Starting phenix.real_space_refine on Tue Mar 19 08:54:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/03_2024/8eby_28002_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/03_2024/8eby_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/03_2024/8eby_28002.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/03_2024/8eby_28002.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/03_2024/8eby_28002_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eby_28002/03_2024/8eby_28002_updated.pdb" } 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 Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 109": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "A PHE 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 30": "NH1" <-> "NH2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 112": "NH1" <-> "NH2" Residue "B ARG 166": "NH1" <-> "NH2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 497": "NH1" <-> "NH2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 911": "OE1" <-> "OE2" Residue "K TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 211": "NH1" <-> "NH2" Residue "K ARG 237": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.41, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.71 Conformation dependent library (CDL) restraints added in 3.9 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... running ksdssp... Secondary structure from input PDB file: 120 helices and 20 sheets defined 45.3% alpha, 9.6% beta 21 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 10.75 Creating SS restraints... Processing helix chain 'A' and resid 93 through 103 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.831A pdb=" N GLN A 186 " --> pdb=" O PRO A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 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 192 through 196' Processing helix chain 'A' and resid 274 through 286 removed outlier: 3.533A pdb=" N ILE A 277 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLU A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N CYS A 284 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 285 " --> pdb=" O LYS A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 327 Processing helix chain 'A' and resid 347 through 357 Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 421 through 432 removed outlier: 3.848A pdb=" N THR A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 446 Processing helix chain 'A' and resid 452 through 457 removed outlier: 4.046A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 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 493 through 498 Processing helix chain 'A' and resid 516 through 524 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 531 through 535 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 565 through 573 removed outlier: 4.122A pdb=" N GLU A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 597 removed outlier: 4.100A pdb=" N LYS A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'A' and resid 668 through 676 Processing helix chain 'A' and resid 678 through 683 Processing helix chain 'A' and resid 706 through 717 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 19 through 34 Processing helix chain 'B' and resid 48 through 62 Processing helix chain 'B' and resid 77 through 98 Processing helix chain 'B' and resid 119 through 122 No H-bonds generated for 'chain 'B' and resid 119 through 122' Processing helix chain 'B' and resid 127 through 137 removed outlier: 4.646A pdb=" N ASP B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLY B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 removed outlier: 3.949A pdb=" N GLN B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 removed outlier: 4.650A pdb=" N ALA B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 209 through 213 removed outlier: 4.264A pdb=" N LEU B 213 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 221 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 239 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 253 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 334 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) Processing helix chain 'B' and resid 336 through 345 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 356 through 364 Processing helix chain 'B' and resid 370 through 379 removed outlier: 3.643A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 395 through 409 Processing helix chain 'B' and resid 442 through 448 Proline residue: B 446 - end of helix No H-bonds generated for 'chain 'B' and resid 442 through 448' Processing helix chain 'B' and resid 467 through 470 No H-bonds generated for 'chain 'B' and resid 467 through 470' Processing helix chain 'B' and resid 508 through 510 No H-bonds generated for 'chain 'B' and resid 508 through 510' Processing helix chain 'B' and resid 514 through 528 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 558 through 564 removed outlier: 3.735A pdb=" N ASN B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 589 Processing helix chain 'B' and resid 603 through 607 Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 648 through 667 removed outlier: 4.228A pdb=" N ARG B 666 " --> pdb=" O GLN B 662 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N ALA B 667 " --> pdb=" O CYS B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 685 Processing helix chain 'B' and resid 687 through 692 removed outlier: 4.286A pdb=" N LYS B 692 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 710 through 724 Processing helix chain 'C' and resid 112 through 120 removed outlier: 3.546A pdb=" N MET C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 139 through 146 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 399 through 412 Processing helix chain 'C' and resid 419 through 421 No H-bonds generated for 'chain 'C' and resid 419 through 421' Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 455 through 478 removed outlier: 3.503A pdb=" N GLU C 460 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 515 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 521 through 546 removed outlier: 3.833A pdb=" N ILE C 525 " --> pdb=" O LEU C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 28 through 36 removed outlier: 3.809A pdb=" N GLY D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 50 through 61 removed outlier: 3.545A pdb=" N ASN D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N PHE D 61 " --> pdb=" O MET D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 74 removed outlier: 3.699A pdb=" N TRP D 74 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 145 through 164 Processing helix chain 'D' and resid 173 through 181 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 226 removed outlier: 4.592A pdb=" N GLN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N SER D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG D 226 " --> pdb=" O THR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 285 through 291 removed outlier: 4.330A pdb=" N SER D 291 " --> pdb=" O ALA D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 330 Processing helix chain 'D' and resid 348 through 356 Processing helix chain 'D' and resid 361 through 370 Processing helix chain 'D' and resid 374 through 378 Processing helix chain 'D' and resid 385 through 398 removed outlier: 4.145A pdb=" N ARG D 398 " --> pdb=" O TRP D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 445 through 461 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 18 through 21 removed outlier: 3.553A pdb=" N ILE E 21 " --> pdb=" O THR E 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 21' Processing helix chain 'E' and resid 29 through 41 Processing helix chain 'E' and resid 69 through 72 Processing helix chain 'E' and resid 80 through 98 Processing helix chain 'E' and resid 124 through 136 removed outlier: 4.513A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 158 removed outlier: 4.639A pdb=" N HIS E 158 " --> pdb=" O GLN E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 192 Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 225 through 236 Processing helix chain 'E' and resid 273 through 277 removed outlier: 3.681A pdb=" N ASP E 277 " --> pdb=" O MET E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 273 through 277' Processing helix chain 'E' and resid 315 through 325 removed outlier: 4.443A pdb=" N SER E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N HIS E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU E 325 " --> pdb=" O SER E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 377 Processing helix chain 'E' and resid 383 through 386 No H-bonds generated for 'chain 'E' and resid 383 through 386' Processing helix chain 'F' and resid 19 through 27 Processing helix chain 'F' and resid 34 through 51 Processing helix chain 'F' and resid 102 through 120 Processing helix chain 'F' and resid 133 through 150 removed outlier: 3.576A pdb=" N GLU F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 201 through 210 Processing helix chain 'F' and resid 220 through 230 removed outlier: 4.705A pdb=" N LEU F 224 " --> pdb=" O PRO F 221 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F 230 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 removed outlier: 3.958A pdb=" N GLN F 240 " --> pdb=" O ASP F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 287 Processing helix chain 'G' and resid 14 through 26 Processing helix chain 'G' and resid 47 through 63 removed outlier: 3.695A pdb=" N VAL G 50 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ASN G 51 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL G 52 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN G 63 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 890 through 901 Processing helix chain 'H' and resid 909 through 914 Processing helix chain 'H' and resid 924 through 933 Processing helix chain 'H' and resid 936 through 938 No H-bonds generated for 'chain 'H' and resid 936 through 938' Processing helix chain 'K' and resid 116 through 121 Processing helix chain 'K' and resid 141 through 148 Processing helix chain 'K' and resid 152 through 156 Processing helix chain 'K' and resid 183 through 194 Processing helix chain 'K' and resid 200 through 231 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= A, first strand: chain 'A' and resid 76 through 78 removed outlier: 5.381A pdb=" N LYS A 117 " --> pdb=" O PRO A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 166 through 171 Processing sheet with id= C, first strand: chain 'A' and resid 438 through 441 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: 8.590A pdb=" N VAL A 339 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N LEU A 488 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 361 through 365 removed outlier: 4.667A pdb=" N THR A 409 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 688 through 690 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) removed outlier: 7.687A pdb=" N ALA A 657 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ALA A 508 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE A 659 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 663 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 623 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= G, 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: 3.523A pdb=" N THR B 457 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS B 69 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N VAL B 232 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 71 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ASP B 234 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N CYS B 73 " --> pdb=" O ASP B 234 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.922A pdb=" N VAL B 204 " --> pdb=" O LEU B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 414 through 419 Processing sheet with id= J, first strand: chain 'B' and resid 490 through 495 removed outlier: 8.258A pdb=" N GLY B 675 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N MET B 493 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE B 495 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE B 679 " --> pdb=" O ILE B 495 " (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= K, first strand: chain 'D' and resid 96 through 100 removed outlier: 3.627A pdb=" N ILE D 109 " --> pdb=" O HIS D 97 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 248 through 250 Processing sheet with id= M, first strand: chain 'D' and resid 307 through 310 removed outlier: 3.757A pdb=" N ARG D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN D 345 " --> pdb=" O MET D 334 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N MET D 334 " --> pdb=" O GLN D 345 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 407 through 409 removed outlier: 3.644A pdb=" N PHE D 433 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 113 through 118 removed outlier: 6.683A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N SER E 164 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N TYR E 62 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU E 166 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N VAL E 64 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU E 168 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ASP E 66 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE E 170 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG E 195 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE E 169 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER E 197 " --> pdb=" O ILE E 169 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 332 through 335 Processing sheet with id= Q, first strand: chain 'F' and resid 67 through 69 removed outlier: 6.343A pdb=" N GLU F 156 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU F 10 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LYS F 158 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N VAL F 12 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG F 160 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL F 14 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU F 162 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASP F 16 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ILE F 164 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU F 190 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL F 163 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP F 192 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N LYS F 165 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N CYS F 194 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 8 through 11 removed outlier: 3.776A pdb=" N GLN G 36 " --> pdb=" O PHE G 44 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 138 through 140 Processing sheet with id= T, first strand: chain 'K' and resid 250 through 252 removed outlier: 3.798A pdb=" N MET K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) 866 hydrogen bonds defined for protein. 2430 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: 8.40 Time building geometry restraints manager: 9.47 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: 73.70 - 85.77: 12 85.77 - 97.83: 0 97.83 - 109.89: 3199 109.89 - 121.95: 24942 121.95 - 134.01: 4882 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: 507 2.69 - 3.25: 23429 3.25 - 3.80: 37907 3.80 - 4.35: 49117 4.35 - 4.90: 79200 Nonbonded interactions: 190160 Sorted by model distance: nonbonded pdb=" O ILE H 899 " pdb=" OG SER H 903 " model vdw 2.142 2.440 nonbonded pdb=" O PHE A 378 " pdb=" OG SER A 382 " model vdw 2.184 2.440 nonbonded pdb=" O LEU B 382 " pdb=" OG1 THR B 385 " model vdw 2.225 2.440 nonbonded pdb=" OG SER E 243 " pdb=" O ALA F 288 " model vdw 2.231 2.440 nonbonded pdb=" O LEU E 30 " pdb=" OG1 THR E 33 " model vdw 2.239 2.440 ... (remaining 190155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.420 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: 6.640 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 75.480 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.130 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.860 ------------------------------------------------------------------------------- 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 24295 Z= 0.134 Angle : 0.472 8.097 33035 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 *********************** 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 fitting. rotamer outliers: 56 poor density : 900 time to evaluate : 2.571 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: 0.4083 time to fit residues: 558.4883 Evaluate side-chains 788 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 758 time to evaluate : 2.511 ------------------------------------------------------------------------------- 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: 6.9990 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 222 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 165 optimal weight: 0.9990 chunk 257 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 241 ASN B 560 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 700 HIS ** D 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN D 363 GLN ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 349 GLN ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN F 185 GLN F 248 HIS ** H 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24295 Z= 0.339 Angle : 0.624 11.069 33035 Z= 0.323 Chirality : 0.044 0.175 3696 Planarity : 0.005 0.072 4058 Dihedral : 13.281 142.606 3631 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 4.98 % Allowed : 13.99 % Favored : 81.03 % 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: 0.29 (0.16), residues: 2804 helix: 1.29 (0.15), residues: 1326 sheet: 0.07 (0.27), residues: 378 loop : -1.10 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 511 HIS 0.023 0.002 HIS D 424 PHE 0.031 0.002 PHE A 659 TYR 0.021 0.002 TYR K 116 ARG 0.011 0.001 ARG D 226 *********************** 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 924 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 799 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8106 (mm110) REVERT: A 65 MET cc_start: 0.7577 (ptt) cc_final: 0.7119 (ptt) REVERT: A 68 LYS cc_start: 0.6564 (mtmt) cc_final: 0.5899 (tttm) REVERT: A 94 LYS cc_start: 0.7552 (ptpt) cc_final: 0.6965 (ptpt) REVERT: A 98 ASP cc_start: 0.7521 (m-30) cc_final: 0.7253 (m-30) REVERT: A 117 LYS cc_start: 0.8098 (tttt) cc_final: 0.7781 (tttt) REVERT: A 138 GLU cc_start: 0.7731 (pt0) cc_final: 0.7365 (tp30) REVERT: A 157 LYS cc_start: 0.8098 (ptmm) cc_final: 0.7739 (ttpp) REVERT: A 158 LEU cc_start: 0.8330 (mt) cc_final: 0.8105 (mt) REVERT: A 163 TYR cc_start: 0.7996 (t80) cc_final: 0.7662 (t80) REVERT: A 169 VAL cc_start: 0.8367 (p) cc_final: 0.7722 (m) REVERT: A 173 ASN cc_start: 0.7889 (m-40) cc_final: 0.7017 (m-40) REVERT: A 174 ARG cc_start: 0.7813 (mmm-85) cc_final: 0.7262 (ttm110) REVERT: A 175 TYR cc_start: 0.8045 (m-80) cc_final: 0.7807 (m-80) REVERT: A 176 PHE cc_start: 0.7840 (m-80) cc_final: 0.6923 (m-10) REVERT: A 191 ASP cc_start: 0.7084 (t0) cc_final: 0.6812 (t0) REVERT: A 273 LYS cc_start: 0.8118 (ttmt) cc_final: 0.7806 (ttmm) REVERT: A 275 GLU cc_start: 0.8076 (pm20) cc_final: 0.7860 (pm20) REVERT: A 276 MET cc_start: 0.7566 (ttm) cc_final: 0.7318 (ttm) REVERT: A 282 LYS cc_start: 0.8361 (tttt) cc_final: 0.8036 (ttmm) REVERT: A 287 LEU cc_start: 0.8570 (mt) cc_final: 0.8165 (mt) REVERT: A 288 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7312 (mp0) REVERT: A 294 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6447 (tp30) REVERT: A 299 ASN cc_start: 0.8134 (p0) cc_final: 0.7384 (p0) REVERT: A 309 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6483 (p0) REVERT: A 310 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7851 (pt) REVERT: A 321 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7185 (tm-30) REVERT: A 332 ARG cc_start: 0.8023 (mpp80) cc_final: 0.7118 (mtp85) REVERT: A 347 SER cc_start: 0.8603 (m) cc_final: 0.7854 (t) REVERT: A 370 SER cc_start: 0.8178 (m) cc_final: 0.7962 (m) REVERT: A 372 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6784 (tp30) REVERT: A 373 GLN cc_start: 0.7802 (tp40) cc_final: 0.7585 (tp40) REVERT: A 375 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7893 (tttm) REVERT: A 389 ILE cc_start: 0.7571 (mm) cc_final: 0.7135 (tt) REVERT: A 392 PHE cc_start: 0.7472 (t80) cc_final: 0.7076 (t80) REVERT: A 412 MET cc_start: 0.7475 (ttp) cc_final: 0.7260 (ttt) REVERT: A 418 LYS cc_start: 0.7889 (tmmt) cc_final: 0.7506 (tmmt) REVERT: A 419 ARG cc_start: 0.8208 (ttm170) cc_final: 0.7751 (tpp80) REVERT: A 424 GLU cc_start: 0.7768 (tp30) cc_final: 0.7556 (mm-30) REVERT: A 428 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7668 (mm-30) REVERT: A 434 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7471 (mm-30) REVERT: A 438 MET cc_start: 0.8077 (ttp) cc_final: 0.7831 (ttp) REVERT: A 453 ARG cc_start: 0.7233 (ptm160) cc_final: 0.6813 (ptp-170) REVERT: A 457 ILE cc_start: 0.8144 (tt) cc_final: 0.7877 (tt) REVERT: A 470 LEU cc_start: 0.8784 (tp) cc_final: 0.8239 (tp) REVERT: A 476 LYS cc_start: 0.8077 (mttt) cc_final: 0.7579 (mttm) REVERT: A 478 VAL cc_start: 0.8348 (t) cc_final: 0.8115 (m) REVERT: A 487 LYS cc_start: 0.8628 (ttmt) cc_final: 0.7897 (ttmm) REVERT: A 504 LYS cc_start: 0.8516 (ttpt) cc_final: 0.7802 (ttpt) REVERT: A 505 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8185 (m) REVERT: A 525 ILE cc_start: 0.8272 (tp) cc_final: 0.7879 (tp) REVERT: A 526 LYS cc_start: 0.7796 (tmtt) cc_final: 0.7156 (tppt) REVERT: A 528 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7921 (mptt) REVERT: A 530 ARG cc_start: 0.6816 (ptt-90) cc_final: 0.6245 (ptt-90) REVERT: A 556 ASP cc_start: 0.7395 (m-30) cc_final: 0.7041 (m-30) REVERT: A 564 ASN cc_start: 0.8436 (t0) cc_final: 0.7874 (t0) REVERT: A 570 GLU cc_start: 0.7232 (pm20) cc_final: 0.6785 (pm20) REVERT: A 579 TYR cc_start: 0.7577 (p90) cc_final: 0.7074 (p90) REVERT: A 586 GLN cc_start: 0.8496 (tp40) cc_final: 0.8136 (tp40) REVERT: A 590 MET cc_start: 0.7688 (tpp) cc_final: 0.7458 (tpt) REVERT: A 632 SER cc_start: 0.8276 (p) cc_final: 0.7994 (p) REVERT: A 642 ARG cc_start: 0.7244 (mtp85) cc_final: 0.6630 (mmt180) REVERT: A 644 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8110 (pp) REVERT: A 659 PHE cc_start: 0.8301 (OUTLIER) cc_final: 0.7168 (p90) REVERT: A 668 GLN cc_start: 0.7366 (mt0) cc_final: 0.7101 (mt0) REVERT: A 669 GLU cc_start: 0.7547 (tt0) cc_final: 0.7308 (tt0) REVERT: A 670 MET cc_start: 0.8072 (mmm) cc_final: 0.7709 (mmm) REVERT: A 677 GLN cc_start: 0.7815 (mt0) cc_final: 0.7601 (mt0) REVERT: A 678 ARG cc_start: 0.7450 (ptt180) cc_final: 0.7152 (ptt180) REVERT: A 682 ASP cc_start: 0.6965 (m-30) cc_final: 0.6763 (m-30) REVERT: A 683 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7062 (mm-40) REVERT: A 700 ASP cc_start: 0.7586 (t0) cc_final: 0.7384 (t0) REVERT: A 701 LEU cc_start: 0.8084 (mm) cc_final: 0.7847 (mm) REVERT: A 706 LYS cc_start: 0.7779 (tmmt) cc_final: 0.7332 (tmtt) REVERT: B 25 MET cc_start: 0.7699 (mmm) cc_final: 0.7466 (mpp) REVERT: B 40 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8108 (mt) REVERT: B 42 MET cc_start: 0.7420 (mtp) cc_final: 0.6747 (mtp) REVERT: B 48 LYS cc_start: 0.7657 (ttpp) cc_final: 0.7077 (mtpt) REVERT: B 53 LEU cc_start: 0.7919 (mt) cc_final: 0.7688 (mt) REVERT: B 91 LEU cc_start: 0.7976 (mm) cc_final: 0.7533 (mm) REVERT: B 158 TYR cc_start: 0.7442 (t80) cc_final: 0.6941 (t80) REVERT: B 235 GLU cc_start: 0.7689 (tp30) cc_final: 0.7407 (tp30) REVERT: B 243 CYS cc_start: 0.8459 (m) cc_final: 0.8233 (m) REVERT: B 247 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7316 (mpp) REVERT: B 341 LYS cc_start: 0.8325 (ptpt) cc_final: 0.8111 (pttm) REVERT: B 414 PHE cc_start: 0.7100 (m-80) cc_final: 0.6083 (m-80) REVERT: B 445 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7664 (mmtt) REVERT: B 455 ILE cc_start: 0.7675 (mm) cc_final: 0.7252 (mm) REVERT: B 464 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7137 (mt) REVERT: B 466 ILE cc_start: 0.7595 (tt) cc_final: 0.7161 (tp) REVERT: B 512 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7230 (mm-30) REVERT: B 518 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7737 (mtm110) REVERT: B 533 ASP cc_start: 0.7200 (p0) cc_final: 0.6880 (p0) REVERT: B 545 MET cc_start: 0.7819 (tmm) cc_final: 0.7467 (ttp) REVERT: B 548 THR cc_start: 0.8577 (m) cc_final: 0.8200 (t) REVERT: B 559 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7160 (mp0) REVERT: B 570 GLU cc_start: 0.5796 (tm-30) cc_final: 0.5217 (tm-30) REVERT: B 586 GLU cc_start: 0.7591 (pp20) cc_final: 0.7295 (pp20) REVERT: B 588 CYS cc_start: 0.7875 (m) cc_final: 0.7663 (m) REVERT: B 620 MET cc_start: 0.7861 (mmm) cc_final: 0.7270 (mmm) REVERT: B 634 LYS cc_start: 0.7262 (ptpp) cc_final: 0.6986 (mttm) REVERT: B 638 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6475 (mm-30) REVERT: B 641 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.6671 (mtm-85) REVERT: B 648 GLU cc_start: 0.6899 (tm-30) cc_final: 0.6453 (tm-30) REVERT: B 662 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7635 (pp30) REVERT: B 664 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8188 (p) REVERT: B 669 ARG cc_start: 0.6499 (mpt90) cc_final: 0.6272 (mpt90) REVERT: B 681 ASP cc_start: 0.7763 (t0) cc_final: 0.7504 (t0) REVERT: B 692 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7788 (mptt) REVERT: B 707 ASN cc_start: 0.7573 (t0) cc_final: 0.7265 (t0) REVERT: B 712 GLU cc_start: 0.6791 (pt0) cc_final: 0.6221 (pt0) REVERT: B 724 MET cc_start: 0.7129 (mmm) cc_final: 0.6633 (mmm) REVERT: C 405 GLN cc_start: 0.7957 (mt0) cc_final: 0.7560 (mt0) REVERT: C 408 ARG cc_start: 0.7885 (ttt180) cc_final: 0.7654 (ttm-80) REVERT: C 441 MET cc_start: 0.6800 (mmm) cc_final: 0.6353 (mmt) REVERT: C 442 GLN cc_start: 0.5305 (OUTLIER) cc_final: 0.3995 (pp30) REVERT: C 473 ARG cc_start: 0.7842 (tmt170) cc_final: 0.7601 (ttt180) REVERT: C 475 PHE cc_start: 0.7829 (t80) cc_final: 0.7303 (t80) REVERT: C 498 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8389 (mt-10) REVERT: C 501 GLN cc_start: 0.8076 (tp40) cc_final: 0.7571 (tp40) REVERT: C 528 MET cc_start: 0.8968 (mtp) cc_final: 0.8446 (mtm) REVERT: D 20 GLN cc_start: 0.8844 (mt0) cc_final: 0.8454 (mp10) REVERT: D 34 LEU cc_start: 0.8756 (mt) cc_final: 0.8528 (mt) REVERT: D 50 SER cc_start: 0.8140 (m) cc_final: 0.7508 (t) REVERT: D 55 TRP cc_start: 0.7864 (m-10) cc_final: 0.7661 (m-10) REVERT: D 77 LYS cc_start: 0.8122 (mttt) cc_final: 0.7877 (mttt) REVERT: D 78 GLU cc_start: 0.7645 (pt0) cc_final: 0.7015 (pt0) REVERT: D 79 PHE cc_start: 0.7740 (m-80) cc_final: 0.7518 (m-80) REVERT: D 81 LYS cc_start: 0.8808 (tttt) cc_final: 0.8348 (tttm) REVERT: D 85 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7462 (mt-10) REVERT: D 154 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7441 (mt-10) REVERT: D 173 GLN cc_start: 0.8950 (tt0) cc_final: 0.8608 (pp30) REVERT: D 174 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8493 (p0) REVERT: D 177 GLN cc_start: 0.7950 (pt0) cc_final: 0.7639 (pp30) REVERT: D 185 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6474 (mpp) REVERT: D 215 PHE cc_start: 0.8439 (t80) cc_final: 0.7987 (t80) REVERT: D 216 MET cc_start: 0.7928 (mmm) cc_final: 0.7627 (mmm) REVERT: D 218 GLN cc_start: 0.7715 (mm110) cc_final: 0.7283 (tm-30) REVERT: D 221 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7788 (mm-40) REVERT: D 228 MET cc_start: 0.5241 (mtm) cc_final: 0.3791 (mtm) REVERT: D 243 SER cc_start: 0.8063 (m) cc_final: 0.7587 (p) REVERT: D 244 THR cc_start: 0.8099 (m) cc_final: 0.7852 (t) REVERT: D 254 MET cc_start: 0.6897 (mtt) cc_final: 0.5862 (mtp) REVERT: D 258 LEU cc_start: 0.8526 (mt) cc_final: 0.8071 (tp) REVERT: D 260 ASN cc_start: 0.7929 (t0) cc_final: 0.7275 (t0) REVERT: D 261 PHE cc_start: 0.8369 (t80) cc_final: 0.8049 (t80) REVERT: D 263 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8264 (mm-40) REVERT: D 264 HIS cc_start: 0.8306 (m170) cc_final: 0.8095 (m170) REVERT: D 267 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8234 (mt-10) REVERT: D 272 PHE cc_start: 0.8148 (t80) cc_final: 0.7716 (t80) REVERT: D 276 ARG cc_start: 0.7488 (ttt90) cc_final: 0.6984 (ttt90) REVERT: D 284 THR cc_start: 0.8431 (OUTLIER) cc_final: 0.8084 (p) REVERT: D 322 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7225 (mm-30) REVERT: D 371 ARG cc_start: 0.7825 (mmt180) cc_final: 0.7607 (mpt180) REVERT: D 397 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6943 (mm-30) REVERT: D 433 PHE cc_start: 0.7940 (t80) cc_final: 0.7349 (t80) REVERT: D 439 ARG cc_start: 0.7971 (mtm180) cc_final: 0.7558 (mtp85) REVERT: E 12 GLU cc_start: 0.7693 (pt0) cc_final: 0.7406 (pt0) REVERT: E 36 ASP cc_start: 0.7845 (t0) cc_final: 0.7605 (t0) REVERT: E 59 ARG cc_start: 0.7381 (mtp180) cc_final: 0.7122 (mtp180) REVERT: E 70 THR cc_start: 0.8232 (p) cc_final: 0.7787 (t) REVERT: E 72 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7507 (mm-30) REVERT: E 73 ASP cc_start: 0.6993 (t0) cc_final: 0.5398 (t0) REVERT: E 75 ASP cc_start: 0.7056 (m-30) cc_final: 0.5870 (m-30) REVERT: E 79 ASN cc_start: 0.7866 (p0) cc_final: 0.7657 (p0) REVERT: E 80 ARG cc_start: 0.7877 (mtt180) cc_final: 0.6953 (mtt180) REVERT: E 89 GLU cc_start: 0.6608 (mt-10) cc_final: 0.6218 (mt-10) REVERT: E 93 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6752 (mt-10) REVERT: E 96 PHE cc_start: 0.7388 (m-80) cc_final: 0.6931 (m-80) REVERT: E 101 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8206 (pt) REVERT: E 103 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7601 (mt0) REVERT: E 112 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7673 (mttt) REVERT: E 125 ARG cc_start: 0.7331 (mtt180) cc_final: 0.7035 (mtt180) REVERT: E 132 LYS cc_start: 0.8532 (mttt) cc_final: 0.8273 (mttt) REVERT: E 154 GLN cc_start: 0.7589 (tm-30) cc_final: 0.7184 (tm-30) REVERT: E 157 LYS cc_start: 0.8233 (tttt) cc_final: 0.7834 (tttt) REVERT: E 166 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6857 (mt-10) REVERT: E 177 CYS cc_start: 0.7620 (m) cc_final: 0.6984 (m) REVERT: E 181 ASN cc_start: 0.8276 (t0) cc_final: 0.7778 (t0) REVERT: E 184 ASP cc_start: 0.7150 (m-30) cc_final: 0.6734 (m-30) REVERT: E 190 LYS cc_start: 0.8125 (tptt) cc_final: 0.7920 (tptt) REVERT: E 193 LYS cc_start: 0.8441 (mttt) cc_final: 0.7755 (ttmm) REVERT: E 256 GLN cc_start: 0.7478 (mt0) cc_final: 0.7014 (mt0) REVERT: E 299 CYS cc_start: 0.7682 (m) cc_final: 0.7348 (m) REVERT: E 304 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7218 (tm-30) REVERT: E 329 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6201 (p0) REVERT: E 331 PHE cc_start: 0.8490 (m-10) cc_final: 0.8264 (m-80) REVERT: E 332 GLN cc_start: 0.7501 (mt0) cc_final: 0.7283 (mt0) REVERT: E 333 GLU cc_start: 0.7793 (tt0) cc_final: 0.7402 (tt0) REVERT: E 353 LYS cc_start: 0.8359 (mttt) cc_final: 0.7778 (mttt) REVERT: F 16 ASP cc_start: 0.7879 (t0) cc_final: 0.7423 (t0) REVERT: F 55 ASN cc_start: 0.8032 (m-40) cc_final: 0.7656 (m-40) REVERT: F 56 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7627 (mmtt) REVERT: F 60 ILE cc_start: 0.8572 (mt) cc_final: 0.8209 (tt) REVERT: F 105 THR cc_start: 0.7976 (m) cc_final: 0.7708 (p) REVERT: F 109 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7575 (mt-10) REVERT: F 116 LYS cc_start: 0.8044 (mttt) cc_final: 0.7612 (mmmm) REVERT: F 131 THR cc_start: 0.8366 (m) cc_final: 0.8161 (p) REVERT: F 139 LYS cc_start: 0.8525 (mttt) cc_final: 0.8195 (mtpp) REVERT: F 158 LYS cc_start: 0.8181 (mttt) cc_final: 0.7936 (mttt) REVERT: F 172 LEU cc_start: 0.8368 (mt) cc_final: 0.8124 (mm) REVERT: F 186 LYS cc_start: 0.8474 (tttt) cc_final: 0.8068 (mtpp) REVERT: F 187 GLN cc_start: 0.8256 (mt0) cc_final: 0.8007 (mt0) REVERT: F 197 ASP cc_start: 0.8158 (t0) cc_final: 0.7840 (t0) REVERT: F 200 SER cc_start: 0.8697 (OUTLIER) cc_final: 0.8356 (p) REVERT: F 205 GLN cc_start: 0.8219 (mt0) cc_final: 0.7963 (mt0) REVERT: F 213 LEU cc_start: 0.8303 (tt) cc_final: 0.8000 (tt) REVERT: F 216 LYS cc_start: 0.8485 (tttt) cc_final: 0.8093 (tttt) REVERT: F 226 TYR cc_start: 0.8238 (m-80) cc_final: 0.7942 (m-80) REVERT: F 249 VAL cc_start: 0.7952 (t) cc_final: 0.7563 (p) REVERT: F 252 ARG cc_start: 0.7752 (mtm180) cc_final: 0.7508 (ptp-110) REVERT: F 266 TYR cc_start: 0.8224 (m-80) cc_final: 0.7857 (m-80) REVERT: F 267 VAL cc_start: 0.8447 (t) cc_final: 0.7912 (m) REVERT: G 9 LEU cc_start: 0.8233 (tt) cc_final: 0.7994 (tp) REVERT: G 12 CYS cc_start: 0.8724 (p) cc_final: 0.8170 (p) REVERT: G 16 MET cc_start: 0.8467 (mmt) cc_final: 0.7477 (mmm) REVERT: H 926 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6302 (tp30) REVERT: K 148 TYR cc_start: 0.7800 (m-80) cc_final: 0.7514 (m-80) REVERT: K 150 LEU cc_start: 0.8190 (mt) cc_final: 0.7952 (mt) REVERT: K 178 MET cc_start: 0.7671 (mtm) cc_final: 0.7143 (mtm) REVERT: K 188 LYS cc_start: 0.8040 (tttt) cc_final: 0.7801 (tttt) REVERT: K 208 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7729 (tp-100) REVERT: K 222 LYS cc_start: 0.8145 (pttm) cc_final: 0.7919 (pttp) REVERT: K 263 MET cc_start: 0.5637 (mmm) cc_final: 0.5248 (mmm) outliers start: 125 outliers final: 73 residues processed: 870 average time/residue: 0.3951 time to fit residues: 503.7302 Evaluate side-chains 862 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 769 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 144 SER 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 309 ASP 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 393 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 474 ASP 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 515 SER Chi-restraints excluded: chain A residue 608 SER 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 199 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 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 559 GLU 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 C residue 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 SER 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 174 ASP Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 256 ASP 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 340 ASN Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 280 THR 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 192 ASP Chi-restraints excluded: chain F residue 200 SER 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 177 ASP 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 143 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 214 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 71 optimal weight: 0.0870 chunk 258 optimal weight: 0.8980 chunk 279 optimal weight: 6.9990 chunk 230 optimal weight: 0.5980 chunk 256 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS A 499 ASN A 555 ASN ** A 625 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS D 218 GLN D 263 GLN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 GLN F 48 HIS F 155 GLN F 179 ASN F 185 GLN F 188 ASN F 204 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24295 Z= 0.192 Angle : 0.543 9.018 33035 Z= 0.277 Chirality : 0.041 0.182 3696 Planarity : 0.004 0.056 4058 Dihedral : 13.216 147.015 3626 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.71 % Favored : 95.26 % Rotamer: Outliers : 4.70 % Allowed : 17.18 % Favored : 78.12 % 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: 0.33 (0.16), residues: 2804 helix: 1.32 (0.15), residues: 1310 sheet: 0.10 (0.27), residues: 380 loop : -1.06 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 11 HIS 0.018 0.001 HIS C 474 PHE 0.021 0.001 PHE A 703 TYR 0.017 0.001 TYR K 116 ARG 0.006 0.001 ARG A 334 *********************** 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 898 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 780 time to evaluate : 2.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8126 (mm110) REVERT: A 65 MET cc_start: 0.7519 (ptt) cc_final: 0.7258 (ptt) REVERT: A 68 LYS cc_start: 0.6410 (mtmt) cc_final: 0.5805 (tttm) REVERT: A 94 LYS cc_start: 0.7570 (ptpt) cc_final: 0.7006 (ptpt) REVERT: A 98 ASP cc_start: 0.7543 (m-30) cc_final: 0.7246 (m-30) REVERT: A 100 LEU cc_start: 0.8051 (mt) cc_final: 0.7835 (mm) REVERT: A 117 LYS cc_start: 0.8154 (tttt) cc_final: 0.7802 (tttt) REVERT: A 121 TYR cc_start: 0.7237 (m-80) cc_final: 0.6690 (m-80) REVERT: A 138 GLU cc_start: 0.7610 (pt0) cc_final: 0.7212 (tp30) REVERT: A 146 THR cc_start: 0.7685 (p) cc_final: 0.7078 (p) REVERT: A 157 LYS cc_start: 0.8053 (ptmm) cc_final: 0.7640 (ttpp) REVERT: A 158 LEU cc_start: 0.8369 (mt) cc_final: 0.8127 (mt) REVERT: A 163 TYR cc_start: 0.8001 (t80) cc_final: 0.7631 (t80) REVERT: A 167 LYS cc_start: 0.7455 (mttp) cc_final: 0.7248 (ttmm) REVERT: A 169 VAL cc_start: 0.8276 (p) cc_final: 0.7934 (m) REVERT: A 173 ASN cc_start: 0.7876 (m-40) cc_final: 0.7002 (m-40) REVERT: A 174 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7479 (ttm110) REVERT: A 176 PHE cc_start: 0.7677 (m-80) cc_final: 0.7441 (m-80) REVERT: A 191 ASP cc_start: 0.7241 (t0) cc_final: 0.6937 (t0) REVERT: A 273 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7864 (ttpt) REVERT: A 282 LYS cc_start: 0.8351 (tttt) cc_final: 0.7887 (ttmm) REVERT: A 287 LEU cc_start: 0.8547 (mt) cc_final: 0.8128 (mt) REVERT: A 288 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7185 (mp0) REVERT: A 294 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6437 (tp30) REVERT: A 299 ASN cc_start: 0.8126 (p0) cc_final: 0.7389 (p0) REVERT: A 310 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7796 (pt) REVERT: A 321 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7128 (tm-30) REVERT: A 332 ARG cc_start: 0.8053 (mpp80) cc_final: 0.7241 (mtp85) REVERT: A 347 SER cc_start: 0.8594 (m) cc_final: 0.7853 (t) REVERT: A 372 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6729 (tp30) REVERT: A 392 PHE cc_start: 0.7311 (t80) cc_final: 0.7001 (t80) REVERT: A 418 LYS cc_start: 0.7826 (tmmt) cc_final: 0.7434 (tmmt) REVERT: A 419 ARG cc_start: 0.8106 (ttm170) cc_final: 0.7683 (tpp80) REVERT: A 424 GLU cc_start: 0.7759 (tp30) cc_final: 0.7461 (mm-30) REVERT: A 428 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7737 (mm-30) REVERT: A 434 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7471 (mm-30) REVERT: A 438 MET cc_start: 0.8069 (ttp) cc_final: 0.7865 (ttp) REVERT: A 457 ILE cc_start: 0.8239 (tt) cc_final: 0.7946 (tt) REVERT: A 470 LEU cc_start: 0.8777 (tp) cc_final: 0.8213 (tp) REVERT: A 476 LYS cc_start: 0.8126 (mttt) cc_final: 0.7635 (mttm) REVERT: A 478 VAL cc_start: 0.8335 (t) cc_final: 0.8092 (m) REVERT: A 487 LYS cc_start: 0.8419 (ttmt) cc_final: 0.7998 (ttmm) REVERT: A 504 LYS cc_start: 0.8498 (ttpt) cc_final: 0.7785 (ttpt) REVERT: A 505 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8156 (m) REVERT: A 525 ILE cc_start: 0.8287 (tp) cc_final: 0.7931 (tp) REVERT: A 526 LYS cc_start: 0.7778 (tmtt) cc_final: 0.7126 (tppt) REVERT: A 530 ARG cc_start: 0.6803 (ptt-90) cc_final: 0.6324 (ptt-90) REVERT: A 556 ASP cc_start: 0.7357 (m-30) cc_final: 0.6934 (m-30) REVERT: A 564 ASN cc_start: 0.8413 (t0) cc_final: 0.7786 (t0) REVERT: A 570 GLU cc_start: 0.7327 (pm20) cc_final: 0.6788 (pm20) REVERT: A 579 TYR cc_start: 0.7636 (p90) cc_final: 0.7108 (p90) REVERT: A 586 GLN cc_start: 0.8455 (tp40) cc_final: 0.8124 (tp40) REVERT: A 588 GLU cc_start: 0.7412 (tp30) cc_final: 0.6752 (tp30) REVERT: A 590 MET cc_start: 0.7712 (tpp) cc_final: 0.7422 (tpt) REVERT: A 642 ARG cc_start: 0.7171 (mtp85) cc_final: 0.6526 (mmt180) REVERT: A 659 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7035 (p90) REVERT: A 669 GLU cc_start: 0.7409 (tt0) cc_final: 0.7189 (tt0) REVERT: A 670 MET cc_start: 0.8047 (mmm) cc_final: 0.7791 (mmm) REVERT: A 682 ASP cc_start: 0.6970 (m-30) cc_final: 0.6725 (m-30) REVERT: A 683 GLN cc_start: 0.7487 (mm-40) cc_final: 0.6953 (mm-40) REVERT: A 688 LYS cc_start: 0.8140 (tttt) cc_final: 0.7705 (ttmt) REVERT: A 701 LEU cc_start: 0.8148 (mm) cc_final: 0.7904 (mm) REVERT: A 703 PHE cc_start: 0.8378 (m-80) cc_final: 0.7959 (m-80) REVERT: A 706 LYS cc_start: 0.7762 (tmmt) cc_final: 0.7531 (tmtt) REVERT: B 25 MET cc_start: 0.7738 (mmm) cc_final: 0.7511 (mpp) REVERT: B 40 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8234 (mm) REVERT: B 42 MET cc_start: 0.7590 (mtp) cc_final: 0.6924 (mtp) REVERT: B 48 LYS cc_start: 0.7663 (ttpp) cc_final: 0.7374 (ttpp) REVERT: B 91 LEU cc_start: 0.8033 (mm) cc_final: 0.7624 (mm) REVERT: B 158 TYR cc_start: 0.7433 (t80) cc_final: 0.6931 (t80) REVERT: B 235 GLU cc_start: 0.7783 (tp30) cc_final: 0.7460 (tp30) REVERT: B 243 CYS cc_start: 0.8554 (m) cc_final: 0.8217 (m) REVERT: B 247 MET cc_start: 0.8095 (mtt) cc_final: 0.7340 (mpp) REVERT: B 414 PHE cc_start: 0.7211 (m-80) cc_final: 0.6044 (m-80) REVERT: B 416 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6572 (pt) REVERT: B 445 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7710 (mmtt) REVERT: B 455 ILE cc_start: 0.7804 (mm) cc_final: 0.7437 (mm) REVERT: B 466 ILE cc_start: 0.7524 (tt) cc_final: 0.7090 (tp) REVERT: B 469 LYS cc_start: 0.7927 (ptpp) cc_final: 0.7604 (ptpp) REVERT: B 512 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7176 (mm-30) REVERT: B 518 ARG cc_start: 0.7954 (mtp85) cc_final: 0.7716 (mtm110) REVERT: B 533 ASP cc_start: 0.7044 (p0) cc_final: 0.6717 (p0) REVERT: B 545 MET cc_start: 0.7895 (tmm) cc_final: 0.7565 (ttp) REVERT: B 548 THR cc_start: 0.8661 (m) cc_final: 0.8238 (t) REVERT: B 559 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: B 570 GLU cc_start: 0.5843 (tm-30) cc_final: 0.5257 (tm-30) REVERT: B 586 GLU cc_start: 0.7540 (pp20) cc_final: 0.7207 (pp20) REVERT: B 588 CYS cc_start: 0.7888 (m) cc_final: 0.7668 (m) REVERT: B 620 MET cc_start: 0.7828 (mmm) cc_final: 0.7099 (mmm) REVERT: B 634 LYS cc_start: 0.7297 (ptpp) cc_final: 0.7006 (mttm) REVERT: B 638 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6567 (mm-30) REVERT: B 641 ARG cc_start: 0.7855 (ttm-80) cc_final: 0.6919 (mtm-85) REVERT: B 648 GLU cc_start: 0.6819 (tm-30) cc_final: 0.6459 (tm-30) REVERT: B 662 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7603 (pp30) REVERT: B 669 ARG cc_start: 0.6393 (mpt90) cc_final: 0.6090 (mpt90) REVERT: B 681 ASP cc_start: 0.7772 (t0) cc_final: 0.7499 (t0) REVERT: B 692 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7788 (mptt) REVERT: B 707 ASN cc_start: 0.7521 (t0) cc_final: 0.7219 (t0) REVERT: B 712 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6135 (pt0) REVERT: B 724 MET cc_start: 0.7121 (mmm) cc_final: 0.6767 (mmm) REVERT: C 405 GLN cc_start: 0.7906 (mt0) cc_final: 0.7534 (mt0) REVERT: C 411 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7737 (tpp) REVERT: C 441 MET cc_start: 0.6889 (mmm) cc_final: 0.6408 (mmt) REVERT: C 442 GLN cc_start: 0.5273 (OUTLIER) cc_final: 0.3936 (pp30) REVERT: C 473 ARG cc_start: 0.7859 (tmt170) cc_final: 0.7595 (ttt180) REVERT: C 475 PHE cc_start: 0.7764 (t80) cc_final: 0.7206 (t80) REVERT: C 501 GLN cc_start: 0.7897 (tp40) cc_final: 0.7497 (tp40) REVERT: D 20 GLN cc_start: 0.8884 (mt0) cc_final: 0.8476 (mp10) REVERT: D 50 SER cc_start: 0.8102 (m) cc_final: 0.7045 (p) REVERT: D 55 TRP cc_start: 0.7861 (m-10) cc_final: 0.7572 (m-10) REVERT: D 77 LYS cc_start: 0.8125 (mttt) cc_final: 0.7845 (mttt) REVERT: D 78 GLU cc_start: 0.7715 (pt0) cc_final: 0.7205 (pt0) REVERT: D 79 PHE cc_start: 0.7772 (m-80) cc_final: 0.7509 (m-80) REVERT: D 81 LYS cc_start: 0.8818 (tttt) cc_final: 0.8312 (tttt) REVERT: D 85 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7502 (mt-10) REVERT: D 140 LYS cc_start: 0.7468 (pttm) cc_final: 0.7251 (pttm) REVERT: D 154 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7450 (mt-10) REVERT: D 155 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7705 (mmm160) REVERT: D 173 GLN cc_start: 0.8898 (tt0) cc_final: 0.8450 (pp30) REVERT: D 174 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8326 (p0) REVERT: D 177 GLN cc_start: 0.7929 (pt0) cc_final: 0.7689 (pp30) REVERT: D 185 MET cc_start: 0.7301 (OUTLIER) cc_final: 0.6883 (mpp) REVERT: D 201 PHE cc_start: 0.8187 (m-80) cc_final: 0.7937 (m-80) REVERT: D 215 PHE cc_start: 0.8380 (t80) cc_final: 0.7923 (t80) REVERT: D 216 MET cc_start: 0.7943 (mmm) cc_final: 0.7705 (mmm) REVERT: D 218 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7301 (tm-30) REVERT: D 221 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7776 (mm-40) REVERT: D 243 SER cc_start: 0.8145 (m) cc_final: 0.7632 (p) REVERT: D 244 THR cc_start: 0.8074 (m) cc_final: 0.7775 (t) REVERT: D 254 MET cc_start: 0.6998 (mtt) cc_final: 0.5785 (mtp) REVERT: D 258 LEU cc_start: 0.8422 (mt) cc_final: 0.8031 (tp) REVERT: D 260 ASN cc_start: 0.7846 (t0) cc_final: 0.7552 (t0) REVERT: D 261 PHE cc_start: 0.8392 (t80) cc_final: 0.7923 (t80) REVERT: D 267 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8114 (mt-10) REVERT: D 276 ARG cc_start: 0.7377 (ttt90) cc_final: 0.7146 (mmm-85) REVERT: D 281 TYR cc_start: 0.7284 (p90) cc_final: 0.6583 (p90) REVERT: D 284 THR cc_start: 0.8334 (OUTLIER) cc_final: 0.8017 (p) REVERT: D 362 GLN cc_start: 0.7908 (tp40) cc_final: 0.7571 (tp40) REVERT: D 371 ARG cc_start: 0.7798 (mmt180) cc_final: 0.7535 (mpt180) REVERT: D 397 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6920 (mm-30) REVERT: D 433 PHE cc_start: 0.7896 (t80) cc_final: 0.7269 (t80) REVERT: D 435 ASN cc_start: 0.7040 (t0) cc_final: 0.6687 (t0) REVERT: D 439 ARG cc_start: 0.8056 (mtm180) cc_final: 0.7568 (mtp85) REVERT: E 12 GLU cc_start: 0.7682 (pt0) cc_final: 0.7232 (pt0) REVERT: E 70 THR cc_start: 0.8183 (p) cc_final: 0.7730 (t) REVERT: E 72 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7601 (mm-30) REVERT: E 73 ASP cc_start: 0.6988 (t0) cc_final: 0.5315 (t0) REVERT: E 75 ASP cc_start: 0.7033 (m-30) cc_final: 0.5822 (m-30) REVERT: E 79 ASN cc_start: 0.7917 (p0) cc_final: 0.7667 (p0) REVERT: E 80 ARG cc_start: 0.7874 (mtt180) cc_final: 0.6883 (mtt180) REVERT: E 93 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6895 (mt-10) REVERT: E 96 PHE cc_start: 0.7335 (m-80) cc_final: 0.7044 (m-80) REVERT: E 112 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7599 (mttt) REVERT: E 119 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7717 (tm-30) REVERT: E 125 ARG cc_start: 0.7319 (mtt180) cc_final: 0.6992 (mtt180) REVERT: E 132 LYS cc_start: 0.8531 (mttt) cc_final: 0.8294 (mttt) REVERT: E 144 SER cc_start: 0.8531 (t) cc_final: 0.7936 (p) REVERT: E 154 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7131 (tm-30) REVERT: E 157 LYS cc_start: 0.8188 (tttt) cc_final: 0.7822 (tttt) REVERT: E 166 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6921 (mt-10) REVERT: E 177 CYS cc_start: 0.7666 (m) cc_final: 0.7116 (m) REVERT: E 181 ASN cc_start: 0.8282 (t0) cc_final: 0.7798 (t0) REVERT: E 184 ASP cc_start: 0.7134 (m-30) cc_final: 0.6798 (m-30) REVERT: E 186 ILE cc_start: 0.8032 (mt) cc_final: 0.7816 (mt) REVERT: E 190 LYS cc_start: 0.8086 (tptt) cc_final: 0.7800 (tptt) REVERT: E 193 LYS cc_start: 0.8399 (mttt) cc_final: 0.7721 (ttmm) REVERT: E 214 GLU cc_start: 0.7553 (tt0) cc_final: 0.7203 (tt0) REVERT: E 256 GLN cc_start: 0.7463 (mt0) cc_final: 0.7190 (mt0) REVERT: E 289 TYR cc_start: 0.8204 (m-80) cc_final: 0.7918 (m-80) REVERT: E 299 CYS cc_start: 0.7652 (m) cc_final: 0.7355 (m) REVERT: E 304 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7135 (tm-30) REVERT: E 329 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6212 (p0) REVERT: E 333 GLU cc_start: 0.7787 (tt0) cc_final: 0.7425 (tt0) REVERT: E 353 LYS cc_start: 0.8372 (mttt) cc_final: 0.7832 (mttt) REVERT: E 366 VAL cc_start: 0.8376 (OUTLIER) cc_final: 0.8120 (m) REVERT: F 16 ASP cc_start: 0.7855 (t0) cc_final: 0.7368 (t0) REVERT: F 28 LYS cc_start: 0.7984 (tttt) cc_final: 0.7722 (tttt) REVERT: F 56 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7484 (mmtt) REVERT: F 60 ILE cc_start: 0.8586 (mt) cc_final: 0.8187 (tt) REVERT: F 109 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7478 (mt-10) REVERT: F 116 LYS cc_start: 0.8102 (mttt) cc_final: 0.7726 (mmmm) REVERT: F 131 THR cc_start: 0.8404 (m) cc_final: 0.8202 (p) REVERT: F 139 LYS cc_start: 0.8511 (mttt) cc_final: 0.8182 (mtpp) REVERT: F 150 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7216 (mt-10) REVERT: F 158 LYS cc_start: 0.8226 (mttt) cc_final: 0.7962 (mttt) REVERT: F 172 LEU cc_start: 0.8369 (mt) cc_final: 0.8127 (mm) REVERT: F 187 GLN cc_start: 0.8286 (mt0) cc_final: 0.8038 (mt0) REVERT: F 200 SER cc_start: 0.8702 (t) cc_final: 0.8411 (p) REVERT: F 205 GLN cc_start: 0.8134 (mt0) cc_final: 0.7890 (mt0) REVERT: F 213 LEU cc_start: 0.8327 (tt) cc_final: 0.8100 (tt) REVERT: F 216 LYS cc_start: 0.8494 (tttt) cc_final: 0.8046 (ttpp) REVERT: F 217 VAL cc_start: 0.8998 (p) cc_final: 0.8754 (t) REVERT: F 237 GLN cc_start: 0.7324 (mt0) cc_final: 0.6838 (mt0) REVERT: F 242 ILE cc_start: 0.8260 (mt) cc_final: 0.8015 (mt) REVERT: F 249 VAL cc_start: 0.7878 (t) cc_final: 0.7586 (p) REVERT: F 252 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7526 (ptp-110) REVERT: F 264 ILE cc_start: 0.8482 (mp) cc_final: 0.8112 (mm) REVERT: F 266 TYR cc_start: 0.8308 (m-80) cc_final: 0.7914 (m-80) REVERT: F 267 VAL cc_start: 0.8445 (t) cc_final: 0.7951 (m) REVERT: G 9 LEU cc_start: 0.8241 (tt) cc_final: 0.8019 (tp) REVERT: G 12 CYS cc_start: 0.8797 (p) cc_final: 0.8191 (p) REVERT: G 16 MET cc_start: 0.8497 (mmt) cc_final: 0.7382 (mmm) REVERT: G 66 PHE cc_start: 0.8474 (t80) cc_final: 0.7905 (t80) REVERT: H 926 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6290 (tp30) REVERT: K 148 TYR cc_start: 0.7785 (m-80) cc_final: 0.7499 (m-80) REVERT: K 163 LYS cc_start: 0.8007 (mttt) cc_final: 0.7680 (mttt) REVERT: K 178 MET cc_start: 0.7587 (mtm) cc_final: 0.7168 (mtm) REVERT: K 187 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8289 (m) REVERT: K 188 LYS cc_start: 0.8092 (tttt) cc_final: 0.7734 (tttt) REVERT: K 208 GLN cc_start: 0.7891 (tp-100) cc_final: 0.7667 (tp-100) REVERT: K 212 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: K 222 LYS cc_start: 0.8146 (pttm) cc_final: 0.7916 (pttm) REVERT: K 263 MET cc_start: 0.5608 (mmm) cc_final: 0.5229 (mmm) outliers start: 118 outliers final: 69 residues processed: 842 average time/residue: 0.4069 time to fit residues: 501.4664 Evaluate side-chains 848 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 761 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 279 GLU 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 382 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 479 ASP 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 656 ASN 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 138 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 482 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 546 GLU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 612 HIS Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 682 LYS Chi-restraints excluded: chain 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 423 SER Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 SER 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 71 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 250 ILE 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 128 HIS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain H residue 926 GLU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 162 LEU Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 271 GLU Chi-restraints excluded: chain K residue 273 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 1.9990 chunk 194 optimal weight: 0.4980 chunk 134 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 173 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 24295 Z= 0.244 Angle : 0.574 12.616 33035 Z= 0.294 Chirality : 0.042 0.160 3696 Planarity : 0.004 0.065 4058 Dihedral : 13.323 147.810 3622 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 6.10 % Allowed : 16.50 % Favored : 77.40 % 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: 0.17 (0.16), residues: 2804 helix: 1.17 (0.15), residues: 1313 sheet: -0.12 (0.26), residues: 389 loop : -1.05 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 511 HIS 0.016 0.001 HIS C 474 PHE 0.024 0.002 PHE A 659 TYR 0.032 0.002 TYR A 581 ARG 0.007 0.001 ARG A 141 *********************** 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 951 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 798 time to evaluate : 2.620 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: 0.8317 (mttt) cc_final: 0.7919 (mptt) REVERT: A 64 GLN cc_start: 0.8383 (mm-40) cc_final: 0.8101 (mm110) REVERT: A 65 MET cc_start: 0.7544 (ptt) cc_final: 0.7311 (ptt) REVERT: A 68 LYS cc_start: 0.6390 (mtmt) cc_final: 0.5793 (tttm) REVERT: A 94 LYS cc_start: 0.7676 (ptpt) cc_final: 0.7164 (ptpt) REVERT: A 98 ASP cc_start: 0.7508 (m-30) cc_final: 0.7204 (m-30) REVERT: A 100 LEU cc_start: 0.8051 (mt) cc_final: 0.7851 (mm) REVERT: A 117 LYS cc_start: 0.8193 (tttt) cc_final: 0.7870 (tttt) REVERT: A 138 GLU cc_start: 0.7673 (pt0) cc_final: 0.7327 (tp30) REVERT: A 141 ARG cc_start: 0.7748 (ttm-80) cc_final: 0.7458 (ttm-80) REVERT: A 146 THR cc_start: 0.7788 (p) cc_final: 0.7292 (p) REVERT: A 157 LYS cc_start: 0.8160 (ptmm) cc_final: 0.7743 (ttpp) REVERT: A 163 TYR cc_start: 0.8023 (t80) cc_final: 0.7653 (t80) REVERT: A 167 LYS cc_start: 0.7545 (mttp) cc_final: 0.7159 (mtpp) REVERT: A 169 VAL cc_start: 0.8260 (p) cc_final: 0.7912 (m) REVERT: A 173 ASN cc_start: 0.7947 (m-40) cc_final: 0.6681 (m-40) REVERT: A 174 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7470 (tpp80) REVERT: A 178 GLU cc_start: 0.6685 (pm20) cc_final: 0.6309 (pm20) REVERT: A 191 ASP cc_start: 0.7662 (t0) cc_final: 0.7445 (t0) REVERT: A 273 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7701 (tppp) REVERT: A 275 GLU cc_start: 0.7957 (pm20) cc_final: 0.7724 (pm20) REVERT: A 282 LYS cc_start: 0.8367 (tttt) cc_final: 0.7890 (ttmm) REVERT: A 287 LEU cc_start: 0.8579 (mt) cc_final: 0.8172 (mt) REVERT: A 288 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7248 (mp0) REVERT: A 299 ASN cc_start: 0.8138 (p0) cc_final: 0.7509 (p0) REVERT: A 309 ASP cc_start: 0.6910 (OUTLIER) cc_final: 0.6527 (p0) REVERT: A 310 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7827 (pt) REVERT: A 321 GLU cc_start: 0.7423 (mm-30) cc_final: 0.7159 (tm-30) REVERT: A 332 ARG cc_start: 0.8062 (mpp80) cc_final: 0.7767 (mtp85) REVERT: A 334 ARG cc_start: 0.6960 (ptp90) cc_final: 0.6714 (ptp90) REVERT: A 347 SER cc_start: 0.8626 (m) cc_final: 0.7907 (t) REVERT: A 372 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6661 (tp30) REVERT: A 389 ILE cc_start: 0.7633 (mm) cc_final: 0.7345 (tt) REVERT: A 392 PHE cc_start: 0.7292 (t80) cc_final: 0.6630 (t80) REVERT: A 412 MET cc_start: 0.7259 (ttt) cc_final: 0.7059 (ttt) REVERT: A 418 LYS cc_start: 0.7864 (tmmt) cc_final: 0.7457 (tmmt) REVERT: A 419 ARG cc_start: 0.7914 (ttm170) cc_final: 0.7627 (tpp80) REVERT: A 424 GLU cc_start: 0.7889 (tp30) cc_final: 0.7439 (mm-30) REVERT: A 428 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7709 (mm-30) REVERT: A 434 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7525 (mm-30) REVERT: A 457 ILE cc_start: 0.8300 (tt) cc_final: 0.7941 (tt) REVERT: A 476 LYS cc_start: 0.8197 (mttt) cc_final: 0.7695 (mttm) REVERT: A 487 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8118 (ttmm) REVERT: A 490 GLU cc_start: 0.6721 (mp0) cc_final: 0.6391 (mm-30) REVERT: A 502 ILE cc_start: 0.7813 (mm) cc_final: 0.7549 (mt) REVERT: A 504 LYS cc_start: 0.8493 (ttpt) cc_final: 0.7688 (ttpt) REVERT: A 505 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8054 (m) REVERT: A 520 ARG cc_start: 0.7680 (mmm160) cc_final: 0.6874 (tpt-90) REVERT: A 521 GLU cc_start: 0.7752 (mp0) cc_final: 0.7374 (mp0) REVERT: A 525 ILE cc_start: 0.8303 (tp) cc_final: 0.7964 (tp) REVERT: A 526 LYS cc_start: 0.7879 (tmtt) cc_final: 0.7154 (tppt) REVERT: A 528 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7998 (mptt) REVERT: A 530 ARG cc_start: 0.7128 (ptt-90) cc_final: 0.6470 (ptt-90) REVERT: A 554 ARG cc_start: 0.7499 (ttm-80) cc_final: 0.7181 (ttp80) REVERT: A 556 ASP cc_start: 0.7300 (m-30) cc_final: 0.6912 (m-30) REVERT: A 564 ASN cc_start: 0.8405 (t0) cc_final: 0.7691 (t0) REVERT: A 569 LYS cc_start: 0.8013 (mmmt) cc_final: 0.7510 (mmmm) REVERT: A 570 GLU cc_start: 0.7458 (pm20) cc_final: 0.7087 (pm20) REVERT: A 579 TYR cc_start: 0.7555 (p90) cc_final: 0.7110 (p90) REVERT: A 586 GLN cc_start: 0.8425 (tp40) cc_final: 0.8090 (tp40) REVERT: A 588 GLU cc_start: 0.7467 (tp30) cc_final: 0.6764 (tp30) REVERT: A 590 MET cc_start: 0.7776 (tpp) cc_final: 0.7489 (tpt) REVERT: A 632 SER cc_start: 0.8297 (p) cc_final: 0.7944 (p) REVERT: A 642 ARG cc_start: 0.7256 (mtp85) cc_final: 0.6641 (mmt180) REVERT: A 659 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.6915 (p90) REVERT: A 669 GLU cc_start: 0.7559 (tt0) cc_final: 0.7277 (tt0) REVERT: A 670 MET cc_start: 0.7998 (mmm) cc_final: 0.7763 (mmm) REVERT: A 677 GLN cc_start: 0.7676 (mt0) cc_final: 0.7226 (mt0) REVERT: A 682 ASP cc_start: 0.6973 (m-30) cc_final: 0.6742 (m-30) REVERT: A 683 GLN cc_start: 0.7458 (mm-40) cc_final: 0.6992 (mm-40) REVERT: A 700 ASP cc_start: 0.7402 (t0) cc_final: 0.7201 (t0) REVERT: A 704 SER cc_start: 0.8500 (p) cc_final: 0.8263 (p) REVERT: A 706 LYS cc_start: 0.7847 (tmmt) cc_final: 0.7568 (tmtt) REVERT: B 1 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5784 (ppp) REVERT: B 40 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 42 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7188 (mtp) REVERT: B 75 ARG cc_start: 0.7435 (ttp80) cc_final: 0.7042 (ttp80) REVERT: B 91 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7645 (mm) REVERT: B 113 LYS cc_start: 0.7890 (ttpp) cc_final: 0.7530 (ttmm) REVERT: B 158 TYR cc_start: 0.7472 (t80) cc_final: 0.6965 (t80) REVERT: B 243 CYS cc_start: 0.8530 (m) cc_final: 0.8111 (m) REVERT: B 247 MET cc_start: 0.7998 (mtt) cc_final: 0.7371 (mpp) REVERT: B 384 HIS cc_start: 0.5128 (OUTLIER) cc_final: 0.4819 (p-80) REVERT: B 414 PHE cc_start: 0.7287 (m-80) cc_final: 0.6101 (m-80) REVERT: B 416 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6570 (pt) REVERT: B 445 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7909 (mmtt) REVERT: B 455 ILE cc_start: 0.7883 (mm) cc_final: 0.7429 (mm) REVERT: B 464 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7236 (mt) REVERT: B 466 ILE cc_start: 0.7609 (tt) cc_final: 0.7261 (tp) REVERT: B 469 LYS cc_start: 0.8010 (ptpp) cc_final: 0.7752 (ptpp) REVERT: B 512 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7249 (mm-30) REVERT: B 518 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7715 (mtp-110) REVERT: B 533 ASP cc_start: 0.6978 (p0) cc_final: 0.6649 (p0) REVERT: B 545 MET cc_start: 0.7901 (tmm) cc_final: 0.7656 (ttp) REVERT: B 548 THR cc_start: 0.8663 (m) cc_final: 0.8307 (t) REVERT: B 570 GLU cc_start: 0.6362 (tm-30) cc_final: 0.5670 (tm-30) REVERT: B 586 GLU cc_start: 0.7576 (pp20) cc_final: 0.7235 (pp20) REVERT: B 588 CYS cc_start: 0.7960 (m) cc_final: 0.7757 (m) REVERT: B 589 GLU cc_start: 0.6919 (mm-30) cc_final: 0.6559 (mm-30) REVERT: B 604 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8203 (t) REVERT: B 620 MET cc_start: 0.7827 (mmm) cc_final: 0.6949 (mmm) REVERT: B 633 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7155 (tp) REVERT: B 638 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6492 (mm-30) REVERT: B 641 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.6925 (mtm-85) REVERT: B 648 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6515 (tm-30) REVERT: B 664 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8156 (p) REVERT: B 681 ASP cc_start: 0.7782 (t0) cc_final: 0.7537 (t0) REVERT: B 688 ASP cc_start: 0.8074 (p0) cc_final: 0.7780 (p0) REVERT: B 692 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7802 (mptt) REVERT: B 707 ASN cc_start: 0.7571 (t0) cc_final: 0.7273 (t0) REVERT: B 712 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6377 (pt0) REVERT: B 723 GLN cc_start: 0.7645 (mm110) cc_final: 0.7436 (tp40) REVERT: B 724 MET cc_start: 0.7236 (mmm) cc_final: 0.6818 (mmm) REVERT: C 405 GLN cc_start: 0.7937 (mt0) cc_final: 0.7557 (mt0) REVERT: C 408 ARG cc_start: 0.7922 (ttt180) cc_final: 0.7601 (ttm-80) REVERT: C 411 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7732 (tpp) REVERT: C 442 GLN cc_start: 0.5338 (OUTLIER) cc_final: 0.4073 (pp30) REVERT: C 473 ARG cc_start: 0.7973 (tmt170) cc_final: 0.7726 (ttt180) REVERT: C 475 PHE cc_start: 0.7826 (t80) cc_final: 0.7206 (t80) REVERT: C 501 GLN cc_start: 0.7882 (tp40) cc_final: 0.7481 (tp40) REVERT: C 528 MET cc_start: 0.8882 (mtp) cc_final: 0.8420 (mtm) REVERT: D 20 GLN cc_start: 0.8698 (mt0) cc_final: 0.8403 (mp10) REVERT: D 40 THR cc_start: 0.8045 (p) cc_final: 0.7803 (p) REVERT: D 50 SER cc_start: 0.8077 (m) cc_final: 0.7053 (p) REVERT: D 77 LYS cc_start: 0.8246 (mttt) cc_final: 0.7930 (mttt) REVERT: D 78 GLU cc_start: 0.7850 (pt0) cc_final: 0.7379 (pt0) REVERT: D 79 PHE cc_start: 0.7988 (m-80) cc_final: 0.7682 (m-80) REVERT: D 81 LYS cc_start: 0.8817 (tttt) cc_final: 0.8452 (tttt) REVERT: D 85 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7449 (mt-10) REVERT: D 114 PHE cc_start: 0.8423 (t80) cc_final: 0.8157 (t80) REVERT: D 154 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7573 (mt-10) REVERT: D 155 ARG cc_start: 0.8231 (mmm160) cc_final: 0.7985 (mmm160) REVERT: D 173 GLN cc_start: 0.8891 (tt0) cc_final: 0.8470 (pp30) REVERT: D 174 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8417 (p0) REVERT: D 177 GLN cc_start: 0.7966 (pt0) cc_final: 0.7502 (pp30) REVERT: D 178 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8265 (tp) REVERT: D 185 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6914 (mpp) REVERT: D 201 PHE cc_start: 0.8363 (m-80) cc_final: 0.8010 (m-80) REVERT: D 218 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7288 (tm-30) REVERT: D 243 SER cc_start: 0.8198 (m) cc_final: 0.7711 (p) REVERT: D 244 THR cc_start: 0.8018 (m) cc_final: 0.7740 (t) REVERT: D 249 TYR cc_start: 0.7961 (m-80) cc_final: 0.7667 (m-80) REVERT: D 258 LEU cc_start: 0.8431 (mt) cc_final: 0.8045 (tp) REVERT: D 260 ASN cc_start: 0.7975 (t0) cc_final: 0.7635 (t0) REVERT: D 261 PHE cc_start: 0.8505 (t80) cc_final: 0.8194 (t80) REVERT: D 267 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8070 (mt-10) REVERT: D 276 ARG cc_start: 0.7408 (ttt90) cc_final: 0.7191 (mmm-85) REVERT: D 281 TYR cc_start: 0.7192 (p90) cc_final: 0.6550 (p90) REVERT: D 282 TYR cc_start: 0.7857 (m-80) cc_final: 0.7589 (m-80) REVERT: D 284 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8007 (p) REVERT: D 313 TYR cc_start: 0.8353 (m-80) cc_final: 0.8039 (m-80) REVERT: D 316 TYR cc_start: 0.8441 (m-80) cc_final: 0.8105 (m-10) REVERT: D 362 GLN cc_start: 0.7921 (tp40) cc_final: 0.7598 (tp40) REVERT: D 371 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7488 (mpt180) REVERT: D 378 LYS cc_start: 0.8054 (mttt) cc_final: 0.7777 (mttp) REVERT: D 397 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7042 (mm-30) REVERT: D 398 ARG cc_start: 0.7771 (ttt90) cc_final: 0.7502 (ttt90) REVERT: D 433 PHE cc_start: 0.7915 (t80) cc_final: 0.7288 (t80) REVERT: D 435 ASN cc_start: 0.7114 (t0) cc_final: 0.6779 (t0) REVERT: E 9 LYS cc_start: 0.7492 (mmmm) cc_final: 0.7225 (mmmm) REVERT: E 12 GLU cc_start: 0.7744 (pt0) cc_final: 0.7254 (pt0) REVERT: E 70 THR cc_start: 0.8161 (p) cc_final: 0.7727 (t) REVERT: E 72 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7589 (mm-30) REVERT: E 73 ASP cc_start: 0.7052 (t0) cc_final: 0.5353 (t0) REVERT: E 75 ASP cc_start: 0.7007 (m-30) cc_final: 0.5623 (m-30) REVERT: E 79 ASN cc_start: 0.7855 (p0) cc_final: 0.7583 (p0) REVERT: E 80 ARG cc_start: 0.7966 (mtt180) cc_final: 0.6924 (mtt180) REVERT: E 96 PHE cc_start: 0.7334 (m-80) cc_final: 0.7004 (m-80) REVERT: E 103 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7572 (mt0) REVERT: E 112 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7723 (mttt) REVERT: E 119 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7794 (tm-30) REVERT: E 125 ARG cc_start: 0.7357 (mtt180) cc_final: 0.7005 (mtt180) REVERT: E 132 LYS cc_start: 0.8538 (mttt) cc_final: 0.8308 (mttt) REVERT: E 144 SER cc_start: 0.8535 (t) cc_final: 0.7959 (p) REVERT: E 154 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7013 (tm-30) REVERT: E 157 LYS cc_start: 0.8190 (tttt) cc_final: 0.7827 (tttt) REVERT: E 166 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6861 (mt-10) REVERT: E 177 CYS cc_start: 0.7626 (m) cc_final: 0.7208 (m) REVERT: E 181 ASN cc_start: 0.8267 (t0) cc_final: 0.7772 (t0) REVERT: E 184 ASP cc_start: 0.7029 (m-30) cc_final: 0.6667 (m-30) REVERT: E 190 LYS cc_start: 0.8171 (tptt) cc_final: 0.7892 (tptt) REVERT: E 193 LYS cc_start: 0.8408 (mttt) cc_final: 0.7762 (ttmm) REVERT: E 214 GLU cc_start: 0.7645 (tt0) cc_final: 0.7292 (tt0) REVERT: E 237 SER cc_start: 0.8422 (m) cc_final: 0.7867 (p) REVERT: E 256 GLN cc_start: 0.7614 (mt0) cc_final: 0.7317 (mt0) REVERT: E 268 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7240 (mtmm) REVERT: E 289 TYR cc_start: 0.8259 (m-80) cc_final: 0.7895 (m-80) REVERT: E 295 ARG cc_start: 0.7581 (mmt180) cc_final: 0.7202 (ttm-80) REVERT: E 299 CYS cc_start: 0.7656 (m) cc_final: 0.7378 (m) REVERT: E 304 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7143 (tm-30) REVERT: E 329 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6278 (p0) REVERT: E 333 GLU cc_start: 0.7754 (tt0) cc_final: 0.7446 (tt0) REVERT: E 353 LYS cc_start: 0.8325 (mttt) cc_final: 0.7806 (mttt) REVERT: F 16 ASP cc_start: 0.7859 (t0) cc_final: 0.7408 (t0) REVERT: F 28 LYS cc_start: 0.8189 (tttt) cc_final: 0.7979 (tttt) REVERT: F 56 LYS cc_start: 0.7827 (mmtt) cc_final: 0.7611 (mmtt) REVERT: F 60 ILE cc_start: 0.8607 (mt) cc_final: 0.8186 (tt) REVERT: F 109 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7506 (mt-10) REVERT: F 116 LYS cc_start: 0.8121 (mttt) cc_final: 0.7672 (mmmm) REVERT: F 139 LYS cc_start: 0.8529 (mttt) cc_final: 0.8182 (mtpp) REVERT: F 172 LEU cc_start: 0.8396 (mt) cc_final: 0.8150 (mm) REVERT: F 187 GLN cc_start: 0.8300 (mt0) cc_final: 0.8085 (mt0) REVERT: F 194 CYS cc_start: 0.8015 (t) cc_final: 0.7320 (t) REVERT: F 195 VAL cc_start: 0.8567 (t) cc_final: 0.8022 (p) REVERT: F 197 ASP cc_start: 0.7951 (t0) cc_final: 0.7743 (t0) REVERT: F 200 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8388 (p) REVERT: F 205 GLN cc_start: 0.8280 (mt0) cc_final: 0.8055 (mt0) REVERT: F 213 LEU cc_start: 0.8179 (tt) cc_final: 0.7968 (tt) REVERT: F 216 LYS cc_start: 0.8471 (tttt) cc_final: 0.7902 (ttpp) REVERT: F 237 GLN cc_start: 0.7416 (mt0) cc_final: 0.6904 (mt0) REVERT: F 242 ILE cc_start: 0.8197 (mt) cc_final: 0.7811 (mt) REVERT: F 249 VAL cc_start: 0.7988 (t) cc_final: 0.7667 (p) REVERT: F 252 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7515 (ptp-110) REVERT: F 264 ILE cc_start: 0.8454 (mp) cc_final: 0.8148 (mm) REVERT: F 266 TYR cc_start: 0.8337 (m-80) cc_final: 0.7905 (m-80) REVERT: F 267 VAL cc_start: 0.8378 (t) cc_final: 0.7918 (m) REVERT: G 9 LEU cc_start: 0.8250 (tt) cc_final: 0.8034 (tp) REVERT: G 12 CYS cc_start: 0.8771 (p) cc_final: 0.8228 (p) REVERT: G 16 MET cc_start: 0.8561 (mmt) cc_final: 0.7267 (mmm) REVERT: H 926 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6312 (tp30) REVERT: K 143 GLU cc_start: 0.7761 (tt0) cc_final: 0.7263 (tt0) REVERT: K 163 LYS cc_start: 0.7994 (mttt) cc_final: 0.7706 (mttt) REVERT: K 178 MET cc_start: 0.7720 (mtm) cc_final: 0.7249 (mtm) REVERT: K 187 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8340 (m) REVERT: K 188 LYS cc_start: 0.8132 (tttt) cc_final: 0.7920 (tttt) REVERT: K 208 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7461 (tp-100) REVERT: K 212 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: K 214 MET cc_start: 0.7061 (mmt) cc_final: 0.6852 (mmt) REVERT: K 222 LYS cc_start: 0.8297 (pttm) cc_final: 0.8018 (pttm) REVERT: K 263 MET cc_start: 0.5722 (mmm) cc_final: 0.5324 (mmm) outliers start: 153 outliers final: 90 residues processed: 872 average time/residue: 0.4043 time to fit residues: 517.8201 Evaluate side-chains 891 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 772 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 144 SER 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 309 ASP 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 382 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 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 40 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 THR 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 397 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 464 LEU 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 546 GLU 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 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 428 SER Chi-restraints excluded: chain C residue 429 SER 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 C residue 531 THR 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 174 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 256 ASP 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 327 LEU Chi-restraints excluded: chain D residue 340 ASN Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 ILE 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 226 SER Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 280 THR 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 199 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 229 TRP 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 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 162 LEU Chi-restraints excluded: chain K residue 183 LYS Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG 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 228 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 204 optimal weight: 0.5980 chunk 113 optimal weight: 0.4980 chunk 234 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 chunk 246 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN B 328 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24295 Z= 0.197 Angle : 0.561 9.829 33035 Z= 0.283 Chirality : 0.041 0.161 3696 Planarity : 0.004 0.050 4058 Dihedral : 13.326 149.239 3620 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 5.54 % Allowed : 19.25 % Favored : 75.21 % 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: 0.20 (0.16), residues: 2804 helix: 1.21 (0.15), residues: 1323 sheet: -0.12 (0.26), residues: 384 loop : -1.08 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 55 HIS 0.019 0.001 HIS D 424 PHE 0.026 0.001 PHE A 703 TYR 0.017 0.001 TYR K 116 ARG 0.006 0.000 ARG E 213 *********************** 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 916 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 777 time to evaluate : 2.868 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 59 LYS cc_start: 0.8305 (mttt) cc_final: 0.7997 (mptt) REVERT: A 64 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8102 (mm110) REVERT: A 65 MET cc_start: 0.7552 (ptt) cc_final: 0.7263 (ptt) REVERT: A 68 LYS cc_start: 0.6376 (mtmt) cc_final: 0.5724 (tttm) REVERT: A 94 LYS cc_start: 0.7782 (ptpt) cc_final: 0.7307 (ptpt) REVERT: A 98 ASP cc_start: 0.7498 (m-30) cc_final: 0.7192 (m-30) REVERT: A 117 LYS cc_start: 0.8177 (tttt) cc_final: 0.7882 (tttt) REVERT: A 138 GLU cc_start: 0.7729 (pt0) cc_final: 0.7423 (tp30) REVERT: A 146 THR cc_start: 0.7647 (p) cc_final: 0.7177 (p) REVERT: A 157 LYS cc_start: 0.8123 (ptmm) cc_final: 0.7638 (ttpp) REVERT: A 160 THR cc_start: 0.8006 (m) cc_final: 0.7779 (t) REVERT: A 163 TYR cc_start: 0.8014 (t80) cc_final: 0.7617 (t80) REVERT: A 167 LYS cc_start: 0.7610 (mttp) cc_final: 0.7120 (mtpp) REVERT: A 169 VAL cc_start: 0.8343 (p) cc_final: 0.7997 (m) REVERT: A 173 ASN cc_start: 0.7954 (m-40) cc_final: 0.6747 (m-40) REVERT: A 176 PHE cc_start: 0.7707 (m-10) cc_final: 0.7478 (m-10) REVERT: A 178 GLU cc_start: 0.6678 (pm20) cc_final: 0.6361 (pm20) REVERT: A 191 ASP cc_start: 0.7701 (t0) cc_final: 0.7438 (t0) REVERT: A 203 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.6190 (pm20) REVERT: A 273 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7561 (tppp) REVERT: A 275 GLU cc_start: 0.7979 (pm20) cc_final: 0.7713 (pm20) REVERT: A 287 LEU cc_start: 0.8561 (mt) cc_final: 0.8152 (mt) REVERT: A 288 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7312 (mp0) REVERT: A 294 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6625 (mm-30) REVERT: A 299 ASN cc_start: 0.8198 (p0) cc_final: 0.7626 (p0) REVERT: A 309 ASP cc_start: 0.6946 (p0) cc_final: 0.6608 (p0) REVERT: A 310 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7837 (pt) REVERT: A 321 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7208 (tm-30) REVERT: A 332 ARG cc_start: 0.8091 (mpp80) cc_final: 0.7033 (mtp85) REVERT: A 334 ARG cc_start: 0.6965 (ptp90) cc_final: 0.6098 (ptp90) REVERT: A 347 SER cc_start: 0.8632 (m) cc_final: 0.7895 (t) REVERT: A 372 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6770 (tp30) REVERT: A 375 LYS cc_start: 0.8153 (tttm) cc_final: 0.7894 (ttpp) REVERT: A 389 ILE cc_start: 0.7562 (mm) cc_final: 0.7292 (tt) REVERT: A 418 LYS cc_start: 0.7851 (tmmt) cc_final: 0.7460 (tmmt) REVERT: A 419 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7558 (tpp80) REVERT: A 424 GLU cc_start: 0.7910 (tp30) cc_final: 0.7478 (mm-30) REVERT: A 428 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7761 (mm-30) REVERT: A 434 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7542 (mm-30) REVERT: A 457 ILE cc_start: 0.8300 (tt) cc_final: 0.7946 (tt) REVERT: A 476 LYS cc_start: 0.8173 (mttt) cc_final: 0.7639 (mttm) REVERT: A 487 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7660 (ttpp) REVERT: A 490 GLU cc_start: 0.6741 (mp0) cc_final: 0.6143 (mm-30) REVERT: A 504 LYS cc_start: 0.8464 (ttpt) cc_final: 0.7713 (ttpt) REVERT: A 505 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8057 (m) REVERT: A 520 ARG cc_start: 0.7533 (mmm160) cc_final: 0.6604 (tpt-90) REVERT: A 521 GLU cc_start: 0.7865 (mp0) cc_final: 0.7464 (mp0) REVERT: A 525 ILE cc_start: 0.8298 (tp) cc_final: 0.7967 (tp) REVERT: A 526 LYS cc_start: 0.7893 (tmtt) cc_final: 0.7135 (tppt) REVERT: A 528 LYS cc_start: 0.8269 (mmtt) cc_final: 0.7991 (mptt) REVERT: A 530 ARG cc_start: 0.7104 (ptt-90) cc_final: 0.6432 (ptt-90) REVERT: A 556 ASP cc_start: 0.7291 (m-30) cc_final: 0.6881 (m-30) REVERT: A 564 ASN cc_start: 0.8389 (t0) cc_final: 0.7612 (t0) REVERT: A 569 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7508 (mmmt) REVERT: A 570 GLU cc_start: 0.7515 (pm20) cc_final: 0.6767 (pm20) REVERT: A 579 TYR cc_start: 0.7529 (p90) cc_final: 0.7168 (p90) REVERT: A 586 GLN cc_start: 0.8394 (tp40) cc_final: 0.8087 (tp40) REVERT: A 588 GLU cc_start: 0.7445 (tp30) cc_final: 0.6687 (tp30) REVERT: A 632 SER cc_start: 0.8272 (p) cc_final: 0.7888 (p) REVERT: A 642 ARG cc_start: 0.7243 (mtp85) cc_final: 0.6620 (mmt180) REVERT: A 658 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7490 (p90) REVERT: A 659 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.6841 (p90) REVERT: A 669 GLU cc_start: 0.7525 (tt0) cc_final: 0.7254 (tt0) REVERT: A 676 ARG cc_start: 0.7942 (ptm160) cc_final: 0.7739 (ptp-170) REVERT: A 677 GLN cc_start: 0.7641 (mt0) cc_final: 0.7265 (mt0) REVERT: A 682 ASP cc_start: 0.6969 (m-30) cc_final: 0.6725 (m-30) REVERT: A 683 GLN cc_start: 0.7462 (mm-40) cc_final: 0.6976 (mm-40) REVERT: A 696 MET cc_start: 0.7631 (mmm) cc_final: 0.7041 (tmm) REVERT: A 700 ASP cc_start: 0.7426 (t0) cc_final: 0.7213 (t0) REVERT: A 704 SER cc_start: 0.8441 (p) cc_final: 0.8221 (p) REVERT: A 706 LYS cc_start: 0.7827 (tmmt) cc_final: 0.7397 (tmtt) REVERT: B 1 MET cc_start: 0.6137 (OUTLIER) cc_final: 0.5731 (ppp) REVERT: B 25 MET cc_start: 0.7845 (mmm) cc_final: 0.7627 (mpp) REVERT: B 40 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8158 (mt) REVERT: B 42 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7101 (mtm) REVERT: B 48 LYS cc_start: 0.7686 (ttpp) cc_final: 0.6993 (mtpp) REVERT: B 75 ARG cc_start: 0.7500 (ttp80) cc_final: 0.7046 (ttp80) REVERT: B 91 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7671 (mm) REVERT: B 113 LYS cc_start: 0.8072 (ttpp) cc_final: 0.7701 (ttmm) REVERT: B 158 TYR cc_start: 0.7467 (t80) cc_final: 0.6963 (t80) REVERT: B 243 CYS cc_start: 0.8548 (m) cc_final: 0.8158 (m) REVERT: B 247 MET cc_start: 0.8096 (mtt) cc_final: 0.7407 (mpp) REVERT: B 384 HIS cc_start: 0.5140 (OUTLIER) cc_final: 0.4823 (p-80) REVERT: B 414 PHE cc_start: 0.7327 (m-80) cc_final: 0.6171 (m-80) REVERT: B 416 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6798 (mt) REVERT: B 445 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7860 (mmtt) REVERT: B 455 ILE cc_start: 0.7978 (mm) cc_final: 0.7479 (mm) REVERT: B 512 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7259 (mm-30) REVERT: B 518 ARG cc_start: 0.8018 (mtp85) cc_final: 0.7710 (mtp-110) REVERT: B 545 MET cc_start: 0.8010 (tmm) cc_final: 0.7557 (ttp) REVERT: B 548 THR cc_start: 0.8677 (m) cc_final: 0.8305 (t) REVERT: B 570 GLU cc_start: 0.6256 (tm-30) cc_final: 0.5669 (tm-30) REVERT: B 586 GLU cc_start: 0.7518 (pp20) cc_final: 0.7190 (pp20) REVERT: B 589 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6585 (mm-30) REVERT: B 613 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7305 (p90) REVERT: B 620 MET cc_start: 0.7802 (mmm) cc_final: 0.6956 (mmm) REVERT: B 633 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7232 (tp) REVERT: B 636 ARG cc_start: 0.7283 (ttt180) cc_final: 0.7055 (ttt180) REVERT: B 641 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7325 (mtm-85) REVERT: B 648 GLU cc_start: 0.6944 (tm-30) cc_final: 0.6566 (tm-30) REVERT: B 655 ASP cc_start: 0.7839 (t0) cc_final: 0.7299 (m-30) REVERT: B 664 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8178 (p) REVERT: B 681 ASP cc_start: 0.7816 (t0) cc_final: 0.7586 (t0) REVERT: B 688 ASP cc_start: 0.8055 (p0) cc_final: 0.7768 (p0) REVERT: B 692 LYS cc_start: 0.8151 (mmmt) cc_final: 0.7815 (mptt) REVERT: B 707 ASN cc_start: 0.7529 (t0) cc_final: 0.7261 (t0) REVERT: B 712 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6377 (pt0) REVERT: B 723 GLN cc_start: 0.7686 (mm110) cc_final: 0.7455 (tp40) REVERT: B 724 MET cc_start: 0.7239 (mmm) cc_final: 0.6810 (mmm) REVERT: C 405 GLN cc_start: 0.7897 (mt0) cc_final: 0.7501 (mt0) REVERT: C 408 ARG cc_start: 0.7947 (ttt180) cc_final: 0.7573 (ttm-80) REVERT: C 411 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7682 (tpp) REVERT: C 441 MET cc_start: 0.6704 (mmm) cc_final: 0.6249 (mmt) REVERT: C 442 GLN cc_start: 0.5422 (OUTLIER) cc_final: 0.4076 (pp30) REVERT: C 473 ARG cc_start: 0.7976 (tmt170) cc_final: 0.7737 (ttt180) REVERT: C 475 PHE cc_start: 0.7735 (t80) cc_final: 0.7169 (t80) REVERT: C 501 GLN cc_start: 0.7869 (tp40) cc_final: 0.7459 (tp40) REVERT: D 20 GLN cc_start: 0.8668 (mt0) cc_final: 0.8355 (mp10) REVERT: D 33 ARG cc_start: 0.8234 (mmm-85) cc_final: 0.7945 (mtm-85) REVERT: D 40 THR cc_start: 0.8151 (p) cc_final: 0.7909 (p) REVERT: D 50 SER cc_start: 0.7748 (m) cc_final: 0.6735 (p) REVERT: D 54 ASN cc_start: 0.8501 (m-40) cc_final: 0.8033 (m-40) REVERT: D 77 LYS cc_start: 0.8265 (mttt) cc_final: 0.7954 (mttt) REVERT: D 78 GLU cc_start: 0.7910 (pt0) cc_final: 0.7412 (pt0) REVERT: D 79 PHE cc_start: 0.8059 (m-80) cc_final: 0.7716 (m-80) REVERT: D 81 LYS cc_start: 0.8851 (tttt) cc_final: 0.8583 (tttt) REVERT: D 85 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7534 (mt-10) REVERT: D 140 LYS cc_start: 0.7522 (pttm) cc_final: 0.6879 (mmtm) REVERT: D 154 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7644 (mt-10) REVERT: D 155 ARG cc_start: 0.8261 (mmm160) cc_final: 0.8037 (mmm160) REVERT: D 173 GLN cc_start: 0.8892 (tt0) cc_final: 0.8418 (pp30) REVERT: D 174 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8313 (p0) REVERT: D 177 GLN cc_start: 0.7958 (pt0) cc_final: 0.7573 (pp30) REVERT: D 178 LEU cc_start: 0.8772 (tt) cc_final: 0.8446 (pp) REVERT: D 185 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6925 (mpp) REVERT: D 201 PHE cc_start: 0.8372 (m-80) cc_final: 0.8035 (m-80) REVERT: D 218 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7271 (tm-30) REVERT: D 243 SER cc_start: 0.8211 (m) cc_final: 0.7781 (p) REVERT: D 244 THR cc_start: 0.7972 (m) cc_final: 0.7698 (t) REVERT: D 249 TYR cc_start: 0.7988 (m-80) cc_final: 0.7730 (m-80) REVERT: D 258 LEU cc_start: 0.8431 (mt) cc_final: 0.8027 (tp) REVERT: D 260 ASN cc_start: 0.8014 (t0) cc_final: 0.7675 (t0) REVERT: D 261 PHE cc_start: 0.8455 (t80) cc_final: 0.8203 (t80) REVERT: D 267 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8180 (mt-10) REVERT: D 276 ARG cc_start: 0.7637 (ttt90) cc_final: 0.7243 (mmm-85) REVERT: D 281 TYR cc_start: 0.7136 (p90) cc_final: 0.6528 (p90) REVERT: D 282 TYR cc_start: 0.7743 (m-80) cc_final: 0.7541 (m-80) REVERT: D 284 THR cc_start: 0.8302 (OUTLIER) cc_final: 0.8041 (p) REVERT: D 313 TYR cc_start: 0.8329 (m-80) cc_final: 0.8009 (m-80) REVERT: D 371 ARG cc_start: 0.7786 (mmt180) cc_final: 0.7523 (mpt180) REVERT: D 378 LYS cc_start: 0.8038 (mttt) cc_final: 0.7745 (mttp) REVERT: D 395 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7290 (tm-30) REVERT: D 397 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7039 (mm-30) REVERT: D 398 ARG cc_start: 0.7793 (ttt90) cc_final: 0.7513 (ttt90) REVERT: D 433 PHE cc_start: 0.7918 (t80) cc_final: 0.7280 (t80) REVERT: E 12 GLU cc_start: 0.7727 (pt0) cc_final: 0.7243 (pt0) REVERT: E 36 ASP cc_start: 0.7835 (t0) cc_final: 0.7599 (t0) REVERT: E 70 THR cc_start: 0.8144 (p) cc_final: 0.7709 (t) REVERT: E 72 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7577 (mm-30) REVERT: E 73 ASP cc_start: 0.7056 (t0) cc_final: 0.5275 (t0) REVERT: E 75 ASP cc_start: 0.6997 (m-30) cc_final: 0.5612 (m-30) REVERT: E 79 ASN cc_start: 0.7878 (p0) cc_final: 0.7596 (p0) REVERT: E 80 ARG cc_start: 0.7963 (mtt180) cc_final: 0.6896 (mtt180) REVERT: E 96 PHE cc_start: 0.7512 (m-80) cc_final: 0.7177 (m-80) REVERT: E 112 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7716 (mttt) REVERT: E 125 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6960 (mtt180) REVERT: E 132 LYS cc_start: 0.8532 (mttt) cc_final: 0.8298 (mttt) REVERT: E 144 SER cc_start: 0.8455 (t) cc_final: 0.7912 (p) REVERT: E 154 GLN cc_start: 0.7503 (tm-30) cc_final: 0.6949 (tm-30) REVERT: E 157 LYS cc_start: 0.8170 (tttt) cc_final: 0.7823 (tttt) REVERT: E 166 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6840 (mt-10) REVERT: E 177 CYS cc_start: 0.7648 (m) cc_final: 0.7189 (m) REVERT: E 181 ASN cc_start: 0.8237 (t0) cc_final: 0.7778 (t0) REVERT: E 184 ASP cc_start: 0.7025 (m-30) cc_final: 0.6692 (m-30) REVERT: E 190 LYS cc_start: 0.8172 (tptt) cc_final: 0.7892 (tptt) REVERT: E 193 LYS cc_start: 0.8404 (mttt) cc_final: 0.7751 (ttmm) REVERT: E 195 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7563 (ttm110) REVERT: E 214 GLU cc_start: 0.7626 (tt0) cc_final: 0.7291 (tt0) REVERT: E 237 SER cc_start: 0.8414 (m) cc_final: 0.7914 (p) REVERT: E 256 GLN cc_start: 0.7612 (mt0) cc_final: 0.7304 (mt0) REVERT: E 289 TYR cc_start: 0.8257 (m-80) cc_final: 0.7751 (m-80) REVERT: E 299 CYS cc_start: 0.7664 (m) cc_final: 0.7389 (m) REVERT: E 304 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7130 (tm-30) REVERT: E 329 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6418 (p0) REVERT: E 333 GLU cc_start: 0.7723 (tt0) cc_final: 0.7420 (tt0) REVERT: E 353 LYS cc_start: 0.8352 (mttt) cc_final: 0.7828 (mttt) REVERT: F 16 ASP cc_start: 0.7677 (t0) cc_final: 0.7169 (t0) REVERT: F 28 LYS cc_start: 0.8179 (tttt) cc_final: 0.7975 (tttt) REVERT: F 56 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7595 (mmtt) REVERT: F 60 ILE cc_start: 0.8625 (mt) cc_final: 0.8191 (tt) REVERT: F 109 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7482 (mt-10) REVERT: F 116 LYS cc_start: 0.8132 (mttt) cc_final: 0.7739 (mmmm) REVERT: F 139 LYS cc_start: 0.8502 (mttt) cc_final: 0.8170 (mtpp) REVERT: F 147 MET cc_start: 0.7663 (mmm) cc_final: 0.7117 (tpp) REVERT: F 172 LEU cc_start: 0.8389 (mt) cc_final: 0.8144 (mm) REVERT: F 187 GLN cc_start: 0.8315 (mt0) cc_final: 0.8074 (mt0) REVERT: F 195 VAL cc_start: 0.8559 (t) cc_final: 0.8074 (p) REVERT: F 197 ASP cc_start: 0.7952 (t0) cc_final: 0.7700 (t0) REVERT: F 200 SER cc_start: 0.8655 (t) cc_final: 0.8386 (p) REVERT: F 205 GLN cc_start: 0.8282 (mt0) cc_final: 0.8059 (mt0) REVERT: F 213 LEU cc_start: 0.8146 (tt) cc_final: 0.7942 (tt) REVERT: F 216 LYS cc_start: 0.8443 (tttt) cc_final: 0.7892 (ttpp) REVERT: F 237 GLN cc_start: 0.7378 (mt0) cc_final: 0.6822 (mt0) REVERT: F 242 ILE cc_start: 0.8210 (mt) cc_final: 0.7986 (mt) REVERT: F 249 VAL cc_start: 0.7930 (t) cc_final: 0.7649 (p) REVERT: F 252 ARG cc_start: 0.7734 (mtm180) cc_final: 0.7510 (ptp-110) REVERT: F 264 ILE cc_start: 0.8436 (mp) cc_final: 0.8146 (mm) REVERT: F 266 TYR cc_start: 0.8305 (m-80) cc_final: 0.7854 (m-80) REVERT: F 267 VAL cc_start: 0.8371 (t) cc_final: 0.7928 (m) REVERT: G 9 LEU cc_start: 0.8254 (tt) cc_final: 0.8043 (tp) REVERT: G 12 CYS cc_start: 0.8741 (p) cc_final: 0.8259 (p) REVERT: G 16 MET cc_start: 0.8527 (mmt) cc_final: 0.7549 (mmm) REVERT: G 18 GLN cc_start: 0.8579 (mm110) cc_final: 0.8191 (mm-40) REVERT: H 926 GLU cc_start: 0.6707 (OUTLIER) cc_final: 0.6306 (tp30) REVERT: K 143 GLU cc_start: 0.7716 (tt0) cc_final: 0.7222 (tt0) REVERT: K 163 LYS cc_start: 0.8026 (mttt) cc_final: 0.7725 (mttt) REVERT: K 178 MET cc_start: 0.7707 (mtm) cc_final: 0.7206 (mtm) REVERT: K 187 VAL cc_start: 0.8563 (p) cc_final: 0.8288 (m) REVERT: K 188 LYS cc_start: 0.8125 (tttt) cc_final: 0.7913 (tttt) REVERT: K 208 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7483 (tp-100) REVERT: K 212 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: K 214 MET cc_start: 0.6941 (mmt) cc_final: 0.6717 (mmt) REVERT: K 263 MET cc_start: 0.5695 (mmm) cc_final: 0.5293 (mmm) outliers start: 139 outliers final: 84 residues processed: 847 average time/residue: 0.4034 time to fit residues: 500.3804 Evaluate side-chains 874 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 766 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 GLU 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 355 CYS 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 393 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 469 THR Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 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 40 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 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 546 GLU 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 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 428 SER Chi-restraints excluded: chain C residue 429 SER 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 71 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 196 ILE 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 284 THR 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 417 ASP Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 39 PHE Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 280 THR 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 128 HIS Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 229 TRP 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 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 162 LEU Chi-restraints excluded: chain K residue 184 LEU Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG 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 92 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 274 optimal weight: 0.5980 chunk 228 optimal weight: 0.8980 chunk 127 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN B 37 HIS B 328 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 24295 Z= 0.230 Angle : 0.588 10.546 33035 Z= 0.296 Chirality : 0.041 0.200 3696 Planarity : 0.004 0.061 4058 Dihedral : 13.321 148.814 3618 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.06 % Favored : 94.90 % Rotamer: Outliers : 5.70 % Allowed : 19.49 % Favored : 74.81 % 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: 0.13 (0.16), residues: 2804 helix: 1.18 (0.15), residues: 1324 sheet: -0.26 (0.26), residues: 382 loop : -1.10 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 55 HIS 0.014 0.001 HIS D 424 PHE 0.024 0.001 PHE B 12 TYR 0.019 0.001 TYR D 316 ARG 0.010 0.001 ARG B 185 *********************** 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 927 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 784 time to evaluate : 2.797 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: 0.8339 (mttt) cc_final: 0.7994 (mptt) REVERT: A 64 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8121 (mm110) REVERT: A 65 MET cc_start: 0.7582 (ptt) cc_final: 0.7274 (ptt) REVERT: A 68 LYS cc_start: 0.6404 (mtmt) cc_final: 0.5779 (tttm) REVERT: A 94 LYS cc_start: 0.7811 (ptpt) cc_final: 0.7346 (ptpt) REVERT: A 98 ASP cc_start: 0.7478 (m-30) cc_final: 0.7146 (m-30) REVERT: A 117 LYS cc_start: 0.8179 (tttt) cc_final: 0.7881 (tttt) REVERT: A 121 TYR cc_start: 0.7201 (m-80) cc_final: 0.6835 (m-80) REVERT: A 146 THR cc_start: 0.7650 (p) cc_final: 0.7223 (p) REVERT: A 157 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7650 (ttpp) REVERT: A 160 THR cc_start: 0.8057 (m) cc_final: 0.7825 (t) REVERT: A 163 TYR cc_start: 0.8060 (t80) cc_final: 0.7675 (t80) REVERT: A 167 LYS cc_start: 0.7632 (mttp) cc_final: 0.7096 (mtpp) REVERT: A 169 VAL cc_start: 0.8351 (p) cc_final: 0.7992 (m) REVERT: A 173 ASN cc_start: 0.8008 (m-40) cc_final: 0.6397 (m-40) REVERT: A 174 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7001 (mtp-110) REVERT: A 175 TYR cc_start: 0.8088 (m-80) cc_final: 0.7882 (m-10) REVERT: A 178 GLU cc_start: 0.6684 (pm20) cc_final: 0.6407 (pm20) REVERT: A 191 ASP cc_start: 0.7895 (t0) cc_final: 0.7558 (t0) REVERT: A 203 GLU cc_start: 0.6474 (OUTLIER) cc_final: 0.6208 (pm20) REVERT: A 273 LYS cc_start: 0.8200 (ttmt) cc_final: 0.7568 (tppp) REVERT: A 275 GLU cc_start: 0.7973 (pm20) cc_final: 0.7740 (pm20) REVERT: A 287 LEU cc_start: 0.8612 (mt) cc_final: 0.8051 (mt) REVERT: A 288 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7291 (mp0) REVERT: A 294 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6587 (mm-30) REVERT: A 299 ASN cc_start: 0.8011 (p0) cc_final: 0.7528 (p0) REVERT: A 309 ASP cc_start: 0.6981 (p0) cc_final: 0.6666 (p0) REVERT: A 310 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7883 (pt) REVERT: A 321 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7216 (tm-30) REVERT: A 332 ARG cc_start: 0.8153 (mpp80) cc_final: 0.7104 (mtp85) REVERT: A 334 ARG cc_start: 0.7060 (ptp90) cc_final: 0.6303 (ptp90) REVERT: A 347 SER cc_start: 0.8647 (m) cc_final: 0.7929 (t) REVERT: A 372 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6770 (tp30) REVERT: A 375 LYS cc_start: 0.8225 (tttm) cc_final: 0.7934 (ttpp) REVERT: A 389 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7300 (tt) REVERT: A 418 LYS cc_start: 0.7797 (tmmt) cc_final: 0.7500 (tmmt) REVERT: A 419 ARG cc_start: 0.7772 (ttm170) cc_final: 0.7437 (tpp80) REVERT: A 424 GLU cc_start: 0.8013 (tp30) cc_final: 0.7423 (tp30) REVERT: A 434 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7511 (mm-30) REVERT: A 457 ILE cc_start: 0.8345 (tt) cc_final: 0.7977 (tt) REVERT: A 476 LYS cc_start: 0.8114 (mttt) cc_final: 0.7601 (mttm) REVERT: A 487 LYS cc_start: 0.8281 (ttmt) cc_final: 0.7761 (tttt) REVERT: A 490 GLU cc_start: 0.6746 (mp0) cc_final: 0.6101 (mm-30) REVERT: A 504 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8127 (ttmt) REVERT: A 505 VAL cc_start: 0.8387 (OUTLIER) cc_final: 0.8040 (m) REVERT: A 517 GLU cc_start: 0.7575 (mp0) cc_final: 0.6831 (mp0) REVERT: A 525 ILE cc_start: 0.8303 (tp) cc_final: 0.7994 (tp) REVERT: A 526 LYS cc_start: 0.7912 (tmtt) cc_final: 0.7379 (tppt) REVERT: A 528 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8070 (mptt) REVERT: A 556 ASP cc_start: 0.7313 (m-30) cc_final: 0.6883 (m-30) REVERT: A 564 ASN cc_start: 0.8389 (t0) cc_final: 0.7645 (t0) REVERT: A 569 LYS cc_start: 0.8023 (mmmt) cc_final: 0.7647 (mmmt) REVERT: A 570 GLU cc_start: 0.7574 (pm20) cc_final: 0.7125 (pm20) REVERT: A 586 GLN cc_start: 0.8428 (tp40) cc_final: 0.8085 (tp40) REVERT: A 588 GLU cc_start: 0.7469 (tp30) cc_final: 0.6649 (tp30) REVERT: A 632 SER cc_start: 0.8308 (p) cc_final: 0.7825 (p) REVERT: A 642 ARG cc_start: 0.7259 (mtp85) cc_final: 0.6526 (mmt180) REVERT: A 658 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.7383 (p90) REVERT: A 659 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.6764 (p90) REVERT: A 669 GLU cc_start: 0.7520 (tt0) cc_final: 0.7247 (tt0) REVERT: A 676 ARG cc_start: 0.7864 (ptm160) cc_final: 0.7146 (ttm170) REVERT: A 677 GLN cc_start: 0.7620 (mt0) cc_final: 0.7150 (mt0) REVERT: A 682 ASP cc_start: 0.6976 (m-30) cc_final: 0.6750 (m-30) REVERT: A 683 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7053 (mm-40) REVERT: A 696 MET cc_start: 0.7612 (mmm) cc_final: 0.7004 (tmm) REVERT: A 704 SER cc_start: 0.8404 (p) cc_final: 0.8189 (p) REVERT: A 706 LYS cc_start: 0.7857 (tmmt) cc_final: 0.7270 (tmmt) REVERT: A 710 GLN cc_start: 0.7878 (pp30) cc_final: 0.7556 (pp30) REVERT: B 1 MET cc_start: 0.6199 (OUTLIER) cc_final: 0.5810 (ppp) REVERT: B 25 MET cc_start: 0.7868 (mmm) cc_final: 0.7640 (mmm) REVERT: B 40 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8222 (mt) REVERT: B 42 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7231 (mtm) REVERT: B 75 ARG cc_start: 0.7389 (ttp80) cc_final: 0.7050 (ttp80) REVERT: B 91 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7702 (mm) REVERT: B 113 LYS cc_start: 0.8119 (ttpp) cc_final: 0.7724 (ttmm) REVERT: B 158 TYR cc_start: 0.7450 (t80) cc_final: 0.6945 (t80) REVERT: B 196 ARG cc_start: 0.8133 (mmp80) cc_final: 0.7715 (mmp80) REVERT: B 243 CYS cc_start: 0.8559 (m) cc_final: 0.8169 (m) REVERT: B 247 MET cc_start: 0.8057 (mtt) cc_final: 0.7392 (mpp) REVERT: B 384 HIS cc_start: 0.5160 (OUTLIER) cc_final: 0.4829 (p-80) REVERT: B 414 PHE cc_start: 0.7345 (m-80) cc_final: 0.6455 (m-80) REVERT: B 416 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.7030 (mt) REVERT: B 438 MET cc_start: 0.8077 (mtm) cc_final: 0.7647 (mtm) REVERT: B 445 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7903 (mmtt) REVERT: B 455 ILE cc_start: 0.7994 (mm) cc_final: 0.7507 (mm) REVERT: B 512 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7293 (mm-30) REVERT: B 518 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7788 (mtp-110) REVERT: B 545 MET cc_start: 0.8015 (tmm) cc_final: 0.7465 (ttp) REVERT: B 548 THR cc_start: 0.8682 (m) cc_final: 0.8323 (t) REVERT: B 570 GLU cc_start: 0.6320 (tm-30) cc_final: 0.5742 (tm-30) REVERT: B 586 GLU cc_start: 0.7546 (pp20) cc_final: 0.7176 (pp20) REVERT: B 589 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6570 (tm-30) REVERT: B 603 LYS cc_start: 0.7815 (ptmm) cc_final: 0.7603 (ptmm) REVERT: B 620 MET cc_start: 0.7794 (mmm) cc_final: 0.6958 (mmm) REVERT: B 633 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7344 (tp) REVERT: B 641 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7391 (mtm-85) REVERT: B 664 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8180 (p) REVERT: B 681 ASP cc_start: 0.7867 (t0) cc_final: 0.7614 (t0) REVERT: B 688 ASP cc_start: 0.8046 (p0) cc_final: 0.7780 (p0) REVERT: B 692 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7809 (mptt) REVERT: B 707 ASN cc_start: 0.7576 (t0) cc_final: 0.7337 (t0) REVERT: B 712 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6392 (pt0) REVERT: B 724 MET cc_start: 0.7294 (mmm) cc_final: 0.6803 (mmm) REVERT: C 408 ARG cc_start: 0.7968 (ttt180) cc_final: 0.7616 (ttm-80) REVERT: C 411 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7681 (tpp) REVERT: C 441 MET cc_start: 0.6812 (mmm) cc_final: 0.6363 (mmt) REVERT: C 442 GLN cc_start: 0.5416 (OUTLIER) cc_final: 0.4566 (pp30) REVERT: C 473 ARG cc_start: 0.8003 (tmt170) cc_final: 0.7765 (ttt180) REVERT: C 475 PHE cc_start: 0.7796 (t80) cc_final: 0.7183 (t80) REVERT: C 493 MET cc_start: 0.8117 (tpp) cc_final: 0.7820 (mpp) REVERT: C 501 GLN cc_start: 0.7855 (tp40) cc_final: 0.7430 (tp40) REVERT: D 20 GLN cc_start: 0.8687 (mt0) cc_final: 0.8355 (mp10) REVERT: D 33 ARG cc_start: 0.8264 (mmm-85) cc_final: 0.7974 (mtm-85) REVERT: D 40 THR cc_start: 0.8118 (p) cc_final: 0.7888 (p) REVERT: D 50 SER cc_start: 0.7702 (m) cc_final: 0.6866 (p) REVERT: D 77 LYS cc_start: 0.8298 (mttt) cc_final: 0.7996 (mttt) REVERT: D 78 GLU cc_start: 0.7986 (pt0) cc_final: 0.7548 (pt0) REVERT: D 79 PHE cc_start: 0.8108 (m-80) cc_final: 0.7714 (m-80) REVERT: D 81 LYS cc_start: 0.8860 (tttt) cc_final: 0.8615 (tttt) REVERT: D 85 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7625 (mt-10) REVERT: D 94 ARG cc_start: 0.7436 (mtp-110) cc_final: 0.6886 (mtp-110) REVERT: D 140 LYS cc_start: 0.7530 (pttm) cc_final: 0.6904 (mmtm) REVERT: D 154 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7592 (mt-10) REVERT: D 155 ARG cc_start: 0.8303 (mmm160) cc_final: 0.8017 (mmm160) REVERT: D 173 GLN cc_start: 0.8988 (tt0) cc_final: 0.8442 (pp30) REVERT: D 174 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8324 (p0) REVERT: D 177 GLN cc_start: 0.8064 (pt0) cc_final: 0.7647 (pp30) REVERT: D 178 LEU cc_start: 0.8792 (tt) cc_final: 0.8463 (pp) REVERT: D 185 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6890 (mpp) REVERT: D 201 PHE cc_start: 0.8450 (m-80) cc_final: 0.8134 (m-80) REVERT: D 216 MET cc_start: 0.7993 (mmm) cc_final: 0.7763 (mmm) REVERT: D 218 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7366 (tm-30) REVERT: D 243 SER cc_start: 0.8215 (m) cc_final: 0.7800 (p) REVERT: D 244 THR cc_start: 0.7954 (m) cc_final: 0.7678 (t) REVERT: D 258 LEU cc_start: 0.8406 (mt) cc_final: 0.7974 (tp) REVERT: D 260 ASN cc_start: 0.8095 (t0) cc_final: 0.7623 (t0) REVERT: D 261 PHE cc_start: 0.8443 (t80) cc_final: 0.8235 (t80) REVERT: D 267 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8175 (mt-10) REVERT: D 276 ARG cc_start: 0.7715 (ttt90) cc_final: 0.7316 (mmm-85) REVERT: D 281 TYR cc_start: 0.7151 (p90) cc_final: 0.6691 (p90) REVERT: D 284 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.8024 (p) REVERT: D 313 TYR cc_start: 0.8322 (m-80) cc_final: 0.8008 (m-80) REVERT: D 362 GLN cc_start: 0.7903 (tp40) cc_final: 0.7613 (tp40) REVERT: D 371 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7539 (mpt180) REVERT: D 378 LYS cc_start: 0.8030 (mttt) cc_final: 0.7754 (mttp) REVERT: D 397 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7041 (mm-30) REVERT: D 398 ARG cc_start: 0.7821 (ttt90) cc_final: 0.7522 (ttt90) REVERT: D 426 ARG cc_start: 0.8688 (tpp80) cc_final: 0.8480 (tpp80) REVERT: D 433 PHE cc_start: 0.7954 (t80) cc_final: 0.7282 (t80) REVERT: E 12 GLU cc_start: 0.7661 (pt0) cc_final: 0.7171 (pt0) REVERT: E 36 ASP cc_start: 0.7843 (t0) cc_final: 0.7620 (t0) REVERT: E 70 THR cc_start: 0.8162 (p) cc_final: 0.7741 (t) REVERT: E 72 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7605 (mm-30) REVERT: E 73 ASP cc_start: 0.7080 (t0) cc_final: 0.5252 (t0) REVERT: E 75 ASP cc_start: 0.7002 (m-30) cc_final: 0.5586 (m-30) REVERT: E 79 ASN cc_start: 0.7882 (p0) cc_final: 0.7596 (p0) REVERT: E 80 ARG cc_start: 0.7992 (mtt180) cc_final: 0.6881 (mtt180) REVERT: E 96 PHE cc_start: 0.7595 (m-80) cc_final: 0.7266 (m-80) REVERT: E 103 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7643 (mt0) REVERT: E 112 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7593 (mttt) REVERT: E 119 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7275 (tm-30) REVERT: E 125 ARG cc_start: 0.7317 (mtt180) cc_final: 0.6954 (mtt180) REVERT: E 132 LYS cc_start: 0.8557 (mttt) cc_final: 0.8342 (mttt) REVERT: E 144 SER cc_start: 0.8456 (t) cc_final: 0.7914 (p) REVERT: E 154 GLN cc_start: 0.7500 (tm-30) cc_final: 0.6973 (tm-30) REVERT: E 157 LYS cc_start: 0.8197 (tttt) cc_final: 0.7823 (tttt) REVERT: E 166 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6806 (mt-10) REVERT: E 177 CYS cc_start: 0.7655 (m) cc_final: 0.7367 (t) REVERT: E 181 ASN cc_start: 0.8222 (t0) cc_final: 0.7769 (t0) REVERT: E 184 ASP cc_start: 0.7037 (m-30) cc_final: 0.6719 (m-30) REVERT: E 193 LYS cc_start: 0.8416 (mttt) cc_final: 0.7748 (ttmm) REVERT: E 195 ARG cc_start: 0.7794 (ttm110) cc_final: 0.7555 (ttm110) REVERT: E 214 GLU cc_start: 0.7641 (tt0) cc_final: 0.7292 (tt0) REVERT: E 237 SER cc_start: 0.8529 (m) cc_final: 0.8032 (p) REVERT: E 256 GLN cc_start: 0.7752 (mt0) cc_final: 0.7414 (mt0) REVERT: E 289 TYR cc_start: 0.8222 (m-80) cc_final: 0.7878 (m-80) REVERT: E 299 CYS cc_start: 0.7644 (m) cc_final: 0.7393 (m) REVERT: E 304 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7129 (tm-30) REVERT: E 333 GLU cc_start: 0.7731 (tt0) cc_final: 0.7456 (tt0) REVERT: E 353 LYS cc_start: 0.8349 (mttt) cc_final: 0.7836 (mttt) REVERT: F 16 ASP cc_start: 0.7706 (t0) cc_final: 0.7210 (t0) REVERT: F 28 LYS cc_start: 0.8231 (tttt) cc_final: 0.8015 (tttt) REVERT: F 56 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7599 (mmtt) REVERT: F 60 ILE cc_start: 0.8663 (mt) cc_final: 0.8231 (tt) REVERT: F 109 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7483 (mt-10) REVERT: F 116 LYS cc_start: 0.8166 (mttt) cc_final: 0.7782 (mmmm) REVERT: F 139 LYS cc_start: 0.8507 (mttt) cc_final: 0.8198 (mtpp) REVERT: F 147 MET cc_start: 0.7671 (mmm) cc_final: 0.7147 (tpp) REVERT: F 172 LEU cc_start: 0.8406 (mt) cc_final: 0.8165 (mm) REVERT: F 187 GLN cc_start: 0.8377 (mt0) cc_final: 0.8081 (mt0) REVERT: F 195 VAL cc_start: 0.8565 (t) cc_final: 0.8220 (p) REVERT: F 197 ASP cc_start: 0.7961 (t0) cc_final: 0.7648 (t0) REVERT: F 200 SER cc_start: 0.8649 (t) cc_final: 0.8376 (p) REVERT: F 205 GLN cc_start: 0.8270 (mt0) cc_final: 0.8039 (mt0) REVERT: F 213 LEU cc_start: 0.8110 (tt) cc_final: 0.7889 (tt) REVERT: F 216 LYS cc_start: 0.8436 (tttt) cc_final: 0.7895 (ttpp) REVERT: F 237 GLN cc_start: 0.7371 (mt0) cc_final: 0.6903 (mt0) REVERT: F 249 VAL cc_start: 0.7948 (t) cc_final: 0.7667 (p) REVERT: F 252 ARG cc_start: 0.7754 (mtm180) cc_final: 0.7552 (ptp-110) REVERT: F 264 ILE cc_start: 0.8449 (mp) cc_final: 0.8172 (mm) REVERT: F 266 TYR cc_start: 0.8352 (m-80) cc_final: 0.7882 (m-80) REVERT: F 267 VAL cc_start: 0.8310 (t) cc_final: 0.7912 (m) REVERT: F 278 PHE cc_start: 0.8434 (t80) cc_final: 0.8142 (t80) REVERT: G 16 MET cc_start: 0.8474 (mmt) cc_final: 0.7628 (mmm) REVERT: G 18 GLN cc_start: 0.8575 (mm110) cc_final: 0.8280 (mm-40) REVERT: G 54 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: H 926 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6303 (tp30) REVERT: K 163 LYS cc_start: 0.8027 (mttt) cc_final: 0.7762 (mttt) REVERT: K 178 MET cc_start: 0.7737 (mtm) cc_final: 0.7201 (mtm) REVERT: K 208 GLN cc_start: 0.7851 (tp-100) cc_final: 0.7486 (tp-100) REVERT: K 212 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: K 263 MET cc_start: 0.5686 (mmm) cc_final: 0.5322 (mmm) outliers start: 143 outliers final: 101 residues processed: 853 average time/residue: 0.3972 time to fit residues: 495.0405 Evaluate side-chains 905 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 779 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 GLU 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 355 CYS 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 389 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU 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 40 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 432 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 546 GLU 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 418 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 SER 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 C residue 531 THR 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 163 MET Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 196 ILE 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 271 VAL 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 340 ASN Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 39 PHE 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 175 THR Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 280 THR 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 128 HIS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 229 TRP 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 177 ASP Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 chunk 200 optimal weight: 0.2980 chunk 155 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 273 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 126 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 499 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN B 37 HIS ** B 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24295 Z= 0.202 Angle : 0.584 10.742 33035 Z= 0.293 Chirality : 0.041 0.184 3696 Planarity : 0.004 0.063 4058 Dihedral : 13.288 149.001 3618 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.74 % Favored : 95.22 % Rotamer: Outliers : 5.74 % Allowed : 19.85 % Favored : 74.41 % 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: 0.16 (0.16), residues: 2804 helix: 1.16 (0.15), residues: 1325 sheet: -0.17 (0.27), residues: 375 loop : -1.07 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP D 55 HIS 0.014 0.001 HIS D 424 PHE 0.022 0.001 PHE B 12 TYR 0.020 0.001 TYR D 316 ARG 0.007 0.000 ARG B 185 *********************** 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 921 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 777 time to evaluate : 2.695 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: 0.8328 (mttt) cc_final: 0.8003 (mptt) REVERT: A 64 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8162 (mm110) REVERT: A 65 MET cc_start: 0.7584 (ptt) cc_final: 0.7302 (ptt) REVERT: A 68 LYS cc_start: 0.6427 (mtmt) cc_final: 0.5753 (tttm) REVERT: A 94 LYS cc_start: 0.7810 (ptpt) cc_final: 0.7323 (ptpt) REVERT: A 98 ASP cc_start: 0.7467 (m-30) cc_final: 0.7130 (m-30) REVERT: A 117 LYS cc_start: 0.8124 (tttt) cc_final: 0.7765 (tppt) REVERT: A 121 TYR cc_start: 0.7193 (m-80) cc_final: 0.6758 (m-80) REVERT: A 146 THR cc_start: 0.7700 (p) cc_final: 0.7349 (p) REVERT: A 157 LYS cc_start: 0.8140 (ptmm) cc_final: 0.7718 (ttpp) REVERT: A 163 TYR cc_start: 0.8055 (t80) cc_final: 0.7629 (t80) REVERT: A 167 LYS cc_start: 0.7654 (mttp) cc_final: 0.7080 (mtpp) REVERT: A 169 VAL cc_start: 0.8358 (p) cc_final: 0.8015 (m) REVERT: A 173 ASN cc_start: 0.7978 (m-40) cc_final: 0.6353 (m-40) REVERT: A 174 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7115 (mtp-110) REVERT: A 175 TYR cc_start: 0.8144 (m-80) cc_final: 0.7487 (m-80) REVERT: A 176 PHE cc_start: 0.7671 (m-10) cc_final: 0.7032 (m-80) REVERT: A 178 GLU cc_start: 0.6678 (pm20) cc_final: 0.6415 (pm20) REVERT: A 191 ASP cc_start: 0.7908 (t0) cc_final: 0.7562 (t0) REVERT: A 203 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.6138 (pm20) REVERT: A 273 LYS cc_start: 0.8225 (ttmt) cc_final: 0.7576 (tppp) REVERT: A 275 GLU cc_start: 0.7971 (pm20) cc_final: 0.7693 (pm20) REVERT: A 287 LEU cc_start: 0.8603 (mt) cc_final: 0.8040 (mt) REVERT: A 288 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7303 (mp0) REVERT: A 294 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6904 (mm-30) REVERT: A 299 ASN cc_start: 0.7999 (p0) cc_final: 0.7556 (p0) REVERT: A 321 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7245 (tm-30) REVERT: A 332 ARG cc_start: 0.8123 (mpp80) cc_final: 0.7504 (mtp85) REVERT: A 347 SER cc_start: 0.8644 (m) cc_final: 0.7936 (t) REVERT: A 375 LYS cc_start: 0.8235 (tttm) cc_final: 0.7917 (ttpp) REVERT: A 389 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7436 (tt) REVERT: A 418 LYS cc_start: 0.7756 (tmmt) cc_final: 0.7410 (tmmt) REVERT: A 419 ARG cc_start: 0.7736 (ttm170) cc_final: 0.7132 (tpp80) REVERT: A 424 GLU cc_start: 0.8032 (tp30) cc_final: 0.7409 (tp30) REVERT: A 434 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7530 (mm-30) REVERT: A 457 ILE cc_start: 0.8308 (tt) cc_final: 0.7942 (tt) REVERT: A 476 LYS cc_start: 0.8111 (mttt) cc_final: 0.7635 (mttm) REVERT: A 487 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7738 (tttt) REVERT: A 490 GLU cc_start: 0.6753 (mp0) cc_final: 0.6089 (mm-30) REVERT: A 504 LYS cc_start: 0.8513 (ttpt) cc_final: 0.8147 (ttmt) REVERT: A 505 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.8035 (m) REVERT: A 517 GLU cc_start: 0.7607 (mp0) cc_final: 0.6825 (mp0) REVERT: A 520 ARG cc_start: 0.7540 (mmm160) cc_final: 0.6590 (tpt-90) REVERT: A 525 ILE cc_start: 0.8306 (tp) cc_final: 0.7992 (tp) REVERT: A 526 LYS cc_start: 0.7882 (tmtt) cc_final: 0.7292 (tppt) REVERT: A 528 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8062 (mptt) REVERT: A 556 ASP cc_start: 0.7295 (m-30) cc_final: 0.6879 (m-30) REVERT: A 564 ASN cc_start: 0.8429 (t0) cc_final: 0.7659 (t0) REVERT: A 569 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7666 (mmmt) REVERT: A 570 GLU cc_start: 0.7594 (pm20) cc_final: 0.7142 (pm20) REVERT: A 586 GLN cc_start: 0.8426 (tp40) cc_final: 0.8095 (tp40) REVERT: A 588 GLU cc_start: 0.7463 (tp30) cc_final: 0.6630 (tp30) REVERT: A 632 SER cc_start: 0.8257 (p) cc_final: 0.7838 (p) REVERT: A 636 GLU cc_start: 0.7055 (tp30) cc_final: 0.6850 (tp30) REVERT: A 642 ARG cc_start: 0.7253 (mtp85) cc_final: 0.6745 (mmt-90) REVERT: A 658 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.7355 (p90) REVERT: A 659 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.6666 (p90) REVERT: A 669 GLU cc_start: 0.7499 (tt0) cc_final: 0.7239 (tt0) REVERT: A 670 MET cc_start: 0.8162 (mmm) cc_final: 0.7945 (mmm) REVERT: A 676 ARG cc_start: 0.7894 (ptm160) cc_final: 0.7522 (ptp-170) REVERT: A 677 GLN cc_start: 0.7565 (mt0) cc_final: 0.7159 (mt0) REVERT: A 682 ASP cc_start: 0.6967 (m-30) cc_final: 0.6729 (m-30) REVERT: A 683 GLN cc_start: 0.7458 (mm-40) cc_final: 0.7045 (mm-40) REVERT: A 692 LYS cc_start: 0.8095 (tptm) cc_final: 0.7447 (tptt) REVERT: A 696 MET cc_start: 0.7537 (mmm) cc_final: 0.7130 (tmm) REVERT: A 704 SER cc_start: 0.8399 (p) cc_final: 0.8169 (p) REVERT: A 706 LYS cc_start: 0.7877 (tmmt) cc_final: 0.7292 (tmmt) REVERT: A 710 GLN cc_start: 0.7886 (pp30) cc_final: 0.7483 (pp30) REVERT: B 1 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.5916 (ppp) REVERT: B 25 MET cc_start: 0.7897 (mmm) cc_final: 0.7671 (mmm) REVERT: B 40 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8143 (mt) REVERT: B 42 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7122 (mtp) REVERT: B 75 ARG cc_start: 0.7322 (ttp80) cc_final: 0.6998 (ttp80) REVERT: B 91 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7664 (mm) REVERT: B 113 LYS cc_start: 0.8148 (ttpp) cc_final: 0.7754 (ttmm) REVERT: B 158 TYR cc_start: 0.7445 (t80) cc_final: 0.6947 (t80) REVERT: B 196 ARG cc_start: 0.8151 (mmp80) cc_final: 0.7632 (mmp80) REVERT: B 243 CYS cc_start: 0.8579 (m) cc_final: 0.8204 (m) REVERT: B 247 MET cc_start: 0.8081 (mtt) cc_final: 0.7459 (mpp) REVERT: B 384 HIS cc_start: 0.5149 (OUTLIER) cc_final: 0.4815 (p-80) REVERT: B 414 PHE cc_start: 0.7383 (m-80) cc_final: 0.6660 (m-80) REVERT: B 416 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7056 (tt) REVERT: B 438 MET cc_start: 0.8085 (mtm) cc_final: 0.7456 (mtm) REVERT: B 455 ILE cc_start: 0.8016 (mm) cc_final: 0.7570 (mm) REVERT: B 512 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7318 (mm-30) REVERT: B 518 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7816 (mtp-110) REVERT: B 526 GLU cc_start: 0.7645 (pt0) cc_final: 0.7379 (pt0) REVERT: B 533 ASP cc_start: 0.6869 (p0) cc_final: 0.6433 (p0) REVERT: B 545 MET cc_start: 0.8028 (tmm) cc_final: 0.7604 (ttp) REVERT: B 570 GLU cc_start: 0.6381 (tm-30) cc_final: 0.5798 (tm-30) REVERT: B 586 GLU cc_start: 0.7572 (pp20) cc_final: 0.7181 (pp20) REVERT: B 589 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6169 (tm-30) REVERT: B 620 MET cc_start: 0.7784 (mmm) cc_final: 0.6958 (mmm) REVERT: B 641 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7354 (mtm-85) REVERT: B 648 GLU cc_start: 0.7022 (tm-30) cc_final: 0.6552 (tm-30) REVERT: B 664 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8177 (p) REVERT: B 672 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8581 (t) REVERT: B 681 ASP cc_start: 0.7876 (t0) cc_final: 0.7626 (t0) REVERT: B 688 ASP cc_start: 0.8030 (p0) cc_final: 0.7727 (p0) REVERT: B 692 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7812 (mptt) REVERT: B 707 ASN cc_start: 0.7538 (t0) cc_final: 0.7281 (t0) REVERT: B 712 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6392 (pt0) REVERT: B 724 MET cc_start: 0.7310 (mmm) cc_final: 0.6840 (mmm) REVERT: C 411 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7714 (tpp) REVERT: C 441 MET cc_start: 0.6799 (mmm) cc_final: 0.6419 (mmt) REVERT: C 442 GLN cc_start: 0.5342 (OUTLIER) cc_final: 0.4449 (pp30) REVERT: C 473 ARG cc_start: 0.8009 (tmt170) cc_final: 0.7772 (ttt180) REVERT: C 475 PHE cc_start: 0.7866 (t80) cc_final: 0.7214 (t80) REVERT: C 493 MET cc_start: 0.8117 (tpp) cc_final: 0.7809 (mpp) REVERT: C 501 GLN cc_start: 0.7891 (tp40) cc_final: 0.7481 (tp40) REVERT: D 20 GLN cc_start: 0.8601 (mt0) cc_final: 0.8301 (mp10) REVERT: D 33 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.8064 (mtp-110) REVERT: D 40 THR cc_start: 0.8153 (p) cc_final: 0.7921 (p) REVERT: D 50 SER cc_start: 0.7477 (m) cc_final: 0.6619 (p) REVERT: D 78 GLU cc_start: 0.8011 (pt0) cc_final: 0.7562 (pt0) REVERT: D 79 PHE cc_start: 0.8110 (m-80) cc_final: 0.7780 (m-80) REVERT: D 81 LYS cc_start: 0.8870 (tttt) cc_final: 0.8578 (tttt) REVERT: D 85 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7705 (mt-10) REVERT: D 94 ARG cc_start: 0.7471 (mtp-110) cc_final: 0.6983 (mtp-110) REVERT: D 140 LYS cc_start: 0.7576 (pttm) cc_final: 0.6957 (mmtm) REVERT: D 153 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7609 (mm-30) REVERT: D 154 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7639 (mt-10) REVERT: D 173 GLN cc_start: 0.8997 (tt0) cc_final: 0.8433 (pp30) REVERT: D 174 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8312 (p0) REVERT: D 177 GLN cc_start: 0.8075 (pt0) cc_final: 0.7648 (pp30) REVERT: D 178 LEU cc_start: 0.8780 (tt) cc_final: 0.8433 (pp) REVERT: D 185 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6910 (mpp) REVERT: D 201 PHE cc_start: 0.8491 (m-80) cc_final: 0.8202 (m-80) REVERT: D 218 GLN cc_start: 0.7899 (mm-40) cc_final: 0.7393 (tm-30) REVERT: D 243 SER cc_start: 0.8226 (m) cc_final: 0.7848 (p) REVERT: D 244 THR cc_start: 0.8040 (m) cc_final: 0.7755 (t) REVERT: D 254 MET cc_start: 0.7153 (mtt) cc_final: 0.6293 (mtt) REVERT: D 258 LEU cc_start: 0.8262 (mt) cc_final: 0.7888 (tp) REVERT: D 260 ASN cc_start: 0.8065 (t0) cc_final: 0.7777 (t0) REVERT: D 267 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8195 (mt-10) REVERT: D 276 ARG cc_start: 0.7716 (ttt90) cc_final: 0.7326 (mmm-85) REVERT: D 282 TYR cc_start: 0.7779 (m-80) cc_final: 0.7540 (m-80) REVERT: D 284 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.8025 (p) REVERT: D 313 TYR cc_start: 0.8327 (m-80) cc_final: 0.8016 (m-80) REVERT: D 316 TYR cc_start: 0.8254 (m-80) cc_final: 0.8038 (m-80) REVERT: D 362 GLN cc_start: 0.7903 (tp40) cc_final: 0.7576 (tp40) REVERT: D 369 ARG cc_start: 0.7540 (tpt90) cc_final: 0.7210 (tpt90) REVERT: D 371 ARG cc_start: 0.7779 (mmt180) cc_final: 0.7482 (mpt180) REVERT: D 378 LYS cc_start: 0.8034 (mttt) cc_final: 0.7788 (mttp) REVERT: D 395 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7263 (tm-30) REVERT: D 397 GLU cc_start: 0.7296 (mm-30) cc_final: 0.7054 (mm-30) REVERT: D 398 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7475 (ttt90) REVERT: D 426 ARG cc_start: 0.8719 (tpp80) cc_final: 0.8493 (tpp80) REVERT: D 433 PHE cc_start: 0.7975 (t80) cc_final: 0.7484 (t80) REVERT: E 12 GLU cc_start: 0.7740 (pt0) cc_final: 0.7271 (pt0) REVERT: E 36 ASP cc_start: 0.7845 (t0) cc_final: 0.7610 (t0) REVERT: E 70 THR cc_start: 0.8150 (p) cc_final: 0.7731 (t) REVERT: E 72 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7607 (mm-30) REVERT: E 73 ASP cc_start: 0.7212 (t0) cc_final: 0.5412 (t0) REVERT: E 75 ASP cc_start: 0.7001 (m-30) cc_final: 0.5544 (m-30) REVERT: E 79 ASN cc_start: 0.7899 (p0) cc_final: 0.7628 (p0) REVERT: E 80 ARG cc_start: 0.7989 (mtt180) cc_final: 0.6878 (mtt180) REVERT: E 96 PHE cc_start: 0.7549 (m-80) cc_final: 0.7233 (m-80) REVERT: E 112 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7604 (mttt) REVERT: E 119 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7416 (tm-30) REVERT: E 125 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6594 (mtt180) REVERT: E 132 LYS cc_start: 0.8559 (mttt) cc_final: 0.8345 (mttt) REVERT: E 144 SER cc_start: 0.8438 (t) cc_final: 0.7919 (p) REVERT: E 154 GLN cc_start: 0.7484 (tm-30) cc_final: 0.6871 (tm-30) REVERT: E 157 LYS cc_start: 0.8172 (tttt) cc_final: 0.7827 (tttt) REVERT: E 166 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6810 (mt-10) REVERT: E 177 CYS cc_start: 0.7636 (m) cc_final: 0.7342 (t) REVERT: E 181 ASN cc_start: 0.8209 (t0) cc_final: 0.7786 (t0) REVERT: E 184 ASP cc_start: 0.7037 (m-30) cc_final: 0.6767 (m-30) REVERT: E 193 LYS cc_start: 0.8455 (mttt) cc_final: 0.7765 (ttmm) REVERT: E 195 ARG cc_start: 0.7785 (ttm110) cc_final: 0.7561 (ttm110) REVERT: E 214 GLU cc_start: 0.7633 (tt0) cc_final: 0.7292 (tt0) REVERT: E 223 LEU cc_start: 0.8502 (tp) cc_final: 0.8140 (mt) REVERT: E 237 SER cc_start: 0.8540 (m) cc_final: 0.8049 (p) REVERT: E 256 GLN cc_start: 0.7692 (mt0) cc_final: 0.7378 (mt0) REVERT: E 289 TYR cc_start: 0.8249 (m-80) cc_final: 0.7829 (m-80) REVERT: E 299 CYS cc_start: 0.7634 (m) cc_final: 0.7392 (m) REVERT: E 300 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6668 (mt-10) REVERT: E 304 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7126 (tm-30) REVERT: E 333 GLU cc_start: 0.7715 (tt0) cc_final: 0.7510 (tt0) REVERT: E 353 LYS cc_start: 0.8360 (mttt) cc_final: 0.7851 (mttt) REVERT: F 16 ASP cc_start: 0.7745 (t0) cc_final: 0.7259 (t0) REVERT: F 28 LYS cc_start: 0.8281 (tttt) cc_final: 0.8055 (tttt) REVERT: F 56 LYS cc_start: 0.7780 (mmtt) cc_final: 0.7573 (mmtt) REVERT: F 109 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7508 (mt-10) REVERT: F 116 LYS cc_start: 0.8179 (mttt) cc_final: 0.7787 (mmmm) REVERT: F 139 LYS cc_start: 0.8514 (mttt) cc_final: 0.8209 (mtpp) REVERT: F 172 LEU cc_start: 0.8412 (mt) cc_final: 0.8160 (mm) REVERT: F 187 GLN cc_start: 0.8394 (mt0) cc_final: 0.8116 (mt0) REVERT: F 194 CYS cc_start: 0.7806 (t) cc_final: 0.7284 (t) REVERT: F 195 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.8166 (p) REVERT: F 197 ASP cc_start: 0.7956 (t0) cc_final: 0.7622 (t0) REVERT: F 200 SER cc_start: 0.8643 (OUTLIER) cc_final: 0.8396 (p) REVERT: F 205 GLN cc_start: 0.8273 (mt0) cc_final: 0.8002 (mt0) REVERT: F 216 LYS cc_start: 0.8549 (tttt) cc_final: 0.7999 (ttpp) REVERT: F 237 GLN cc_start: 0.7369 (mt0) cc_final: 0.6919 (mt0) REVERT: F 240 GLN cc_start: 0.7595 (mm-40) cc_final: 0.7229 (mt0) REVERT: F 242 ILE cc_start: 0.8072 (mt) cc_final: 0.7841 (mp) REVERT: F 249 VAL cc_start: 0.7981 (t) cc_final: 0.7690 (p) REVERT: F 264 ILE cc_start: 0.8446 (mp) cc_final: 0.8171 (mm) REVERT: F 266 TYR cc_start: 0.8378 (m-80) cc_final: 0.7919 (m-80) REVERT: F 267 VAL cc_start: 0.8319 (t) cc_final: 0.7909 (m) REVERT: F 278 PHE cc_start: 0.8412 (t80) cc_final: 0.8151 (t80) REVERT: G 16 MET cc_start: 0.8488 (mmt) cc_final: 0.7635 (mmm) REVERT: G 27 ASN cc_start: 0.8200 (t0) cc_final: 0.7909 (t0) REVERT: G 54 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: H 926 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6301 (tp30) REVERT: K 178 MET cc_start: 0.7743 (mtm) cc_final: 0.7189 (mtm) REVERT: K 192 GLU cc_start: 0.7560 (mt-10) cc_final: 0.6916 (mt-10) REVERT: K 208 GLN cc_start: 0.7937 (tp-100) cc_final: 0.7590 (tp-100) REVERT: K 212 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: K 263 MET cc_start: 0.5712 (mmm) cc_final: 0.5343 (mmm) outliers start: 144 outliers final: 100 residues processed: 845 average time/residue: 0.4048 time to fit residues: 502.5567 Evaluate side-chains 891 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 767 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU 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 40 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 447 VAL 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 604 VAL Chi-restraints excluded: chain B residue 613 HIS 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 418 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 SER 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 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 163 MET Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 196 ILE 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 256 ASP Chi-restraints excluded: chain D residue 271 VAL 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 417 ASP Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 39 PHE 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 139 CYS Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 280 THR 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 195 VAL Chi-restraints excluded: chain F residue 199 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 229 TRP 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 162 LEU Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 271 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 0.3980 chunk 109 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 174 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 215 optimal weight: 0.1980 chunk 249 optimal weight: 3.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 HIS A 499 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN B 37 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24295 Z= 0.219 Angle : 0.606 11.636 33035 Z= 0.303 Chirality : 0.042 0.168 3696 Planarity : 0.004 0.085 4058 Dihedral : 13.292 148.729 3618 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 5.34 % Allowed : 21.00 % Favored : 73.65 % 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: 0.13 (0.16), residues: 2804 helix: 1.14 (0.15), residues: 1324 sheet: -0.23 (0.27), residues: 375 loop : -1.05 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 55 HIS 0.014 0.001 HIS D 424 PHE 0.021 0.001 PHE A 659 TYR 0.021 0.001 TYR D 281 ARG 0.014 0.001 ARG A 317 *********************** 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 912 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 778 time to evaluate : 2.179 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: 0.8358 (mttt) cc_final: 0.8079 (mptt) REVERT: A 64 GLN cc_start: 0.8481 (mm-40) cc_final: 0.8172 (mm110) REVERT: A 65 MET cc_start: 0.7560 (ptt) cc_final: 0.6733 (ptt) REVERT: A 68 LYS cc_start: 0.6419 (mtmt) cc_final: 0.5738 (tttm) REVERT: A 73 SER cc_start: 0.6489 (m) cc_final: 0.6144 (t) REVERT: A 94 LYS cc_start: 0.7813 (ptpt) cc_final: 0.7324 (ptpt) REVERT: A 98 ASP cc_start: 0.7482 (m-30) cc_final: 0.7161 (m-30) REVERT: A 105 GLU cc_start: 0.7552 (pm20) cc_final: 0.6579 (pm20) REVERT: A 117 LYS cc_start: 0.8114 (tttt) cc_final: 0.7445 (tppt) REVERT: A 121 TYR cc_start: 0.7205 (m-80) cc_final: 0.6757 (m-80) REVERT: A 146 THR cc_start: 0.7769 (p) cc_final: 0.6509 (t) REVERT: A 163 TYR cc_start: 0.8102 (t80) cc_final: 0.7669 (t80) REVERT: A 167 LYS cc_start: 0.7674 (mttp) cc_final: 0.7051 (mtpp) REVERT: A 169 VAL cc_start: 0.8376 (p) cc_final: 0.7993 (m) REVERT: A 173 ASN cc_start: 0.8041 (m-40) cc_final: 0.6402 (m-40) REVERT: A 174 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7116 (mtp-110) REVERT: A 175 TYR cc_start: 0.8106 (m-80) cc_final: 0.7470 (m-80) REVERT: A 176 PHE cc_start: 0.7678 (m-10) cc_final: 0.7055 (m-80) REVERT: A 178 GLU cc_start: 0.6686 (pm20) cc_final: 0.6415 (pm20) REVERT: A 191 ASP cc_start: 0.7904 (t0) cc_final: 0.7568 (t0) REVERT: A 203 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.6062 (pm20) REVERT: A 273 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7929 (ttpt) REVERT: A 287 LEU cc_start: 0.8613 (mt) cc_final: 0.8059 (mt) REVERT: A 288 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7305 (mp0) REVERT: A 294 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6552 (mm-30) REVERT: A 298 ARG cc_start: 0.8007 (mmm160) cc_final: 0.7405 (mmm160) REVERT: A 299 ASN cc_start: 0.7986 (p0) cc_final: 0.7628 (p0) REVERT: A 321 GLU cc_start: 0.7628 (mm-30) cc_final: 0.6721 (tp30) REVERT: A 332 ARG cc_start: 0.8121 (mpp80) cc_final: 0.7037 (mtp85) REVERT: A 347 SER cc_start: 0.8675 (m) cc_final: 0.7917 (t) REVERT: A 375 LYS cc_start: 0.8217 (tttm) cc_final: 0.7887 (ttpp) REVERT: A 385 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6589 (p0) REVERT: A 389 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7480 (tt) REVERT: A 392 PHE cc_start: 0.7286 (t80) cc_final: 0.6803 (t80) REVERT: A 412 MET cc_start: 0.7313 (ttp) cc_final: 0.6783 (ttp) REVERT: A 418 LYS cc_start: 0.7757 (tmmt) cc_final: 0.7436 (tmmt) REVERT: A 419 ARG cc_start: 0.7721 (ttm170) cc_final: 0.7110 (tpp80) REVERT: A 434 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7570 (mm-30) REVERT: A 457 ILE cc_start: 0.8323 (tt) cc_final: 0.7931 (tt) REVERT: A 476 LYS cc_start: 0.8104 (mttt) cc_final: 0.7624 (mttm) REVERT: A 487 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7773 (tttt) REVERT: A 490 GLU cc_start: 0.6769 (mp0) cc_final: 0.6142 (mm-30) REVERT: A 504 LYS cc_start: 0.8507 (ttpt) cc_final: 0.8151 (ttmt) REVERT: A 505 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8043 (m) REVERT: A 517 GLU cc_start: 0.7635 (mp0) cc_final: 0.6876 (mp0) REVERT: A 520 ARG cc_start: 0.7556 (mmm160) cc_final: 0.6585 (tpt-90) REVERT: A 525 ILE cc_start: 0.8300 (tp) cc_final: 0.7599 (tp) REVERT: A 528 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7961 (mptt) REVERT: A 556 ASP cc_start: 0.7331 (m-30) cc_final: 0.6899 (m-30) REVERT: A 564 ASN cc_start: 0.8408 (t0) cc_final: 0.7618 (t0) REVERT: A 569 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7701 (mmmt) REVERT: A 570 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: A 586 GLN cc_start: 0.8438 (tp40) cc_final: 0.8093 (tp40) REVERT: A 588 GLU cc_start: 0.7476 (tp30) cc_final: 0.6629 (tp30) REVERT: A 632 SER cc_start: 0.8287 (p) cc_final: 0.7865 (p) REVERT: A 636 GLU cc_start: 0.7083 (tp30) cc_final: 0.6876 (tp30) REVERT: A 642 ARG cc_start: 0.7267 (mtp85) cc_final: 0.6747 (mmt90) REVERT: A 658 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7417 (p90) REVERT: A 659 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.6524 (p90) REVERT: A 669 GLU cc_start: 0.7488 (tt0) cc_final: 0.7218 (tt0) REVERT: A 670 MET cc_start: 0.8146 (mmm) cc_final: 0.7912 (mmm) REVERT: A 676 ARG cc_start: 0.7872 (ptm160) cc_final: 0.7517 (ptp-170) REVERT: A 677 GLN cc_start: 0.7586 (mt0) cc_final: 0.7208 (mt0) REVERT: A 682 ASP cc_start: 0.6978 (m-30) cc_final: 0.6734 (m-30) REVERT: A 683 GLN cc_start: 0.7456 (mm-40) cc_final: 0.6877 (mm-40) REVERT: A 696 MET cc_start: 0.7676 (mmm) cc_final: 0.7148 (tmm) REVERT: A 699 GLU cc_start: 0.8064 (pp20) cc_final: 0.7751 (pp20) REVERT: A 704 SER cc_start: 0.8397 (p) cc_final: 0.8159 (p) REVERT: A 706 LYS cc_start: 0.7847 (tmmt) cc_final: 0.7364 (tmtt) REVERT: B 1 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5975 (ppp) REVERT: B 25 MET cc_start: 0.7964 (mmm) cc_final: 0.7716 (mmm) REVERT: B 40 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8172 (mt) REVERT: B 42 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7263 (mtm) REVERT: B 75 ARG cc_start: 0.7330 (ttp80) cc_final: 0.7036 (ttp80) REVERT: B 91 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7722 (mm) REVERT: B 113 LYS cc_start: 0.8293 (ttpp) cc_final: 0.7939 (ttmm) REVERT: B 158 TYR cc_start: 0.7459 (t80) cc_final: 0.6935 (t80) REVERT: B 196 ARG cc_start: 0.8192 (mmp80) cc_final: 0.7635 (mmp80) REVERT: B 207 TYR cc_start: 0.6126 (OUTLIER) cc_final: 0.5902 (p90) REVERT: B 243 CYS cc_start: 0.8654 (m) cc_final: 0.8277 (m) REVERT: B 247 MET cc_start: 0.8099 (mtt) cc_final: 0.7509 (mpp) REVERT: B 384 HIS cc_start: 0.5161 (OUTLIER) cc_final: 0.4840 (p-80) REVERT: B 414 PHE cc_start: 0.7399 (m-80) cc_final: 0.6785 (m-80) REVERT: B 416 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7072 (tt) REVERT: B 438 MET cc_start: 0.8005 (mtm) cc_final: 0.7261 (mtm) REVERT: B 455 ILE cc_start: 0.8030 (mm) cc_final: 0.7601 (mm) REVERT: B 512 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7342 (mm-30) REVERT: B 518 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7834 (mtp-110) REVERT: B 526 GLU cc_start: 0.7655 (pt0) cc_final: 0.7383 (pt0) REVERT: B 533 ASP cc_start: 0.6992 (p0) cc_final: 0.6730 (p0) REVERT: B 545 MET cc_start: 0.8010 (tmm) cc_final: 0.7637 (ttp) REVERT: B 570 GLU cc_start: 0.6412 (tm-30) cc_final: 0.5825 (tm-30) REVERT: B 586 GLU cc_start: 0.7549 (pp20) cc_final: 0.7095 (pp20) REVERT: B 589 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6182 (tm-30) REVERT: B 620 MET cc_start: 0.7797 (mmm) cc_final: 0.6955 (mmm) REVERT: B 641 ARG cc_start: 0.7767 (ttm-80) cc_final: 0.7385 (mtm-85) REVERT: B 664 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8196 (p) REVERT: B 712 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6385 (pt0) REVERT: B 724 MET cc_start: 0.7364 (mmm) cc_final: 0.6812 (mmm) REVERT: C 411 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7760 (tpp) REVERT: C 442 GLN cc_start: 0.5314 (OUTLIER) cc_final: 0.4054 (pp30) REVERT: C 473 ARG cc_start: 0.8030 (tmt170) cc_final: 0.7821 (ttt180) REVERT: C 475 PHE cc_start: 0.7919 (t80) cc_final: 0.7260 (t80) REVERT: C 493 MET cc_start: 0.8137 (tpp) cc_final: 0.7779 (mpp) REVERT: C 501 GLN cc_start: 0.7879 (tp40) cc_final: 0.7460 (tp40) REVERT: C 528 MET cc_start: 0.8788 (mtp) cc_final: 0.8569 (mmm) REVERT: D 20 GLN cc_start: 0.8655 (mt0) cc_final: 0.8333 (mp10) REVERT: D 33 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7928 (mtp-110) REVERT: D 40 THR cc_start: 0.8138 (p) cc_final: 0.7912 (p) REVERT: D 42 LEU cc_start: 0.8319 (tp) cc_final: 0.8068 (mp) REVERT: D 55 TRP cc_start: 0.8029 (m-90) cc_final: 0.7783 (m-90) REVERT: D 77 LYS cc_start: 0.8394 (mttt) cc_final: 0.8122 (mmtt) REVERT: D 78 GLU cc_start: 0.8024 (pt0) cc_final: 0.7569 (pt0) REVERT: D 79 PHE cc_start: 0.8175 (m-80) cc_final: 0.7708 (m-80) REVERT: D 81 LYS cc_start: 0.8888 (tttt) cc_final: 0.8625 (tttt) REVERT: D 85 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7798 (mt-10) REVERT: D 94 ARG cc_start: 0.7585 (mtp-110) cc_final: 0.7065 (mtp-110) REVERT: D 140 LYS cc_start: 0.7662 (pttm) cc_final: 0.7119 (mmtt) REVERT: D 153 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7603 (mm-30) REVERT: D 154 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7656 (mt-10) REVERT: D 173 GLN cc_start: 0.9017 (tt0) cc_final: 0.8473 (pp30) REVERT: D 177 GLN cc_start: 0.8161 (pt0) cc_final: 0.7686 (pp30) REVERT: D 178 LEU cc_start: 0.8770 (tt) cc_final: 0.8371 (pp) REVERT: D 185 MET cc_start: 0.7274 (mpp) cc_final: 0.6956 (mpp) REVERT: D 201 PHE cc_start: 0.8525 (m-80) cc_final: 0.8260 (m-80) REVERT: D 218 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7399 (tm-30) REVERT: D 243 SER cc_start: 0.8216 (m) cc_final: 0.7941 (p) REVERT: D 244 THR cc_start: 0.8026 (m) cc_final: 0.7726 (t) REVERT: D 254 MET cc_start: 0.7162 (mtt) cc_final: 0.6297 (mtt) REVERT: D 258 LEU cc_start: 0.8283 (mt) cc_final: 0.7911 (tp) REVERT: D 260 ASN cc_start: 0.8089 (t0) cc_final: 0.7791 (t0) REVERT: D 276 ARG cc_start: 0.7742 (ttt90) cc_final: 0.7353 (mmm-85) REVERT: D 282 TYR cc_start: 0.7799 (m-80) cc_final: 0.7555 (m-80) REVERT: D 284 THR cc_start: 0.8203 (OUTLIER) cc_final: 0.7977 (p) REVERT: D 313 TYR cc_start: 0.8337 (m-80) cc_final: 0.8018 (m-80) REVERT: D 362 GLN cc_start: 0.7897 (tp40) cc_final: 0.7568 (tp40) REVERT: D 369 ARG cc_start: 0.7459 (tpt90) cc_final: 0.7127 (tpt90) REVERT: D 371 ARG cc_start: 0.7801 (mmt180) cc_final: 0.7555 (mpt180) REVERT: D 378 LYS cc_start: 0.8041 (mttt) cc_final: 0.7787 (mttp) REVERT: D 397 GLU cc_start: 0.7313 (mm-30) cc_final: 0.7049 (mm-30) REVERT: D 398 ARG cc_start: 0.7756 (ttt90) cc_final: 0.7481 (ttt90) REVERT: D 433 PHE cc_start: 0.7985 (t80) cc_final: 0.7506 (t80) REVERT: E 12 GLU cc_start: 0.7694 (pt0) cc_final: 0.7280 (pt0) REVERT: E 36 ASP cc_start: 0.7834 (t0) cc_final: 0.7587 (t0) REVERT: E 70 THR cc_start: 0.8163 (p) cc_final: 0.7734 (t) REVERT: E 72 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7617 (mm-30) REVERT: E 73 ASP cc_start: 0.7174 (t0) cc_final: 0.5435 (t0) REVERT: E 75 ASP cc_start: 0.7004 (m-30) cc_final: 0.5558 (m-30) REVERT: E 79 ASN cc_start: 0.7916 (p0) cc_final: 0.7634 (p0) REVERT: E 80 ARG cc_start: 0.8012 (mtt180) cc_final: 0.6894 (mtt180) REVERT: E 96 PHE cc_start: 0.7533 (m-80) cc_final: 0.7216 (m-80) REVERT: E 103 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: E 112 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7618 (mttt) REVERT: E 119 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7476 (tm-30) REVERT: E 125 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6592 (mtt180) REVERT: E 132 LYS cc_start: 0.8554 (mttt) cc_final: 0.8340 (mttt) REVERT: E 144 SER cc_start: 0.8362 (t) cc_final: 0.7933 (p) REVERT: E 154 GLN cc_start: 0.7471 (tm-30) cc_final: 0.6877 (tm-30) REVERT: E 157 LYS cc_start: 0.8183 (tttt) cc_final: 0.7834 (tttt) REVERT: E 166 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6796 (mt-10) REVERT: E 177 CYS cc_start: 0.7640 (m) cc_final: 0.7330 (t) REVERT: E 181 ASN cc_start: 0.8205 (t0) cc_final: 0.7663 (t0) REVERT: E 193 LYS cc_start: 0.8473 (mttt) cc_final: 0.7806 (ttmm) REVERT: E 214 GLU cc_start: 0.7647 (tt0) cc_final: 0.7295 (tt0) REVERT: E 223 LEU cc_start: 0.8518 (tp) cc_final: 0.8215 (mt) REVERT: E 237 SER cc_start: 0.8566 (m) cc_final: 0.8097 (p) REVERT: E 256 GLN cc_start: 0.7554 (mt0) cc_final: 0.7342 (mt0) REVERT: E 289 TYR cc_start: 0.8232 (m-80) cc_final: 0.7820 (m-80) REVERT: E 299 CYS cc_start: 0.7633 (m) cc_final: 0.7392 (m) REVERT: E 300 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6706 (mt-10) REVERT: E 304 GLU cc_start: 0.7315 (tm-30) cc_final: 0.7062 (tm-30) REVERT: E 331 PHE cc_start: 0.8611 (m-10) cc_final: 0.8350 (m-80) REVERT: E 333 GLU cc_start: 0.7664 (tt0) cc_final: 0.7444 (tt0) REVERT: E 353 LYS cc_start: 0.8379 (mttt) cc_final: 0.7855 (mttt) REVERT: F 16 ASP cc_start: 0.7791 (t0) cc_final: 0.7291 (t0) REVERT: F 28 LYS cc_start: 0.8413 (tttt) cc_final: 0.8192 (tttt) REVERT: F 56 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7601 (mmtt) REVERT: F 116 LYS cc_start: 0.8181 (mttt) cc_final: 0.7750 (mmmm) REVERT: F 139 LYS cc_start: 0.8517 (mttt) cc_final: 0.8228 (mtpp) REVERT: F 172 LEU cc_start: 0.8428 (mt) cc_final: 0.8171 (mm) REVERT: F 187 GLN cc_start: 0.8402 (mt0) cc_final: 0.8126 (mt0) REVERT: F 194 CYS cc_start: 0.7773 (t) cc_final: 0.7258 (t) REVERT: F 195 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8182 (p) REVERT: F 197 ASP cc_start: 0.7963 (t0) cc_final: 0.7639 (t0) REVERT: F 200 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8379 (p) REVERT: F 205 GLN cc_start: 0.8287 (mt0) cc_final: 0.8019 (mt0) REVERT: F 216 LYS cc_start: 0.8449 (tttt) cc_final: 0.7880 (ttpp) REVERT: F 237 GLN cc_start: 0.7328 (mt0) cc_final: 0.7015 (mt0) REVERT: F 242 ILE cc_start: 0.8091 (mt) cc_final: 0.7702 (mp) REVERT: F 249 VAL cc_start: 0.8014 (t) cc_final: 0.7702 (p) REVERT: F 252 ARG cc_start: 0.8403 (mtm110) cc_final: 0.8121 (mtm110) REVERT: F 264 ILE cc_start: 0.8403 (mp) cc_final: 0.8150 (mm) REVERT: F 267 VAL cc_start: 0.8324 (t) cc_final: 0.7922 (m) REVERT: G 16 MET cc_start: 0.8530 (mmt) cc_final: 0.7790 (mmm) REVERT: G 27 ASN cc_start: 0.8261 (t0) cc_final: 0.7954 (t0) REVERT: G 54 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: H 926 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6289 (tp30) REVERT: K 143 GLU cc_start: 0.7656 (tt0) cc_final: 0.7128 (tt0) REVERT: K 178 MET cc_start: 0.7788 (mtm) cc_final: 0.7209 (mtm) REVERT: K 208 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7581 (tp-100) REVERT: K 212 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: K 263 MET cc_start: 0.5778 (mmm) cc_final: 0.5339 (mmm) outliers start: 134 outliers final: 88 residues processed: 848 average time/residue: 0.4094 time to fit residues: 511.1469 Evaluate side-chains 884 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 771 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 203 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 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 40 LEU Chi-restraints excluded: chain B residue 42 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 207 TYR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 447 VAL 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 604 VAL Chi-restraints excluded: chain B residue 613 HIS 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 418 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 SER 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 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 163 MET 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 271 VAL 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 417 ASP Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 39 PHE 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 139 CYS Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 280 THR 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 128 HIS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 200 SER 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 177 ASP Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 271 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 0.3980 chunk 239 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 200 optimal weight: 0.0770 chunk 78 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 241 optimal weight: 0.0070 chunk 254 optimal weight: 1.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** A 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 555 ASN B 37 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** F 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24295 Z= 0.180 Angle : 0.617 16.809 33035 Z= 0.304 Chirality : 0.041 0.239 3696 Planarity : 0.004 0.077 4058 Dihedral : 13.252 148.848 3615 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.92 % Favored : 95.04 % Rotamer: Outliers : 4.94 % Allowed : 21.92 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.13 (0.16), residues: 2804 helix: 1.15 (0.15), residues: 1320 sheet: -0.12 (0.27), residues: 366 loop : -1.09 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP D 55 HIS 0.013 0.001 HIS D 424 PHE 0.016 0.001 PHE A 703 TYR 0.024 0.001 TYR D 281 ARG 0.016 0.001 ARG A 317 *********************** 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 906 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 782 time to evaluate : 2.809 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: 0.8375 (mttt) cc_final: 0.8056 (mptt) REVERT: A 64 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8158 (mm110) REVERT: A 65 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.7284 (ptt) REVERT: A 68 LYS cc_start: 0.6393 (mtmt) cc_final: 0.5699 (tttm) REVERT: A 73 SER cc_start: 0.6654 (m) cc_final: 0.6338 (t) REVERT: A 94 LYS cc_start: 0.7794 (ptpt) cc_final: 0.7316 (ptpt) REVERT: A 98 ASP cc_start: 0.7453 (m-30) cc_final: 0.7163 (m-30) REVERT: A 105 GLU cc_start: 0.7532 (pm20) cc_final: 0.6638 (pm20) REVERT: A 117 LYS cc_start: 0.8089 (tttt) cc_final: 0.7428 (tttt) REVERT: A 121 TYR cc_start: 0.7165 (m-80) cc_final: 0.6714 (m-80) REVERT: A 146 THR cc_start: 0.7745 (p) cc_final: 0.7433 (p) REVERT: A 163 TYR cc_start: 0.8094 (t80) cc_final: 0.7685 (t80) REVERT: A 167 LYS cc_start: 0.7617 (mttp) cc_final: 0.7021 (mttp) REVERT: A 169 VAL cc_start: 0.8361 (p) cc_final: 0.7986 (m) REVERT: A 173 ASN cc_start: 0.8017 (m-40) cc_final: 0.6384 (m-40) REVERT: A 174 ARG cc_start: 0.7880 (mmm-85) cc_final: 0.7125 (mtp-110) REVERT: A 175 TYR cc_start: 0.8015 (m-80) cc_final: 0.7606 (m-80) REVERT: A 176 PHE cc_start: 0.7614 (m-10) cc_final: 0.7096 (m-80) REVERT: A 178 GLU cc_start: 0.6639 (pm20) cc_final: 0.6385 (pm20) REVERT: A 191 ASP cc_start: 0.7917 (t0) cc_final: 0.7589 (t0) REVERT: A 203 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.6035 (pm20) REVERT: A 270 PHE cc_start: 0.8107 (p90) cc_final: 0.7778 (p90) REVERT: A 273 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7263 (mttp) REVERT: A 287 LEU cc_start: 0.8619 (mt) cc_final: 0.8055 (mt) REVERT: A 288 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7284 (mp0) REVERT: A 294 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6512 (mm-30) REVERT: A 298 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7393 (mmm160) REVERT: A 299 ASN cc_start: 0.7967 (p0) cc_final: 0.7549 (p0) REVERT: A 311 LYS cc_start: 0.8188 (ptpp) cc_final: 0.7951 (ptpp) REVERT: A 321 GLU cc_start: 0.7594 (mm-30) cc_final: 0.6148 (tp30) REVERT: A 325 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.6775 (ttm-80) REVERT: A 326 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8149 (mtpp) REVERT: A 332 ARG cc_start: 0.8120 (mpp80) cc_final: 0.6983 (mtp85) REVERT: A 347 SER cc_start: 0.8656 (m) cc_final: 0.7890 (t) REVERT: A 375 LYS cc_start: 0.8180 (tttm) cc_final: 0.7906 (tttm) REVERT: A 385 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6572 (p0) REVERT: A 389 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7428 (tt) REVERT: A 392 PHE cc_start: 0.7267 (t80) cc_final: 0.6835 (t80) REVERT: A 412 MET cc_start: 0.7155 (ttp) cc_final: 0.6802 (ttt) REVERT: A 418 LYS cc_start: 0.7740 (tmmt) cc_final: 0.7422 (tmmt) REVERT: A 419 ARG cc_start: 0.7693 (ttm170) cc_final: 0.7102 (tpp80) REVERT: A 434 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7484 (mm-30) REVERT: A 457 ILE cc_start: 0.8329 (tt) cc_final: 0.7931 (tt) REVERT: A 490 GLU cc_start: 0.6780 (mp0) cc_final: 0.6418 (mm-30) REVERT: A 504 LYS cc_start: 0.8512 (ttpt) cc_final: 0.7906 (ttpt) REVERT: A 505 VAL cc_start: 0.8372 (OUTLIER) cc_final: 0.8055 (m) REVERT: A 517 GLU cc_start: 0.7652 (mp0) cc_final: 0.6886 (mp0) REVERT: A 525 ILE cc_start: 0.8092 (tp) cc_final: 0.7818 (tp) REVERT: A 528 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7890 (mmtp) REVERT: A 552 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7100 (mm-30) REVERT: A 556 ASP cc_start: 0.7207 (m-30) cc_final: 0.6814 (m-30) REVERT: A 564 ASN cc_start: 0.8407 (t0) cc_final: 0.7604 (t0) REVERT: A 569 LYS cc_start: 0.8076 (mmmt) cc_final: 0.7670 (mmmt) REVERT: A 570 GLU cc_start: 0.7693 (pm20) cc_final: 0.7229 (pm20) REVERT: A 586 GLN cc_start: 0.8427 (tp40) cc_final: 0.8087 (tp40) REVERT: A 588 GLU cc_start: 0.7434 (tp30) cc_final: 0.6584 (tp30) REVERT: A 609 LYS cc_start: 0.8289 (tttt) cc_final: 0.8079 (tttm) REVERT: A 636 GLU cc_start: 0.7027 (tp30) cc_final: 0.6825 (tp30) REVERT: A 642 ARG cc_start: 0.7261 (mtp85) cc_final: 0.6872 (mmt-90) REVERT: A 658 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7399 (p90) REVERT: A 659 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.6507 (p90) REVERT: A 670 MET cc_start: 0.8152 (mmm) cc_final: 0.7907 (mmm) REVERT: A 675 LYS cc_start: 0.8527 (ptmt) cc_final: 0.8189 (ttpt) REVERT: A 676 ARG cc_start: 0.7874 (ptm160) cc_final: 0.7499 (ptp-170) REVERT: A 677 GLN cc_start: 0.7548 (mt0) cc_final: 0.7152 (mt0) REVERT: A 682 ASP cc_start: 0.6956 (m-30) cc_final: 0.6693 (m-30) REVERT: A 683 GLN cc_start: 0.7462 (mm-40) cc_final: 0.6880 (mm-40) REVERT: A 696 MET cc_start: 0.7665 (mmm) cc_final: 0.7153 (tmm) REVERT: A 699 GLU cc_start: 0.8040 (pp20) cc_final: 0.7789 (pp20) REVERT: A 704 SER cc_start: 0.8368 (p) cc_final: 0.8156 (p) REVERT: A 706 LYS cc_start: 0.7810 (tmmt) cc_final: 0.6352 (tmmt) REVERT: A 710 GLN cc_start: 0.7856 (pp30) cc_final: 0.7197 (pm20) REVERT: B 1 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.5935 (ppp) REVERT: B 25 MET cc_start: 0.7991 (mmm) cc_final: 0.7720 (mmm) REVERT: B 42 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.7245 (mtm) REVERT: B 55 LEU cc_start: 0.7683 (tt) cc_final: 0.7459 (tp) REVERT: B 75 ARG cc_start: 0.7294 (ttp80) cc_final: 0.7047 (ttp80) REVERT: B 91 LEU cc_start: 0.8033 (mm) cc_final: 0.7722 (mm) REVERT: B 113 LYS cc_start: 0.8296 (ttpp) cc_final: 0.7950 (ttmm) REVERT: B 158 TYR cc_start: 0.7586 (t80) cc_final: 0.7029 (t80) REVERT: B 196 ARG cc_start: 0.8195 (mmp80) cc_final: 0.7628 (mmp80) REVERT: B 243 CYS cc_start: 0.8657 (m) cc_final: 0.8291 (m) REVERT: B 247 MET cc_start: 0.8094 (mtt) cc_final: 0.7549 (mpp) REVERT: B 384 HIS cc_start: 0.5138 (OUTLIER) cc_final: 0.4811 (p-80) REVERT: B 414 PHE cc_start: 0.7388 (m-80) cc_final: 0.6875 (m-80) REVERT: B 416 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7091 (tt) REVERT: B 438 MET cc_start: 0.8018 (mtm) cc_final: 0.7256 (mtm) REVERT: B 455 ILE cc_start: 0.8120 (mm) cc_final: 0.7715 (mm) REVERT: B 512 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7333 (mm-30) REVERT: B 518 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7811 (mtp-110) REVERT: B 526 GLU cc_start: 0.7593 (pt0) cc_final: 0.7311 (pt0) REVERT: B 533 ASP cc_start: 0.6968 (p0) cc_final: 0.6552 (p0) REVERT: B 545 MET cc_start: 0.8046 (tmm) cc_final: 0.7825 (ttt) REVERT: B 570 GLU cc_start: 0.6429 (tm-30) cc_final: 0.5842 (tm-30) REVERT: B 586 GLU cc_start: 0.7529 (pp20) cc_final: 0.7087 (pp20) REVERT: B 589 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6221 (tm-30) REVERT: B 613 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7106 (p90) REVERT: B 620 MET cc_start: 0.7765 (mmm) cc_final: 0.6946 (mmm) REVERT: B 641 ARG cc_start: 0.7702 (ttm-80) cc_final: 0.7210 (mtm-85) REVERT: B 664 VAL cc_start: 0.8435 (OUTLIER) cc_final: 0.8162 (p) REVERT: B 681 ASP cc_start: 0.7885 (t0) cc_final: 0.7644 (t0) REVERT: B 712 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6334 (pt0) REVERT: B 724 MET cc_start: 0.7352 (mmm) cc_final: 0.6849 (mmm) REVERT: C 411 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7712 (tpp) REVERT: C 441 MET cc_start: 0.6620 (mmm) cc_final: 0.6134 (mmt) REVERT: C 442 GLN cc_start: 0.5204 (OUTLIER) cc_final: 0.3970 (pp30) REVERT: C 473 ARG cc_start: 0.8020 (tmt170) cc_final: 0.7800 (ttt180) REVERT: C 475 PHE cc_start: 0.7924 (t80) cc_final: 0.7284 (t80) REVERT: C 493 MET cc_start: 0.8134 (tpp) cc_final: 0.7802 (mpp) REVERT: C 501 GLN cc_start: 0.7884 (tp40) cc_final: 0.7457 (tp40) REVERT: D 20 GLN cc_start: 0.8641 (mt0) cc_final: 0.8312 (mp10) REVERT: D 33 ARG cc_start: 0.8159 (mmm-85) cc_final: 0.7911 (mtp-110) REVERT: D 40 THR cc_start: 0.8103 (p) cc_final: 0.7877 (p) REVERT: D 42 LEU cc_start: 0.8218 (tp) cc_final: 0.8012 (mp) REVERT: D 55 TRP cc_start: 0.7967 (m-90) cc_final: 0.7729 (m-90) REVERT: D 77 LYS cc_start: 0.8384 (mttt) cc_final: 0.8093 (mmtt) REVERT: D 78 GLU cc_start: 0.8023 (pt0) cc_final: 0.7594 (pt0) REVERT: D 79 PHE cc_start: 0.8167 (m-80) cc_final: 0.7715 (m-10) REVERT: D 81 LYS cc_start: 0.8889 (tttt) cc_final: 0.8631 (tttt) REVERT: D 85 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7805 (mt-10) REVERT: D 94 ARG cc_start: 0.7577 (mtp-110) cc_final: 0.7036 (mtp-110) REVERT: D 140 LYS cc_start: 0.7653 (pttm) cc_final: 0.7115 (mmtm) REVERT: D 153 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7591 (mm-30) REVERT: D 154 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7616 (mt-10) REVERT: D 173 GLN cc_start: 0.8925 (tt0) cc_final: 0.8501 (pp30) REVERT: D 177 GLN cc_start: 0.8145 (pt0) cc_final: 0.7051 (pp30) REVERT: D 178 LEU cc_start: 0.8753 (tt) cc_final: 0.8213 (pp) REVERT: D 181 GLN cc_start: 0.8782 (mt0) cc_final: 0.8539 (mm-40) REVERT: D 185 MET cc_start: 0.7187 (mpp) cc_final: 0.6849 (mpp) REVERT: D 201 PHE cc_start: 0.8528 (m-80) cc_final: 0.7897 (m-80) REVERT: D 218 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7406 (tm-30) REVERT: D 243 SER cc_start: 0.8192 (m) cc_final: 0.7888 (p) REVERT: D 244 THR cc_start: 0.8036 (m) cc_final: 0.7727 (t) REVERT: D 254 MET cc_start: 0.7134 (mtt) cc_final: 0.6302 (mtt) REVERT: D 258 LEU cc_start: 0.8275 (mt) cc_final: 0.7919 (tp) REVERT: D 260 ASN cc_start: 0.8082 (t0) cc_final: 0.7833 (t0) REVERT: D 276 ARG cc_start: 0.7707 (ttt90) cc_final: 0.7364 (mmm-85) REVERT: D 282 TYR cc_start: 0.7860 (m-80) cc_final: 0.7637 (m-80) REVERT: D 316 TYR cc_start: 0.8371 (m-80) cc_final: 0.8108 (m-10) REVERT: D 341 MET cc_start: 0.7168 (ttm) cc_final: 0.6934 (ttp) REVERT: D 362 GLN cc_start: 0.7875 (tp40) cc_final: 0.7543 (tp40) REVERT: D 369 ARG cc_start: 0.7440 (tpt90) cc_final: 0.7105 (tpt90) REVERT: D 371 ARG cc_start: 0.7778 (mmt180) cc_final: 0.7422 (mpt180) REVERT: D 378 LYS cc_start: 0.8035 (mttt) cc_final: 0.7758 (mttp) REVERT: D 398 ARG cc_start: 0.7736 (ttt90) cc_final: 0.7447 (ttt90) REVERT: D 433 PHE cc_start: 0.7984 (t80) cc_final: 0.7479 (t80) REVERT: E 12 GLU cc_start: 0.7689 (pt0) cc_final: 0.7274 (pt0) REVERT: E 36 ASP cc_start: 0.7836 (t0) cc_final: 0.7586 (t0) REVERT: E 70 THR cc_start: 0.8143 (p) cc_final: 0.7687 (t) REVERT: E 72 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7590 (mm-30) REVERT: E 73 ASP cc_start: 0.7158 (t0) cc_final: 0.5603 (t0) REVERT: E 75 ASP cc_start: 0.6989 (m-30) cc_final: 0.5698 (m-30) REVERT: E 79 ASN cc_start: 0.7934 (p0) cc_final: 0.7623 (p0) REVERT: E 80 ARG cc_start: 0.7992 (mtt180) cc_final: 0.6945 (mtt180) REVERT: E 96 PHE cc_start: 0.7500 (m-80) cc_final: 0.7217 (m-80) REVERT: E 103 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: E 112 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7615 (mttt) REVERT: E 119 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7521 (tm-30) REVERT: E 125 ARG cc_start: 0.7227 (mtt180) cc_final: 0.6560 (mtt180) REVERT: E 132 LYS cc_start: 0.8537 (mttt) cc_final: 0.8305 (mttt) REVERT: E 144 SER cc_start: 0.8326 (t) cc_final: 0.7923 (p) REVERT: E 154 GLN cc_start: 0.7451 (tm-30) cc_final: 0.6869 (tm-30) REVERT: E 157 LYS cc_start: 0.8165 (tttt) cc_final: 0.7825 (tttt) REVERT: E 166 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6782 (mt-10) REVERT: E 177 CYS cc_start: 0.7618 (m) cc_final: 0.7306 (t) REVERT: E 181 ASN cc_start: 0.8110 (t0) cc_final: 0.7439 (t0) REVERT: E 193 LYS cc_start: 0.8486 (mttt) cc_final: 0.7811 (ttmm) REVERT: E 214 GLU cc_start: 0.7637 (tt0) cc_final: 0.7288 (tt0) REVERT: E 223 LEU cc_start: 0.8448 (tp) cc_final: 0.8186 (mt) REVERT: E 237 SER cc_start: 0.8549 (m) cc_final: 0.8089 (p) REVERT: E 256 GLN cc_start: 0.7411 (mt0) cc_final: 0.7207 (mt0) REVERT: E 289 TYR cc_start: 0.8237 (m-80) cc_final: 0.7771 (m-80) REVERT: E 299 CYS cc_start: 0.7618 (m) cc_final: 0.7390 (m) REVERT: E 300 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6674 (mt-10) REVERT: E 304 GLU cc_start: 0.7298 (tm-30) cc_final: 0.7042 (tm-30) REVERT: E 353 LYS cc_start: 0.8374 (mttt) cc_final: 0.7855 (mttt) REVERT: F 16 ASP cc_start: 0.7796 (t0) cc_final: 0.7303 (t0) REVERT: F 28 LYS cc_start: 0.8411 (tttt) cc_final: 0.8179 (tttt) REVERT: F 56 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7590 (mmtt) REVERT: F 109 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7433 (tt0) REVERT: F 116 LYS cc_start: 0.8156 (mttt) cc_final: 0.7822 (mmmm) REVERT: F 139 LYS cc_start: 0.8493 (mttt) cc_final: 0.8228 (mtpp) REVERT: F 158 LYS cc_start: 0.8299 (mtmt) cc_final: 0.8014 (mtmt) REVERT: F 172 LEU cc_start: 0.8422 (mt) cc_final: 0.8157 (mm) REVERT: F 187 GLN cc_start: 0.8408 (mt0) cc_final: 0.8092 (mt0) REVERT: F 194 CYS cc_start: 0.7798 (t) cc_final: 0.7296 (t) REVERT: F 197 ASP cc_start: 0.7946 (t0) cc_final: 0.7593 (t0) REVERT: F 200 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8386 (p) REVERT: F 205 GLN cc_start: 0.8278 (mt0) cc_final: 0.8005 (mt0) REVERT: F 213 LEU cc_start: 0.8366 (tp) cc_final: 0.8102 (tt) REVERT: F 216 LYS cc_start: 0.8555 (tttt) cc_final: 0.8095 (ttpp) REVERT: F 237 GLN cc_start: 0.7326 (mt0) cc_final: 0.6991 (mt0) REVERT: F 242 ILE cc_start: 0.8137 (mt) cc_final: 0.7802 (mp) REVERT: F 249 VAL cc_start: 0.8010 (t) cc_final: 0.7701 (p) REVERT: F 264 ILE cc_start: 0.8399 (mp) cc_final: 0.8103 (mm) REVERT: F 267 VAL cc_start: 0.8333 (t) cc_final: 0.7931 (m) REVERT: G 16 MET cc_start: 0.8561 (mmt) cc_final: 0.7731 (mmm) REVERT: G 27 ASN cc_start: 0.8250 (t0) cc_final: 0.7967 (t0) REVERT: H 926 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6285 (tp30) REVERT: K 135 LYS cc_start: 0.8434 (tttt) cc_final: 0.7944 (tttt) REVERT: K 143 GLU cc_start: 0.7626 (tt0) cc_final: 0.7060 (tt0) REVERT: K 178 MET cc_start: 0.7745 (mtm) cc_final: 0.7182 (mtm) REVERT: K 192 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6816 (mt-10) REVERT: K 208 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7588 (tp-100) REVERT: K 212 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: K 263 MET cc_start: 0.5746 (mmm) cc_final: 0.5313 (mmm) outliers start: 124 outliers final: 90 residues processed: 845 average time/residue: 0.4432 time to fit residues: 551.4287 Evaluate side-chains 872 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 762 time to evaluate : 2.465 ------------------------------------------------------------------------------- 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 203 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 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 42 MET Chi-restraints excluded: chain B residue 77 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 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 447 VAL 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 604 VAL Chi-restraints excluded: chain B residue 613 HIS 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 407 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 429 SER 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 531 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 163 MET 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 250 SER 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 380 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 39 PHE 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 175 THR Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 328 LEU 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 195 VAL Chi-restraints excluded: chain F residue 200 SER 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 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 177 ASP Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 271 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 0.9990 chunk 164 optimal weight: 0.0670 chunk 127 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 225 optimal weight: 1.9990 chunk 23 optimal weight: 0.0000 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 overall best weight: 0.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN A 555 ASN B 37 HIS ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 340 ASN D 435 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24295 Z= 0.196 Angle : 0.618 13.945 33035 Z= 0.306 Chirality : 0.042 0.198 3696 Planarity : 0.004 0.059 4058 Dihedral : 13.253 148.347 3612 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 4.50 % Allowed : 22.76 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.31 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.16), residues: 2804 helix: 1.14 (0.15), residues: 1317 sheet: -0.18 (0.27), residues: 366 loop : -1.09 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP D 55 HIS 0.013 0.001 HIS D 424 PHE 0.018 0.001 PHE A 659 TYR 0.025 0.001 TYR D 281 ARG 0.009 0.001 ARG E 10 ********************** 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 883 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 770 time to evaluate : 3.004 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: 0.8345 (mttt) cc_final: 0.8015 (mptt) REVERT: A 64 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8179 (mm110) REVERT: A 65 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6752 (ptt) REVERT: A 68 LYS cc_start: 0.6424 (mtmt) cc_final: 0.5738 (tttm) REVERT: A 73 SER cc_start: 0.6496 (m) cc_final: 0.6187 (t) REVERT: A 94 LYS cc_start: 0.7803 (ptpt) cc_final: 0.7316 (ptpt) REVERT: A 98 ASP cc_start: 0.7454 (m-30) cc_final: 0.7135 (m-30) REVERT: A 105 GLU cc_start: 0.7514 (pm20) cc_final: 0.6648 (pm20) REVERT: A 117 LYS cc_start: 0.8069 (tttt) cc_final: 0.7375 (tttt) REVERT: A 121 TYR cc_start: 0.7188 (m-80) cc_final: 0.6705 (m-80) REVERT: A 146 THR cc_start: 0.7762 (p) cc_final: 0.6548 (t) REVERT: A 163 TYR cc_start: 0.8113 (t80) cc_final: 0.7693 (t80) REVERT: A 167 LYS cc_start: 0.7611 (mttp) cc_final: 0.7004 (mttp) REVERT: A 169 VAL cc_start: 0.8349 (p) cc_final: 0.8019 (m) REVERT: A 173 ASN cc_start: 0.8019 (m-40) cc_final: 0.6423 (m-40) REVERT: A 174 ARG cc_start: 0.7878 (mmm-85) cc_final: 0.7100 (mtp-110) REVERT: A 175 TYR cc_start: 0.8028 (m-80) cc_final: 0.7582 (m-80) REVERT: A 176 PHE cc_start: 0.7601 (m-10) cc_final: 0.7135 (m-80) REVERT: A 178 GLU cc_start: 0.6640 (pm20) cc_final: 0.6408 (pm20) REVERT: A 191 ASP cc_start: 0.7948 (t0) cc_final: 0.7611 (t0) REVERT: A 203 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.6033 (pm20) REVERT: A 270 PHE cc_start: 0.8088 (p90) cc_final: 0.7793 (p90) REVERT: A 273 LYS cc_start: 0.8238 (ttmt) cc_final: 0.7261 (mttp) REVERT: A 279 GLU cc_start: 0.7578 (mp0) cc_final: 0.6935 (mp0) REVERT: A 287 LEU cc_start: 0.8628 (mt) cc_final: 0.8039 (mt) REVERT: A 288 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7295 (mp0) REVERT: A 294 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6533 (mm-30) REVERT: A 299 ASN cc_start: 0.7928 (p0) cc_final: 0.7435 (p0) REVERT: A 311 LYS cc_start: 0.8172 (ptpp) cc_final: 0.7970 (ptpp) REVERT: A 317 ARG cc_start: 0.7229 (tpp80) cc_final: 0.6302 (mmm-85) REVERT: A 321 GLU cc_start: 0.7620 (mm-30) cc_final: 0.6708 (tp30) REVERT: A 325 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.7134 (ttm-80) REVERT: A 326 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8317 (mtpp) REVERT: A 332 ARG cc_start: 0.8060 (mpp80) cc_final: 0.6914 (mtp85) REVERT: A 347 SER cc_start: 0.8668 (m) cc_final: 0.7917 (t) REVERT: A 375 LYS cc_start: 0.8181 (tttm) cc_final: 0.7890 (tttm) REVERT: A 385 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6561 (p0) REVERT: A 389 ILE cc_start: 0.7862 (OUTLIER) cc_final: 0.7501 (tt) REVERT: A 392 PHE cc_start: 0.7288 (t80) cc_final: 0.6865 (t80) REVERT: A 412 MET cc_start: 0.7257 (ttp) cc_final: 0.6932 (ttt) REVERT: A 418 LYS cc_start: 0.7756 (tmmt) cc_final: 0.7450 (tmmt) REVERT: A 419 ARG cc_start: 0.7776 (ttm170) cc_final: 0.7357 (tpp80) REVERT: A 434 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7478 (mm-30) REVERT: A 457 ILE cc_start: 0.8338 (tt) cc_final: 0.7938 (tt) REVERT: A 463 LYS cc_start: 0.8561 (mttp) cc_final: 0.8354 (mttp) REVERT: A 490 GLU cc_start: 0.6807 (mp0) cc_final: 0.6498 (mm-30) REVERT: A 504 LYS cc_start: 0.8507 (ttpt) cc_final: 0.7906 (ttpt) REVERT: A 505 VAL cc_start: 0.8404 (OUTLIER) cc_final: 0.8090 (m) REVERT: A 517 GLU cc_start: 0.7665 (mp0) cc_final: 0.6906 (mp0) REVERT: A 525 ILE cc_start: 0.8117 (tp) cc_final: 0.7841 (tp) REVERT: A 528 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7967 (mptt) REVERT: A 552 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7116 (mm-30) REVERT: A 556 ASP cc_start: 0.7211 (m-30) cc_final: 0.6786 (m-30) REVERT: A 564 ASN cc_start: 0.8390 (t0) cc_final: 0.7595 (t0) REVERT: A 569 LYS cc_start: 0.8086 (mmmt) cc_final: 0.7678 (mmmt) REVERT: A 570 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7263 (pm20) REVERT: A 586 GLN cc_start: 0.8445 (tp40) cc_final: 0.8110 (tp40) REVERT: A 588 GLU cc_start: 0.7460 (tp30) cc_final: 0.6594 (tp30) REVERT: A 609 LYS cc_start: 0.8312 (tttt) cc_final: 0.8100 (tttm) REVERT: A 642 ARG cc_start: 0.7278 (mtp85) cc_final: 0.6874 (mmt-90) REVERT: A 658 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7394 (p90) REVERT: A 659 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.6367 (p90) REVERT: A 669 GLU cc_start: 0.7552 (tt0) cc_final: 0.7149 (tt0) REVERT: A 670 MET cc_start: 0.8176 (mmm) cc_final: 0.7872 (mmm) REVERT: A 675 LYS cc_start: 0.8502 (ptmt) cc_final: 0.8181 (ttpt) REVERT: A 676 ARG cc_start: 0.7853 (ptm160) cc_final: 0.7479 (ptp-170) REVERT: A 677 GLN cc_start: 0.7533 (mt0) cc_final: 0.7138 (mt0) REVERT: A 682 ASP cc_start: 0.6964 (m-30) cc_final: 0.6697 (m-30) REVERT: A 683 GLN cc_start: 0.7452 (mm-40) cc_final: 0.6874 (mm-40) REVERT: A 696 MET cc_start: 0.7689 (mmm) cc_final: 0.7172 (tmm) REVERT: A 699 GLU cc_start: 0.8048 (pp20) cc_final: 0.7790 (pp20) REVERT: A 704 SER cc_start: 0.8369 (p) cc_final: 0.8152 (p) REVERT: A 706 LYS cc_start: 0.7759 (tmmt) cc_final: 0.7223 (tmmt) REVERT: A 710 GLN cc_start: 0.7869 (pp30) cc_final: 0.7522 (pp30) REVERT: B 1 MET cc_start: 0.6308 (OUTLIER) cc_final: 0.5936 (ppp) REVERT: B 25 MET cc_start: 0.8016 (mmm) cc_final: 0.7735 (mmm) REVERT: B 42 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.7230 (mtm) REVERT: B 91 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7739 (mm) REVERT: B 113 LYS cc_start: 0.8305 (ttpp) cc_final: 0.7962 (ttmm) REVERT: B 158 TYR cc_start: 0.7596 (t80) cc_final: 0.7046 (t80) REVERT: B 196 ARG cc_start: 0.8226 (mmp80) cc_final: 0.7638 (mmp80) REVERT: B 243 CYS cc_start: 0.8653 (m) cc_final: 0.8300 (m) REVERT: B 247 MET cc_start: 0.8234 (mtt) cc_final: 0.7643 (mpp) REVERT: B 384 HIS cc_start: 0.5130 (OUTLIER) cc_final: 0.4801 (p-80) REVERT: B 414 PHE cc_start: 0.7374 (m-80) cc_final: 0.6907 (m-80) REVERT: B 416 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7092 (tt) REVERT: B 438 MET cc_start: 0.8019 (mtm) cc_final: 0.7283 (mtm) REVERT: B 512 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7362 (mm-30) REVERT: B 518 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7816 (mtp-110) REVERT: B 526 GLU cc_start: 0.7609 (pt0) cc_final: 0.7276 (pt0) REVERT: B 533 ASP cc_start: 0.7032 (p0) cc_final: 0.6568 (p0) REVERT: B 570 GLU cc_start: 0.6394 (tm-30) cc_final: 0.5817 (tm-30) REVERT: B 586 GLU cc_start: 0.7528 (pp20) cc_final: 0.7100 (pp20) REVERT: B 589 GLU cc_start: 0.7149 (mm-30) cc_final: 0.6227 (tm-30) REVERT: B 620 MET cc_start: 0.7797 (mmm) cc_final: 0.6976 (mmm) REVERT: B 641 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7267 (mtm-85) REVERT: B 664 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8203 (p) REVERT: B 677 MET cc_start: 0.7158 (mtp) cc_final: 0.6857 (mtm) REVERT: B 681 ASP cc_start: 0.8164 (t0) cc_final: 0.7912 (t0) REVERT: B 712 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6338 (pt0) REVERT: B 724 MET cc_start: 0.7368 (mmm) cc_final: 0.6837 (mmm) REVERT: C 441 MET cc_start: 0.6787 (mmm) cc_final: 0.6289 (mmt) REVERT: C 442 GLN cc_start: 0.5115 (OUTLIER) cc_final: 0.3879 (pp30) REVERT: C 473 ARG cc_start: 0.8028 (tmt170) cc_final: 0.7808 (ttt180) REVERT: C 475 PHE cc_start: 0.7948 (t80) cc_final: 0.7298 (t80) REVERT: C 493 MET cc_start: 0.8121 (tpp) cc_final: 0.7715 (mpp) REVERT: C 501 GLN cc_start: 0.7874 (tp40) cc_final: 0.7461 (tp40) REVERT: D 20 GLN cc_start: 0.8644 (mt0) cc_final: 0.8321 (mp10) REVERT: D 33 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7981 (mtp-110) REVERT: D 40 THR cc_start: 0.8113 (p) cc_final: 0.7882 (p) REVERT: D 42 LEU cc_start: 0.8305 (tp) cc_final: 0.8076 (mp) REVERT: D 55 TRP cc_start: 0.7992 (m-90) cc_final: 0.7745 (m-90) REVERT: D 77 LYS cc_start: 0.8378 (mttt) cc_final: 0.8105 (mmtt) REVERT: D 78 GLU cc_start: 0.8030 (pt0) cc_final: 0.7624 (pt0) REVERT: D 79 PHE cc_start: 0.8163 (m-80) cc_final: 0.7690 (m-10) REVERT: D 85 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7835 (mt-10) REVERT: D 94 ARG cc_start: 0.7608 (mtp-110) cc_final: 0.6956 (mtp-110) REVERT: D 140 LYS cc_start: 0.7677 (pttm) cc_final: 0.7146 (mmtm) REVERT: D 153 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7639 (mm-30) REVERT: D 154 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7650 (mt-10) REVERT: D 161 HIS cc_start: 0.8044 (m90) cc_final: 0.7508 (m-70) REVERT: D 173 GLN cc_start: 0.8951 (tt0) cc_final: 0.8537 (pp30) REVERT: D 177 GLN cc_start: 0.8154 (pt0) cc_final: 0.7070 (pp30) REVERT: D 178 LEU cc_start: 0.8760 (tt) cc_final: 0.8225 (pp) REVERT: D 181 GLN cc_start: 0.8787 (mt0) cc_final: 0.8545 (mm-40) REVERT: D 185 MET cc_start: 0.7177 (mpp) cc_final: 0.6841 (mpp) REVERT: D 201 PHE cc_start: 0.8545 (m-80) cc_final: 0.7926 (m-80) REVERT: D 218 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7413 (tm-30) REVERT: D 243 SER cc_start: 0.8214 (m) cc_final: 0.7857 (p) REVERT: D 244 THR cc_start: 0.8041 (m) cc_final: 0.7731 (t) REVERT: D 254 MET cc_start: 0.7171 (mtt) cc_final: 0.6241 (mtt) REVERT: D 258 LEU cc_start: 0.8282 (mt) cc_final: 0.7904 (tp) REVERT: D 260 ASN cc_start: 0.8115 (t0) cc_final: 0.7839 (t0) REVERT: D 276 ARG cc_start: 0.7706 (ttt90) cc_final: 0.7383 (mmm-85) REVERT: D 282 TYR cc_start: 0.7934 (m-80) cc_final: 0.7705 (m-80) REVERT: D 313 TYR cc_start: 0.8364 (m-80) cc_final: 0.7985 (m-80) REVERT: D 362 GLN cc_start: 0.7873 (tp40) cc_final: 0.7550 (tp40) REVERT: D 369 ARG cc_start: 0.7418 (tpt90) cc_final: 0.7098 (tpt90) REVERT: D 371 ARG cc_start: 0.7787 (mmt180) cc_final: 0.7491 (mpt180) REVERT: D 398 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7459 (ttt90) REVERT: D 433 PHE cc_start: 0.8008 (t80) cc_final: 0.7505 (t80) REVERT: E 12 GLU cc_start: 0.7670 (pt0) cc_final: 0.7260 (pt0) REVERT: E 36 ASP cc_start: 0.7835 (t0) cc_final: 0.7588 (t0) REVERT: E 70 THR cc_start: 0.8166 (p) cc_final: 0.7737 (t) REVERT: E 72 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7591 (mm-30) REVERT: E 73 ASP cc_start: 0.7178 (t0) cc_final: 0.5411 (t0) REVERT: E 75 ASP cc_start: 0.6988 (m-30) cc_final: 0.5545 (m-30) REVERT: E 79 ASN cc_start: 0.7925 (p0) cc_final: 0.7599 (p0) REVERT: E 80 ARG cc_start: 0.7997 (mtt180) cc_final: 0.6885 (mtt180) REVERT: E 96 PHE cc_start: 0.7506 (m-80) cc_final: 0.7225 (m-80) REVERT: E 103 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7612 (mt0) REVERT: E 112 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7672 (mttt) REVERT: E 119 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7493 (tm-30) REVERT: E 125 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6570 (mtt180) REVERT: E 132 LYS cc_start: 0.8533 (mttt) cc_final: 0.8309 (mttt) REVERT: E 144 SER cc_start: 0.8346 (t) cc_final: 0.7937 (p) REVERT: E 154 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6864 (tm-30) REVERT: E 157 LYS cc_start: 0.8168 (tttt) cc_final: 0.7832 (tttt) REVERT: E 166 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6762 (mt-10) REVERT: E 181 ASN cc_start: 0.8105 (t0) cc_final: 0.7807 (t0) REVERT: E 184 ASP cc_start: 0.7032 (m-30) cc_final: 0.6612 (m-30) REVERT: E 193 LYS cc_start: 0.8486 (mttt) cc_final: 0.7807 (ttmm) REVERT: E 214 GLU cc_start: 0.7628 (tt0) cc_final: 0.7289 (tt0) REVERT: E 223 LEU cc_start: 0.8477 (tp) cc_final: 0.8165 (mt) REVERT: E 237 SER cc_start: 0.8565 (m) cc_final: 0.8105 (p) REVERT: E 256 GLN cc_start: 0.7490 (mt0) cc_final: 0.7127 (mt0) REVERT: E 289 TYR cc_start: 0.8234 (m-80) cc_final: 0.7757 (m-80) REVERT: E 299 CYS cc_start: 0.7614 (m) cc_final: 0.7390 (m) REVERT: E 300 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6817 (mt-10) REVERT: E 304 GLU cc_start: 0.7281 (tm-30) cc_final: 0.7050 (tm-30) REVERT: E 331 PHE cc_start: 0.8505 (m-10) cc_final: 0.8263 (m-80) REVERT: E 353 LYS cc_start: 0.8375 (mttt) cc_final: 0.7860 (mttt) REVERT: F 16 ASP cc_start: 0.7812 (t0) cc_final: 0.7302 (t0) REVERT: F 20 ILE cc_start: 0.8285 (mm) cc_final: 0.8060 (mm) REVERT: F 56 LYS cc_start: 0.7746 (mmtt) cc_final: 0.7533 (mmtt) REVERT: F 109 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7365 (tt0) REVERT: F 116 LYS cc_start: 0.8170 (mttt) cc_final: 0.7834 (mmmm) REVERT: F 139 LYS cc_start: 0.8497 (mttt) cc_final: 0.8234 (mtpp) REVERT: F 158 LYS cc_start: 0.8303 (mtmt) cc_final: 0.8007 (mtmt) REVERT: F 172 LEU cc_start: 0.8398 (mt) cc_final: 0.8119 (mm) REVERT: F 187 GLN cc_start: 0.8409 (mt0) cc_final: 0.8076 (mt0) REVERT: F 194 CYS cc_start: 0.7790 (t) cc_final: 0.7300 (t) REVERT: F 197 ASP cc_start: 0.7945 (t0) cc_final: 0.7591 (t0) REVERT: F 200 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8377 (p) REVERT: F 213 LEU cc_start: 0.8525 (tp) cc_final: 0.8263 (tt) REVERT: F 216 LYS cc_start: 0.8567 (tttt) cc_final: 0.8107 (ttpp) REVERT: F 237 GLN cc_start: 0.7314 (mt0) cc_final: 0.6995 (mt0) REVERT: F 242 ILE cc_start: 0.8150 (mt) cc_final: 0.7803 (mp) REVERT: F 249 VAL cc_start: 0.8048 (t) cc_final: 0.7726 (p) REVERT: F 252 ARG cc_start: 0.8451 (mtm110) cc_final: 0.7986 (mtm110) REVERT: F 264 ILE cc_start: 0.8327 (mp) cc_final: 0.8074 (mm) REVERT: F 266 TYR cc_start: 0.8045 (m-80) cc_final: 0.7546 (m-10) REVERT: F 267 VAL cc_start: 0.8330 (t) cc_final: 0.7909 (m) REVERT: F 278 PHE cc_start: 0.8127 (t80) cc_final: 0.7865 (t80) REVERT: G 16 MET cc_start: 0.8551 (mmt) cc_final: 0.7730 (mmm) REVERT: G 21 LEU cc_start: 0.8303 (mm) cc_final: 0.8079 (mm) REVERT: G 27 ASN cc_start: 0.8253 (t0) cc_final: 0.7974 (t0) REVERT: H 926 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6374 (tp30) REVERT: K 135 LYS cc_start: 0.8493 (tttt) cc_final: 0.8021 (tttt) REVERT: K 143 GLU cc_start: 0.7613 (tt0) cc_final: 0.7030 (tt0) REVERT: K 178 MET cc_start: 0.7774 (mtm) cc_final: 0.7203 (mtm) REVERT: K 208 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7587 (tp-100) REVERT: K 212 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: K 263 MET cc_start: 0.5836 (mmm) cc_final: 0.5353 (mmm) outliers start: 113 outliers final: 86 residues processed: 831 average time/residue: 0.4117 time to fit residues: 496.7899 Evaluate side-chains 874 residues out of total 2510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 768 time to evaluate : 2.808 ------------------------------------------------------------------------------- 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 203 GLU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 571 TYR Chi-restraints excluded: chain A residue 581 TYR Chi-restraints excluded: chain A residue 629 HIS Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 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 42 MET Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 403 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 447 VAL 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 604 VAL Chi-restraints excluded: chain B residue 613 HIS 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 712 GLU 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 428 SER Chi-restraints excluded: chain C residue 429 SER 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 531 THR 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 250 SER 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 417 ASP Chi-restraints excluded: chain D residue 434 GLU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 444 THR Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 39 PHE 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 268 LYS Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 200 SER 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 177 ASP Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 212 GLU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 271 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 231 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** B 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 GLN ** C 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** K 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.149556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.121351 restraints weight = 40205.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125313 restraints weight = 19064.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.127832 restraints weight = 11554.545| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.368 24295 Z= 0.279 Angle : 0.751 59.200 33035 Z= 0.412 Chirality : 0.046 0.852 3696 Planarity : 0.004 0.057 4058 Dihedral : 13.253 148.320 3612 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 4.50 % Allowed : 23.00 % Favored : 72.50 % 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: 0.11 (0.16), residues: 2804 helix: 1.13 (0.15), residues: 1317 sheet: -0.20 (0.27), residues: 366 loop : -1.07 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 77 HIS 0.008 0.001 HIS D 424 PHE 0.019 0.001 PHE D 454 TYR 0.024 0.001 TYR D 281 ARG 0.008 0.000 ARG E 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7722.25 seconds wall clock time: 137 minutes 33.99 seconds (8253.99 seconds total)