ttm170) cc_final: 0.7666 (tpp80) REVERT: A 424 GLU cc_start: 0.7429 (tp30) cc_final: 0.6982 (mm-30) REVERT: A 438 MET cc_start: 0.8003 (ttp) cc_final: 0.7748 (ttp) REVERT: A 457 ILE cc_start: 0.8159 (tt) cc_final: 0.7933 (tt) REVERT: A 470 LEU cc_start: 0.8810 (tp) cc_final: 0.8197 (tp) REVERT: A 476 LYS cc_start: 0.8230 (mttt) cc_final: 0.7768 (mttm) REVERT: A 478 VAL cc_start: 0.8483 (t) cc_final: 0.8270 (m) REVERT: A 487 LYS cc_start: 0.8598 (ttmt) cc_final: 0.7795 (ttmm) REVERT: A 504 LYS cc_start: 0.8550 (ttpt) cc_final: 0.8340 (ttpt) REVERT: A 514 MET cc_start: 0.8206 (mmt) cc_final: 0.7861 (tpp) REVERT: A 525 ILE cc_start: 0.8379 (tp) cc_final: 0.8100 (tp) REVERT: A 537 ASN cc_start: 0.8231 (t0) cc_final: 0.7477 (t0) REVERT: A 555 ASN cc_start: 0.7734 (p0) cc_final: 0.7534 (p0) REVERT: A 556 ASP cc_start: 0.7414 (m-30) cc_final: 0.7125 (m-30) REVERT: A 564 ASN cc_start: 0.8370 (t0) cc_final: 0.7725 (t0) REVERT: A 570 GLU cc_start: 0.7025 (pm20) cc_final: 0.6518 (pm20) REVERT: A 579 TYR cc_start: 0.7533 (p90) cc_final: 0.6867 (p90) REVERT: A 588 GLU cc_start: 0.7194 (tp30) cc_final: 0.6548 (tp30) REVERT: A 632 SER cc_start: 0.8089 (p) cc_final: 0.7746 (p) REVERT: A 642 ARG cc_start: 0.7484 (mtp85) cc_final: 0.7086 (mmt180) REVERT: A 644 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8272 (pp) REVERT: A 659 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7225 (p90) REVERT: A 668 GLN cc_start: 0.7459 (mt0) cc_final: 0.7172 (mt0) REVERT: A 669 GLU cc_start: 0.7258 (tt0) cc_final: 0.6967 (tt0) REVERT: A 670 MET cc_start: 0.8106 (mmm) cc_final: 0.7720 (mmm) REVERT: A 677 GLN cc_start: 0.7837 (mt0) cc_final: 0.7466 (mt0) REVERT: A 682 ASP cc_start: 0.6943 (m-30) cc_final: 0.6722 (m-30) REVERT: A 683 GLN cc_start: 0.7582 (mm-40) cc_final: 0.7332 (mm-40) REVERT: A 688 LYS cc_start: 0.8364 (tttt) cc_final: 0.7920 (ttmt) REVERT: A 701 LEU cc_start: 0.8079 (mm) cc_final: 0.7732 (mm) REVERT: A 706 LYS cc_start: 0.7743 (tmmt) cc_final: 0.7374 (tmtt) REVERT: B 40 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8106 (mt) REVERT: B 42 MET cc_start: 0.7158 (mtp) cc_final: 0.6748 (mtp) REVERT: B 48 LYS cc_start: 0.7875 (ttpp) cc_final: 0.7366 (mtpt) REVERT: B 91 LEU cc_start: 0.7919 (mm) cc_final: 0.7553 (mm) REVERT: B 158 TYR cc_start: 0.7339 (t80) cc_final: 0.6886 (t80) REVERT: B 243 CYS cc_start: 0.8301 (m) cc_final: 0.7941 (m) REVERT: B 414 PHE cc_start: 0.7016 (m-80) cc_final: 0.6469 (m-80) REVERT: B 445 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7471 (mmtt) REVERT: B 455 ILE cc_start: 0.8019 (mm) cc_final: 0.7695 (mm) REVERT: B 464 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7092 (mt) REVERT: B 512 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6806 (mm-30) REVERT: B 533 ASP cc_start: 0.6933 (p0) cc_final: 0.6630 (p0) REVERT: B 546 GLU cc_start: 0.7549 (pp20) cc_final: 0.7305 (pp20) REVERT: B 548 THR cc_start: 0.8624 (m) cc_final: 0.8317 (t) REVERT: B 570 GLU cc_start: 0.5777 (tm-30) cc_final: 0.5312 (tm-30) REVERT: B 586 GLU cc_start: 0.7258 (pp20) cc_final: 0.6852 (pp20) REVERT: B 588 CYS cc_start: 0.7923 (m) cc_final: 0.7677 (m) REVERT: B 589 GLU cc_start: 0.6862 (mm-30) cc_final: 0.6501 (mm-30) REVERT: B 620 MET cc_start: 0.7812 (mmm) cc_final: 0.7180 (mmm) REVERT: B 638 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6338 (mm-30) REVERT: B 639 TYR cc_start: 0.7621 (t80) cc_final: 0.7309 (t80) REVERT: B 641 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7015 (mtm-85) REVERT: B 648 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6704 (tm-30) REVERT: B 677 MET cc_start: 0.6806 (mtp) cc_final: 0.6559 (mtm) REVERT: B 681 ASP cc_start: 0.8010 (t0) cc_final: 0.7755 (t0) REVERT: B 719 TYR cc_start: 0.8171 (t80) cc_final: 0.7953 (t80) REVERT: C 405 GLN cc_start: 0.7852 (mt0) cc_final: 0.7591 (mt0) REVERT: C 442 GLN cc_start: 0.4892 (OUTLIER) cc_final: 0.3844 (pp30) REVERT: C 475 PHE cc_start: 0.7196 (t80) cc_final: 0.6822 (t80) REVERT: C 501 GLN cc_start: 0.8258 (tp40) cc_final: 0.7834 (tp40) REVERT: C 528 MET cc_start: 0.8620 (mtp) cc_final: 0.8284 (mtp) REVERT: D 34 LEU cc_start: 0.8534 (mt) cc_final: 0.8329 (mt) REVERT: D 47 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7438 (mm-30) REVERT: D 50 SER cc_start: 0.8395 (m) cc_final: 0.7956 (t) REVERT: D 81 LYS cc_start: 0.8701 (tttt) cc_final: 0.8172 (tttm) REVERT: D 154 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7150 (mt-10) REVERT: D 178 LEU cc_start: 0.8491 (tp) cc_final: 0.8178 (tt) REVERT: D 185 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6457 (mpp) REVERT: D 215 PHE cc_start: 0.8299 (t80) cc_final: 0.7579 (t80) REVERT: D 216 MET cc_start: 0.7795 (mmm) cc_final: 0.7555 (mmm) REVERT: D 218 GLN cc_start: 0.7556 (mm-40) cc_final: 0.7293 (tm-30) REVERT: D 219 TYR cc_start: 0.7776 (t80) cc_final: 0.7504 (t80) REVERT: D 221 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7544 (mm-40) REVERT: D 228 MET cc_start: 0.4547 (mtm) cc_final: 0.3180 (mtm) REVERT: D 243 SER cc_start: 0.7992 (m) cc_final: 0.7651 (p) REVERT: D 254 MET cc_start: 0.6364 (mtt) cc_final: 0.5506 (mtp) REVERT: D 258 LEU cc_start: 0.8246 (mt) cc_final: 0.7908 (tp) REVERT: D 259 LEU cc_start: 0.8757 (mt) cc_final: 0.8498 (mm) REVERT: D 260 ASN cc_start: 0.7614 (t0) cc_final: 0.6855 (t0) REVERT: D 261 PHE cc_start: 0.8138 (t80) cc_final: 0.7688 (t80) REVERT: D 263 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8093 (mm-40) REVERT: D 267 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7691 (mt-10) REVERT: D 276 ARG cc_start: 0.7020 (ttt90) cc_final: 0.6588 (ttt90) REVERT: D 284 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8290 (p) REVERT: D 313 TYR cc_start: 0.8357 (m-80) cc_final: 0.7877 (m-80) REVERT: D 322 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7155 (mm-30) REVERT: D 362 GLN cc_start: 0.8099 (tp40) cc_final: 0.7733 (tp40) REVERT: D 395 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7037 (tm-30) REVERT: D 397 GLU cc_start: 0.7220 (mm-30) cc_final: 0.6960 (mm-30) REVERT: D 433 PHE cc_start: 0.7519 (t80) cc_final: 0.7028 (t80) REVERT: E 70 THR cc_start: 0.8307 (p) cc_final: 0.7951 (t) REVERT: E 72 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7212 (mm-30) REVERT: E 73 ASP cc_start: 0.7282 (t0) cc_final: 0.5790 (t0) REVERT: E 75 ASP cc_start: 0.7219 (m-30) cc_final: 0.6576 (m-30) REVERT: E 80 ARG cc_start: 0.8212 (mtt180) cc_final: 0.7181 (mtt180) REVERT: E 89 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6055 (mt-10) REVERT: E 93 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6725 (mp0) REVERT: E 96 PHE cc_start: 0.7602 (m-80) cc_final: 0.7106 (m-80) REVERT: E 103 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7560 (mt0) REVERT: E 112 LYS cc_start: 0.8004 (mtmt) cc_final: 0.7755 (mttt) REVERT: E 125 ARG cc_start: 0.7170 (mtt180) cc_final: 0.6864 (mtt180) REVERT: E 132 LYS cc_start: 0.8492 (mttt) cc_final: 0.8272 (mttt) REVERT: E 144 SER cc_start: 0.8311 (t) cc_final: 0.7925 (t) REVERT: E 154 GLN cc_start: 0.7394 (tm-30) cc_final: 0.7059 (tm-30) REVERT: E 157 LYS cc_start: 0.8149 (tttt) cc_final: 0.7938 (tttt) REVERT: E 166 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6766 (mt-10) REVERT: E 177 CYS cc_start: 0.7624 (m) cc_final: 0.7116 (m) REVERT: E 181 ASN cc_start: 0.8138 (t0) cc_final: 0.7829 (t0) REVERT: E 184 ASP cc_start: 0.6899 (m-30) cc_final: 0.6571 (m-30) REVERT: E 193 LYS cc_start: 0.8374 (mttt) cc_final: 0.7695 (ttmm) REVERT: E 256 GLN cc_start: 0.7320 (mt0) cc_final: 0.6905 (mt0) REVERT: E 289 TYR cc_start: 0.8370 (m-80) cc_final: 0.7553 (m-80) REVERT: E 299 CYS cc_start: 0.7608 (m) cc_final: 0.7324 (m) REVERT: E 320 ARG cc_start: 0.8268 (ttm170) cc_final: 0.7960 (ttm170) REVERT: E 322 TYR cc_start: 0.8260 (m-10) cc_final: 0.7850 (m-80) REVERT: E 333 GLU cc_start: 0.7790 (tt0) cc_final: 0.7490 (tt0) REVERT: E 353 LYS cc_start: 0.8164 (mttt) cc_final: 0.7659 (mttt) REVERT: F 16 ASP cc_start: 0.7884 (t0) cc_final: 0.7499 (t0) REVERT: F 50 PHE cc_start: 0.7901 (m-10) cc_final: 0.7632 (m-10) REVERT: F 60 ILE cc_start: 0.8709 (mt) cc_final: 0.8446 (tt) REVERT: F 106 SER cc_start: 0.7984 (m) cc_final: 0.7730 (p) REVERT: F 116 LYS cc_start: 0.8277 (mttt) cc_final: 0.7980 (mmmm) REVERT: F 131 THR cc_start: 0.8209 (m) cc_final: 0.7909 (p) REVERT: F 139 LYS cc_start: 0.8698 (mttt) cc_final: 0.8413 (mtpp) REVERT: F 147 MET cc_start: 0.7315 (mmm) cc_final: 0.7032 (mmm) REVERT: F 150 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6987 (mt-10) REVERT: F 158 LYS cc_start: 0.8226 (mttt) cc_final: 0.8003 (mttt) REVERT: F 172 LEU cc_start: 0.8338 (mt) cc_final: 0.8131 (mm) REVERT: F 197 ASP cc_start: 0.7972 (t0) cc_final: 0.7767 (t0) REVERT: F 213 LEU cc_start: 0.8257 (tt) cc_final: 0.7978 (tt) REVERT: F 216 LYS cc_start: 0.8439 (tttt) cc_final: 0.8146 (tttt) REVERT: F 224 LEU cc_start: 0.8675 (tp) cc_final: 0.8367 (tp) REVERT: F 225 GLN cc_start: 0.8831 (tp40) cc_final: 0.8572 (tp40) REVERT: F 249 VAL cc_start: 0.8172 (t) cc_final: 0.7854 (p) REVERT: G 16 MET cc_start: 0.8236 (mmt) cc_final: 0.7598 (mmm) REVERT: G 53 LEU cc_start: 0.8089 (tt) cc_final: 0.7810 (tt) REVERT: H 926 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6187 (tp30) REVERT: K 148 TYR cc_start: 0.7654 (m-80) cc_final: 0.7444 (m-80) REVERT: K 178 MET cc_start: 0.7701 (mtm) cc_final: 0.7417 (mtm) REVERT: K 187 VAL cc_start: 0.8858 (t) cc_final: 0.8538 (p) REVERT: K 188 LYS cc_start: 0.8156 (tttt) cc_final: 0.7814 (tttt) REVERT: K 208 GLN cc_start: 0.7555 (tp-100) cc_final: 0.7291 (tp-100) REVERT: K 222 LYS cc_start: 0.8319 (pttm) cc_final: 0.8115 (pttp) REVERT: K 263 MET cc_start: 0.4997 (mmm) cc_final: 0.4741 (mmm) outliers start: 106 outliers final: 58 residues processed: 869 average time/residue: 0.4094 time to fit residues: 524.9924 Evaluate side-chains 820 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 751 time to evaluate : 2.717 ------------------------------------------------------------------------------- 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 177 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 355 CYS 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 512 CYS 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 205 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 464 LEU 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 526 GLU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 672 THR 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 435 SER 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 185 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain E residue 103 GLN 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 313 VAL 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 255 CYS Chi-restraints excluded: chain F residue 281 ILE 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 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 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 249 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 229 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 415 HIS A 625 GLN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 263 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 GLN F 179 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.153585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.124803 restraints weight = 40349.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.128716 restraints weight = 19251.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131263 restraints weight = 11725.846| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 24323 Z= 0.148 Angle : 0.614 14.154 33080 Z= 0.304 Chirality : 0.042 0.170 3696 Planarity : 0.004 0.051 4058 Dihedral : 13.248 146.241 3622 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 4.15 % Allowed : 18.13 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.16), residues: 2804 helix: 1.33 (0.15), residues: 1350 sheet: -0.03 (0.27), residues: 381 loop : -1.06 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 55 HIS 0.018 0.001 HIS C 474 PHE 0.024 0.001 PHE A 703 TYR 0.018 0.001 TYR K 116 ARG 0.008 0.001 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 1106) hydrogen bonds : angle 4.43011 ( 3154) metal coordination : bond 0.00587 ( 28) metal coordination : angle 4.75318 ( 45) covalent geometry : bond 0.00329 (24295) covalent geometry : angle 0.58888 (33035) *********************** 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 876 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 772 time to evaluate : 2.634 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: 0.7026 (OUTLIER) cc_final: 0.6825 (ptt) REVERT: A 68 LYS cc_start: 0.6355 (mtmt) cc_final: 0.5788 (tttm) REVERT: A 94 LYS cc_start: 0.7583 (ptpt) cc_final: 0.7197 (ptpt) REVERT: A 146 THR cc_start: 0.7388 (p) cc_final: 0.7153 (p) REVERT: A 157 LYS cc_start: 0.8260 (ptmm) cc_final: 0.7861 (ttpp) REVERT: A 158 LEU cc_start: 0.8359 (mt) cc_final: 0.8077 (mt) REVERT: A 162 SER cc_start: 0.8230 (p) cc_final: 0.7945 (p) REVERT: A 163 TYR cc_start: 0.7859 (t80) cc_final: 0.7522 (t80) REVERT: A 169 VAL cc_start: 0.8649 (p) cc_final: 0.8140 (m) REVERT: A 173 ASN cc_start: 0.7849 (m-40) cc_final: 0.7224 (m-40) REVERT: A 174 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7544 (tpp80) REVERT: A 178 GLU cc_start: 0.6608 (pm20) cc_final: 0.6346 (pm20) REVERT: A 273 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7915 (ttpt) REVERT: A 279 GLU cc_start: 0.7767 (mp0) cc_final: 0.7503 (mp0) REVERT: A 282 LYS cc_start: 0.8550 (tttt) cc_final: 0.8095 (ttmm) REVERT: A 287 LEU cc_start: 0.8549 (mt) cc_final: 0.7362 (mt) REVERT: A 288 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7367 (mp0) REVERT: A 299 ASN cc_start: 0.7358 (p0) cc_final: 0.6874 (p0) REVERT: A 310 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8028 (pt) REVERT: A 332 ARG cc_start: 0.8094 (mpp80) cc_final: 0.7736 (mtp85) REVERT: A 334 ARG cc_start: 0.7233 (ptp90) cc_final: 0.6906 (ptp90) REVERT: A 347 SER cc_start: 0.8515 (m) cc_final: 0.7690 (t) REVERT: A 372 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6741 (tp30) REVERT: A 375 LYS cc_start: 0.8190 (ttpt) cc_final: 0.7966 (tttm) REVERT: A 392 PHE cc_start: 0.7483 (t80) cc_final: 0.7112 (t80) REVERT: A 418 LYS cc_start: 0.7678 (tmmt) cc_final: 0.7387 (tmmt) REVERT: A 419 ARG cc_start: 0.8016 (ttm170) cc_final: 0.7587 (tpp80) REVERT: A 424 GLU cc_start: 0.7400 (tp30) cc_final: 0.7072 (mm-30) REVERT: A 434 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7082 (mm-30) REVERT: A 438 MET cc_start: 0.8034 (ttp) cc_final: 0.7796 (ttp) REVERT: A 457 ILE cc_start: 0.8157 (tt) cc_final: 0.7955 (tt) REVERT: A 470 LEU cc_start: 0.8802 (tp) cc_final: 0.8449 (tp) REVERT: A 476 LYS cc_start: 0.8239 (mttt) cc_final: 0.7804 (mttm) REVERT: A 487 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7534 (tttm) REVERT: A 505 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8139 (m) REVERT: A 520 ARG cc_start: 0.7512 (mmm160) cc_final: 0.6755 (tpt-90) REVERT: A 525 ILE cc_start: 0.8359 (tp) cc_final: 0.7820 (tp) REVERT: A 556 ASP cc_start: 0.7453 (m-30) cc_final: 0.7163 (m-30) REVERT: A 564 ASN cc_start: 0.8307 (t0) cc_final: 0.7595 (t0) REVERT: A 570 GLU cc_start: 0.7046 (pm20) cc_final: 0.6638 (pm20) REVERT: A 579 TYR cc_start: 0.7535 (p90) cc_final: 0.6936 (p90) REVERT: A 588 GLU cc_start: 0.7112 (tp30) cc_final: 0.6792 (tp30) REVERT: A 590 MET cc_start: 0.7768 (tpp) cc_final: 0.7554 (tpt) REVERT: A 632 SER cc_start: 0.8042 (p) cc_final: 0.7736 (p) REVERT: A 644 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8276 (pp) REVERT: A 659 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7164 (p90) REVERT: A 668 GLN cc_start: 0.7391 (mt0) cc_final: 0.7072 (mt0) REVERT: A 669 GLU cc_start: 0.7224 (tt0) cc_final: 0.6974 (tt0) REVERT: A 670 MET cc_start: 0.8061 (mmm) cc_final: 0.7794 (mmm) REVERT: A 677 GLN cc_start: 0.7792 (mt0) cc_final: 0.7486 (mt0) REVERT: A 682 ASP cc_start: 0.6926 (m-30) cc_final: 0.6671 (m-30) REVERT: A 688 LYS cc_start: 0.8370 (tttt) cc_final: 0.7938 (ttmt) REVERT: A 692 LYS cc_start: 0.7641 (tptm) cc_final: 0.7078 (tptt) REVERT: A 703 PHE cc_start: 0.8211 (m-80) cc_final: 0.7537 (m-80) REVERT: A 706 LYS cc_start: 0.7788 (tmmt) cc_final: 0.7509 (tmtt) REVERT: B 40 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8226 (mt) REVERT: B 42 MET cc_start: 0.7277 (mtp) cc_final: 0.6982 (mtp) REVERT: B 48 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7411 (ttpp) REVERT: B 75 ARG cc_start: 0.7379 (ttp80) cc_final: 0.7095 (ttp80) REVERT: B 91 LEU cc_start: 0.7923 (mm) cc_final: 0.7596 (mm) REVERT: B 158 TYR cc_start: 0.7308 (t80) cc_final: 0.6856 (t80) REVERT: B 243 CYS cc_start: 0.8410 (m) cc_final: 0.8201 (m) REVERT: B 414 PHE cc_start: 0.7086 (m-80) cc_final: 0.6515 (m-80) REVERT: B 416 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7043 (mp) REVERT: B 438 MET cc_start: 0.7671 (mtm) cc_final: 0.7391 (mtm) REVERT: B 445 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7611 (mmtt) REVERT: B 455 ILE cc_start: 0.8030 (mm) cc_final: 0.7696 (mm) REVERT: B 512 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6891 (mm-30) REVERT: B 533 ASP cc_start: 0.6777 (p0) cc_final: 0.6346 (p0) REVERT: B 570 GLU cc_start: 0.6159 (tm-30) cc_final: 0.5522 (tm-30) REVERT: B 586 GLU cc_start: 0.7208 (pp20) cc_final: 0.6854 (pp20) REVERT: B 589 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6507 (mm-30) REVERT: B 613 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.7212 (p90) REVERT: B 638 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6908 (mm-30) REVERT: B 639 TYR cc_start: 0.7481 (t80) cc_final: 0.7156 (t80) REVERT: B 641 ARG cc_start: 0.7892 (ttm-80) cc_final: 0.7185 (mtm-85) REVERT: B 648 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6854 (tm-30) REVERT: B 681 ASP cc_start: 0.8019 (t0) cc_final: 0.7778 (t0) REVERT: B 724 MET cc_start: 0.7575 (mmm) cc_final: 0.6950 (mmm) REVERT: C 405 GLN cc_start: 0.7823 (mt0) cc_final: 0.7558 (mt0) REVERT: C 442 GLN cc_start: 0.4762 (OUTLIER) cc_final: 0.4263 (pp30) REVERT: C 475 PHE cc_start: 0.7096 (t80) cc_final: 0.6709 (t80) REVERT: C 501 GLN cc_start: 0.8210 (tp40) cc_final: 0.7773 (tp40) REVERT: C 524 HIS cc_start: 0.7830 (t-170) cc_final: 0.7324 (t-170) REVERT: C 528 MET cc_start: 0.8575 (mtp) cc_final: 0.8244 (mtm) REVERT: D 22 PHE cc_start: 0.8377 (t80) cc_final: 0.8076 (t80) REVERT: D 50 SER cc_start: 0.8146 (m) cc_final: 0.7368 (p) REVERT: D 155 ARG cc_start: 0.7766 (mmm160) cc_final: 0.7484 (mmm160) REVERT: D 175 LEU cc_start: 0.8451 (tp) cc_final: 0.8246 (tp) REVERT: D 185 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6590 (mpp) REVERT: D 215 PHE cc_start: 0.8167 (t80) cc_final: 0.7676 (t80) REVERT: D 216 MET cc_start: 0.7736 (mmm) cc_final: 0.7526 (mmm) REVERT: D 218 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7287 (tm-30) REVERT: D 219 TYR cc_start: 0.7819 (t80) cc_final: 0.7529 (t80) REVERT: D 233 ILE cc_start: 0.8414 (mt) cc_final: 0.8193 (mm) REVERT: D 243 SER cc_start: 0.8006 (m) cc_final: 0.7632 (p) REVERT: D 254 MET cc_start: 0.6385 (mtt) cc_final: 0.5553 (mtp) REVERT: D 258 LEU cc_start: 0.8286 (mt) cc_final: 0.7947 (tp) REVERT: D 260 ASN cc_start: 0.7460 (t0) cc_final: 0.7073 (t0) REVERT: D 261 PHE cc_start: 0.8189 (t80) cc_final: 0.7791 (t80) REVERT: D 267 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7455 (mt-10) REVERT: D 284 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8378 (p) REVERT: D 313 TYR cc_start: 0.8315 (m-80) cc_final: 0.7953 (m-80) REVERT: D 327 LEU cc_start: 0.8388 (mt) cc_final: 0.8176 (mm) REVERT: D 362 GLN cc_start: 0.8041 (tp40) cc_final: 0.7681 (tp40) REVERT: D 378 LYS cc_start: 0.8071 (mttt) cc_final: 0.7813 (mttp) REVERT: D 397 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6940 (mm-30) REVERT: D 433 PHE cc_start: 0.6879 (t80) cc_final: 0.6440 (t80) REVERT: E 16 GLU cc_start: 0.6535 (mm-30) cc_final: 0.6226 (mm-30) REVERT: E 70 THR cc_start: 0.8218 (p) cc_final: 0.7791 (t) REVERT: E 73 ASP cc_start: 0.7342 (t0) cc_final: 0.5837 (t0) REVERT: E 75 ASP cc_start: 0.7222 (m-30) cc_final: 0.6586 (m-30) REVERT: E 80 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7103 (mtt180) REVERT: E 96 PHE cc_start: 0.7565 (m-80) cc_final: 0.7263 (m-80) REVERT: E 112 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7766 (mttt) REVERT: E 125 ARG cc_start: 0.7164 (mtt180) cc_final: 0.6877 (mtt180) REVERT: E 132 LYS cc_start: 0.8501 (mttt) cc_final: 0.8164 (mttt) REVERT: E 144 SER cc_start: 0.8250 (t) cc_final: 0.7846 (t) REVERT: E 154 GLN cc_start: 0.7339 (tm-30) cc_final: 0.6926 (tm-30) REVERT: E 157 LYS cc_start: 0.8126 (tttt) cc_final: 0.7901 (tttt) REVERT: E 166 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6733 (mt-10) REVERT: E 177 CYS cc_start: 0.7666 (m) cc_final: 0.7135 (m) REVERT: E 181 ASN cc_start: 0.8133 (t0) cc_final: 0.7801 (t0) REVERT: E 184 ASP cc_start: 0.6917 (m-30) cc_final: 0.6581 (m-30) REVERT: E 193 LYS cc_start: 0.8329 (mttt) cc_final: 0.7693 (ttmm) REVERT: E 256 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6923 (mt0) REVERT: E 299 CYS cc_start: 0.7567 (m) cc_final: 0.7354 (m) REVERT: E 320 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7969 (ttm170) REVERT: E 322 TYR cc_start: 0.8100 (m-10) cc_final: 0.7744 (m-80) REVERT: E 333 GLU cc_start: 0.7744 (tt0) cc_final: 0.7416 (tt0) REVERT: E 353 LYS cc_start: 0.8202 (mttt) cc_final: 0.7710 (mttt) REVERT: E 366 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8282 (m) REVERT: F 16 ASP cc_start: 0.7779 (t0) cc_final: 0.7312 (t0) REVERT: F 28 LYS cc_start: 0.7884 (tttt) cc_final: 0.7648 (tttt) REVERT: F 60 ILE cc_start: 0.8705 (mt) cc_final: 0.8426 (tt) REVERT: F 106 SER cc_start: 0.7952 (m) cc_final: 0.7735 (p) REVERT: F 110 VAL cc_start: 0.8483 (t) cc_final: 0.8238 (p) REVERT: F 116 LYS cc_start: 0.8287 (mttt) cc_final: 0.7920 (mmmm) REVERT: F 131 THR cc_start: 0.8374 (m) cc_final: 0.7921 (p) REVERT: F 139 LYS cc_start: 0.8673 (mttt) cc_final: 0.8379 (mtpp) REVERT: F 187 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7919 (mp10) REVERT: F 216 LYS cc_start: 0.8387 (tttt) cc_final: 0.8074 (ttpp) REVERT: F 217 VAL cc_start: 0.8973 (p) cc_final: 0.8679 (t) REVERT: F 224 LEU cc_start: 0.8659 (tp) cc_final: 0.8397 (tp) REVERT: F 225 GLN cc_start: 0.8768 (tp40) cc_final: 0.8501 (tp40) REVERT: F 237 GLN cc_start: 0.7029 (mt0) cc_final: 0.6791 (mt0) REVERT: F 249 VAL cc_start: 0.8270 (t) cc_final: 0.7997 (p) REVERT: G 16 MET cc_start: 0.8298 (mmt) cc_final: 0.7607 (mmm) REVERT: H 926 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6184 (tp30) REVERT: K 163 LYS cc_start: 0.8166 (mttt) cc_final: 0.7925 (mttt) REVERT: K 178 MET cc_start: 0.7659 (mtm) cc_final: 0.7413 (mtm) REVERT: K 188 LYS cc_start: 0.8173 (tttt) cc_final: 0.7811 (tttt) REVERT: K 208 GLN cc_start: 0.7597 (tp-100) cc_final: 0.7350 (tp-100) REVERT: K 212 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: K 214 MET cc_start: 0.6573 (mmt) cc_final: 0.6342 (mmt) REVERT: K 263 MET cc_start: 0.4961 (mmm) cc_final: 0.4722 (mmm) outliers start: 104 outliers final: 63 residues processed: 822 average time/residue: 0.4134 time to fit residues: 499.3211 Evaluate side-chains 820 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 740 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 177 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 372 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 505 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 656 ASN 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 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 531 VAL Chi-restraints excluded: chain B residue 603 LYS 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 663 CYS Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 712 GLU 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 457 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 525 ILE 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 185 MET Chi-restraints excluded: chain D residue 234 LEU 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 321 SER Chi-restraints excluded: chain D residue 323 LEU 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 104 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 256 GLN 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 E residue 366 VAL Chi-restraints excluded: chain F residue 105 THR 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 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 113 MET Chi-restraints excluded: chain K residue 147 GLU 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 66 optimal weight: 0.8980 chunk 273 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN A 668 GLN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.122767 restraints weight = 40777.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.126640 restraints weight = 19306.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.129126 restraints weight = 11700.951| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24323 Z= 0.175 Angle : 0.636 14.380 33080 Z= 0.315 Chirality : 0.042 0.181 3696 Planarity : 0.004 0.060 4058 Dihedral : 13.331 147.388 3621 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 5.46 % Allowed : 18.06 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.16), residues: 2804 helix: 1.24 (0.14), residues: 1353 sheet: -0.15 (0.27), residues: 371 loop : -1.13 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 55 HIS 0.021 0.001 HIS D 424 PHE 0.020 0.002 PHE A 659 TYR 0.017 0.002 TYR A 534 ARG 0.014 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 1106) hydrogen bonds : angle 4.38338 ( 3154) metal coordination : bond 0.00743 ( 28) metal coordination : angle 5.07708 ( 45) covalent geometry : bond 0.00385 (24295) covalent geometry : angle 0.60815 (33035) *********************** 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 910 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 773 time to evaluate : 2.708 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 59 LYS cc_start: 0.8310 (mttt) cc_final: 0.7952 (mmmt) REVERT: A 65 MET cc_start: 0.7017 (OUTLIER) cc_final: 0.6802 (ptt) REVERT: A 68 LYS cc_start: 0.6390 (mtmt) cc_final: 0.5807 (tttm) REVERT: A 94 LYS cc_start: 0.7634 (ptpt) cc_final: 0.7268 (ptpt) REVERT: A 146 THR cc_start: 0.7511 (p) cc_final: 0.7139 (p) REVERT: A 157 LYS cc_start: 0.8340 (ptmm) cc_final: 0.7925 (ttpp) REVERT: A 158 LEU cc_start: 0.8355 (mt) cc_final: 0.8145 (mt) REVERT: A 162 SER cc_start: 0.8322 (p) cc_final: 0.6980 (p) REVERT: A 163 TYR cc_start: 0.7920 (t80) cc_final: 0.7592 (t80) REVERT: A 167 LYS cc_start: 0.7888 (mttp) cc_final: 0.7458 (mtpp) REVERT: A 169 VAL cc_start: 0.8609 (p) cc_final: 0.8169 (m) REVERT: A 173 ASN cc_start: 0.7833 (m-40) cc_final: 0.7473 (m-40) REVERT: A 273 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7822 (ttpt) REVERT: A 279 GLU cc_start: 0.7780 (mp0) cc_final: 0.7524 (mp0) REVERT: A 282 LYS cc_start: 0.8518 (tttt) cc_final: 0.8089 (ttmm) REVERT: A 288 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7235 (tp30) REVERT: A 299 ASN cc_start: 0.7458 (p0) cc_final: 0.6789 (p0) REVERT: A 310 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8289 (pt) REVERT: A 325 ARG cc_start: 0.7391 (mtp85) cc_final: 0.7125 (mtp-110) REVERT: A 332 ARG cc_start: 0.8135 (mpp80) cc_final: 0.7403 (mtp85) REVERT: A 334 ARG cc_start: 0.7264 (ptp90) cc_final: 0.6581 (ptp90) REVERT: A 347 SER cc_start: 0.8566 (m) cc_final: 0.7802 (t) REVERT: A 372 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6515 (tp30) REVERT: A 389 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7267 (tt) REVERT: A 418 LYS cc_start: 0.7716 (tmmt) cc_final: 0.7459 (tmmt) REVERT: A 419 ARG cc_start: 0.7814 (ttm170) cc_final: 0.7192 (tpp80) REVERT: A 424 GLU cc_start: 0.7609 (tp30) cc_final: 0.7268 (mm-30) REVERT: A 434 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7155 (mp0) REVERT: A 457 ILE cc_start: 0.8254 (tt) cc_final: 0.7949 (tt) REVERT: A 476 LYS cc_start: 0.8281 (mttt) cc_final: 0.7804 (mttm) REVERT: A 487 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7543 (tttm) REVERT: A 490 GLU cc_start: 0.6425 (mp0) cc_final: 0.6031 (mp0) REVERT: A 504 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8124 (ttmm) REVERT: A 505 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8016 (m) REVERT: A 521 GLU cc_start: 0.7321 (mp0) cc_final: 0.7031 (mp0) REVERT: A 525 ILE cc_start: 0.8408 (tp) cc_final: 0.8187 (tp) REVERT: A 526 LYS cc_start: 0.7664 (tppt) cc_final: 0.7442 (tppt) REVERT: A 556 ASP cc_start: 0.7476 (m-30) cc_final: 0.7179 (m-30) REVERT: A 564 ASN cc_start: 0.8225 (t0) cc_final: 0.7572 (t0) REVERT: A 570 GLU cc_start: 0.7119 (pm20) cc_final: 0.6660 (pm20) REVERT: A 579 TYR cc_start: 0.7538 (p90) cc_final: 0.6983 (p90) REVERT: A 632 SER cc_start: 0.8116 (p) cc_final: 0.7772 (p) REVERT: A 644 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8292 (pp) REVERT: A 659 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.6919 (p90) REVERT: A 669 GLU cc_start: 0.7241 (tt0) cc_final: 0.6908 (tt0) REVERT: A 677 GLN cc_start: 0.7770 (mt0) cc_final: 0.7393 (mt0) REVERT: A 682 ASP cc_start: 0.6865 (m-30) cc_final: 0.6638 (m-30) REVERT: A 692 LYS cc_start: 0.7769 (tptm) cc_final: 0.7242 (tptt) REVERT: A 696 MET cc_start: 0.7471 (mmm) cc_final: 0.7081 (tmm) REVERT: A 706 LYS cc_start: 0.7870 (tmmt) cc_final: 0.7359 (tmmt) REVERT: B 1 MET cc_start: 0.7408 (ppp) cc_final: 0.7150 (ppp) REVERT: B 40 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8312 (mt) REVERT: B 59 TYR cc_start: 0.7008 (t80) cc_final: 0.6713 (t80) REVERT: B 91 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7568 (mm) REVERT: B 113 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7545 (ttmm) REVERT: B 122 THR cc_start: 0.6671 (OUTLIER) cc_final: 0.6458 (p) REVERT: B 158 TYR cc_start: 0.7348 (t80) cc_final: 0.6872 (t80) REVERT: B 233 PHE cc_start: 0.8166 (m-10) cc_final: 0.7640 (m-80) REVERT: B 352 GLU cc_start: 0.6970 (mp0) cc_final: 0.6718 (mp0) REVERT: B 384 HIS cc_start: 0.5132 (OUTLIER) cc_final: 0.4719 (p-80) REVERT: B 414 PHE cc_start: 0.7245 (m-80) cc_final: 0.6463 (m-80) REVERT: B 416 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.7023 (pt) REVERT: B 445 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7785 (mmtt) REVERT: B 455 ILE cc_start: 0.8151 (mm) cc_final: 0.7830 (mm) REVERT: B 464 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7253 (mt) REVERT: B 507 LYS cc_start: 0.8368 (mttt) cc_final: 0.7590 (mttp) REVERT: B 570 GLU cc_start: 0.6354 (tm-30) cc_final: 0.5628 (tm-30) REVERT: B 586 GLU cc_start: 0.7270 (pp20) cc_final: 0.6903 (pp20) REVERT: B 589 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6483 (mm-30) REVERT: B 613 HIS cc_start: 0.7962 (OUTLIER) cc_final: 0.7500 (p90) REVERT: B 641 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7499 (mtm-85) REVERT: B 664 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8474 (p) REVERT: B 669 ARG cc_start: 0.6224 (mpt90) cc_final: 0.5714 (mpt90) REVERT: B 677 MET cc_start: 0.7094 (mtp) cc_final: 0.6847 (mtm) REVERT: B 681 ASP cc_start: 0.8038 (t0) cc_final: 0.7754 (t0) REVERT: B 712 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6223 (pt0) REVERT: C 405 GLN cc_start: 0.7788 (mt0) cc_final: 0.7532 (mt0) REVERT: C 411 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6999 (tpp) REVERT: C 441 MET cc_start: 0.7021 (mmm) cc_final: 0.6661 (mmt) REVERT: C 442 GLN cc_start: 0.4799 (OUTLIER) cc_final: 0.3790 (pp30) REVERT: C 475 PHE cc_start: 0.7112 (t80) cc_final: 0.6772 (t80) REVERT: C 501 GLN cc_start: 0.8167 (tp40) cc_final: 0.7738 (tp40) REVERT: C 528 MET cc_start: 0.8662 (mtp) cc_final: 0.8342 (mtm) REVERT: D 22 PHE cc_start: 0.8433 (t80) cc_final: 0.8183 (t80) REVERT: D 47 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7532 (mm-30) REVERT: D 50 SER cc_start: 0.7879 (m) cc_final: 0.7217 (p) REVERT: D 78 GLU cc_start: 0.7014 (pt0) cc_final: 0.6803 (pt0) REVERT: D 143 ARG cc_start: 0.7240 (mtm110) cc_final: 0.7029 (mtp85) REVERT: D 178 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7902 (tp) REVERT: D 201 PHE cc_start: 0.8453 (m-80) cc_final: 0.8200 (m-80) REVERT: D 218 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7324 (tm-30) REVERT: D 233 ILE cc_start: 0.8434 (mt) cc_final: 0.8214 (mm) REVERT: D 243 SER cc_start: 0.8017 (m) cc_final: 0.7653 (p) REVERT: D 254 MET cc_start: 0.6413 (mtt) cc_final: 0.5666 (mtp) REVERT: D 258 LEU cc_start: 0.8304 (mt) cc_final: 0.7899 (tp) REVERT: D 259 LEU cc_start: 0.8789 (mt) cc_final: 0.8440 (mm) REVERT: D 260 ASN cc_start: 0.7500 (t0) cc_final: 0.7130 (t0) REVERT: D 261 PHE cc_start: 0.8185 (t80) cc_final: 0.7869 (t80) REVERT: D 267 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7400 (mt-10) REVERT: D 275 LYS cc_start: 0.7478 (mttt) cc_final: 0.6962 (mttm) REVERT: D 284 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8442 (p) REVERT: D 313 TYR cc_start: 0.8321 (m-80) cc_final: 0.7943 (m-80) REVERT: D 340 ASN cc_start: 0.8158 (p0) cc_final: 0.7836 (t0) REVERT: D 362 GLN cc_start: 0.8026 (tp40) cc_final: 0.7635 (tp40) REVERT: D 369 ARG cc_start: 0.7165 (tpt90) cc_final: 0.6955 (tpt90) REVERT: D 378 LYS cc_start: 0.8060 (mttt) cc_final: 0.7838 (mttp) REVERT: D 397 GLU cc_start: 0.7215 (mm-30) cc_final: 0.7011 (mm-30) REVERT: D 398 ARG cc_start: 0.7284 (ttt90) cc_final: 0.6888 (mtt90) REVERT: D 433 PHE cc_start: 0.6972 (t80) cc_final: 0.6528 (t80) REVERT: E 16 GLU cc_start: 0.6598 (mm-30) cc_final: 0.6216 (mm-30) REVERT: E 70 THR cc_start: 0.8224 (p) cc_final: 0.7772 (t) REVERT: E 73 ASP cc_start: 0.7381 (t0) cc_final: 0.5837 (t0) REVERT: E 75 ASP cc_start: 0.7267 (m-30) cc_final: 0.6592 (m-30) REVERT: E 80 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7066 (mtt180) REVERT: E 89 GLU cc_start: 0.6312 (mt-10) cc_final: 0.6106 (mt-10) REVERT: E 93 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6931 (mt-10) REVERT: E 96 PHE cc_start: 0.7551 (m-80) cc_final: 0.7247 (m-80) REVERT: E 103 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7601 (mt0) REVERT: E 112 LYS cc_start: 0.8119 (mtmt) cc_final: 0.7837 (mttt) REVERT: E 119 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7342 (tm-30) REVERT: E 125 ARG cc_start: 0.7199 (mtt180) cc_final: 0.6867 (mtt180) REVERT: E 144 SER cc_start: 0.7941 (t) cc_final: 0.7520 (t) REVERT: E 154 GLN cc_start: 0.7353 (tm-30) cc_final: 0.6894 (tm-30) REVERT: E 157 LYS cc_start: 0.8167 (tttt) cc_final: 0.7919 (tttt) REVERT: E 166 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6900 (mt-10) REVERT: E 177 CYS cc_start: 0.7616 (m) cc_final: 0.7173 (m) REVERT: E 181 ASN cc_start: 0.8123 (t0) cc_final: 0.7830 (t0) REVERT: E 184 ASP cc_start: 0.6984 (m-30) cc_final: 0.6657 (m-30) REVERT: E 193 LYS cc_start: 0.8388 (mttt) cc_final: 0.7737 (ttmm) REVERT: E 237 SER cc_start: 0.8225 (m) cc_final: 0.7968 (t) REVERT: E 299 CYS cc_start: 0.7569 (m) cc_final: 0.7359 (m) REVERT: E 322 TYR cc_start: 0.8158 (m-10) cc_final: 0.7859 (m-80) REVERT: E 333 GLU cc_start: 0.7701 (tt0) cc_final: 0.7447 (tt0) REVERT: E 353 LYS cc_start: 0.8160 (mttt) cc_final: 0.7696 (mttt) REVERT: F 16 ASP cc_start: 0.7756 (t0) cc_final: 0.7302 (t0) REVERT: F 28 LYS cc_start: 0.8026 (tttt) cc_final: 0.7820 (tttt) REVERT: F 34 LEU cc_start: 0.8064 (tt) cc_final: 0.7850 (tt) REVERT: F 56 LYS cc_start: 0.8255 (mmtt) cc_final: 0.8055 (mmtt) REVERT: F 60 ILE cc_start: 0.8730 (mt) cc_final: 0.8449 (tt) REVERT: F 68 ARG cc_start: 0.8358 (tpp80) cc_final: 0.8040 (tpp80) REVERT: F 105 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.8124 (p) REVERT: F 110 VAL cc_start: 0.8486 (t) cc_final: 0.8262 (p) REVERT: F 116 LYS cc_start: 0.8292 (mttt) cc_final: 0.7929 (mmmm) REVERT: F 131 THR cc_start: 0.8389 (m) cc_final: 0.7941 (p) REVERT: F 139 LYS cc_start: 0.8692 (mttt) cc_final: 0.8405 (mtpp) REVERT: F 158 LYS cc_start: 0.8350 (mttt) cc_final: 0.8062 (mttt) REVERT: F 187 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7961 (mp10) REVERT: F 200 SER cc_start: 0.8351 (t) cc_final: 0.7812 (p) REVERT: F 216 LYS cc_start: 0.8361 (tttt) cc_final: 0.8093 (ttpp) REVERT: F 224 LEU cc_start: 0.8713 (tp) cc_final: 0.8421 (tp) REVERT: F 225 GLN cc_start: 0.8751 (tp40) cc_final: 0.8513 (tp40) REVERT: F 237 GLN cc_start: 0.7087 (mt0) cc_final: 0.6873 (mt0) REVERT: F 249 VAL cc_start: 0.8436 (t) cc_final: 0.8106 (p) REVERT: G 16 MET cc_start: 0.8308 (mmt) cc_final: 0.7554 (mmm) REVERT: H 926 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6167 (tp30) REVERT: K 143 GLU cc_start: 0.7620 (tt0) cc_final: 0.7249 (tt0) REVERT: K 178 MET cc_start: 0.7762 (mtm) cc_final: 0.7469 (mtm) REVERT: K 187 VAL cc_start: 0.8922 (t) cc_final: 0.8608 (m) REVERT: K 188 LYS cc_start: 0.8191 (tttt) cc_final: 0.7990 (tttt) REVERT: K 200 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6198 (mm) REVERT: K 208 GLN cc_start: 0.7579 (tp-100) cc_final: 0.7324 (tp-100) REVERT: K 212 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: K 214 MET cc_start: 0.6741 (mmt) cc_final: 0.6495 (mmt) REVERT: K 263 MET cc_start: 0.4943 (mmm) cc_final: 0.4674 (mmm) outliers start: 137 outliers final: 80 residues processed: 848 average time/residue: 0.4078 time to fit residues: 510.2962 Evaluate side-chains 857 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 751 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 177 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 310 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 372 GLU 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 415 HIS Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 625 GLN 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 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 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 464 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 478 MET 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 564 ASN 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 633 LEU Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 664 VAL 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 B residue 712 GLU 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 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 71 VAL 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 234 LEU Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 436 SER 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 163 THR Chi-restraints excluded: chain E residue 174 LEU 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 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 105 THR 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 252 ARG 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 125 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 150 optimal weight: 0.3980 chunk 188 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 259 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN A 677 GLN B 37 HIS B 328 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.151744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123000 restraints weight = 40681.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.126960 restraints weight = 19328.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.129464 restraints weight = 11671.681| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24323 Z= 0.140 Angle : 0.641 14.947 33080 Z= 0.313 Chirality : 0.042 0.216 3696 Planarity : 0.004 0.065 4058 Dihedral : 13.334 148.617 3621 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 5.18 % Allowed : 19.65 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2804 helix: 1.25 (0.14), residues: 1365 sheet: -0.15 (0.27), residues: 366 loop : -1.12 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP D 55 HIS 0.021 0.001 HIS D 424 PHE 0.027 0.001 PHE A 703 TYR 0.018 0.001 TYR A 61 ARG 0.012 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03572 ( 1106) hydrogen bonds : angle 4.30460 ( 3154) metal coordination : bond 0.00639 ( 28) metal coordination : angle 4.96311 ( 45) covalent geometry : bond 0.00312 (24295) covalent geometry : angle 0.61487 (33035) *********************** 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 912 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 782 time to evaluate : 2.887 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: 0.8399 (mttt) cc_final: 0.8151 (mttt) REVERT: A 65 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6047 (ptt) REVERT: A 68 LYS cc_start: 0.6345 (mtmt) cc_final: 0.5848 (tttm) REVERT: A 94 LYS cc_start: 0.7755 (ptpt) cc_final: 0.7467 (ptpt) REVERT: A 146 THR cc_start: 0.7454 (p) cc_final: 0.6229 (t) REVERT: A 157 LYS cc_start: 0.8320 (ptmm) cc_final: 0.7898 (ttpp) REVERT: A 158 LEU cc_start: 0.8324 (mt) cc_final: 0.8119 (mt) REVERT: A 162 SER cc_start: 0.8320 (p) cc_final: 0.7185 (p) REVERT: A 163 TYR cc_start: 0.7888 (t80) cc_final: 0.7541 (t80) REVERT: A 167 LYS cc_start: 0.7813 (mttp) cc_final: 0.7433 (mtpp) REVERT: A 169 VAL cc_start: 0.8501 (p) cc_final: 0.8203 (m) REVERT: A 173 ASN cc_start: 0.7853 (m-40) cc_final: 0.7448 (m-40) REVERT: A 178 GLU cc_start: 0.6625 (pm20) cc_final: 0.6357 (pm20) REVERT: A 273 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7664 (tppp) REVERT: A 279 GLU cc_start: 0.7779 (mp0) cc_final: 0.7529 (mp0) REVERT: A 282 LYS cc_start: 0.8491 (tttt) cc_final: 0.8012 (ttmm) REVERT: A 288 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7172 (tp30) REVERT: A 294 GLU cc_start: 0.6855 (tp30) cc_final: 0.6456 (tp30) REVERT: A 298 ARG cc_start: 0.7759 (mmm160) cc_final: 0.7255 (mmm160) REVERT: A 299 ASN cc_start: 0.7540 (p0) cc_final: 0.6988 (p0) REVERT: A 310 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8251 (pt) REVERT: A 325 ARG cc_start: 0.7343 (mtp85) cc_final: 0.6965 (mtp-110) REVERT: A 332 ARG cc_start: 0.8066 (mpp80) cc_final: 0.7458 (mtp85) REVERT: A 347 SER cc_start: 0.8553 (m) cc_final: 0.7780 (t) REVERT: A 372 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6660 (tp30) REVERT: A 375 LYS cc_start: 0.8263 (tttm) cc_final: 0.7956 (ttpp) REVERT: A 389 ILE cc_start: 0.7684 (mm) cc_final: 0.7303 (tt) REVERT: A 392 PHE cc_start: 0.7358 (t80) cc_final: 0.6836 (t80) REVERT: A 412 MET cc_start: 0.7289 (ttt) cc_final: 0.7033 (ttt) REVERT: A 418 LYS cc_start: 0.7657 (tmmt) cc_final: 0.7430 (tmmt) REVERT: A 419 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7351 (tpp80) REVERT: A 434 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7206 (mm-30) REVERT: A 457 ILE cc_start: 0.8256 (tt) cc_final: 0.7936 (tt) REVERT: A 476 LYS cc_start: 0.8328 (mttt) cc_final: 0.7883 (mttm) REVERT: A 487 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7746 (tttm) REVERT: A 490 GLU cc_start: 0.6407 (mp0) cc_final: 0.5962 (mp0) REVERT: A 504 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8232 (ttmt) REVERT: A 505 VAL cc_start: 0.8335 (OUTLIER) cc_final: 0.7997 (m) REVERT: A 525 ILE cc_start: 0.8352 (tp) cc_final: 0.7985 (tp) REVERT: A 530 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.7140 (mtm-85) REVERT: A 556 ASP cc_start: 0.7338 (m-30) cc_final: 0.7003 (m-30) REVERT: A 570 GLU cc_start: 0.7123 (pm20) cc_final: 0.6822 (pm20) REVERT: A 579 TYR cc_start: 0.7519 (p90) cc_final: 0.7028 (p90) REVERT: A 632 SER cc_start: 0.8086 (p) cc_final: 0.7727 (p) REVERT: A 642 ARG cc_start: 0.7423 (mtp85) cc_final: 0.6742 (mmt180) REVERT: A 659 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.6850 (p90) REVERT: A 669 GLU cc_start: 0.7139 (tt0) cc_final: 0.6874 (tt0) REVERT: A 677 GLN cc_start: 0.7663 (mt0) cc_final: 0.7404 (mt0) REVERT: A 682 ASP cc_start: 0.6822 (m-30) cc_final: 0.6620 (m-30) REVERT: A 683 GLN cc_start: 0.7616 (tp40) cc_final: 0.7273 (mm-40) REVERT: A 692 LYS cc_start: 0.7740 (tptm) cc_final: 0.7225 (tptt) REVERT: A 696 MET cc_start: 0.7419 (mmm) cc_final: 0.6973 (tmm) REVERT: A 704 SER cc_start: 0.8540 (p) cc_final: 0.8216 (p) REVERT: A 706 LYS cc_start: 0.7876 (tmmt) cc_final: 0.7417 (tmmt) REVERT: B 1 MET cc_start: 0.7418 (ppp) cc_final: 0.7165 (ppp) REVERT: B 42 MET cc_start: 0.7150 (mtp) cc_final: 0.6776 (mtp) REVERT: B 48 LYS cc_start: 0.8020 (ttpp) cc_final: 0.7495 (mtpp) REVERT: B 91 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7586 (mm) REVERT: B 113 LYS cc_start: 0.8107 (ttpp) cc_final: 0.7717 (ttmm) REVERT: B 122 THR cc_start: 0.6655 (OUTLIER) cc_final: 0.6292 (p) REVERT: B 158 TYR cc_start: 0.7399 (t80) cc_final: 0.6902 (t80) REVERT: B 233 PHE cc_start: 0.8159 (m-10) cc_final: 0.7846 (m-80) REVERT: B 384 HIS cc_start: 0.5130 (OUTLIER) cc_final: 0.4726 (p-80) REVERT: B 393 ASP cc_start: 0.7622 (m-30) cc_final: 0.7373 (t70) REVERT: B 414 PHE cc_start: 0.7228 (m-80) cc_final: 0.6489 (m-80) REVERT: B 416 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7081 (pt) REVERT: B 445 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7846 (mmtt) REVERT: B 464 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7214 (mt) REVERT: B 469 LYS cc_start: 0.8146 (ptpt) cc_final: 0.7690 (ptpp) REVERT: B 533 ASP cc_start: 0.6813 (p0) cc_final: 0.6546 (p0) REVERT: B 570 GLU cc_start: 0.6624 (tm-30) cc_final: 0.5896 (tm-30) REVERT: B 586 GLU cc_start: 0.7232 (pp20) cc_final: 0.6881 (pp20) REVERT: B 589 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6512 (mm-30) REVERT: B 613 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7337 (p90) REVERT: B 641 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7447 (mtm-85) REVERT: B 677 MET cc_start: 0.6949 (mtp) cc_final: 0.6709 (mtm) REVERT: B 681 ASP cc_start: 0.7981 (t0) cc_final: 0.7715 (t0) REVERT: B 712 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6209 (pt0) REVERT: C 405 GLN cc_start: 0.7763 (mt0) cc_final: 0.7484 (mt0) REVERT: C 441 MET cc_start: 0.7155 (mmm) cc_final: 0.6940 (mmt) REVERT: C 442 GLN cc_start: 0.4724 (OUTLIER) cc_final: 0.4284 (pp30) REVERT: C 475 PHE cc_start: 0.7103 (t80) cc_final: 0.6695 (t80) REVERT: C 493 MET cc_start: 0.7583 (tpp) cc_final: 0.7347 (mpp) REVERT: C 501 GLN cc_start: 0.8164 (tp40) cc_final: 0.7752 (tp40) REVERT: D 35 TYR cc_start: 0.8535 (m-10) cc_final: 0.8232 (m-80) REVERT: D 47 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7516 (mm-30) REVERT: D 50 SER cc_start: 0.7725 (m) cc_final: 0.7062 (p) REVERT: D 78 GLU cc_start: 0.7034 (pt0) cc_final: 0.6798 (pt0) REVERT: D 114 PHE cc_start: 0.8476 (t80) cc_final: 0.8272 (t80) REVERT: D 150 LYS cc_start: 0.7519 (tttt) cc_final: 0.7144 (tttt) REVERT: D 201 PHE cc_start: 0.8543 (m-80) cc_final: 0.8157 (m-80) REVERT: D 218 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7291 (tm-30) REVERT: D 233 ILE cc_start: 0.8482 (mt) cc_final: 0.8193 (mm) REVERT: D 243 SER cc_start: 0.7969 (m) cc_final: 0.7674 (p) REVERT: D 254 MET cc_start: 0.6511 (mtt) cc_final: 0.5655 (mtp) REVERT: D 258 LEU cc_start: 0.8299 (mt) cc_final: 0.7911 (tp) REVERT: D 259 LEU cc_start: 0.8793 (mt) cc_final: 0.8461 (mm) REVERT: D 260 ASN cc_start: 0.7556 (t0) cc_final: 0.7103 (t0) REVERT: D 261 PHE cc_start: 0.8177 (t80) cc_final: 0.7854 (t80) REVERT: D 281 TYR cc_start: 0.7654 (p90) cc_final: 0.7177 (p90) REVERT: D 284 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8451 (p) REVERT: D 313 TYR cc_start: 0.8312 (m-80) cc_final: 0.7942 (m-80) REVERT: D 316 TYR cc_start: 0.8366 (m-80) cc_final: 0.8054 (m-10) REVERT: D 318 TYR cc_start: 0.7923 (m-10) cc_final: 0.7709 (m-80) REVERT: D 340 ASN cc_start: 0.8142 (p0) cc_final: 0.7842 (t0) REVERT: D 341 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6498 (ttt) REVERT: D 362 GLN cc_start: 0.7996 (tp40) cc_final: 0.7599 (tp40) REVERT: D 378 LYS cc_start: 0.8052 (mttt) cc_final: 0.7822 (mttp) REVERT: D 398 ARG cc_start: 0.7295 (ttt90) cc_final: 0.6873 (mtt90) REVERT: D 433 PHE cc_start: 0.6939 (t80) cc_final: 0.6509 (t80) REVERT: E 16 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6167 (mm-30) REVERT: E 20 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7291 (mt-10) REVERT: E 70 THR cc_start: 0.8181 (p) cc_final: 0.7764 (t) REVERT: E 73 ASP cc_start: 0.7384 (t0) cc_final: 0.6188 (t0) REVERT: E 75 ASP cc_start: 0.7263 (m-30) cc_final: 0.6677 (m-30) REVERT: E 80 ARG cc_start: 0.8183 (mtt180) cc_final: 0.7310 (mtt180) REVERT: E 96 PHE cc_start: 0.7681 (m-80) cc_final: 0.7405 (m-80) REVERT: E 112 LYS cc_start: 0.8125 (mtmt) cc_final: 0.7716 (mttt) REVERT: E 125 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6627 (mtt180) REVERT: E 132 LYS cc_start: 0.8550 (mttt) cc_final: 0.8318 (mmtm) REVERT: E 144 SER cc_start: 0.7915 (t) cc_final: 0.7464 (t) REVERT: E 154 GLN cc_start: 0.7319 (tm-30) cc_final: 0.6864 (tm-30) REVERT: E 157 LYS cc_start: 0.8159 (tttt) cc_final: 0.7916 (tttt) REVERT: E 166 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6896 (mt-10) REVERT: E 181 ASN cc_start: 0.8079 (t0) cc_final: 0.7869 (t0) REVERT: E 184 ASP cc_start: 0.6752 (m-30) cc_final: 0.6495 (m-30) REVERT: E 193 LYS cc_start: 0.8390 (mttt) cc_final: 0.7728 (ttmm) REVERT: E 251 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.7847 (mtp180) REVERT: E 322 TYR cc_start: 0.8160 (m-10) cc_final: 0.7854 (m-80) REVERT: E 333 GLU cc_start: 0.7631 (tt0) cc_final: 0.7407 (tt0) REVERT: E 353 LYS cc_start: 0.8194 (mttt) cc_final: 0.7726 (mttt) REVERT: F 16 ASP cc_start: 0.7577 (t0) cc_final: 0.7149 (t0) REVERT: F 28 LYS cc_start: 0.8075 (tttt) cc_final: 0.7865 (tttt) REVERT: F 60 ILE cc_start: 0.8744 (mt) cc_final: 0.8458 (tt) REVERT: F 68 ARG cc_start: 0.8374 (tpp80) cc_final: 0.8058 (tpp80) REVERT: F 105 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.8085 (p) REVERT: F 110 VAL cc_start: 0.8436 (t) cc_final: 0.8234 (p) REVERT: F 116 LYS cc_start: 0.8282 (mttt) cc_final: 0.7912 (mmmm) REVERT: F 131 THR cc_start: 0.8375 (m) cc_final: 0.8154 (p) REVERT: F 139 LYS cc_start: 0.8672 (mttt) cc_final: 0.8384 (mtpp) REVERT: F 149 LYS cc_start: 0.8269 (mttt) cc_final: 0.8034 (mttt) REVERT: F 158 LYS cc_start: 0.8371 (mttt) cc_final: 0.8085 (mttt) REVERT: F 200 SER cc_start: 0.8313 (t) cc_final: 0.7805 (p) REVERT: F 213 LEU cc_start: 0.8508 (tp) cc_final: 0.8186 (tt) REVERT: F 216 LYS cc_start: 0.8352 (tttt) cc_final: 0.8076 (ttpp) REVERT: F 224 LEU cc_start: 0.8696 (tp) cc_final: 0.8416 (tp) REVERT: F 225 GLN cc_start: 0.8706 (tp40) cc_final: 0.8475 (tp40) REVERT: F 229 TRP cc_start: 0.8284 (t60) cc_final: 0.8051 (t60) REVERT: F 249 VAL cc_start: 0.8444 (t) cc_final: 0.8151 (p) REVERT: G 16 MET cc_start: 0.8237 (mmt) cc_final: 0.7437 (mmm) REVERT: H 926 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6166 (tp30) REVERT: K 143 GLU cc_start: 0.7580 (tt0) cc_final: 0.7158 (tt0) REVERT: K 178 MET cc_start: 0.7725 (mtm) cc_final: 0.7433 (mtm) REVERT: K 187 VAL cc_start: 0.8917 (t) cc_final: 0.8601 (m) REVERT: K 188 LYS cc_start: 0.8208 (tttt) cc_final: 0.8007 (tttt) REVERT: K 208 GLN cc_start: 0.7613 (tp-100) cc_final: 0.7338 (tp-100) REVERT: K 212 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: K 214 MET cc_start: 0.6750 (mmt) cc_final: 0.6491 (mmt) REVERT: K 263 MET cc_start: 0.4909 (mmm) cc_final: 0.4636 (mmm) outliers start: 130 outliers final: 80 residues processed: 851 average time/residue: 0.4206 time to fit residues: 526.7472 Evaluate side-chains 846 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 748 time to evaluate : 2.563 ------------------------------------------------------------------------------- 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 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 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 372 GLU 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 480 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 625 GLN 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 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 464 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 478 MET 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 603 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain B residue 712 GLU 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 71 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 212 LEU 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 284 THR Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 341 MET Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 174 LEU 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 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 105 THR 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 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 186 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 14 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 chunk 193 optimal weight: 7.9990 chunk 280 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 142 optimal weight: 0.0370 overall best weight: 1.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS A 461 HIS ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN A 564 ASN A 677 GLN B 37 HIS B 499 ASN ** C 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.145940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117387 restraints weight = 40238.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.121224 restraints weight = 19231.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123630 restraints weight = 11719.901| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 24323 Z= 0.214 Angle : 0.684 14.972 33080 Z= 0.338 Chirality : 0.044 0.214 3696 Planarity : 0.005 0.114 4058 Dihedral : 13.375 148.058 3615 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 5.38 % Allowed : 19.97 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2804 helix: 1.15 (0.14), residues: 1359 sheet: -0.29 (0.27), residues: 368 loop : -1.18 (0.19), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D 55 HIS 0.015 0.001 HIS D 424 PHE 0.029 0.002 PHE A 659 TYR 0.020 0.002 TYR A 501 ARG 0.015 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 1106) hydrogen bonds : angle 4.41915 ( 3154) metal coordination : bond 0.00882 ( 28) metal coordination : angle 5.77484 ( 45) covalent geometry : bond 0.00468 (24295) covalent geometry : angle 0.65057 (33035) *********************** 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 902 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 767 time to evaluate : 2.714 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: 0.8369 (mttt) cc_final: 0.8155 (mttt) REVERT: A 65 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6108 (ptt) REVERT: A 68 LYS cc_start: 0.6381 (mtmt) cc_final: 0.5910 (tttm) REVERT: A 146 THR cc_start: 0.7440 (p) cc_final: 0.6462 (t) REVERT: A 157 LYS cc_start: 0.8370 (ptmm) cc_final: 0.7975 (ttpp) REVERT: A 162 SER cc_start: 0.8366 (p) cc_final: 0.8010 (p) REVERT: A 163 TYR cc_start: 0.7932 (t80) cc_final: 0.7639 (t80) REVERT: A 167 LYS cc_start: 0.7894 (mttp) cc_final: 0.7347 (mtpp) REVERT: A 169 VAL cc_start: 0.8564 (p) cc_final: 0.8295 (m) REVERT: A 173 ASN cc_start: 0.7827 (m-40) cc_final: 0.7557 (m-40) REVERT: A 273 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7656 (tppp) REVERT: A 279 GLU cc_start: 0.7764 (mp0) cc_final: 0.7548 (mp0) REVERT: A 282 LYS cc_start: 0.8504 (tttt) cc_final: 0.8080 (ttmm) REVERT: A 288 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7232 (mp0) REVERT: A 298 ARG cc_start: 0.7783 (mmm160) cc_final: 0.7305 (mmm160) REVERT: A 299 ASN cc_start: 0.7750 (p0) cc_final: 0.7186 (p0) REVERT: A 310 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8294 (pt) REVERT: A 325 ARG cc_start: 0.7527 (mtp85) cc_final: 0.7159 (mtp-110) REVERT: A 332 ARG cc_start: 0.8113 (mpp80) cc_final: 0.7479 (mtp85) REVERT: A 334 ARG cc_start: 0.7281 (ptp90) cc_final: 0.6891 (ptp90) REVERT: A 347 SER cc_start: 0.8597 (m) cc_final: 0.7867 (t) REVERT: A 372 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6641 (tp30) REVERT: A 375 LYS cc_start: 0.8314 (tttm) cc_final: 0.7992 (ttpp) REVERT: A 389 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7400 (tt) REVERT: A 418 LYS cc_start: 0.7770 (tmmt) cc_final: 0.7451 (tmmt) REVERT: A 419 ARG cc_start: 0.7631 (ttm170) cc_final: 0.7318 (tpp80) REVERT: A 424 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 434 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7084 (mp0) REVERT: A 457 ILE cc_start: 0.8328 (tt) cc_final: 0.7994 (tt) REVERT: A 476 LYS cc_start: 0.8336 (mttt) cc_final: 0.7895 (mttm) REVERT: A 487 LYS cc_start: 0.8446 (ttmt) cc_final: 0.7854 (tttm) REVERT: A 490 GLU cc_start: 0.6401 (mp0) cc_final: 0.5925 (mp0) REVERT: A 504 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8234 (ttmt) REVERT: A 520 ARG cc_start: 0.7503 (mmm160) cc_final: 0.7253 (mmm-85) REVERT: A 521 GLU cc_start: 0.7304 (mp0) cc_final: 0.7066 (mp0) REVERT: A 525 ILE cc_start: 0.8406 (tp) cc_final: 0.8185 (tp) REVERT: A 526 LYS cc_start: 0.7520 (tppt) cc_final: 0.7218 (tppt) REVERT: A 556 ASP cc_start: 0.7379 (m-30) cc_final: 0.7010 (m-30) REVERT: A 570 GLU cc_start: 0.7191 (pm20) cc_final: 0.6640 (pm20) REVERT: A 579 TYR cc_start: 0.7490 (p90) cc_final: 0.7040 (p90) REVERT: A 632 SER cc_start: 0.8131 (p) cc_final: 0.7764 (p) REVERT: A 642 ARG cc_start: 0.7471 (mtp85) cc_final: 0.7046 (mmt90) REVERT: A 658 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7510 (p90) REVERT: A 659 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.6609 (p90) REVERT: A 669 GLU cc_start: 0.7159 (tt0) cc_final: 0.6838 (tt0) REVERT: A 677 GLN cc_start: 0.7650 (mt0) cc_final: 0.7315 (mt0) REVERT: A 682 ASP cc_start: 0.6855 (m-30) cc_final: 0.6577 (m-30) REVERT: A 692 LYS cc_start: 0.7883 (tptm) cc_final: 0.7407 (tptt) REVERT: A 696 MET cc_start: 0.7441 (mmm) cc_final: 0.6961 (tmm) REVERT: A 704 SER cc_start: 0.8533 (p) cc_final: 0.8174 (p) REVERT: A 706 LYS cc_start: 0.7966 (tmmt) cc_final: 0.7413 (tmmt) REVERT: B 1 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7219 (ppp) REVERT: B 27 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6523 (tm-30) REVERT: B 42 MET cc_start: 0.7147 (mtp) cc_final: 0.6727 (mtp) REVERT: B 48 LYS cc_start: 0.8310 (ttpp) cc_final: 0.7504 (mtpp) REVERT: B 91 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7625 (mm) REVERT: B 113 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7862 (ttmm) REVERT: B 122 THR cc_start: 0.6813 (OUTLIER) cc_final: 0.6589 (p) REVERT: B 158 TYR cc_start: 0.7403 (t80) cc_final: 0.6953 (t80) REVERT: B 352 GLU cc_start: 0.7290 (mp0) cc_final: 0.7056 (mp0) REVERT: B 384 HIS cc_start: 0.5147 (OUTLIER) cc_final: 0.4710 (p-80) REVERT: B 414 PHE cc_start: 0.7310 (m-80) cc_final: 0.6881 (m-80) REVERT: B 416 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7292 (mt) REVERT: B 438 MET cc_start: 0.7651 (mtm) cc_final: 0.7147 (mtm) REVERT: B 445 LYS cc_start: 0.8243 (mmtt) cc_final: 0.8028 (mmtt) REVERT: B 455 ILE cc_start: 0.8335 (mt) cc_final: 0.7930 (mm) REVERT: B 507 LYS cc_start: 0.8427 (mttt) cc_final: 0.8101 (mttm) REVERT: B 533 ASP cc_start: 0.6754 (p0) cc_final: 0.6364 (p0) REVERT: B 570 GLU cc_start: 0.6636 (tm-30) cc_final: 0.5987 (tm-30) REVERT: B 586 GLU cc_start: 0.7236 (pp20) cc_final: 0.6872 (pp20) REVERT: B 589 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6562 (mm-30) REVERT: B 604 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8358 (t) REVERT: B 613 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.7314 (p90) REVERT: B 641 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.7421 (mtm-85) REVERT: B 677 MET cc_start: 0.6903 (mtp) cc_final: 0.6701 (mtt) REVERT: B 712 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6526 (pt0) REVERT: C 411 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.7003 (tpp) REVERT: C 442 GLN cc_start: 0.4829 (OUTLIER) cc_final: 0.4283 (pp30) REVERT: C 475 PHE cc_start: 0.7032 (t80) cc_final: 0.6658 (t80) REVERT: C 493 MET cc_start: 0.7651 (tpp) cc_final: 0.7407 (mpp) REVERT: C 501 GLN cc_start: 0.8182 (tp40) cc_final: 0.7701 (tp40) REVERT: D 47 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7556 (mm-30) REVERT: D 78 GLU cc_start: 0.7139 (pt0) cc_final: 0.6751 (pt0) REVERT: D 79 PHE cc_start: 0.7566 (m-80) cc_final: 0.6656 (m-80) REVERT: D 81 LYS cc_start: 0.8722 (tttm) cc_final: 0.8334 (tttm) REVERT: D 84 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7278 (mt-10) REVERT: D 150 LYS cc_start: 0.7652 (tttt) cc_final: 0.7267 (tttt) REVERT: D 155 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7836 (mmm160) REVERT: D 201 PHE cc_start: 0.8652 (m-80) cc_final: 0.8261 (m-80) REVERT: D 218 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7344 (tm-30) REVERT: D 233 ILE cc_start: 0.8483 (mt) cc_final: 0.8242 (mm) REVERT: D 243 SER cc_start: 0.8118 (m) cc_final: 0.7877 (p) REVERT: D 258 LEU cc_start: 0.8241 (mt) cc_final: 0.7868 (tp) REVERT: D 259 LEU cc_start: 0.8858 (mt) cc_final: 0.8530 (mm) REVERT: D 260 ASN cc_start: 0.7533 (t0) cc_final: 0.7195 (t0) REVERT: D 313 TYR cc_start: 0.8326 (m-80) cc_final: 0.7910 (m-80) REVERT: D 340 ASN cc_start: 0.8096 (p0) cc_final: 0.7565 (t0) REVERT: D 362 GLN cc_start: 0.7998 (tp40) cc_final: 0.7714 (tp40) REVERT: D 369 ARG cc_start: 0.7211 (tpt90) cc_final: 0.6981 (tpt90) REVERT: D 378 LYS cc_start: 0.8099 (mttt) cc_final: 0.7854 (mttp) REVERT: D 397 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7234 (mm-30) REVERT: D 398 ARG cc_start: 0.7300 (ttt90) cc_final: 0.6937 (mtt90) REVERT: D 433 PHE cc_start: 0.7141 (t80) cc_final: 0.6664 (t80) REVERT: E 31 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7995 (ptmt) REVERT: E 42 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7481 (tmtt) REVERT: E 70 THR cc_start: 0.8204 (p) cc_final: 0.7788 (t) REVERT: E 73 ASP cc_start: 0.7372 (t0) cc_final: 0.6240 (t0) REVERT: E 75 ASP cc_start: 0.7247 (m-30) cc_final: 0.6696 (m-30) REVERT: E 80 ARG cc_start: 0.8220 (mtt180) cc_final: 0.7346 (mtt180) REVERT: E 96 PHE cc_start: 0.7710 (m-80) cc_final: 0.7411 (m-80) REVERT: E 103 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: E 112 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7753 (mttt) REVERT: E 125 ARG cc_start: 0.7101 (mtt180) cc_final: 0.6867 (mtt180) REVERT: E 132 LYS cc_start: 0.8550 (mttt) cc_final: 0.8328 (mmtt) REVERT: E 144 SER cc_start: 0.8000 (t) cc_final: 0.7452 (p) REVERT: E 154 GLN cc_start: 0.7365 (tm-30) cc_final: 0.6780 (tm-30) REVERT: E 157 LYS cc_start: 0.8210 (tttt) cc_final: 0.7982 (tttt) REVERT: E 166 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6731 (mt-10) REVERT: E 184 ASP cc_start: 0.6754 (m-30) cc_final: 0.6440 (m-30) REVERT: E 193 LYS cc_start: 0.8434 (mttt) cc_final: 0.7755 (ttmm) REVERT: E 251 ARG cc_start: 0.8300 (mmm-85) cc_final: 0.7984 (mmm160) REVERT: E 322 TYR cc_start: 0.8198 (m-10) cc_final: 0.7780 (m-80) REVERT: E 353 LYS cc_start: 0.8202 (mttt) cc_final: 0.7733 (mttt) REVERT: F 16 ASP cc_start: 0.7607 (t0) cc_final: 0.7253 (t0) REVERT: F 60 ILE cc_start: 0.8771 (mt) cc_final: 0.8481 (tt) REVERT: F 68 ARG cc_start: 0.8412 (tpp80) cc_final: 0.8087 (tpp80) REVERT: F 116 LYS cc_start: 0.8301 (mttt) cc_final: 0.7958 (mmmm) REVERT: F 139 LYS cc_start: 0.8688 (mttt) cc_final: 0.8337 (mtpp) REVERT: F 158 LYS cc_start: 0.8455 (mttt) cc_final: 0.8182 (mttt) REVERT: F 213 LEU cc_start: 0.8522 (tp) cc_final: 0.8207 (tt) REVERT: F 216 LYS cc_start: 0.8359 (tttt) cc_final: 0.8095 (ttpp) REVERT: F 224 LEU cc_start: 0.8694 (tp) cc_final: 0.8394 (tp) REVERT: F 225 GLN cc_start: 0.8716 (tp40) cc_final: 0.8500 (tp40) REVERT: F 237 GLN cc_start: 0.7138 (mt0) cc_final: 0.6903 (mt0) REVERT: F 249 VAL cc_start: 0.8482 (t) cc_final: 0.8169 (p) REVERT: F 252 ARG cc_start: 0.8430 (mtp85) cc_final: 0.8220 (mtp85) REVERT: G 16 MET cc_start: 0.8298 (mmt) cc_final: 0.7686 (mmm) REVERT: G 54 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7557 (tm-30) REVERT: H 926 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.6128 (tp30) REVERT: K 118 MET cc_start: 0.6761 (tpp) cc_final: 0.6436 (tpp) REVERT: K 143 GLU cc_start: 0.7627 (tt0) cc_final: 0.7118 (tt0) REVERT: K 178 MET cc_start: 0.7821 (mtm) cc_final: 0.7483 (mtm) REVERT: K 208 GLN cc_start: 0.7731 (tp-100) cc_final: 0.7439 (tp-100) REVERT: K 212 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: K 214 MET cc_start: 0.6922 (mmt) cc_final: 0.6713 (mmt) REVERT: K 263 MET cc_start: 0.4944 (mmm) cc_final: 0.4680 (mmm) outliers start: 135 outliers final: 96 residues processed: 830 average time/residue: 0.4163 time to fit residues: 511.3842 Evaluate side-chains 870 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 752 time to evaluate : 2.578 ------------------------------------------------------------------------------- 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 107 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain A residue 380 MET 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 427 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 480 LEU 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 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 B residue 1 MET 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 357 PHE 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 470 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 473 PHE Chi-restraints excluded: chain B residue 478 MET 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 603 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 649 ASN Chi-restraints excluded: chain B residue 663 CYS 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 B residue 712 GLU 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 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 215 PHE Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 LYS 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 174 LEU 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 64 ILE Chi-restraints excluded: chain F residue 128 HIS 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 263 GLU 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 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 147 GLU Chi-restraints excluded: chain K residue 164 PHE Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 271 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 226 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 115 optimal weight: 0.0670 chunk 39 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 177 optimal weight: 0.0670 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.147596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118994 restraints weight = 40661.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.122921 restraints weight = 19361.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.125379 restraints weight = 11783.017| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.4665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24323 Z= 0.152 Angle : 0.686 15.590 33080 Z= 0.335 Chirality : 0.042 0.198 3696 Planarity : 0.004 0.095 4058 Dihedral : 13.349 148.959 3614 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 5.18 % Allowed : 21.40 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.16), residues: 2804 helix: 1.20 (0.15), residues: 1360 sheet: -0.30 (0.27), residues: 354 loop : -1.13 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 55 HIS 0.016 0.001 HIS D 424 PHE 0.020 0.001 PHE A 703 TYR 0.023 0.001 TYR F 266 ARG 0.024 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03672 ( 1106) hydrogen bonds : angle 4.36550 ( 3154) metal coordination : bond 0.01040 ( 28) metal coordination : angle 5.39237 ( 45) covalent geometry : bond 0.00340 (24295) covalent geometry : angle 0.65719 (33035) *********************** 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 888 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 758 time to evaluate : 2.972 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: 0.8381 (mttt) cc_final: 0.8111 (mttt) REVERT: A 65 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6086 (ptt) REVERT: A 68 LYS cc_start: 0.6367 (mtmt) cc_final: 0.5884 (tttm) REVERT: A 146 THR cc_start: 0.7429 (p) cc_final: 0.6441 (t) REVERT: A 157 LYS cc_start: 0.8288 (ptmm) cc_final: 0.7963 (ttpp) REVERT: A 162 SER cc_start: 0.8330 (p) cc_final: 0.7953 (p) REVERT: A 163 TYR cc_start: 0.7902 (t80) cc_final: 0.7585 (t80) REVERT: A 167 LYS cc_start: 0.7781 (mttp) cc_final: 0.7283 (mtpp) REVERT: A 173 ASN cc_start: 0.7821 (m-40) cc_final: 0.7538 (m-40) REVERT: A 178 GLU cc_start: 0.6509 (pm20) cc_final: 0.6228 (pm20) REVERT: A 273 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7797 (ttpt) REVERT: A 279 GLU cc_start: 0.7770 (mp0) cc_final: 0.7559 (mp0) REVERT: A 282 LYS cc_start: 0.8503 (tttt) cc_final: 0.8056 (ttmm) REVERT: A 288 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7136 (mp0) REVERT: A 298 ARG cc_start: 0.7771 (mmm160) cc_final: 0.7269 (mmm160) REVERT: A 299 ASN cc_start: 0.7743 (p0) cc_final: 0.7146 (p0) REVERT: A 325 ARG cc_start: 0.7393 (mtp85) cc_final: 0.7049 (mtp-110) REVERT: A 332 ARG cc_start: 0.8088 (mpp80) cc_final: 0.7786 (mtp85) REVERT: A 347 SER cc_start: 0.8589 (m) cc_final: 0.7844 (t) REVERT: A 372 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6605 (tp30) REVERT: A 375 LYS cc_start: 0.8283 (tttm) cc_final: 0.7958 (ttpp) REVERT: A 389 ILE cc_start: 0.7833 (mm) cc_final: 0.7334 (tt) REVERT: A 418 LYS cc_start: 0.7621 (tmmt) cc_final: 0.7316 (tmmt) REVERT: A 419 ARG cc_start: 0.7548 (ttm170) cc_final: 0.7254 (tpp80) REVERT: A 424 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7436 (mm-30) REVERT: A 434 GLU cc_start: 0.7520 (mm-30) cc_final: 0.6983 (mp0) REVERT: A 457 ILE cc_start: 0.8333 (tt) cc_final: 0.7998 (tt) REVERT: A 476 LYS cc_start: 0.8357 (mttt) cc_final: 0.7915 (mttm) REVERT: A 487 LYS cc_start: 0.8368 (ttmt) cc_final: 0.7827 (tttm) REVERT: A 490 GLU cc_start: 0.6383 (mp0) cc_final: 0.5930 (mp0) REVERT: A 504 LYS cc_start: 0.8547 (ttpt) cc_final: 0.8207 (ttmt) REVERT: A 505 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.7996 (m) REVERT: A 521 GLU cc_start: 0.7306 (mp0) cc_final: 0.7071 (mp0) REVERT: A 525 ILE cc_start: 0.8405 (tp) cc_final: 0.8175 (tp) REVERT: A 526 LYS cc_start: 0.7465 (tppt) cc_final: 0.7134 (tppt) REVERT: A 556 ASP cc_start: 0.7353 (m-30) cc_final: 0.6970 (m-30) REVERT: A 570 GLU cc_start: 0.7207 (pm20) cc_final: 0.6853 (pm20) REVERT: A 579 TYR cc_start: 0.7492 (p90) cc_final: 0.7107 (p90) REVERT: A 588 GLU cc_start: 0.7232 (tp30) cc_final: 0.6677 (tp30) REVERT: A 632 SER cc_start: 0.8065 (p) cc_final: 0.7723 (p) REVERT: A 636 GLU cc_start: 0.7383 (tp30) cc_final: 0.6861 (tp30) REVERT: A 642 ARG cc_start: 0.7452 (mtp85) cc_final: 0.7103 (mmt90) REVERT: A 658 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7515 (p90) REVERT: A 659 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.6734 (p90) REVERT: A 669 GLU cc_start: 0.7134 (tt0) cc_final: 0.6841 (tt0) REVERT: A 677 GLN cc_start: 0.7610 (mt0) cc_final: 0.7367 (mt0) REVERT: A 682 ASP cc_start: 0.6838 (m-30) cc_final: 0.6553 (m-30) REVERT: A 692 LYS cc_start: 0.7828 (tptm) cc_final: 0.7335 (tptt) REVERT: A 696 MET cc_start: 0.7364 (mmm) cc_final: 0.6923 (tmm) REVERT: A 704 SER cc_start: 0.8492 (p) cc_final: 0.8146 (p) REVERT: A 706 LYS cc_start: 0.7954 (tmmt) cc_final: 0.7557 (tmmt) REVERT: B 1 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7210 (ppp) REVERT: B 27 GLU cc_start: 0.6757 (tm-30) cc_final: 0.6490 (tm-30) REVERT: B 42 MET cc_start: 0.7134 (mtp) cc_final: 0.6718 (mtp) REVERT: B 48 LYS cc_start: 0.8284 (ttpp) cc_final: 0.7510 (mtpp) REVERT: B 63 TYR cc_start: 0.8081 (m-80) cc_final: 0.7818 (m-80) REVERT: B 91 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7604 (mm) REVERT: B 113 LYS cc_start: 0.8358 (ttpp) cc_final: 0.8009 (ttmm) REVERT: B 122 THR cc_start: 0.6830 (OUTLIER) cc_final: 0.6469 (p) REVERT: B 158 TYR cc_start: 0.7384 (t80) cc_final: 0.6942 (t80) REVERT: B 352 GLU cc_start: 0.7295 (mp0) cc_final: 0.7053 (mp0) REVERT: B 384 HIS cc_start: 0.5142 (OUTLIER) cc_final: 0.4695 (p-80) REVERT: B 414 PHE cc_start: 0.7316 (m-80) cc_final: 0.6957 (m-80) REVERT: B 416 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7322 (mt) REVERT: B 438 MET cc_start: 0.7617 (mtm) cc_final: 0.7071 (mtm) REVERT: B 455 ILE cc_start: 0.8363 (mt) cc_final: 0.7910 (mm) REVERT: B 507 LYS cc_start: 0.8342 (mttt) cc_final: 0.8000 (mttm) REVERT: B 533 ASP cc_start: 0.6790 (p0) cc_final: 0.6507 (p0) REVERT: B 570 GLU cc_start: 0.6686 (tm-30) cc_final: 0.6026 (tm-30) REVERT: B 586 GLU cc_start: 0.7160 (pp20) cc_final: 0.6843 (pp20) REVERT: B 589 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6538 (mm-30) REVERT: B 613 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7383 (p90) REVERT: B 641 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7447 (mtm-85) REVERT: C 411 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.7044 (tpp) REVERT: C 442 GLN cc_start: 0.4729 (OUTLIER) cc_final: 0.3576 (pp30) REVERT: C 475 PHE cc_start: 0.7085 (t80) cc_final: 0.6692 (t80) REVERT: C 493 MET cc_start: 0.7680 (tpp) cc_final: 0.7412 (mpp) REVERT: C 501 GLN cc_start: 0.8170 (tp40) cc_final: 0.7800 (tp40) REVERT: D 20 GLN cc_start: 0.8155 (mp10) cc_final: 0.7891 (mp10) REVERT: D 35 TYR cc_start: 0.8519 (m-10) cc_final: 0.8240 (m-80) REVERT: D 47 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7477 (mm-30) REVERT: D 55 TRP cc_start: 0.7969 (m-90) cc_final: 0.7734 (m-90) REVERT: D 78 GLU cc_start: 0.7153 (pt0) cc_final: 0.6756 (pt0) REVERT: D 79 PHE cc_start: 0.7426 (m-80) cc_final: 0.6588 (m-80) REVERT: D 81 LYS cc_start: 0.8722 (tttm) cc_final: 0.8466 (tttm) REVERT: D 85 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7398 (mp0) REVERT: D 150 LYS cc_start: 0.7648 (tttt) cc_final: 0.7270 (tttt) REVERT: D 161 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.7217 (m-70) REVERT: D 201 PHE cc_start: 0.8685 (m-80) cc_final: 0.8299 (m-80) REVERT: D 218 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7320 (tm-30) REVERT: D 233 ILE cc_start: 0.8486 (mt) cc_final: 0.8234 (mm) REVERT: D 243 SER cc_start: 0.8070 (m) cc_final: 0.7830 (p) REVERT: D 258 LEU cc_start: 0.8216 (mt) cc_final: 0.7910 (tp) REVERT: D 259 LEU cc_start: 0.8790 (mt) cc_final: 0.8480 (mm) REVERT: D 260 ASN cc_start: 0.7505 (t0) cc_final: 0.7171 (t0) REVERT: D 281 TYR cc_start: 0.7708 (p90) cc_final: 0.7454 (p90) REVERT: D 313 TYR cc_start: 0.8335 (m-80) cc_final: 0.7960 (m-80) REVERT: D 316 TYR cc_start: 0.8382 (m-80) cc_final: 0.8105 (m-10) REVERT: D 318 TYR cc_start: 0.7899 (m-10) cc_final: 0.7680 (m-80) REVERT: D 340 ASN cc_start: 0.8072 (p0) cc_final: 0.7584 (t0) REVERT: D 362 GLN cc_start: 0.7937 (tp40) cc_final: 0.7316 (tp40) REVERT: D 369 ARG cc_start: 0.7182 (tpt90) cc_final: 0.6931 (tpt90) REVERT: D 378 LYS cc_start: 0.8072 (mttt) cc_final: 0.7836 (mttp) REVERT: D 397 GLU cc_start: 0.7375 (mm-30) cc_final: 0.7085 (mm-30) REVERT: D 398 ARG cc_start: 0.7317 (ttt90) cc_final: 0.6939 (mtt90) REVERT: D 433 PHE cc_start: 0.7064 (t80) cc_final: 0.6625 (t80) REVERT: E 16 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6461 (mt-10) REVERT: E 31 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7947 (ptmt) REVERT: E 42 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7577 (tmtt) REVERT: E 70 THR cc_start: 0.8175 (p) cc_final: 0.7755 (t) REVERT: E 73 ASP cc_start: 0.7371 (t0) cc_final: 0.6190 (t0) REVERT: E 75 ASP cc_start: 0.7239 (m-30) cc_final: 0.6688 (m-30) REVERT: E 80 ARG cc_start: 0.8202 (mtt180) cc_final: 0.7295 (mtt180) REVERT: E 96 PHE cc_start: 0.7703 (m-80) cc_final: 0.7427 (m-80) REVERT: E 125 ARG cc_start: 0.7063 (mtt180) cc_final: 0.6855 (mtt180) REVERT: E 132 LYS cc_start: 0.8553 (mttt) cc_final: 0.8329 (mmtt) REVERT: E 144 SER cc_start: 0.7903 (t) cc_final: 0.7449 (t) REVERT: E 154 GLN cc_start: 0.7331 (tm-30) cc_final: 0.6768 (tm-30) REVERT: E 157 LYS cc_start: 0.8168 (tttt) cc_final: 0.7953 (tttt) REVERT: E 193 LYS cc_start: 0.8420 (mttt) cc_final: 0.7744 (ttmm) REVERT: E 322 TYR cc_start: 0.8197 (m-10) cc_final: 0.7789 (m-80) REVERT: E 353 LYS cc_start: 0.8200 (mttt) cc_final: 0.7738 (mttt) REVERT: F 8 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7545 (tp) REVERT: F 16 ASP cc_start: 0.7748 (t0) cc_final: 0.7215 (t0) REVERT: F 60 ILE cc_start: 0.8765 (mt) cc_final: 0.8482 (tt) REVERT: F 68 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8094 (tpp80) REVERT: F 116 LYS cc_start: 0.8270 (mttt) cc_final: 0.7896 (mmmm) REVERT: F 139 LYS cc_start: 0.8661 (mttt) cc_final: 0.8407 (mtpp) REVERT: F 158 LYS cc_start: 0.8443 (mttt) cc_final: 0.8173 (mttt) REVERT: F 213 LEU cc_start: 0.8512 (tp) cc_final: 0.8209 (tt) REVERT: F 216 LYS cc_start: 0.8366 (tttt) cc_final: 0.8077 (ttpp) REVERT: F 224 LEU cc_start: 0.8717 (tp) cc_final: 0.8445 (tp) REVERT: F 225 GLN cc_start: 0.8687 (tp40) cc_final: 0.8478 (tp40) REVERT: F 249 VAL cc_start: 0.8482 (t) cc_final: 0.8187 (p) REVERT: F 252 ARG cc_start: 0.8430 (mtp85) cc_final: 0.8004 (mtp85) REVERT: G 16 MET cc_start: 0.8324 (mmt) cc_final: 0.7533 (mmm) REVERT: H 926 GLU cc_start: 0.6604 (OUTLIER) cc_final: 0.6133 (tp30) REVERT: K 118 MET cc_start: 0.6727 (tpp) cc_final: 0.6472 (tpp) REVERT: K 178 MET cc_start: 0.7827 (mtm) cc_final: 0.7515 (mtm) REVERT: K 212 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: K 214 MET cc_start: 0.6942 (mmt) cc_final: 0.6731 (mmt) REVERT: K 259 LYS cc_start: 0.6494 (mmtm) cc_final: 0.6197 (mppt) REVERT: K 263 MET cc_start: 0.4761 (mmm) cc_final: 0.4547 (mmm) outliers start: 130 outliers final: 92 residues processed: 814 average time/residue: 0.4090 time to fit residues: 489.5091 Evaluate side-chains 862 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 751 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 189 LEU Chi-restraints excluded: chain A residue 193 VAL 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 357 VAL Chi-restraints excluded: chain A residue 372 GLU 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 427 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 625 GLN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 656 ASN 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 B residue 1 MET 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 478 MET Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 483 MET 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 603 LYS Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 663 CYS 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 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 31 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS 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 241 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 237 SER 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 E residue 340 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 128 HIS 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 240 GLN Chi-restraints excluded: chain F residue 263 GLU 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 146 GLN Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 96 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 253 optimal weight: 0.6980 chunk 145 optimal weight: 10.0000 chunk 259 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN B 37 HIS ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 210 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117313 restraints weight = 40774.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121229 restraints weight = 19399.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.123696 restraints weight = 11761.752| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24323 Z= 0.168 Angle : 0.695 16.002 33080 Z= 0.342 Chirality : 0.043 0.214 3696 Planarity : 0.004 0.057 4058 Dihedral : 13.382 148.534 3610 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 5.22 % Allowed : 21.92 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2804 helix: 1.09 (0.15), residues: 1361 sheet: -0.24 (0.27), residues: 343 loop : -1.15 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 55 HIS 0.010 0.001 HIS D 424 PHE 0.023 0.001 PHE A 659 TYR 0.023 0.002 TYR F 266 ARG 0.017 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03738 ( 1106) hydrogen bonds : angle 4.39501 ( 3154) metal coordination : bond 0.00765 ( 28) metal coordination : angle 5.35797 ( 45) covalent geometry : bond 0.00375 (24295) covalent geometry : angle 0.66638 (33035) *********************** 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 899 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 768 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8411 (mttt) cc_final: 0.8135 (mttt) REVERT: A 65 MET cc_start: 0.6951 (OUTLIER) cc_final: 0.6528 (ptt) REVERT: A 68 LYS cc_start: 0.6405 (mtmt) cc_final: 0.5962 (tttm) REVERT: A 146 THR cc_start: 0.7496 (p) cc_final: 0.6875 (m) REVERT: A 157 LYS cc_start: 0.8302 (ptmm) cc_final: 0.7939 (ttpp) REVERT: A 162 SER cc_start: 0.8316 (p) cc_final: 0.7936 (p) REVERT: A 163 TYR cc_start: 0.7915 (t80) cc_final: 0.7620 (t80) REVERT: A 173 ASN cc_start: 0.7761 (m-40) cc_final: 0.7545 (m-40) REVERT: A 176 PHE cc_start: 0.8136 (m-10) cc_final: 0.7906 (m-10) REVERT: A 273 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7981 (ttpt) REVERT: A 279 GLU cc_start: 0.7775 (mp0) cc_final: 0.7571 (mp0) REVERT: A 282 LYS cc_start: 0.8511 (tttt) cc_final: 0.8067 (ttmm) REVERT: A 288 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7149 (mp0) REVERT: A 298 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7254 (mmm160) REVERT: A 299 ASN cc_start: 0.7818 (p0) cc_final: 0.7225 (p0) REVERT: A 321 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6313 (tm-30) REVERT: A 326 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8389 (tttm) REVERT: A 330 ASN cc_start: 0.7689 (p0) cc_final: 0.7435 (p0) REVERT: A 332 ARG cc_start: 0.8094 (mpp80) cc_final: 0.7640 (mtp85) REVERT: A 347 SER cc_start: 0.8602 (m) cc_final: 0.7846 (t) REVERT: A 372 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6609 (tp30) REVERT: A 375 LYS cc_start: 0.8285 (tttm) cc_final: 0.7945 (ttpp) REVERT: A 389 ILE cc_start: 0.7878 (OUTLIER) cc_final: 0.7453 (tt) REVERT: A 434 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7046 (mp0) REVERT: A 457 ILE cc_start: 0.8366 (tt) cc_final: 0.8008 (tt) REVERT: A 476 LYS cc_start: 0.8358 (mttt) cc_final: 0.7632 (mttm) REVERT: A 487 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7584 (tttm) REVERT: A 490 GLU cc_start: 0.6429 (mp0) cc_final: 0.5951 (mp0) REVERT: A 504 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8040 (ttmt) REVERT: A 505 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8018 (m) REVERT: A 514 MET cc_start: 0.8113 (tpp) cc_final: 0.7801 (tpp) REVERT: A 525 ILE cc_start: 0.8402 (tp) cc_final: 0.8143 (tp) REVERT: A 526 LYS cc_start: 0.7389 (tppt) cc_final: 0.7106 (tppt) REVERT: A 556 ASP cc_start: 0.7291 (m-30) cc_final: 0.6947 (m-30) REVERT: A 570 GLU cc_start: 0.7238 (pm20) cc_final: 0.6883 (pm20) REVERT: A 579 TYR cc_start: 0.7495 (p90) cc_final: 0.7177 (p90) REVERT: A 588 GLU cc_start: 0.7255 (tp30) cc_final: 0.6709 (tp30) REVERT: A 632 SER cc_start: 0.8085 (p) cc_final: 0.7716 (p) REVERT: A 642 ARG cc_start: 0.7482 (mtp85) cc_final: 0.7109 (mmt90) REVERT: A 658 PHE cc_start: 0.7736 (OUTLIER) cc_final: 0.7520 (p90) REVERT: A 659 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.6687 (p90) REVERT: A 669 GLU cc_start: 0.7167 (tt0) cc_final: 0.6863 (tt0) REVERT: A 677 GLN cc_start: 0.7618 (mt0) cc_final: 0.7374 (mt0) REVERT: A 682 ASP cc_start: 0.6848 (m-30) cc_final: 0.6550 (m-30) REVERT: A 692 LYS cc_start: 0.7837 (tptm) cc_final: 0.7441 (tptt) REVERT: A 696 MET cc_start: 0.7379 (mmm) cc_final: 0.6858 (tmm) REVERT: A 699 GLU cc_start: 0.8007 (pp20) cc_final: 0.7675 (pp20) REVERT: A 704 SER cc_start: 0.8502 (p) cc_final: 0.8141 (p) REVERT: A 706 LYS cc_start: 0.7962 (tmmt) cc_final: 0.7479 (tmmt) REVERT: B 1 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7211 (ppp) REVERT: B 27 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6527 (tm-30) REVERT: B 42 MET cc_start: 0.7129 (mtp) cc_final: 0.6673 (mtp) REVERT: B 48 LYS cc_start: 0.8323 (ttpp) cc_final: 0.7516 (mtpp) REVERT: B 55 LEU cc_start: 0.8082 (tt) cc_final: 0.7829 (tt) REVERT: B 63 TYR cc_start: 0.8138 (m-80) cc_final: 0.7868 (m-80) REVERT: B 70 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7616 (tp) REVERT: B 91 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7568 (mm) REVERT: B 113 LYS cc_start: 0.8387 (ttpp) cc_final: 0.8053 (ttmm) REVERT: B 122 THR cc_start: 0.6887 (OUTLIER) cc_final: 0.6515 (p) REVERT: B 158 TYR cc_start: 0.7311 (t80) cc_final: 0.6859 (t80) REVERT: B 196 ARG cc_start: 0.7705 (mmp80) cc_final: 0.7428 (mmp80) REVERT: B 352 GLU cc_start: 0.7388 (mp0) cc_final: 0.7074 (mp0) REVERT: B 384 HIS cc_start: 0.5147 (OUTLIER) cc_final: 0.4699 (p-80) REVERT: B 414 PHE cc_start: 0.7372 (m-80) cc_final: 0.7022 (m-80) REVERT: B 416 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7413 (mt) REVERT: B 438 MET cc_start: 0.7659 (mtm) cc_final: 0.7063 (mtm) REVERT: B 445 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7895 (mmtt) REVERT: B 455 ILE cc_start: 0.8374 (mt) cc_final: 0.7925 (mm) REVERT: B 533 ASP cc_start: 0.6809 (p0) cc_final: 0.6448 (p0) REVERT: B 570 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6073 (tm-30) REVERT: B 586 GLU cc_start: 0.7172 (pp20) cc_final: 0.6805 (pp20) REVERT: B 589 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6562 (mm-30) REVERT: B 613 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7299 (p90) REVERT: B 641 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7437 (mtm-85) REVERT: B 712 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6634 (mt-10) REVERT: C 408 ARG cc_start: 0.8341 (tpp80) cc_final: 0.8129 (tpp80) REVERT: C 411 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.7062 (tpp) REVERT: C 442 GLN cc_start: 0.4777 (OUTLIER) cc_final: 0.4196 (pp30) REVERT: C 475 PHE cc_start: 0.7142 (t80) cc_final: 0.6729 (t80) REVERT: C 493 MET cc_start: 0.7677 (tpp) cc_final: 0.7406 (mpp) REVERT: C 501 GLN cc_start: 0.8182 (tp40) cc_final: 0.7807 (tp40) REVERT: D 35 TYR cc_start: 0.8533 (m-10) cc_final: 0.8212 (m-80) REVERT: D 55 TRP cc_start: 0.7991 (m-90) cc_final: 0.7705 (m-90) REVERT: D 78 GLU cc_start: 0.7277 (pt0) cc_final: 0.6950 (pt0) REVERT: D 81 LYS cc_start: 0.8675 (tttm) cc_final: 0.8412 (tttm) REVERT: D 84 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7223 (mp0) REVERT: D 85 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7552 (mp0) REVERT: D 150 LYS cc_start: 0.7675 (tttt) cc_final: 0.7305 (tttt) REVERT: D 201 PHE cc_start: 0.8747 (m-80) cc_final: 0.8392 (m-80) REVERT: D 212 LEU cc_start: 0.9023 (tp) cc_final: 0.8780 (mt) REVERT: D 218 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7346 (tm-30) REVERT: D 233 ILE cc_start: 0.8480 (mt) cc_final: 0.8258 (mm) REVERT: D 258 LEU cc_start: 0.8244 (mt) cc_final: 0.7944 (tp) REVERT: D 259 LEU cc_start: 0.8798 (mt) cc_final: 0.8473 (mm) REVERT: D 260 ASN cc_start: 0.7556 (t0) cc_final: 0.7220 (t0) REVERT: D 313 TYR cc_start: 0.8342 (m-80) cc_final: 0.7950 (m-80) REVERT: D 316 TYR cc_start: 0.8406 (m-80) cc_final: 0.8076 (m-10) REVERT: D 318 TYR cc_start: 0.7901 (m-10) cc_final: 0.7675 (m-80) REVERT: D 340 ASN cc_start: 0.8063 (p0) cc_final: 0.7562 (t0) REVERT: D 362 GLN cc_start: 0.7930 (tp40) cc_final: 0.7567 (tp40) REVERT: D 369 ARG cc_start: 0.7244 (tpt90) cc_final: 0.6967 (tpt90) REVERT: D 378 LYS cc_start: 0.8060 (mttt) cc_final: 0.7814 (mttp) REVERT: D 395 GLU cc_start: 0.7324 (tm-30) cc_final: 0.6892 (tm-30) REVERT: D 397 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7177 (mm-30) REVERT: D 398 ARG cc_start: 0.7327 (ttt90) cc_final: 0.7074 (mtt90) REVERT: D 433 PHE cc_start: 0.7054 (t80) cc_final: 0.6625 (t80) REVERT: E 31 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7867 (ptmt) REVERT: E 42 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7654 (tmtt) REVERT: E 70 THR cc_start: 0.8194 (p) cc_final: 0.7739 (t) REVERT: E 73 ASP cc_start: 0.7399 (t0) cc_final: 0.6565 (t0) REVERT: E 75 ASP cc_start: 0.7247 (m-30) cc_final: 0.6649 (m-30) REVERT: E 80 ARG cc_start: 0.8216 (mtt180) cc_final: 0.7658 (mtt180) REVERT: E 103 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7655 (mt0) REVERT: E 112 LYS cc_start: 0.8406 (mttt) cc_final: 0.8193 (mttt) REVERT: E 125 ARG cc_start: 0.7094 (mtt180) cc_final: 0.6852 (mtt180) REVERT: E 132 LYS cc_start: 0.8568 (mttt) cc_final: 0.8339 (mmtt) REVERT: E 144 SER cc_start: 0.7919 (t) cc_final: 0.7490 (t) REVERT: E 154 GLN cc_start: 0.7317 (tm-30) cc_final: 0.6769 (tm-30) REVERT: E 193 LYS cc_start: 0.8443 (mttt) cc_final: 0.7772 (ttmm) REVERT: E 297 LYS cc_start: 0.7687 (ttpt) cc_final: 0.7174 (ttpt) REVERT: E 322 TYR cc_start: 0.8239 (m-10) cc_final: 0.7847 (m-80) REVERT: E 353 LYS cc_start: 0.8208 (mttt) cc_final: 0.7753 (mttt) REVERT: F 16 ASP cc_start: 0.7788 (t0) cc_final: 0.7282 (t0) REVERT: F 68 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8111 (tpp80) REVERT: F 116 LYS cc_start: 0.8264 (mttt) cc_final: 0.7882 (mmmm) REVERT: F 139 LYS cc_start: 0.8662 (mttt) cc_final: 0.8223 (mtpp) REVERT: F 158 LYS cc_start: 0.8501 (mttt) cc_final: 0.8248 (mttt) REVERT: F 213 LEU cc_start: 0.8533 (tp) cc_final: 0.8244 (tt) REVERT: F 216 LYS cc_start: 0.8333 (tttt) cc_final: 0.8081 (ttpp) REVERT: F 224 LEU cc_start: 0.8730 (tp) cc_final: 0.8468 (tp) REVERT: F 225 GLN cc_start: 0.8705 (tp40) cc_final: 0.8486 (tp40) REVERT: F 249 VAL cc_start: 0.8487 (t) cc_final: 0.8188 (p) REVERT: F 252 ARG cc_start: 0.8418 (mtp85) cc_final: 0.8010 (mtp85) REVERT: G 16 MET cc_start: 0.8310 (mmt) cc_final: 0.7500 (mmm) REVERT: G 54 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: G 59 GLU cc_start: 0.7713 (tt0) cc_final: 0.7379 (tt0) REVERT: H 926 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6152 (tp30) REVERT: K 118 MET cc_start: 0.6701 (tpp) cc_final: 0.6485 (tpp) REVERT: K 143 GLU cc_start: 0.7566 (tt0) cc_final: 0.7034 (tt0) REVERT: K 178 MET cc_start: 0.7862 (mtm) cc_final: 0.7532 (mtm) REVERT: K 191 LEU cc_start: 0.7516 (mt) cc_final: 0.7308 (mp) REVERT: K 214 MET cc_start: 0.7023 (mmp) cc_final: 0.6798 (mmt) REVERT: K 259 LYS cc_start: 0.6628 (mmtm) cc_final: 0.6139 (mptt) REVERT: K 263 MET cc_start: 0.4823 (mmm) cc_final: 0.4597 (mmm) outliers start: 131 outliers final: 96 residues processed: 831 average time/residue: 0.4147 time to fit residues: 505.7204 Evaluate side-chains 876 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 760 time to evaluate : 2.767 ------------------------------------------------------------------------------- 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 193 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 GLU 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 427 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 ILE 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 625 GLN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 656 ASN 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 B residue 1 MET 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 470 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 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 663 CYS 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 B residue 724 MET 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 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 100 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 241 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 42 LYS 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 120 LEU Chi-restraints excluded: chain E residue 139 CYS Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 237 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 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 128 HIS 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 240 GLN Chi-restraints excluded: chain F residue 263 GLU 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 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 162 LEU Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 195 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 256 optimal weight: 2.9990 chunk 248 optimal weight: 0.0020 chunk 154 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 555 ASN ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS D 20 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.146452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117992 restraints weight = 40513.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.121895 restraints weight = 19362.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124383 restraints weight = 11786.871| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24323 Z= 0.152 Angle : 0.704 16.315 33080 Z= 0.345 Chirality : 0.042 0.236 3696 Planarity : 0.004 0.048 4058 Dihedral : 13.379 148.753 3610 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 4.90 % Allowed : 23.04 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2804 helix: 1.06 (0.14), residues: 1361 sheet: -0.22 (0.28), residues: 324 loop : -1.09 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP D 55 HIS 0.010 0.001 HIS D 424 PHE 0.020 0.001 PHE A 482 TYR 0.024 0.001 TYR D 281 ARG 0.012 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 1106) hydrogen bonds : angle 4.37586 ( 3154) metal coordination : bond 0.00742 ( 28) metal coordination : angle 5.20309 ( 45) covalent geometry : bond 0.00340 (24295) covalent geometry : angle 0.67782 (33035) *********************** 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 897 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 774 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8387 (mttt) cc_final: 0.8118 (mttt) REVERT: A 65 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6520 (ptt) REVERT: A 68 LYS cc_start: 0.6374 (mtmt) cc_final: 0.5927 (tttm) REVERT: A 146 THR cc_start: 0.7492 (p) cc_final: 0.6865 (m) REVERT: A 157 LYS cc_start: 0.8293 (ptmm) cc_final: 0.7934 (ttpp) REVERT: A 162 SER cc_start: 0.8274 (p) cc_final: 0.7930 (p) REVERT: A 163 TYR cc_start: 0.7918 (t80) cc_final: 0.7608 (t80) REVERT: A 167 LYS cc_start: 0.8343 (ttmm) cc_final: 0.7015 (ttmm) REVERT: A 270 PHE cc_start: 0.8218 (p90) cc_final: 0.7562 (p90) REVERT: A 273 LYS cc_start: 0.8342 (ttmt) cc_final: 0.7998 (ttpt) REVERT: A 279 GLU cc_start: 0.7774 (mp0) cc_final: 0.7558 (mp0) REVERT: A 282 LYS cc_start: 0.8510 (tttt) cc_final: 0.8074 (ttmm) REVERT: A 288 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7154 (mp0) REVERT: A 298 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7372 (mmm160) REVERT: A 299 ASN cc_start: 0.7839 (p0) cc_final: 0.7175 (p0) REVERT: A 321 GLU cc_start: 0.6813 (tm-30) cc_final: 0.6444 (tm-30) REVERT: A 326 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8368 (tttm) REVERT: A 332 ARG cc_start: 0.8007 (mpp80) cc_final: 0.7678 (mtp85) REVERT: A 347 SER cc_start: 0.8600 (m) cc_final: 0.7867 (t) REVERT: A 372 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6338 (tp30) REVERT: A 379 LYS cc_start: 0.8326 (mmtt) cc_final: 0.8078 (mmtt) REVERT: A 389 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7412 (tt) REVERT: A 434 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7294 (mm-30) REVERT: A 457 ILE cc_start: 0.8324 (tt) cc_final: 0.7959 (tt) REVERT: A 476 LYS cc_start: 0.8385 (mttt) cc_final: 0.8041 (mttm) REVERT: A 487 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7836 (tttm) REVERT: A 490 GLU cc_start: 0.6429 (mp0) cc_final: 0.5973 (mp0) REVERT: A 504 LYS cc_start: 0.8402 (ttpt) cc_final: 0.8018 (ttmt) REVERT: A 505 VAL cc_start: 0.8388 (OUTLIER) cc_final: 0.7996 (m) REVERT: A 525 ILE cc_start: 0.8422 (tp) cc_final: 0.8122 (tp) REVERT: A 526 LYS cc_start: 0.7332 (tppt) cc_final: 0.7062 (tppt) REVERT: A 552 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6901 (mm-30) REVERT: A 556 ASP cc_start: 0.7222 (m-30) cc_final: 0.6908 (m-30) REVERT: A 570 GLU cc_start: 0.7219 (pm20) cc_final: 0.6873 (pm20) REVERT: A 579 TYR cc_start: 0.7463 (p90) cc_final: 0.7136 (p90) REVERT: A 588 GLU cc_start: 0.7245 (tp30) cc_final: 0.6683 (tp30) REVERT: A 632 SER cc_start: 0.8031 (p) cc_final: 0.7706 (p) REVERT: A 636 GLU cc_start: 0.7441 (tp30) cc_final: 0.7023 (tp30) REVERT: A 642 ARG cc_start: 0.7446 (mtp85) cc_final: 0.7156 (mmt90) REVERT: A 658 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7495 (p90) REVERT: A 659 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.6752 (p90) REVERT: A 669 GLU cc_start: 0.7113 (tt0) cc_final: 0.6809 (tt0) REVERT: A 677 GLN cc_start: 0.7611 (mt0) cc_final: 0.7359 (mt0) REVERT: A 682 ASP cc_start: 0.6839 (m-30) cc_final: 0.6537 (m-30) REVERT: A 696 MET cc_start: 0.7385 (tmm) cc_final: 0.6793 (tmm) REVERT: A 699 GLU cc_start: 0.8018 (pp20) cc_final: 0.7659 (pp20) REVERT: A 704 SER cc_start: 0.8500 (p) cc_final: 0.8109 (p) REVERT: A 706 LYS cc_start: 0.7922 (tmmt) cc_final: 0.7547 (tmmt) REVERT: B 27 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6510 (tm-30) REVERT: B 42 MET cc_start: 0.7136 (mtp) cc_final: 0.6812 (mtp) REVERT: B 43 PRO cc_start: 0.8457 (Cg_endo) cc_final: 0.8142 (Cg_exo) REVERT: B 55 LEU cc_start: 0.8110 (tt) cc_final: 0.7797 (tt) REVERT: B 63 TYR cc_start: 0.8134 (m-80) cc_final: 0.7868 (m-80) REVERT: B 91 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7551 (mm) REVERT: B 113 LYS cc_start: 0.8393 (ttpp) cc_final: 0.8067 (ttmm) REVERT: B 122 THR cc_start: 0.6900 (OUTLIER) cc_final: 0.6546 (p) REVERT: B 158 TYR cc_start: 0.7272 (t80) cc_final: 0.6837 (t80) REVERT: B 185 ARG cc_start: 0.6282 (ptp-110) cc_final: 0.5958 (ptp90) REVERT: B 196 ARG cc_start: 0.7679 (mmp80) cc_final: 0.7353 (mmp80) REVERT: B 352 GLU cc_start: 0.7351 (mp0) cc_final: 0.7060 (mp0) REVERT: B 384 HIS cc_start: 0.5142 (OUTLIER) cc_final: 0.4692 (p-80) REVERT: B 414 PHE cc_start: 0.7387 (m-80) cc_final: 0.7076 (m-80) REVERT: B 416 ILE cc_start: 0.7877 (OUTLIER) cc_final: 0.7502 (mt) REVERT: B 438 MET cc_start: 0.7527 (mtm) cc_final: 0.7019 (mtm) REVERT: B 439 ASP cc_start: 0.6964 (p0) cc_final: 0.6663 (p0) REVERT: B 445 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7423 (mmtt) REVERT: B 455 ILE cc_start: 0.8406 (mt) cc_final: 0.7954 (mm) REVERT: B 472 ASP cc_start: 0.6894 (t0) cc_final: 0.6230 (p0) REVERT: B 526 GLU cc_start: 0.7571 (pt0) cc_final: 0.7296 (pt0) REVERT: B 533 ASP cc_start: 0.6811 (p0) cc_final: 0.6428 (p0) REVERT: B 570 GLU cc_start: 0.6789 (tm-30) cc_final: 0.6111 (tm-30) REVERT: B 586 GLU cc_start: 0.7144 (pp20) cc_final: 0.6773 (pp20) REVERT: B 589 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6571 (mm-30) REVERT: B 613 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7289 (p90) REVERT: B 641 ARG cc_start: 0.7927 (ttm-80) cc_final: 0.7481 (mtm-85) REVERT: B 707 ASN cc_start: 0.7742 (t0) cc_final: 0.7437 (t0) REVERT: B 712 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6594 (mt-10) REVERT: C 411 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7086 (tpp) REVERT: C 442 GLN cc_start: 0.4676 (OUTLIER) cc_final: 0.4019 (pp30) REVERT: C 475 PHE cc_start: 0.7125 (t80) cc_final: 0.6717 (t80) REVERT: C 493 MET cc_start: 0.7659 (tpp) cc_final: 0.7387 (mpp) REVERT: C 501 GLN cc_start: 0.8175 (tp40) cc_final: 0.7800 (tp40) REVERT: D 33 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7548 (mtm-85) REVERT: D 35 TYR cc_start: 0.8531 (m-10) cc_final: 0.8277 (m-80) REVERT: D 78 GLU cc_start: 0.7395 (pt0) cc_final: 0.7073 (pt0) REVERT: D 81 LYS cc_start: 0.8638 (tttm) cc_final: 0.8342 (tttm) REVERT: D 84 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6818 (mp0) REVERT: D 85 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7464 (mp0) REVERT: D 161 HIS cc_start: 0.7530 (OUTLIER) cc_final: 0.7172 (m-70) REVERT: D 201 PHE cc_start: 0.8817 (m-80) cc_final: 0.8449 (m-80) REVERT: D 212 LEU cc_start: 0.9013 (tp) cc_final: 0.8639 (mt) REVERT: D 218 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7342 (tm-30) REVERT: D 233 ILE cc_start: 0.8474 (mt) cc_final: 0.8249 (mm) REVERT: D 258 LEU cc_start: 0.8238 (mt) cc_final: 0.7954 (tp) REVERT: D 259 LEU cc_start: 0.8749 (mt) cc_final: 0.8421 (mm) REVERT: D 260 ASN cc_start: 0.7571 (t0) cc_final: 0.7219 (t0) REVERT: D 318 TYR cc_start: 0.7892 (m-10) cc_final: 0.7674 (m-80) REVERT: D 340 ASN cc_start: 0.7881 (p0) cc_final: 0.7521 (t0) REVERT: D 362 GLN cc_start: 0.7921 (tp40) cc_final: 0.7653 (tp40) REVERT: D 369 ARG cc_start: 0.7210 (tpt90) cc_final: 0.6893 (tpt90) REVERT: D 378 LYS cc_start: 0.8053 (mttt) cc_final: 0.7801 (mttp) REVERT: D 395 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6804 (tm-30) REVERT: D 397 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7186 (mm-30) REVERT: D 398 ARG cc_start: 0.7311 (ttt90) cc_final: 0.7060 (mtt90) REVERT: D 433 PHE cc_start: 0.7053 (t80) cc_final: 0.6683 (t80) REVERT: E 31 LYS cc_start: 0.8166 (ptmt) cc_final: 0.7811 (ptmt) REVERT: E 70 THR cc_start: 0.8168 (p) cc_final: 0.7713 (t) REVERT: E 73 ASP cc_start: 0.7401 (t0) cc_final: 0.6548 (t0) REVERT: E 75 ASP cc_start: 0.7249 (m-30) cc_final: 0.6650 (m-30) REVERT: E 80 ARG cc_start: 0.8210 (mtt180) cc_final: 0.7659 (mtt180) REVERT: E 103 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: E 125 ARG cc_start: 0.7090 (mtt180) cc_final: 0.6848 (mtt180) REVERT: E 132 LYS cc_start: 0.8563 (mttt) cc_final: 0.8336 (mmtt) REVERT: E 144 SER cc_start: 0.7869 (t) cc_final: 0.7412 (t) REVERT: E 154 GLN cc_start: 0.7304 (tm-30) cc_final: 0.6732 (tm-30) REVERT: E 193 LYS cc_start: 0.8446 (mttt) cc_final: 0.7777 (ttmm) REVERT: E 297 LYS cc_start: 0.7669 (ttpt) cc_final: 0.7169 (ttpt) REVERT: E 322 TYR cc_start: 0.8275 (m-10) cc_final: 0.7928 (m-80) REVERT: E 353 LYS cc_start: 0.8199 (mttt) cc_final: 0.7747 (mttt) REVERT: F 16 ASP cc_start: 0.7593 (t0) cc_final: 0.7109 (t0) REVERT: F 68 ARG cc_start: 0.8439 (tpp80) cc_final: 0.8093 (tpp-160) REVERT: F 116 LYS cc_start: 0.8290 (mttt) cc_final: 0.7891 (mmmm) REVERT: F 139 LYS cc_start: 0.8649 (mttt) cc_final: 0.8224 (mtpp) REVERT: F 158 LYS cc_start: 0.8599 (mttt) cc_final: 0.8332 (mttt) REVERT: F 213 LEU cc_start: 0.8528 (tp) cc_final: 0.8225 (tt) REVERT: F 216 LYS cc_start: 0.8323 (tttt) cc_final: 0.8064 (ttpp) REVERT: F 224 LEU cc_start: 0.8723 (tp) cc_final: 0.8498 (tp) REVERT: F 225 GLN cc_start: 0.8669 (tp40) cc_final: 0.8469 (tp40) REVERT: F 249 VAL cc_start: 0.8525 (t) cc_final: 0.8243 (p) REVERT: F 252 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8012 (mtp85) REVERT: F 267 VAL cc_start: 0.8228 (t) cc_final: 0.7527 (m) REVERT: G 16 MET cc_start: 0.8315 (mmt) cc_final: 0.7321 (mmm) REVERT: G 54 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7548 (tm-30) REVERT: G 59 GLU cc_start: 0.7661 (tt0) cc_final: 0.7378 (tt0) REVERT: H 926 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6140 (tp30) REVERT: K 143 GLU cc_start: 0.7537 (tt0) cc_final: 0.6988 (tt0) REVERT: K 178 MET cc_start: 0.7841 (mtm) cc_final: 0.7534 (mtm) REVERT: K 259 LYS cc_start: 0.6575 (mmtm) cc_final: 0.6105 (mptt) REVERT: K 263 MET cc_start: 0.4827 (mmm) cc_final: 0.4549 (mmm) outliers start: 123 outliers final: 90 residues processed: 830 average time/residue: 0.4137 time to fit residues: 504.6267 Evaluate side-chains 876 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 769 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 280 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 372 GLU 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 427 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 ILE 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 625 GLN Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 656 ASN 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 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 247 MET 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 470 ILE Chi-restraints excluded: chain B residue 471 LEU 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 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 663 CYS 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 B residue 724 MET 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 D residue 34 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 161 HIS 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 244 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 436 SER 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 120 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 237 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 340 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 128 HIS 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 240 GLN Chi-restraints excluded: chain F residue 263 GLU 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 147 GLU Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 74 optimal weight: 9.9990 chunk 248 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 260 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 HIS ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 726 GLN D 340 ASN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.145766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.117100 restraints weight = 40743.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.120964 restraints weight = 19506.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.123468 restraints weight = 11916.695| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24323 Z= 0.161 Angle : 0.731 16.925 33080 Z= 0.356 Chirality : 0.043 0.237 3696 Planarity : 0.004 0.060 4058 Dihedral : 13.457 148.531 3610 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 4.82 % Allowed : 23.52 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2804 helix: 1.05 (0.15), residues: 1361 sheet: -0.29 (0.28), residues: 326 loop : -1.08 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 55 HIS 0.008 0.001 HIS D 424 PHE 0.036 0.001 PHE D 162 TYR 0.025 0.001 TYR D 281 ARG 0.015 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 1106) hydrogen bonds : angle 4.35947 ( 3154) metal coordination : bond 0.00672 ( 28) metal coordination : angle 5.24987 ( 45) covalent geometry : bond 0.00362 (24295) covalent geometry : angle 0.70521 (33035) ********************** 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 892 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 771 time to evaluate : 2.750 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: 0.8295 (mttt) cc_final: 0.8059 (mttt) REVERT: A 65 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6509 (ptt) REVERT: A 68 LYS cc_start: 0.6330 (mtmt) cc_final: 0.5872 (tmtt) REVERT: A 146 THR cc_start: 0.7503 (p) cc_final: 0.6931 (m) REVERT: A 157 LYS cc_start: 0.8302 (ptmm) cc_final: 0.7956 (ttpp) REVERT: A 162 SER cc_start: 0.8291 (p) cc_final: 0.7936 (p) REVERT: A 163 TYR cc_start: 0.7918 (t80) cc_final: 0.7595 (t80) REVERT: A 178 GLU cc_start: 0.7171 (pm20) cc_final: 0.6845 (pm20) REVERT: A 270 PHE cc_start: 0.8246 (p90) cc_final: 0.7468 (p90) REVERT: A 273 LYS cc_start: 0.8351 (ttmt) cc_final: 0.7827 (mmtt) REVERT: A 282 LYS cc_start: 0.8515 (tttt) cc_final: 0.8090 (ttmm) REVERT: A 288 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7147 (mp0) REVERT: A 294 GLU cc_start: 0.6755 (tp30) cc_final: 0.6533 (mm-30) REVERT: A 298 ARG cc_start: 0.7735 (mmm160) cc_final: 0.7383 (mmm160) REVERT: A 299 ASN cc_start: 0.7739 (p0) cc_final: 0.7174 (p0) REVERT: A 326 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8337 (tttm) REVERT: A 332 ARG cc_start: 0.8014 (mpp80) cc_final: 0.7652 (mtp85) REVERT: A 347 SER cc_start: 0.8594 (m) cc_final: 0.7835 (t) REVERT: A 379 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8162 (mmtt) REVERT: A 389 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7528 (tt) REVERT: A 392 PHE cc_start: 0.7244 (t80) cc_final: 0.6915 (t80) REVERT: A 434 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7180 (mp0) REVERT: A 457 ILE cc_start: 0.8346 (tt) cc_final: 0.8004 (tt) REVERT: A 476 LYS cc_start: 0.8382 (mttt) cc_final: 0.8019 (mttm) REVERT: A 487 LYS cc_start: 0.8275 (ttmt) cc_final: 0.7597 (tttm) REVERT: A 490 GLU cc_start: 0.6436 (mp0) cc_final: 0.5947 (mp0) REVERT: A 504 LYS cc_start: 0.8389 (ttpt) cc_final: 0.7995 (ttmm) REVERT: A 505 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8009 (m) REVERT: A 517 GLU cc_start: 0.7334 (mp0) cc_final: 0.6756 (mp0) REVERT: A 525 ILE cc_start: 0.8419 (tp) cc_final: 0.8128 (tp) REVERT: A 526 LYS cc_start: 0.7314 (tppt) cc_final: 0.7016 (tppt) REVERT: A 552 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6869 (mm-30) REVERT: A 556 ASP cc_start: 0.7231 (m-30) cc_final: 0.6812 (m-30) REVERT: A 570 GLU cc_start: 0.7242 (pm20) cc_final: 0.6907 (pm20) REVERT: A 579 TYR cc_start: 0.7446 (p90) cc_final: 0.7174 (p90) REVERT: A 588 GLU cc_start: 0.7241 (tp30) cc_final: 0.6699 (tp30) REVERT: A 632 SER cc_start: 0.8056 (p) cc_final: 0.7703 (p) REVERT: A 642 ARG cc_start: 0.7461 (mtp85) cc_final: 0.7140 (mmt90) REVERT: A 659 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.6613 (p90) REVERT: A 669 GLU cc_start: 0.7115 (tt0) cc_final: 0.6820 (tt0) REVERT: A 677 GLN cc_start: 0.7620 (mt0) cc_final: 0.7374 (mt0) REVERT: A 682 ASP cc_start: 0.6835 (m-30) cc_final: 0.6543 (m-30) REVERT: A 696 MET cc_start: 0.7438 (tmm) cc_final: 0.6829 (tmm) REVERT: A 699 GLU cc_start: 0.8051 (pp20) cc_final: 0.7714 (pp20) REVERT: A 704 SER cc_start: 0.8518 (p) cc_final: 0.8127 (p) REVERT: A 706 LYS cc_start: 0.7919 (tmmt) cc_final: 0.7565 (tmmt) REVERT: B 40 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8477 (mt) REVERT: B 42 MET cc_start: 0.7139 (mtp) cc_final: 0.6807 (mtp) REVERT: B 43 PRO cc_start: 0.8512 (Cg_endo) cc_final: 0.8204 (Cg_exo) REVERT: B 55 LEU cc_start: 0.8129 (tt) cc_final: 0.7794 (tt) REVERT: B 63 TYR cc_start: 0.8144 (m-80) cc_final: 0.7873 (m-80) REVERT: B 91 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7571 (mm) REVERT: B 113 LYS cc_start: 0.8405 (ttpp) cc_final: 0.8081 (ttmm) REVERT: B 122 THR cc_start: 0.6934 (OUTLIER) cc_final: 0.6573 (p) REVERT: B 158 TYR cc_start: 0.7289 (t80) cc_final: 0.6836 (t80) REVERT: B 185 ARG cc_start: 0.6197 (ptp-110) cc_final: 0.5927 (ptp90) REVERT: B 196 ARG cc_start: 0.7703 (mmp80) cc_final: 0.7353 (mmp80) REVERT: B 352 GLU cc_start: 0.7430 (mp0) cc_final: 0.7111 (mp0) REVERT: B 384 HIS cc_start: 0.5134 (OUTLIER) cc_final: 0.4672 (p-80) REVERT: B 414 PHE cc_start: 0.7401 (m-80) cc_final: 0.7095 (m-80) REVERT: B 416 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7543 (mt) REVERT: B 438 MET cc_start: 0.7567 (mtm) cc_final: 0.7087 (mtm) REVERT: B 445 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7365 (mmtt) REVERT: B 450 ARG cc_start: 0.6290 (mmm160) cc_final: 0.6032 (mtp180) REVERT: B 455 ILE cc_start: 0.8409 (mt) cc_final: 0.7936 (mm) REVERT: B 472 ASP cc_start: 0.6900 (t0) cc_final: 0.6346 (p0) REVERT: B 526 GLU cc_start: 0.7571 (pt0) cc_final: 0.7293 (pt0) REVERT: B 533 ASP cc_start: 0.6823 (p0) cc_final: 0.6448 (p0) REVERT: B 570 GLU cc_start: 0.6809 (tm-30) cc_final: 0.6088 (tm-30) REVERT: B 576 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7388 (mp0) REVERT: B 586 GLU cc_start: 0.7144 (pp20) cc_final: 0.6791 (pp20) REVERT: B 589 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6561 (mm-30) REVERT: B 613 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7341 (p90) REVERT: B 641 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7437 (mtm-85) REVERT: B 712 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6578 (mt-10) REVERT: C 411 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7129 (tpp) REVERT: C 442 GLN cc_start: 0.4677 (OUTLIER) cc_final: 0.4058 (pp30) REVERT: C 473 ARG cc_start: 0.8157 (ttm110) cc_final: 0.7785 (ttm110) REVERT: C 475 PHE cc_start: 0.7138 (t80) cc_final: 0.6737 (t80) REVERT: C 493 MET cc_start: 0.7681 (tpp) cc_final: 0.7411 (mpp) REVERT: C 501 GLN cc_start: 0.8166 (tp40) cc_final: 0.7798 (tp40) REVERT: D 33 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7585 (mtm-85) REVERT: D 35 TYR cc_start: 0.8542 (m-10) cc_final: 0.8304 (m-80) REVERT: D 42 LEU cc_start: 0.8257 (tp) cc_final: 0.7894 (mp) REVERT: D 55 TRP cc_start: 0.7907 (OUTLIER) cc_final: 0.7684 (m-90) REVERT: D 64 GLN cc_start: 0.7612 (mp10) cc_final: 0.7405 (mm-40) REVERT: D 78 GLU cc_start: 0.7410 (pt0) cc_final: 0.7103 (pt0) REVERT: D 85 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7575 (mp0) REVERT: D 150 LYS cc_start: 0.7578 (tttt) cc_final: 0.7318 (tttt) REVERT: D 161 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7134 (m-70) REVERT: D 185 MET cc_start: 0.6793 (mtt) cc_final: 0.6554 (mtt) REVERT: D 201 PHE cc_start: 0.8826 (m-80) cc_final: 0.8516 (m-80) REVERT: D 212 LEU cc_start: 0.8996 (tp) cc_final: 0.8738 (mt) REVERT: D 218 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7337 (tm-30) REVERT: D 233 ILE cc_start: 0.8477 (mt) cc_final: 0.8261 (mm) REVERT: D 258 LEU cc_start: 0.8257 (mt) cc_final: 0.7967 (tp) REVERT: D 259 LEU cc_start: 0.8742 (mt) cc_final: 0.8407 (mm) REVERT: D 260 ASN cc_start: 0.7592 (t0) cc_final: 0.7239 (t0) REVERT: D 313 TYR cc_start: 0.8314 (m-80) cc_final: 0.7939 (m-80) REVERT: D 318 TYR cc_start: 0.7881 (m-10) cc_final: 0.7677 (m-80) REVERT: D 340 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7740 (t0) REVERT: D 362 GLN cc_start: 0.7925 (tp40) cc_final: 0.7363 (tp-100) REVERT: D 369 ARG cc_start: 0.7224 (tpt90) cc_final: 0.6898 (tpt90) REVERT: D 378 LYS cc_start: 0.8053 (mttt) cc_final: 0.7801 (mttp) REVERT: D 395 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6813 (tm-30) REVERT: D 397 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7196 (mm-30) REVERT: D 433 PHE cc_start: 0.7102 (t80) cc_final: 0.6713 (t80) REVERT: D 439 ARG cc_start: 0.8128 (mtp85) cc_final: 0.7855 (mtp85) REVERT: E 31 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7814 (ptmt) REVERT: E 70 THR cc_start: 0.8173 (p) cc_final: 0.7707 (t) REVERT: E 73 ASP cc_start: 0.7406 (t0) cc_final: 0.6558 (t0) REVERT: E 75 ASP cc_start: 0.7185 (m-30) cc_final: 0.6625 (m-30) REVERT: E 80 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7677 (mtt180) REVERT: E 103 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7747 (mt0) REVERT: E 125 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6843 (mtt180) REVERT: E 132 LYS cc_start: 0.8566 (mttt) cc_final: 0.8341 (mmtt) REVERT: E 144 SER cc_start: 0.7874 (t) cc_final: 0.7437 (t) REVERT: E 154 GLN cc_start: 0.7328 (tm-30) cc_final: 0.6741 (tm-30) REVERT: E 193 LYS cc_start: 0.8440 (mttt) cc_final: 0.7874 (ttmm) REVERT: E 297 LYS cc_start: 0.7674 (ttpt) cc_final: 0.7204 (ttpt) REVERT: E 322 TYR cc_start: 0.8254 (m-10) cc_final: 0.7879 (m-80) REVERT: E 353 LYS cc_start: 0.8207 (mttt) cc_final: 0.7758 (mttt) REVERT: F 16 ASP cc_start: 0.7577 (t0) cc_final: 0.7119 (t0) REVERT: F 68 ARG cc_start: 0.8426 (tpp80) cc_final: 0.8077 (tpp80) REVERT: F 116 LYS cc_start: 0.8295 (mttt) cc_final: 0.7896 (mmmm) REVERT: F 139 LYS cc_start: 0.8658 (mttt) cc_final: 0.8239 (mtpp) REVERT: F 158 LYS cc_start: 0.8593 (mttt) cc_final: 0.8336 (mttt) REVERT: F 213 LEU cc_start: 0.8520 (tp) cc_final: 0.8226 (tt) REVERT: F 216 LYS cc_start: 0.8333 (tttt) cc_final: 0.8071 (ttpp) REVERT: F 224 LEU cc_start: 0.8725 (tp) cc_final: 0.8489 (tp) REVERT: F 249 VAL cc_start: 0.8512 (t) cc_final: 0.8196 (p) REVERT: F 252 ARG cc_start: 0.8346 (mtp85) cc_final: 0.7948 (mtp85) REVERT: F 267 VAL cc_start: 0.8217 (t) cc_final: 0.7517 (m) REVERT: G 16 MET cc_start: 0.8292 (mmt) cc_final: 0.7374 (mmm) REVERT: G 20 LEU cc_start: 0.8502 (mt) cc_final: 0.8270 (mt) REVERT: G 54 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7551 (tm-30) REVERT: G 59 GLU cc_start: 0.7677 (tt0) cc_final: 0.7368 (tt0) REVERT: H 926 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6149 (tp30) REVERT: K 135 LYS cc_start: 0.8739 (tttt) cc_final: 0.8383 (tttt) REVERT: K 143 GLU cc_start: 0.7509 (tt0) cc_final: 0.6961 (tt0) REVERT: K 178 MET cc_start: 0.7852 (mtm) cc_final: 0.7537 (mtm) REVERT: K 259 LYS cc_start: 0.6590 (mmtm) cc_final: 0.6124 (mptt) REVERT: K 263 MET cc_start: 0.4889 (mmm) cc_final: 0.4608 (mmm) outliers start: 121 outliers final: 91 residues processed: 831 average time/residue: 0.4191 time to fit residues: 511.3564 Evaluate side-chains 879 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 769 time to evaluate : 2.541 ------------------------------------------------------------------------------- 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 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 427 MET Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 502 ILE 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 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 B residue 10 VAL Chi-restraints excluded: chain B residue 40 LEU 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 130 VAL 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 247 MET 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 470 ILE Chi-restraints excluded: chain B residue 471 LEU 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 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 663 CYS 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 B residue 724 MET 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 D residue 34 LEU Chi-restraints excluded: chain D residue 55 TRP Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 140 LYS Chi-restraints excluded: chain D residue 161 HIS 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 244 THR Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain D residue 321 SER Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 31 LYS 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 139 CYS Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 237 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 340 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 64 ILE 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 240 GLN Chi-restraints excluded: chain F residue 263 GLU 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 147 GLU Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 212 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 179 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 256 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS D 20 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 HIS ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.145259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.116953 restraints weight = 40435.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120746 restraints weight = 19339.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123236 restraints weight = 11844.914| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 24323 Z= 0.199 Angle : 0.851 58.837 33080 Z= 0.455 Chirality : 0.047 1.162 3696 Planarity : 0.004 0.056 4058 Dihedral : 13.460 148.521 3610 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.60 % Favored : 94.37 % Rotamer: Outliers : 4.58 % Allowed : 23.91 % Favored : 71.50 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.16), residues: 2804 helix: 1.05 (0.14), residues: 1361 sheet: -0.29 (0.28), residues: 326 loop : -1.08 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 55 HIS 0.007 0.001 HIS B 613 PHE 0.024 0.001 PHE D 162 TYR 0.024 0.001 TYR D 281 ARG 0.016 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 1106) hydrogen bonds : angle 4.36677 ( 3154) metal coordination : bond 0.00650 ( 28) metal coordination : angle 5.25018 ( 45) covalent geometry : bond 0.00436 (24295) covalent geometry : angle 0.82914 (33035) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10889.42 seconds wall clock time: 187 minutes 47.03 seconds (11267.03 seconds total)