Starting phenix.real_space_refine on Wed Mar 20 14:00:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebx_28001/03_2024/8ebx_28001_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebx_28001/03_2024/8ebx_28001.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebx_28001/03_2024/8ebx_28001_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebx_28001/03_2024/8ebx_28001_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebx_28001/03_2024/8ebx_28001_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebx_28001/03_2024/8ebx_28001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebx_28001/03_2024/8ebx_28001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebx_28001/03_2024/8ebx_28001_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ebx_28001/03_2024/8ebx_28001_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= 0.002 sd= 0.031 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 Zn 6 6.06 5 P 80 5.49 5 S 162 5.16 5 C 17288 2.51 5 N 4764 2.21 5 O 5227 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 109": "NH1" <-> "NH2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A TYR 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 520": "NH1" <-> "NH2" Residue "A TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 678": "NH1" <-> "NH2" Residue "B TYR 18": "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 PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "B PHE 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 803": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 911": "OE1" <-> "OE2" Residue "H PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 116": "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: 27533 Number of models: 1 Model: "" Number of chains: 17 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: 2 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: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2332 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 270} Chain breaks: 1 Chain: "J" Number of atoms: 1201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 149, 1192 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'PTRANS': 1, 'TRANS': 147} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Conformer: "B" Number of residues, atoms: 149, 1192 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 3} Link IDs: {'PTRANS': 1, 'TRANS': 147} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 bond proxies already assigned to first conformer: 1192 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: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 810 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Chain: "M" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 810 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} 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: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 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 53.161 37.063 43.608 1.00244.48 S ATOM 6134 SG CYS B 155 49.491 33.676 39.122 1.00283.25 S ATOM 5965 SG CYS B 134 51.433 39.575 37.856 1.00284.98 S ATOM 6423 SG CYS B 190 47.113 38.899 41.848 1.00255.08 S ATOM 18036 SG CYS E 345 37.696 62.447 133.647 1.00136.57 S ATOM 18058 SG CYS E 348 39.545 65.549 134.854 1.00128.75 S ATOM 18215 SG CYS E 368 38.007 65.513 131.352 1.00139.20 S ATOM 18236 SG CYS E 371 41.008 63.360 132.135 1.00135.43 S ATOM 18156 SG CYS E 360 36.061 51.622 128.257 1.00149.73 S ATOM 18174 SG CYS E 363 36.492 51.460 132.048 1.00149.34 S ATOM 18323 SG CYS E 382 39.015 53.281 129.949 1.00136.15 S ATOM 18340 SG CYS E 385 38.854 49.502 129.711 1.00134.73 S ATOM 17600 SG CYS E 291 75.162 37.548 124.435 1.00142.46 S ATOM 17622 SG CYS E 294 78.638 35.999 124.026 1.00155.29 S ATOM 17711 SG CYS E 305 77.456 38.492 121.502 1.00141.59 S ATOM 17734 SG CYS E 308 75.814 35.092 121.625 1.00153.98 S ATOM 20236 SG CYS F 268 55.660 37.937 114.354 1.00122.02 S ATOM 20255 SG CYS F 271 53.087 39.854 116.401 1.00128.00 S ATOM 20340 SG CYS F 282 52.940 36.096 116.304 1.00145.88 S ATOM 20360 SG CYS F 285 52.085 38.072 113.170 1.00153.16 S ATOM 20128 SG CYS F 255 56.547 34.412 126.585 1.00133.99 S ATOM 20145 SG CYS F 257 53.928 31.668 126.415 1.00138.26 S ATOM 20294 SG CYS F 276 57.666 30.748 126.841 1.00140.82 S ATOM 24480 SG CYS K 105 47.120 99.927 24.059 1.00212.58 S ATOM 24504 SG CYS K 108 46.585 99.546 20.306 1.00222.66 S ATOM 24652 SG CYS K 126 49.112 97.337 22.111 1.00202.32 S ATOM 24674 SG CYS K 129 49.823 101.005 21.535 1.00208.97 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALYS J 127 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS J 127 " occ=0.50 Time building chain proxies: 14.07, per 1000 atoms: 0.51 Number of scatterers: 27533 At special positions: 0 Unit cell: (154.38, 176.79, 181.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 Fe 4 26.01 Ca 2 19.99 S 162 16.00 P 80 15.00 O 5227 8.00 N 4764 7.00 C 17288 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: 10.44 Conformation dependent library (CDL) restraints added in 4.3 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 345 " pdb="ZN ZN E 401 " - pdb=" SG CYS E 348 " 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 363 " pdb="ZN ZN E 402 " - pdb=" SG CYS E 385 " pdb=" ZN E 403 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 305 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 294 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 308 " pdb="ZN ZN E 403 " - pdb=" SG CYS E 291 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 268 " 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 271 " 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 108 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 105 " Number of angles added : 33 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 24 sheets defined 45.0% alpha, 8.9% beta 37 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 10.56 Creating SS restraints... Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 152 through 161 Processing helix chain 'A' and resid 182 through 189 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.987A 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: 3.508A pdb=" N ILE A 277 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N GLU A 278 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 284 " --> pdb=" O GLN A 281 " (cutoff:3.500A) removed outlier: 3.925A 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: 3.843A pdb=" N THR A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 445 No H-bonds generated for 'chain 'A' and resid 443 through 445' Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.949A pdb=" N LEU A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.586A pdb=" N ASN A 481 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 4.212A 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: 3.607A pdb=" N ARG A 520 " --> pdb=" O PRO A 516 " (cutoff:3.500A) removed outlier: 4.880A 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: 4.008A pdb=" N GLU A 570 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 597 removed outlier: 4.056A 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: 3.709A pdb=" N LEU A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN A 714 " --> pdb=" O GLN A 710 " (cutoff:3.500A) removed outlier: 3.718A 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: 4.675A pdb=" N ASP B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.995A pdb=" N GLN B 147 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N HIS B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 164 removed outlier: 4.579A 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 198 Processing helix chain 'B' and resid 209 through 213 removed outlier: 4.362A pdb=" N LEU B 213 " --> pdb=" O HIS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 221 removed outlier: 3.867A pdb=" N ASP B 219 " --> pdb=" O PRO B 215 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LEU B 220 " --> pdb=" O LYS B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.898A pdb=" N MET B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 271 removed outlier: 4.094A pdb=" N GLU B 264 " --> pdb=" O GLN B 260 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR B 265 " --> pdb=" O GLY B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 330 No H-bonds generated for 'chain 'B' and resid 327 through 330' Processing helix chain 'B' and resid 334 through 345 removed outlier: 4.098A pdb=" N LEU B 337 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR B 339 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 343 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 364 Processing helix chain 'B' and resid 370 through 379 removed outlier: 3.828A pdb=" N PHE B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA B 376 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 4.742A 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 445 through 448 No H-bonds generated for 'chain 'B' and resid 445 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: 3.547A 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: 4.121A pdb=" N ARG B 666 " --> pdb=" O GLN B 662 " (cutoff:3.500A) removed outlier: 5.770A 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: 4.311A 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: 3.636A pdb=" N MET C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 139 through 146 removed outlier: 3.578A pdb=" N ASN C 145 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 3.614A 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 Processing helix chain 'C' and resid 484 through 515 removed outlier: 3.981A pdb=" N GLU C 488 " --> pdb=" O PRO C 484 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 4.234A 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: 3.988A 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: 3.752A pdb=" N GLY D 36 " --> pdb=" O ASP D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 50 through 61 removed outlier: 4.842A pdb=" N PHE D 61 " --> pdb=" O MET D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 78 through 93 removed outlier: 4.528A pdb=" N LYS D 81 " --> pdb=" O GLU D 78 " (cutoff:3.500A) 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 182 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 223 through 226 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 290 Processing helix chain 'D' and resid 322 through 329 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 400 removed outlier: 4.279A pdb=" N ARG D 398 " --> pdb=" O TRP D 394 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASP D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG D 400 " --> pdb=" O LEU D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 428 Processing helix chain 'D' and resid 445 through 461 removed outlier: 4.505A pdb=" N SER D 449 " --> pdb=" O PRO D 445 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP D 450 " --> pdb=" O ALA D 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' 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: 4.719A pdb=" N ASP E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 156 Processing helix chain 'E' and resid 182 through 191 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: 4.077A 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: 4.427A pdb=" N SER E 321 " --> pdb=" O HIS E 317 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N HIS E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.236A 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: 3.551A pdb=" N LYS F 149 " --> pdb=" O HIS F 145 " (cutoff:3.500A) removed outlier: 3.621A 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 229 removed outlier: 4.659A pdb=" N LEU F 224 " --> pdb=" O PRO F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 removed outlier: 3.615A 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: 3.622A pdb=" N VAL G 50 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ASN G 51 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL G 52 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP G 62 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN G 63 " --> pdb=" O LEU G 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 641 Processing helix chain 'H' and resid 687 through 692 Processing helix chain 'H' and resid 712 through 720 Processing helix chain 'H' and resid 722 through 724 No H-bonds generated for 'chain 'H' and resid 722 through 724' Processing helix chain 'H' and resid 735 through 737 No H-bonds generated for 'chain 'H' and resid 735 through 737' Processing helix chain 'H' and resid 764 through 766 No H-bonds generated for 'chain 'H' and resid 764 through 766' Processing helix chain 'H' and resid 779 through 786 Processing helix chain 'H' and resid 800 through 802 No H-bonds generated for 'chain 'H' and resid 800 through 802' Processing helix chain 'H' and resid 818 through 864 removed outlier: 3.538A pdb=" N THR H 823 " --> pdb=" O ASP H 819 " (cutoff:3.500A) Processing helix chain 'H' and resid 890 through 901 removed outlier: 3.727A pdb=" N ALA H 894 " --> pdb=" O THR H 890 " (cutoff:3.500A) Processing helix chain 'H' and resid 909 through 914 Processing helix chain 'H' and resid 925 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 'J' and resid 29 through 39 Processing helix chain 'J' and resid 50 through 60 removed outlier: 4.315A pdb=" N LYS J 54 " --> pdb=" O LYS J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 76 Processing helix chain 'J' and resid 86 through 113 Processing helix chain 'J' and resid 123 through 132 Processing helix chain 'J' and resid 139 through 148 Processing helix chain 'J' and resid 159 through 167 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: 4.099A pdb=" N LEU K 226 " --> pdb=" O LYS K 222 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG K 228 " --> pdb=" O LYS K 224 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ALA K 229 " --> pdb=" O GLU K 225 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL K 230 " --> pdb=" O LEU K 226 " (cutoff:3.500A) removed outlier: 3.702A 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: 5.372A 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 390 through 392 removed outlier: 4.470A pdb=" N THR A 409 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N CYS A 361 " --> pdb=" O ALA A 406 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N SER A 408 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL A 363 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLY A 336 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N THR A 467 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE A 338 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N VAL A 339 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N LEU A 488 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 688 through 690 removed outlier: 3.660A pdb=" N LYS A 688 " --> pdb=" O CYS A 507 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP A 511 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ALA A 657 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ALA A 508 " --> pdb=" O ALA A 657 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE A 659 " --> pdb=" O ALA A 508 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 510 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N SER A 661 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N CYS A 512 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL A 663 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 623 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= F, first strand: chain 'B' and resid 38 through 41 removed outlier: 3.818A pdb=" N SER B 458 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 106 through 108 removed outlier: 6.973A pdb=" N VAL B 204 " --> pdb=" O LEU B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 417 through 419 Processing sheet with id= I, first strand: chain 'B' and resid 490 through 495 removed outlier: 8.172A pdb=" N GLY B 675 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N MET B 493 " --> pdb=" O GLY B 675 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET B 677 " --> pdb=" O MET B 493 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE B 495 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE B 679 " --> pdb=" O ILE B 495 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU B 566 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 597 " --> pdb=" O LEU B 566 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B 568 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL B 599 " --> pdb=" O PHE B 568 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 96 through 100 Processing sheet with id= K, first strand: chain 'D' and resid 248 through 250 Processing sheet with id= L, first strand: chain 'D' and resid 307 through 310 removed outlier: 3.770A 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: 5.260A pdb=" N MET D 334 " --> pdb=" O GLN D 345 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 407 through 409 removed outlier: 3.594A pdb=" N MET D 441 " --> pdb=" O TYR D 409 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE D 433 " --> pdb=" O VAL D 442 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 113 through 118 removed outlier: 6.709A pdb=" N ILE E 106 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N SER E 164 " --> pdb=" O HIS E 60 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N TYR E 62 " --> pdb=" O SER E 164 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N GLU E 166 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N VAL E 64 " --> pdb=" O GLU E 166 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU E 168 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASP E 66 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE E 170 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ARG E 195 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE E 169 " --> pdb=" O ARG E 195 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER E 197 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N PHE E 171 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE E 199 " --> pdb=" O PHE E 171 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 332 through 335 Processing sheet with id= P, first strand: chain 'F' and resid 67 through 69 removed outlier: 6.369A pdb=" N GLU F 156 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU F 10 " --> pdb=" O GLU F 156 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS F 158 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N VAL F 12 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 160 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL F 14 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU F 162 " --> pdb=" O VAL F 14 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ASP F 16 " --> pdb=" O LEU F 162 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ILE F 164 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU F 190 " --> pdb=" O ILE F 161 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL F 163 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ASP F 192 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LYS F 165 " --> pdb=" O ASP F 192 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N CYS F 194 " --> pdb=" O LYS F 165 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 8 through 11 Processing sheet with id= R, first strand: chain 'H' and resid 647 through 649 removed outlier: 3.968A pdb=" N GLY H 668 " --> pdb=" O VAL H 675 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 695 through 697 Processing sheet with id= T, first strand: chain 'H' and resid 705 through 707 Processing sheet with id= U, first strand: chain 'H' and resid 771 through 774 Processing sheet with id= V, first strand: chain 'H' and resid 794 through 798 removed outlier: 6.906A pdb=" N VAL H 807 " --> pdb=" O THR H 795 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N PHE H 797 " --> pdb=" O HIS H 805 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N HIS H 805 " --> pdb=" O PHE H 797 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 138 through 140 Processing sheet with id= X, first strand: chain 'K' and resid 256 through 260 993 hydrogen bonds defined for protein. 2716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 10.39 Time building geometry restraints manager: 11.34 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: 11915 1.43 - 1.64: 16088 1.64 - 1.86: 244 1.86 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 28259 Sorted by residual: bond pdb=" C4' 3DR L 30 " pdb=" O4' 3DR L 30 " ideal model delta sigma weight residual 1.664 1.278 0.386 2.00e-02 2.50e+03 3.73e+02 bond pdb=" C4' 3DR L 31 " pdb=" O4' 3DR L 31 " ideal model delta sigma weight residual 1.664 1.279 0.385 2.00e-02 2.50e+03 3.70e+02 bond pdb=" C4' 3DR L 30 " pdb=" C3' 3DR L 30 " ideal model delta sigma weight residual 1.336 1.647 -0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" C4' 3DR L 31 " pdb=" C3' 3DR L 31 " ideal model delta sigma weight residual 1.336 1.640 -0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" C3' 3DR L 31 " pdb=" C2' 3DR L 31 " ideal model delta sigma weight residual 1.561 1.288 0.273 2.00e-02 2.50e+03 1.86e+02 ... (remaining 28254 not shown) Histogram of bond angle deviations from ideal: 73.70 - 85.78: 12 85.78 - 97.85: 0 97.85 - 109.92: 4054 109.92 - 121.99: 28845 121.99 - 134.07: 5601 Bond angle restraints: 38512 Sorted by residual: angle pdb=" N MET A 412 " pdb=" CA MET A 412 " pdb=" C MET A 412 " ideal model delta sigma weight residual 114.04 109.60 4.44 1.24e+00 6.50e-01 1.28e+01 angle pdb=" C GLU K 198 " pdb=" N ALA K 199 " pdb=" CA ALA K 199 " ideal model delta sigma weight residual 121.54 127.41 -5.87 1.91e+00 2.74e-01 9.44e+00 angle pdb=" N ASP E 25 " pdb=" CA ASP E 25 " pdb=" C ASP E 25 " ideal model delta sigma weight residual 114.56 110.87 3.69 1.27e+00 6.20e-01 8.46e+00 angle pdb=" C ASP B 423 " pdb=" N ARG B 424 " pdb=" CA ARG B 424 " ideal model delta sigma weight residual 121.54 126.79 -5.25 1.91e+00 2.74e-01 7.54e+00 angle pdb=" N ALA K 199 " pdb=" CA ALA K 199 " pdb=" C ALA K 199 " ideal model delta sigma weight residual 110.80 116.26 -5.46 2.13e+00 2.20e-01 6.57e+00 ... (remaining 38507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 16505 35.09 - 70.18: 428 70.18 - 105.27: 6 105.27 - 140.36: 2 140.36 - 175.46: 2 Dihedral angle restraints: 16943 sinusoidal: 7519 harmonic: 9424 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 -25.54 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLU K 198 " pdb=" C GLU K 198 " pdb=" N ALA K 199 " pdb=" CA ALA K 199 " ideal model delta harmonic sigma weight residual 180.00 -157.90 -22.10 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" C4' DT M 27 " pdb=" C3' DT M 27 " pdb=" O3' DT M 27 " pdb=" P DA M 28 " ideal model delta sinusoidal sigma weight residual -140.00 35.46 -175.46 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 16940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2969 0.031 - 0.062: 911 0.062 - 0.093: 235 0.093 - 0.124: 161 0.124 - 0.155: 9 Chirality restraints: 4285 Sorted by residual: chirality pdb=" C3' 3DR L 30 " pdb=" C4' 3DR L 30 " pdb=" O3' 3DR L 30 " pdb=" C2' 3DR L 30 " both_signs ideal model delta sigma weight residual False -2.43 -2.27 -0.16 2.00e-01 2.50e+01 6.02e-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 -2.49 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA PRO C 454 " pdb=" N PRO C 454 " pdb=" C PRO C 454 " pdb=" CB PRO C 454 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.66e-01 ... (remaining 4282 not shown) Planarity restraints: 4647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 582 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO A 583 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 583 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 583 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 353 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO B 354 " 0.061 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 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO D 374 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 374 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 374 " 0.017 5.00e-02 4.00e+02 ... (remaining 4644 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 363 2.64 - 3.20: 24952 3.20 - 3.77: 43728 3.77 - 4.33: 58242 4.33 - 4.90: 93318 Nonbonded interactions: 220603 Sorted by model distance: nonbonded pdb=" O ILE H 899 " pdb=" OG SER H 903 " model vdw 2.075 2.440 nonbonded pdb=" OE2 GLU B 589 " pdb=" OH TYR B 614 " model vdw 2.170 2.440 nonbonded pdb=" OG SER E 243 " pdb=" O ALA F 288 " model vdw 2.176 2.440 nonbonded pdb=" O LEU B 382 " pdb=" OG1 THR B 385 " model vdw 2.188 2.440 nonbonded pdb=" O PHE A 378 " pdb=" OG SER A 382 " model vdw 2.205 2.440 ... (remaining 220598 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=0.50 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.090 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 85.340 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.386 28259 Z= 0.314 Angle : 0.471 8.231 38512 Z= 0.276 Chirality : 0.037 0.155 4285 Planarity : 0.003 0.056 4647 Dihedral : 13.130 175.456 10841 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.80 % Favored : 96.14 % Rotamer: Outliers : 2.53 % Allowed : 5.35 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: 1.34 (0.16), residues: 3186 helix: 2.19 (0.14), residues: 1479 sheet: 0.33 (0.28), residues: 387 loop : -0.43 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 511 HIS 0.004 0.000 HIS B 613 PHE 0.008 0.001 PHE A 482 TYR 0.010 0.001 TYR E 95 ARG 0.003 0.000 ARG A 676 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1126 time to evaluate : 2.877 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: 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 59 LYS cc_start: 0.8617 (mttt) cc_final: 0.8005 (mttt) REVERT: A 65 MET cc_start: 0.7488 (ptt) cc_final: 0.7007 (ptt) REVERT: A 68 LYS cc_start: 0.6778 (mtmt) cc_final: 0.6505 (tppt) REVERT: A 94 LYS cc_start: 0.7737 (ptpt) cc_final: 0.7169 (ptpt) REVERT: A 108 CYS cc_start: 0.8116 (p) cc_final: 0.7686 (p) REVERT: A 129 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.7971 (t) REVERT: A 131 LEU cc_start: 0.7941 (mp) cc_final: 0.7725 (mp) REVERT: A 150 ASP cc_start: 0.7593 (t0) cc_final: 0.6911 (t0) REVERT: A 157 LYS cc_start: 0.8882 (tppt) cc_final: 0.8588 (mtmm) REVERT: A 175 TYR cc_start: 0.8498 (m-80) cc_final: 0.8198 (m-10) REVERT: A 180 CYS cc_start: 0.8547 (t) cc_final: 0.8148 (p) REVERT: A 181 HIS cc_start: 0.7643 (m-70) cc_final: 0.7298 (m90) REVERT: A 183 ASP cc_start: 0.7914 (p0) cc_final: 0.7664 (p0) REVERT: A 184 VAL cc_start: 0.8797 (p) cc_final: 0.8547 (m) REVERT: A 191 ASP cc_start: 0.8232 (t0) cc_final: 0.6725 (t0) REVERT: A 271 GLU cc_start: 0.7419 (pp20) cc_final: 0.7001 (pp20) REVERT: A 277 ILE cc_start: 0.9066 (tt) cc_final: 0.8846 (tp) REVERT: A 279 GLU cc_start: 0.8499 (tp30) cc_final: 0.8051 (tp30) REVERT: A 282 LYS cc_start: 0.9121 (tttt) cc_final: 0.8511 (ttpp) REVERT: A 283 ARG cc_start: 0.8443 (tpp-160) cc_final: 0.7777 (tpt90) REVERT: A 286 HIS cc_start: 0.9333 (t-90) cc_final: 0.8825 (t-90) REVERT: A 287 LEU cc_start: 0.8913 (mt) cc_final: 0.8613 (tp) REVERT: A 291 LEU cc_start: 0.8771 (mp) cc_final: 0.8221 (mm) REVERT: A 305 ASP cc_start: 0.8562 (p0) cc_final: 0.8344 (p0) REVERT: A 321 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7093 (mm-30) REVERT: A 322 LYS cc_start: 0.8671 (mmtt) cc_final: 0.8211 (mppt) REVERT: A 347 SER cc_start: 0.8771 (m) cc_final: 0.8559 (p) REVERT: A 358 ARG cc_start: 0.8115 (tpt-90) cc_final: 0.7914 (mmm-85) REVERT: A 366 ASN cc_start: 0.8190 (t0) cc_final: 0.7541 (t0) REVERT: A 375 LYS cc_start: 0.8477 (ttpt) cc_final: 0.8155 (ttpt) REVERT: A 379 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8443 (mmmt) REVERT: A 381 TRP cc_start: 0.8222 (m-10) cc_final: 0.7501 (m-10) REVERT: A 385 ASP cc_start: 0.8204 (p0) cc_final: 0.7836 (p0) REVERT: A 386 ASP cc_start: 0.7585 (t0) cc_final: 0.7337 (t0) REVERT: A 390 CYS cc_start: 0.7594 (p) cc_final: 0.7121 (p) REVERT: A 403 CYS cc_start: 0.8311 (p) cc_final: 0.7232 (p) REVERT: A 415 HIS cc_start: 0.7440 (OUTLIER) cc_final: 0.7188 (m-70) REVERT: A 434 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7594 (mp0) REVERT: A 438 MET cc_start: 0.7933 (tmm) cc_final: 0.7724 (ttp) REVERT: A 457 ILE cc_start: 0.8501 (tt) cc_final: 0.8238 (tt) REVERT: A 463 LYS cc_start: 0.8638 (mttt) cc_final: 0.8126 (mtmt) REVERT: A 476 LYS cc_start: 0.8624 (mttt) cc_final: 0.8311 (mtmt) REVERT: A 487 LYS cc_start: 0.8631 (ttmt) cc_final: 0.8181 (tmtt) REVERT: A 490 GLU cc_start: 0.7478 (tp30) cc_final: 0.7255 (tp30) REVERT: A 492 ASN cc_start: 0.8038 (t0) cc_final: 0.7585 (t0) REVERT: A 504 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8017 (tttm) REVERT: A 509 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7054 (tm-30) REVERT: A 521 GLU cc_start: 0.8105 (mp0) cc_final: 0.7884 (mp0) REVERT: A 532 LEU cc_start: 0.8926 (mm) cc_final: 0.8621 (tp) REVERT: A 549 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7883 (ttpp) REVERT: A 555 ASN cc_start: 0.7788 (t0) cc_final: 0.7485 (t0) REVERT: A 613 THR cc_start: 0.5779 (OUTLIER) cc_final: 0.5315 (p) REVERT: A 642 ARG cc_start: 0.7479 (mmm-85) cc_final: 0.7236 (mmt-90) REVERT: A 659 PHE cc_start: 0.8645 (OUTLIER) cc_final: 0.8089 (p90) REVERT: A 677 GLN cc_start: 0.7513 (mt0) cc_final: 0.7218 (mt0) REVERT: A 682 ASP cc_start: 0.7483 (m-30) cc_final: 0.7240 (m-30) REVERT: A 711 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8024 (pp30) REVERT: A 715 LYS cc_start: 0.9088 (ptmt) cc_final: 0.8867 (ptmm) REVERT: B 21 GLN cc_start: 0.8714 (mt0) cc_final: 0.8248 (mp10) REVERT: B 30 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8235 (ttm-80) REVERT: B 41 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6514 (tm-30) REVERT: B 56 ILE cc_start: 0.8748 (mm) cc_final: 0.8137 (mm) REVERT: B 57 MET cc_start: 0.7915 (mmt) cc_final: 0.7598 (mmm) REVERT: B 60 GLN cc_start: 0.8385 (mt0) cc_final: 0.8109 (mt0) REVERT: B 72 TYR cc_start: 0.7529 (t80) cc_final: 0.7025 (t80) REVERT: B 76 THR cc_start: 0.7979 (p) cc_final: 0.7602 (p) REVERT: B 86 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7818 (tm-30) REVERT: B 90 LEU cc_start: 0.8470 (tp) cc_final: 0.8213 (tp) REVERT: B 93 PHE cc_start: 0.7604 (t80) cc_final: 0.7400 (t80) REVERT: B 133 LYS cc_start: 0.8516 (mttt) cc_final: 0.8081 (tppt) REVERT: B 158 TYR cc_start: 0.8285 (t80) cc_final: 0.7207 (t80) REVERT: B 176 ASN cc_start: 0.8521 (t0) cc_final: 0.8145 (t0) REVERT: B 207 TYR cc_start: 0.7870 (p90) cc_final: 0.7423 (p90) REVERT: B 210 HIS cc_start: 0.8247 (m-70) cc_final: 0.7800 (p-80) REVERT: B 228 LYS cc_start: 0.7747 (ptmt) cc_final: 0.7392 (ptmt) REVERT: B 237 HIS cc_start: 0.8647 (p-80) cc_final: 0.8375 (p-80) REVERT: B 243 CYS cc_start: 0.8263 (m) cc_final: 0.7695 (m) REVERT: B 247 MET cc_start: 0.8479 (mpp) cc_final: 0.7887 (mpp) REVERT: B 258 ARG cc_start: 0.8047 (ttt180) cc_final: 0.7662 (ttt180) REVERT: B 341 LYS cc_start: 0.8971 (mtmm) cc_final: 0.8713 (mttt) REVERT: B 382 LEU cc_start: 0.7394 (tt) cc_final: 0.7180 (mt) REVERT: B 397 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8201 (mm) REVERT: B 414 PHE cc_start: 0.8688 (m-80) cc_final: 0.7954 (m-80) REVERT: B 416 ILE cc_start: 0.8842 (mp) cc_final: 0.8510 (mp) REVERT: B 444 ILE cc_start: 0.9112 (tp) cc_final: 0.8872 (tp) REVERT: B 445 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8468 (mmmm) REVERT: B 450 ARG cc_start: 0.7360 (mtp85) cc_final: 0.6925 (mtp180) REVERT: B 460 THR cc_start: 0.8627 (m) cc_final: 0.8000 (p) REVERT: B 469 LYS cc_start: 0.8509 (ptpp) cc_final: 0.8019 (ptmm) REVERT: B 471 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7845 (pp) REVERT: B 472 ASP cc_start: 0.7960 (m-30) cc_final: 0.7692 (m-30) REVERT: B 487 ARG cc_start: 0.8292 (ptt-90) cc_final: 0.7984 (ptt-90) REVERT: B 494 ILE cc_start: 0.8992 (mt) cc_final: 0.8725 (mt) REVERT: B 499 ASN cc_start: 0.8520 (m-40) cc_final: 0.8056 (m-40) REVERT: B 522 ASN cc_start: 0.7484 (t0) cc_final: 0.7017 (t0) REVERT: B 526 GLU cc_start: 0.7601 (pt0) cc_final: 0.6668 (pt0) REVERT: B 570 GLU cc_start: 0.6476 (tm-30) cc_final: 0.6010 (tm-30) REVERT: B 603 LYS cc_start: 0.8709 (ptmm) cc_final: 0.8218 (tmtt) REVERT: B 638 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 644 PHE cc_start: 0.8803 (m-80) cc_final: 0.8588 (m-80) REVERT: B 655 ASP cc_start: 0.8463 (t0) cc_final: 0.7811 (m-30) REVERT: B 662 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8005 (tm-30) REVERT: B 677 MET cc_start: 0.8032 (mtp) cc_final: 0.7823 (mtp) REVERT: B 690 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7468 (mtm-85) REVERT: B 692 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8358 (mmtm) REVERT: B 711 ASP cc_start: 0.7457 (m-30) cc_final: 0.6952 (m-30) REVERT: B 719 TYR cc_start: 0.8725 (t80) cc_final: 0.8401 (t80) REVERT: B 723 GLN cc_start: 0.7413 (pp30) cc_final: 0.7095 (tp-100) REVERT: C 402 ASN cc_start: 0.8253 (m-40) cc_final: 0.7964 (m110) REVERT: C 442 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6401 (pm20) REVERT: C 471 LEU cc_start: 0.9336 (mt) cc_final: 0.9067 (tt) REVERT: C 474 HIS cc_start: 0.8272 (m-70) cc_final: 0.8000 (m90) REVERT: C 475 PHE cc_start: 0.8815 (t80) cc_final: 0.8517 (t80) REVERT: C 493 MET cc_start: 0.8246 (tpp) cc_final: 0.7077 (tpp) REVERT: C 497 LEU cc_start: 0.8454 (mt) cc_final: 0.7473 (mt) REVERT: C 506 CYS cc_start: 0.8675 (t) cc_final: 0.8136 (m) REVERT: C 529 LEU cc_start: 0.9364 (mt) cc_final: 0.8541 (mt) REVERT: C 539 TRP cc_start: 0.8620 (t60) cc_final: 0.7938 (t60) REVERT: D 20 GLN cc_start: 0.8268 (mt0) cc_final: 0.7814 (pm20) REVERT: D 34 LEU cc_start: 0.8645 (mt) cc_final: 0.8367 (mm) REVERT: D 44 VAL cc_start: 0.9296 (t) cc_final: 0.9063 (m) REVERT: D 47 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7975 (mm-30) REVERT: D 48 LEU cc_start: 0.8760 (mt) cc_final: 0.7926 (mt) REVERT: D 50 SER cc_start: 0.8822 (m) cc_final: 0.7168 (p) REVERT: D 51 LEU cc_start: 0.8900 (tp) cc_final: 0.8656 (tp) REVERT: D 53 LYS cc_start: 0.9061 (mttt) cc_final: 0.8654 (mttp) REVERT: D 59 MET cc_start: 0.8098 (mtp) cc_final: 0.7787 (mtp) REVERT: D 81 LYS cc_start: 0.8786 (tttt) cc_final: 0.8252 (tttt) REVERT: D 85 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7762 (mt-10) REVERT: D 91 SER cc_start: 0.8999 (t) cc_final: 0.8756 (p) REVERT: D 150 LYS cc_start: 0.8330 (tttt) cc_final: 0.7769 (tttt) REVERT: D 154 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7829 (mt-10) REVERT: D 215 PHE cc_start: 0.7219 (t80) cc_final: 0.6392 (t80) REVERT: D 239 GLN cc_start: 0.9000 (tt0) cc_final: 0.8302 (tm-30) REVERT: D 254 MET cc_start: 0.5219 (mtt) cc_final: 0.4652 (mtt) REVERT: D 258 LEU cc_start: 0.8501 (mt) cc_final: 0.8167 (tt) REVERT: D 266 ARG cc_start: 0.8555 (ttt180) cc_final: 0.8075 (ttp-170) REVERT: D 270 LEU cc_start: 0.8770 (mt) cc_final: 0.8442 (mm) REVERT: D 271 VAL cc_start: 0.8829 (t) cc_final: 0.8477 (p) REVERT: D 333 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6590 (mt-10) REVERT: D 340 ASN cc_start: 0.8645 (p0) cc_final: 0.8330 (p0) REVERT: D 347 THR cc_start: 0.7951 (p) cc_final: 0.7360 (p) REVERT: D 352 GLN cc_start: 0.8333 (mm110) cc_final: 0.7646 (mm110) REVERT: D 353 GLN cc_start: 0.7978 (tt0) cc_final: 0.7715 (tp40) REVERT: D 360 THR cc_start: 0.8890 (p) cc_final: 0.8393 (p) REVERT: D 363 GLN cc_start: 0.8690 (mt0) cc_final: 0.8340 (mt0) REVERT: D 366 HIS cc_start: 0.8721 (t70) cc_final: 0.8453 (t70) REVERT: D 376 MET cc_start: 0.8058 (mtp) cc_final: 0.7495 (mtp) REVERT: D 378 LYS cc_start: 0.8498 (mttt) cc_final: 0.8252 (mttt) REVERT: D 386 THR cc_start: 0.8814 (p) cc_final: 0.8520 (p) REVERT: D 389 ASP cc_start: 0.7993 (m-30) cc_final: 0.7481 (m-30) REVERT: D 408 LEU cc_start: 0.7835 (tp) cc_final: 0.7482 (tp) REVERT: D 412 PHE cc_start: 0.6895 (m-80) cc_final: 0.5768 (m-80) REVERT: D 418 PHE cc_start: 0.7948 (t80) cc_final: 0.7023 (t80) REVERT: D 421 LEU cc_start: 0.9083 (tp) cc_final: 0.8750 (mt) REVERT: D 435 ASN cc_start: 0.7957 (t0) cc_final: 0.7743 (t0) REVERT: E 12 GLU cc_start: 0.7766 (pt0) cc_final: 0.7280 (pt0) REVERT: E 16 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7402 (mm-30) REVERT: E 19 TRP cc_start: 0.8676 (p90) cc_final: 0.8365 (p90) REVERT: E 20 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7668 (mm-30) REVERT: E 35 GLU cc_start: 0.8462 (tt0) cc_final: 0.8067 (tt0) REVERT: E 40 LYS cc_start: 0.8849 (tppt) cc_final: 0.8639 (tppt) REVERT: E 58 MET cc_start: 0.7478 (mtm) cc_final: 0.7211 (mtm) REVERT: E 59 ARG cc_start: 0.8442 (mtp180) cc_final: 0.8102 (mtp85) REVERT: E 66 ASP cc_start: 0.7180 (t0) cc_final: 0.6898 (t0) REVERT: E 73 ASP cc_start: 0.7866 (t0) cc_final: 0.7039 (t0) REVERT: E 75 ASP cc_start: 0.7360 (m-30) cc_final: 0.6244 (m-30) REVERT: E 80 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7982 (mtt180) REVERT: E 83 CYS cc_start: 0.8099 (t) cc_final: 0.7555 (t) REVERT: E 86 LYS cc_start: 0.8704 (tttt) cc_final: 0.8422 (tttt) REVERT: E 97 ASP cc_start: 0.7856 (t70) cc_final: 0.7634 (t0) REVERT: E 112 LYS cc_start: 0.8315 (mtmt) cc_final: 0.7885 (mttt) REVERT: E 116 LYS cc_start: 0.8542 (tttt) cc_final: 0.8218 (tttt) REVERT: E 125 ARG cc_start: 0.7662 (mtt180) cc_final: 0.7314 (mtt180) REVERT: E 126 LYS cc_start: 0.8266 (tttt) cc_final: 0.7958 (tttt) REVERT: E 144 SER cc_start: 0.8911 (t) cc_final: 0.8194 (p) REVERT: E 153 MET cc_start: 0.7667 (ttp) cc_final: 0.7467 (ttm) REVERT: E 159 MET cc_start: 0.8083 (mmt) cc_final: 0.7753 (mmp) REVERT: E 165 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.7699 (mtt-85) REVERT: E 181 ASN cc_start: 0.8352 (t0) cc_final: 0.7804 (t0) REVERT: E 222 ILE cc_start: 0.8446 (mt) cc_final: 0.8177 (mm) REVERT: E 229 LYS cc_start: 0.8149 (tttt) cc_final: 0.7834 (tttt) REVERT: E 251 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7978 (mmm-85) REVERT: E 256 GLN cc_start: 0.7785 (pm20) cc_final: 0.7389 (tt0) REVERT: E 273 MET cc_start: 0.6410 (mmp) cc_final: 0.6114 (tpp) REVERT: E 298 TYR cc_start: 0.7337 (m-80) cc_final: 0.6401 (m-80) REVERT: E 303 VAL cc_start: 0.8611 (t) cc_final: 0.8089 (p) REVERT: E 304 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7510 (tm-30) REVERT: E 306 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8219 (mmtt) REVERT: E 328 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7148 (tm) REVERT: E 329 ASP cc_start: 0.7789 (m-30) cc_final: 0.7135 (p0) REVERT: E 332 GLN cc_start: 0.6608 (mp-120) cc_final: 0.6063 (mp10) REVERT: E 333 GLU cc_start: 0.7178 (tt0) cc_final: 0.6856 (tt0) REVERT: E 352 LEU cc_start: 0.8542 (mt) cc_final: 0.7703 (mt) REVERT: E 353 LYS cc_start: 0.8812 (mttt) cc_final: 0.7132 (mttt) REVERT: E 357 VAL cc_start: 0.7055 (t) cc_final: 0.6744 (m) REVERT: E 366 VAL cc_start: 0.6684 (OUTLIER) cc_final: 0.6220 (p) REVERT: E 379 LEU cc_start: 0.9122 (tp) cc_final: 0.8867 (tp) REVERT: F 18 ASN cc_start: 0.8706 (t0) cc_final: 0.8502 (t0) REVERT: F 28 LYS cc_start: 0.9045 (mttt) cc_final: 0.8581 (mttt) REVERT: F 55 ASN cc_start: 0.8466 (m-40) cc_final: 0.8261 (m110) REVERT: F 56 LYS cc_start: 0.8164 (mmtt) cc_final: 0.7879 (mmtt) REVERT: F 63 HIS cc_start: 0.8060 (t-90) cc_final: 0.7825 (t-90) REVERT: F 101 TYR cc_start: 0.7902 (t80) cc_final: 0.7600 (t80) REVERT: F 105 THR cc_start: 0.8435 (m) cc_final: 0.7924 (m) REVERT: F 109 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8020 (mt-10) REVERT: F 117 ASP cc_start: 0.8702 (t70) cc_final: 0.7820 (t70) REVERT: F 139 LYS cc_start: 0.9204 (mttt) cc_final: 0.8899 (mtmt) REVERT: F 146 ARG cc_start: 0.8838 (ttt180) cc_final: 0.8549 (tmm-80) REVERT: F 148 ASN cc_start: 0.8298 (t0) cc_final: 0.8021 (m110) REVERT: F 156 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6979 (mt-10) REVERT: F 157 MET cc_start: 0.8004 (ttt) cc_final: 0.7603 (ttp) REVERT: F 158 LYS cc_start: 0.8239 (mttt) cc_final: 0.7897 (mttt) REVERT: F 173 GLN cc_start: 0.8101 (mt0) cc_final: 0.7825 (mt0) REVERT: F 175 MET cc_start: 0.7112 (ttt) cc_final: 0.6667 (ttt) REVERT: F 176 ASN cc_start: 0.8701 (m110) cc_final: 0.8472 (m110) REVERT: F 178 MET cc_start: 0.8604 (mmm) cc_final: 0.8393 (tpp) REVERT: F 179 ASN cc_start: 0.8818 (m110) cc_final: 0.8404 (m110) REVERT: F 194 CYS cc_start: 0.8663 (t) cc_final: 0.7964 (t) REVERT: F 195 VAL cc_start: 0.8488 (t) cc_final: 0.8125 (m) REVERT: F 208 ASP cc_start: 0.7975 (t70) cc_final: 0.7681 (t70) REVERT: F 225 GLN cc_start: 0.9186 (tp40) cc_final: 0.8927 (tp40) REVERT: F 226 TYR cc_start: 0.8732 (m-80) cc_final: 0.8385 (m-10) REVERT: F 236 ASP cc_start: 0.7960 (p0) cc_final: 0.7551 (p0) REVERT: F 237 GLN cc_start: 0.8419 (mt0) cc_final: 0.7458 (mt0) REVERT: F 239 SER cc_start: 0.8685 (m) cc_final: 0.8461 (p) REVERT: F 240 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7149 (mm110) REVERT: F 249 VAL cc_start: 0.7397 (t) cc_final: 0.7096 (p) REVERT: F 252 ARG cc_start: 0.8215 (mtm180) cc_final: 0.7859 (mtm-85) REVERT: F 266 TYR cc_start: 0.7964 (m-80) cc_final: 0.7663 (m-80) REVERT: F 281 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8771 (tp) REVERT: G 13 ASP cc_start: 0.7255 (p0) cc_final: 0.6838 (p0) REVERT: G 16 MET cc_start: 0.8785 (mmt) cc_final: 0.8378 (mmm) REVERT: G 18 GLN cc_start: 0.8441 (mt0) cc_final: 0.8225 (mt0) REVERT: G 36 GLN cc_start: 0.7767 (tp40) cc_final: 0.7487 (tm-30) REVERT: G 43 VAL cc_start: 0.8693 (m) cc_final: 0.8403 (p) REVERT: G 44 PHE cc_start: 0.8018 (t80) cc_final: 0.7794 (t80) REVERT: G 51 ASN cc_start: 0.8406 (m-40) cc_final: 0.8125 (p0) REVERT: H 849 LYS cc_start: 0.8609 (tttt) cc_final: 0.8300 (mmtm) REVERT: H 895 GLU cc_start: 0.8070 (tp30) cc_final: 0.7473 (tp30) REVERT: H 899 ILE cc_start: 0.7973 (mm) cc_final: 0.7457 (mm) REVERT: H 912 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7361 (mt-10) REVERT: H 913 LYS cc_start: 0.7104 (mttt) cc_final: 0.6865 (mttt) REVERT: J 165 ILE cc_start: 0.3448 (OUTLIER) cc_final: 0.3091 (mm) REVERT: K 116 TYR cc_start: 0.8432 (t80) cc_final: 0.8175 (t80) REVERT: K 118 MET cc_start: 0.6909 (tpp) cc_final: 0.6614 (tpp) REVERT: K 135 LYS cc_start: 0.9099 (tttt) cc_final: 0.8591 (tttt) REVERT: K 136 HIS cc_start: 0.8796 (m90) cc_final: 0.8142 (m90) REVERT: K 138 LEU cc_start: 0.8986 (mt) cc_final: 0.8765 (mm) REVERT: K 141 LYS cc_start: 0.8977 (tttt) cc_final: 0.8729 (tttt) REVERT: K 143 GLU cc_start: 0.8650 (tt0) cc_final: 0.7822 (tm-30) REVERT: K 145 LYS cc_start: 0.8231 (mtpt) cc_final: 0.8023 (mtpt) REVERT: K 148 TYR cc_start: 0.8524 (m-80) cc_final: 0.8320 (m-80) REVERT: K 163 LYS cc_start: 0.8408 (mttt) cc_final: 0.8082 (mttt) REVERT: K 178 MET cc_start: 0.8094 (ptp) cc_final: 0.7685 (ptp) REVERT: K 192 GLU cc_start: 0.8555 (mt-10) cc_final: 0.7931 (mt-10) REVERT: K 217 LYS cc_start: 0.8539 (tmtt) cc_final: 0.8185 (tmtt) outliers start: 72 outliers final: 20 residues processed: 1183 average time/residue: 0.4403 time to fit residues: 773.9052 Evaluate side-chains 991 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 957 time to evaluate : 2.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 430 ASN Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 613 HIS 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 D residue 100 LEU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 251 ARG Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain H residue 908 ARG Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 165 ILE Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain K residue 227 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 274 optimal weight: 20.0000 chunk 246 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 189 optimal weight: 0.3980 chunk 295 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 ASN A 683 GLN B 238 ASN B 434 HIS ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 509 GLN C 515 GLN C 524 HIS ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 HIS D 324 GLN D 345 GLN D 379 GLN ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 GLN E 365 ASN F 128 HIS F 176 ASN ** H 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28259 Z= 0.225 Angle : 0.603 14.876 38512 Z= 0.303 Chirality : 0.042 0.280 4285 Planarity : 0.004 0.063 4647 Dihedral : 15.581 176.284 4447 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.41 % Rotamer: Outliers : 4.29 % Allowed : 14.78 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: 1.00 (0.15), residues: 3186 helix: 1.72 (0.14), residues: 1474 sheet: 0.28 (0.28), residues: 382 loop : -0.37 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 511 HIS 0.007 0.001 HIS C 524 PHE 0.020 0.002 PHE A 270 TYR 0.022 0.001 TYR E 339 ARG 0.007 0.001 ARG D 398 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1103 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 981 time to evaluate : 2.878 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8651 (mttt) cc_final: 0.8086 (mttt) REVERT: A 65 MET cc_start: 0.7575 (ptt) cc_final: 0.7105 (ptt) REVERT: A 68 LYS cc_start: 0.7065 (mtmt) cc_final: 0.6589 (tppt) REVERT: A 94 LYS cc_start: 0.7779 (ptpt) cc_final: 0.7243 (ptpt) REVERT: A 124 TYR cc_start: 0.7931 (m-80) cc_final: 0.7721 (m-80) REVERT: A 138 GLU cc_start: 0.7931 (tp30) cc_final: 0.7705 (tp30) REVERT: A 150 ASP cc_start: 0.7447 (t0) cc_final: 0.6578 (t0) REVERT: A 157 LYS cc_start: 0.8893 (tppt) cc_final: 0.8583 (mtmm) REVERT: A 159 CYS cc_start: 0.8379 (m) cc_final: 0.8143 (t) REVERT: A 175 TYR cc_start: 0.8611 (m-80) cc_final: 0.8269 (m-10) REVERT: A 183 ASP cc_start: 0.8120 (p0) cc_final: 0.7914 (p0) REVERT: A 184 VAL cc_start: 0.8848 (p) cc_final: 0.8507 (m) REVERT: A 191 ASP cc_start: 0.8282 (t0) cc_final: 0.6761 (t0) REVERT: A 276 MET cc_start: 0.8406 (mmp) cc_final: 0.8034 (mmp) REVERT: A 279 GLU cc_start: 0.8760 (tp30) cc_final: 0.8448 (mm-30) REVERT: A 282 LYS cc_start: 0.9117 (tttt) cc_final: 0.8561 (ttpp) REVERT: A 305 ASP cc_start: 0.8577 (p0) cc_final: 0.8299 (p0) REVERT: A 306 ILE cc_start: 0.8704 (pt) cc_final: 0.8444 (pt) REVERT: A 321 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7592 (mm-30) REVERT: A 322 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8261 (mppt) REVERT: A 351 VAL cc_start: 0.8983 (t) cc_final: 0.8663 (p) REVERT: A 375 LYS cc_start: 0.8436 (ttpt) cc_final: 0.8152 (ttpt) REVERT: A 379 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8384 (mmmt) REVERT: A 380 MET cc_start: 0.7598 (ttm) cc_final: 0.6949 (ttm) REVERT: A 381 TRP cc_start: 0.8351 (m-10) cc_final: 0.7974 (m-10) REVERT: A 385 ASP cc_start: 0.8160 (p0) cc_final: 0.7883 (p0) REVERT: A 386 ASP cc_start: 0.7683 (t0) cc_final: 0.7457 (t0) REVERT: A 415 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6968 (m-70) REVERT: A 434 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7612 (mp0) REVERT: A 437 LEU cc_start: 0.9018 (tp) cc_final: 0.8685 (tt) REVERT: A 441 ASP cc_start: 0.7948 (t0) cc_final: 0.7709 (t0) REVERT: A 449 LYS cc_start: 0.8438 (tppt) cc_final: 0.8226 (tppt) REVERT: A 450 MET cc_start: 0.7524 (ptm) cc_final: 0.7091 (ptm) REVERT: A 453 ARG cc_start: 0.8239 (ptm160) cc_final: 0.7713 (mtm110) REVERT: A 457 ILE cc_start: 0.8676 (tt) cc_final: 0.8364 (tt) REVERT: A 463 LYS cc_start: 0.8579 (mttt) cc_final: 0.8072 (mtmt) REVERT: A 488 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8121 (mt) REVERT: A 492 ASN cc_start: 0.8034 (t0) cc_final: 0.7558 (t0) REVERT: A 504 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8064 (tttm) REVERT: A 521 GLU cc_start: 0.8166 (mp0) cc_final: 0.7948 (mp0) REVERT: A 532 LEU cc_start: 0.8919 (mm) cc_final: 0.8595 (tp) REVERT: A 549 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7304 (ttpp) REVERT: A 553 ARG cc_start: 0.7986 (mtm-85) cc_final: 0.7498 (mtm-85) REVERT: A 586 GLN cc_start: 0.8044 (tp40) cc_final: 0.7790 (tp-100) REVERT: A 613 THR cc_start: 0.6363 (OUTLIER) cc_final: 0.6121 (p) REVERT: A 656 ASN cc_start: 0.8042 (m110) cc_final: 0.7798 (m-40) REVERT: A 659 PHE cc_start: 0.8664 (OUTLIER) cc_final: 0.8028 (p90) REVERT: A 677 GLN cc_start: 0.7557 (mt0) cc_final: 0.7118 (mt0) REVERT: A 683 GLN cc_start: 0.8181 (mm110) cc_final: 0.7898 (mm-40) REVERT: A 711 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8184 (pp30) REVERT: A 715 LYS cc_start: 0.9215 (ptmt) cc_final: 0.8978 (ptmm) REVERT: B 1 MET cc_start: 0.6326 (ppp) cc_final: 0.5892 (ppp) REVERT: B 27 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7968 (tm-30) REVERT: B 30 ARG cc_start: 0.8492 (ttm-80) cc_final: 0.8236 (ttm-80) REVERT: B 32 LEU cc_start: 0.7550 (mt) cc_final: 0.6997 (mt) REVERT: B 41 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6499 (tm-30) REVERT: B 42 MET cc_start: 0.7782 (mtp) cc_final: 0.7491 (mtp) REVERT: B 48 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8231 (ttmt) REVERT: B 56 ILE cc_start: 0.8774 (mm) cc_final: 0.8350 (tp) REVERT: B 60 GLN cc_start: 0.8745 (mt0) cc_final: 0.8209 (mt0) REVERT: B 61 ARG cc_start: 0.8301 (mmp80) cc_final: 0.7976 (mmp80) REVERT: B 65 LEU cc_start: 0.7864 (tp) cc_final: 0.7570 (pt) REVERT: B 72 TYR cc_start: 0.7782 (t80) cc_final: 0.7203 (t80) REVERT: B 86 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7754 (tm-30) REVERT: B 90 LEU cc_start: 0.8700 (tp) cc_final: 0.8378 (tp) REVERT: B 93 PHE cc_start: 0.7718 (t80) cc_final: 0.7504 (t80) REVERT: B 133 LYS cc_start: 0.8466 (mttt) cc_final: 0.8111 (tppt) REVERT: B 186 ARG cc_start: 0.8678 (ptm160) cc_final: 0.8171 (tmm-80) REVERT: B 207 TYR cc_start: 0.8226 (p90) cc_final: 0.7444 (p90) REVERT: B 210 HIS cc_start: 0.8260 (m-70) cc_final: 0.7917 (p-80) REVERT: B 228 LYS cc_start: 0.7843 (ptmt) cc_final: 0.7453 (ptmt) REVERT: B 243 CYS cc_start: 0.8357 (m) cc_final: 0.7810 (m) REVERT: B 247 MET cc_start: 0.8402 (mpp) cc_final: 0.7536 (mpp) REVERT: B 258 ARG cc_start: 0.8019 (ttt180) cc_final: 0.7608 (ttt180) REVERT: B 334 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7670 (ttp80) REVERT: B 341 LYS cc_start: 0.9134 (mtmm) cc_final: 0.8871 (mttt) REVERT: B 397 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8245 (mm) REVERT: B 414 PHE cc_start: 0.8815 (m-80) cc_final: 0.7740 (m-80) REVERT: B 416 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8778 (mp) REVERT: B 434 HIS cc_start: 0.5958 (OUTLIER) cc_final: 0.5619 (p-80) REVERT: B 444 ILE cc_start: 0.9042 (tp) cc_final: 0.8752 (tp) REVERT: B 445 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8759 (mmmm) REVERT: B 450 ARG cc_start: 0.7247 (mtp85) cc_final: 0.6869 (mtp180) REVERT: B 464 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8190 (mm) REVERT: B 469 LYS cc_start: 0.8660 (ptpp) cc_final: 0.8206 (ptmm) REVERT: B 472 ASP cc_start: 0.7932 (m-30) cc_final: 0.7688 (m-30) REVERT: B 478 MET cc_start: 0.5896 (mmp) cc_final: 0.5645 (mmp) REVERT: B 494 ILE cc_start: 0.9082 (mt) cc_final: 0.8774 (mp) REVERT: B 499 ASN cc_start: 0.8511 (m-40) cc_final: 0.8039 (m-40) REVERT: B 570 GLU cc_start: 0.6650 (tm-30) cc_final: 0.6114 (tm-30) REVERT: B 631 ARG cc_start: 0.7497 (mtp-110) cc_final: 0.7239 (mtp-110) REVERT: B 644 PHE cc_start: 0.8999 (m-80) cc_final: 0.8641 (m-80) REVERT: B 646 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8145 (mm) REVERT: B 655 ASP cc_start: 0.8568 (t0) cc_final: 0.7715 (m-30) REVERT: B 662 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8041 (tm-30) REVERT: B 663 CYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7761 (p) REVERT: B 673 ASP cc_start: 0.7931 (t0) cc_final: 0.7605 (t0) REVERT: B 677 MET cc_start: 0.8001 (mtp) cc_final: 0.7733 (mtp) REVERT: B 682 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8031 (ttmm) REVERT: B 690 ARG cc_start: 0.7844 (mtm110) cc_final: 0.7503 (mtm-85) REVERT: B 711 ASP cc_start: 0.7531 (m-30) cc_final: 0.6994 (m-30) REVERT: B 723 GLN cc_start: 0.7513 (pp30) cc_final: 0.7157 (tp-100) REVERT: C 412 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8393 (tp30) REVERT: C 424 SER cc_start: 0.7295 (p) cc_final: 0.6988 (t) REVERT: C 442 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.6517 (pm20) REVERT: C 471 LEU cc_start: 0.9342 (mt) cc_final: 0.9082 (tt) REVERT: C 474 HIS cc_start: 0.8484 (m-70) cc_final: 0.8279 (m90) REVERT: C 475 PHE cc_start: 0.8788 (t80) cc_final: 0.8360 (t80) REVERT: C 493 MET cc_start: 0.8268 (tpp) cc_final: 0.7391 (tpp) REVERT: C 506 CYS cc_start: 0.8680 (t) cc_final: 0.8441 (m) REVERT: C 528 MET cc_start: 0.9066 (mtm) cc_final: 0.8476 (mtm) REVERT: C 529 LEU cc_start: 0.9111 (mt) cc_final: 0.8790 (mt) REVERT: C 539 TRP cc_start: 0.8541 (t60) cc_final: 0.7938 (t60) REVERT: C 542 ARG cc_start: 0.7742 (tpm170) cc_final: 0.7540 (tpm170) REVERT: D 34 LEU cc_start: 0.8640 (mt) cc_final: 0.8365 (mm) REVERT: D 44 VAL cc_start: 0.9243 (t) cc_final: 0.8962 (m) REVERT: D 47 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8018 (mm-30) REVERT: D 48 LEU cc_start: 0.8720 (mt) cc_final: 0.7959 (mm) REVERT: D 50 SER cc_start: 0.7924 (m) cc_final: 0.6702 (p) REVERT: D 51 LEU cc_start: 0.8362 (tp) cc_final: 0.7571 (tp) REVERT: D 53 LYS cc_start: 0.9125 (mttt) cc_final: 0.8406 (mttp) REVERT: D 60 LEU cc_start: 0.8523 (tp) cc_final: 0.8319 (tt) REVERT: D 79 PHE cc_start: 0.8102 (m-80) cc_final: 0.7760 (m-80) REVERT: D 81 LYS cc_start: 0.9028 (tttt) cc_final: 0.8824 (ttpp) REVERT: D 91 SER cc_start: 0.8933 (t) cc_final: 0.8708 (p) REVERT: D 120 ILE cc_start: 0.9089 (mm) cc_final: 0.8847 (tp) REVERT: D 150 LYS cc_start: 0.8408 (tttt) cc_final: 0.7809 (tttt) REVERT: D 151 TYR cc_start: 0.7785 (t80) cc_final: 0.7245 (t80) REVERT: D 154 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8052 (mt-10) REVERT: D 155 ARG cc_start: 0.8376 (mmp80) cc_final: 0.8035 (mmt90) REVERT: D 213 TRP cc_start: 0.6905 (t-100) cc_final: 0.6411 (t-100) REVERT: D 239 GLN cc_start: 0.9045 (tt0) cc_final: 0.8285 (tm-30) REVERT: D 242 PHE cc_start: 0.8399 (m-10) cc_final: 0.7948 (m-10) REVERT: D 252 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7927 (pp20) REVERT: D 254 MET cc_start: 0.5127 (mtt) cc_final: 0.4322 (mtt) REVERT: D 258 LEU cc_start: 0.8583 (mt) cc_final: 0.8357 (tt) REVERT: D 260 ASN cc_start: 0.8878 (m110) cc_final: 0.8515 (p0) REVERT: D 265 LEU cc_start: 0.8785 (mt) cc_final: 0.8565 (mm) REVERT: D 266 ARG cc_start: 0.8670 (ttt180) cc_final: 0.7899 (ttp-170) REVERT: D 270 LEU cc_start: 0.8540 (mt) cc_final: 0.8266 (mm) REVERT: D 271 VAL cc_start: 0.8840 (t) cc_final: 0.8496 (p) REVERT: D 275 LYS cc_start: 0.8296 (pttt) cc_final: 0.7668 (ptpt) REVERT: D 277 LYS cc_start: 0.9012 (mmpt) cc_final: 0.8754 (mmmt) REVERT: D 290 LEU cc_start: 0.7367 (pp) cc_final: 0.7144 (pp) REVERT: D 316 TYR cc_start: 0.8606 (m-80) cc_final: 0.7727 (m-10) REVERT: D 318 TYR cc_start: 0.8607 (m-10) cc_final: 0.8198 (m-10) REVERT: D 333 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6609 (mt-10) REVERT: D 340 ASN cc_start: 0.8681 (p0) cc_final: 0.8333 (p0) REVERT: D 363 GLN cc_start: 0.8645 (mt0) cc_final: 0.8146 (mt0) REVERT: D 366 HIS cc_start: 0.8822 (t70) cc_final: 0.8448 (t70) REVERT: D 376 MET cc_start: 0.7731 (mtp) cc_final: 0.7491 (mtp) REVERT: D 378 LYS cc_start: 0.8589 (mttt) cc_final: 0.8291 (mttt) REVERT: D 389 ASP cc_start: 0.8053 (m-30) cc_final: 0.7508 (m-30) REVERT: D 405 GLU cc_start: 0.7819 (mp0) cc_final: 0.7606 (mp0) REVERT: D 408 LEU cc_start: 0.7684 (tp) cc_final: 0.7345 (tp) REVERT: D 412 PHE cc_start: 0.6983 (m-80) cc_final: 0.5481 (m-80) REVERT: D 418 PHE cc_start: 0.8008 (t80) cc_final: 0.7297 (t80) REVERT: E 16 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7517 (mm-30) REVERT: E 18 THR cc_start: 0.8414 (p) cc_final: 0.8140 (p) REVERT: E 19 TRP cc_start: 0.8739 (p90) cc_final: 0.8478 (p90) REVERT: E 20 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: E 35 GLU cc_start: 0.8565 (tt0) cc_final: 0.8166 (tt0) REVERT: E 42 LYS cc_start: 0.8616 (mttt) cc_final: 0.8356 (mptt) REVERT: E 57 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7838 (mtp) REVERT: E 66 ASP cc_start: 0.7180 (t0) cc_final: 0.6946 (t0) REVERT: E 73 ASP cc_start: 0.8091 (t0) cc_final: 0.6689 (t0) REVERT: E 75 ASP cc_start: 0.7364 (m-30) cc_final: 0.6179 (m-30) REVERT: E 80 ARG cc_start: 0.8356 (mtt180) cc_final: 0.7993 (mtt180) REVERT: E 86 LYS cc_start: 0.8686 (tttt) cc_final: 0.8443 (tttt) REVERT: E 97 ASP cc_start: 0.7887 (t70) cc_final: 0.7658 (t0) REVERT: E 101 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8152 (mm) REVERT: E 102 SER cc_start: 0.8689 (m) cc_final: 0.7876 (m) REVERT: E 112 LYS cc_start: 0.8371 (mtmt) cc_final: 0.8000 (mttt) REVERT: E 116 LYS cc_start: 0.8507 (tttt) cc_final: 0.8199 (tttt) REVERT: E 125 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7398 (mtt180) REVERT: E 144 SER cc_start: 0.8981 (t) cc_final: 0.8263 (p) REVERT: E 153 MET cc_start: 0.7708 (ttp) cc_final: 0.7495 (ttm) REVERT: E 210 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8348 (p) REVERT: E 222 ILE cc_start: 0.8441 (mt) cc_final: 0.8227 (mm) REVERT: E 229 LYS cc_start: 0.8169 (tttt) cc_final: 0.7849 (tttt) REVERT: E 256 GLN cc_start: 0.7849 (pm20) cc_final: 0.7597 (tt0) REVERT: E 295 ARG cc_start: 0.8020 (mmt180) cc_final: 0.7568 (mmm-85) REVERT: E 303 VAL cc_start: 0.8661 (t) cc_final: 0.8087 (p) REVERT: E 304 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7427 (tm-30) REVERT: E 306 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8161 (mmtt) REVERT: E 322 TYR cc_start: 0.8054 (m-10) cc_final: 0.7817 (m-80) REVERT: E 328 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7004 (tp) REVERT: E 329 ASP cc_start: 0.7767 (m-30) cc_final: 0.7455 (p0) REVERT: E 333 GLU cc_start: 0.7377 (tt0) cc_final: 0.7075 (tt0) REVERT: E 342 GLU cc_start: 0.7420 (tp30) cc_final: 0.6944 (tp30) REVERT: E 351 GLU cc_start: 0.7567 (tm-30) cc_final: 0.6945 (tm-30) REVERT: E 353 LYS cc_start: 0.8450 (mttt) cc_final: 0.7769 (mttt) REVERT: E 357 VAL cc_start: 0.7905 (t) cc_final: 0.7697 (m) REVERT: E 379 LEU cc_start: 0.9173 (tp) cc_final: 0.8791 (tp) REVERT: F 9 ASN cc_start: 0.8198 (m110) cc_final: 0.7822 (t0) REVERT: F 25 GLN cc_start: 0.7959 (tp-100) cc_final: 0.6988 (tp-100) REVERT: F 28 LYS cc_start: 0.9121 (mttt) cc_final: 0.8653 (mttt) REVERT: F 51 MET cc_start: 0.7985 (mtp) cc_final: 0.7640 (mmm) REVERT: F 63 HIS cc_start: 0.8217 (t-90) cc_final: 0.7945 (t-90) REVERT: F 65 GLN cc_start: 0.8349 (mt0) cc_final: 0.7982 (mm-40) REVERT: F 68 ARG cc_start: 0.7806 (tpt-90) cc_final: 0.7306 (tpp80) REVERT: F 101 TYR cc_start: 0.7925 (t80) cc_final: 0.7445 (t80) REVERT: F 105 THR cc_start: 0.8383 (m) cc_final: 0.8013 (m) REVERT: F 109 GLU cc_start: 0.8573 (mt-10) cc_final: 0.7996 (mt-10) REVERT: F 117 ASP cc_start: 0.8555 (t70) cc_final: 0.8033 (t70) REVERT: F 139 LYS cc_start: 0.9298 (mttt) cc_final: 0.8955 (mtmt) REVERT: F 156 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7009 (mt-10) REVERT: F 158 LYS cc_start: 0.8315 (mttt) cc_final: 0.7944 (mttt) REVERT: F 173 GLN cc_start: 0.8184 (mt0) cc_final: 0.7859 (mt0) REVERT: F 194 CYS cc_start: 0.8524 (t) cc_final: 0.7964 (t) REVERT: F 195 VAL cc_start: 0.8435 (t) cc_final: 0.8176 (m) REVERT: F 208 ASP cc_start: 0.8075 (t70) cc_final: 0.7735 (t70) REVERT: F 216 LYS cc_start: 0.8954 (tttt) cc_final: 0.8495 (ttmt) REVERT: F 225 GLN cc_start: 0.9274 (tp40) cc_final: 0.9030 (tp40) REVERT: F 237 GLN cc_start: 0.8256 (mt0) cc_final: 0.7595 (mt0) REVERT: F 240 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7484 (mm110) REVERT: F 248 HIS cc_start: 0.4642 (OUTLIER) cc_final: 0.4415 (m-70) REVERT: F 249 VAL cc_start: 0.7534 (t) cc_final: 0.7284 (p) REVERT: F 281 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8763 (tp) REVERT: G 16 MET cc_start: 0.9043 (mmt) cc_final: 0.8455 (mmm) REVERT: G 18 GLN cc_start: 0.8532 (mt0) cc_final: 0.8321 (mt0) REVERT: G 36 GLN cc_start: 0.7968 (tp40) cc_final: 0.7223 (tm-30) REVERT: G 43 VAL cc_start: 0.8739 (m) cc_final: 0.8342 (p) REVERT: G 44 PHE cc_start: 0.8080 (t80) cc_final: 0.7605 (t80) REVERT: G 51 ASN cc_start: 0.8527 (m-40) cc_final: 0.8315 (p0) REVERT: G 59 GLU cc_start: 0.8539 (tt0) cc_final: 0.8328 (tt0) REVERT: H 862 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6802 (mmtt) REVERT: H 895 GLU cc_start: 0.8200 (tp30) cc_final: 0.7594 (tp30) REVERT: H 899 ILE cc_start: 0.8317 (mm) cc_final: 0.8058 (mm) REVERT: H 912 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7431 (mt-10) REVERT: H 913 LYS cc_start: 0.7200 (mttt) cc_final: 0.6955 (mttt) REVERT: J 162 PHE cc_start: 0.8096 (t80) cc_final: 0.7863 (t80) REVERT: K 118 MET cc_start: 0.6930 (tpp) cc_final: 0.6674 (tpp) REVERT: K 120 HIS cc_start: 0.8747 (m-70) cc_final: 0.8275 (m-70) REVERT: K 121 PHE cc_start: 0.8366 (m-80) cc_final: 0.7654 (m-80) REVERT: K 130 ARG cc_start: 0.7500 (ttt180) cc_final: 0.7287 (ttt180) REVERT: K 135 LYS cc_start: 0.8993 (tttt) cc_final: 0.8730 (tttt) REVERT: K 136 HIS cc_start: 0.8803 (m90) cc_final: 0.8156 (m90) REVERT: K 138 LEU cc_start: 0.8938 (mt) cc_final: 0.8697 (mm) REVERT: K 141 LYS cc_start: 0.8890 (tttt) cc_final: 0.8650 (tttt) REVERT: K 143 GLU cc_start: 0.8718 (tt0) cc_final: 0.7954 (tm-30) REVERT: K 146 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8460 (tm-30) REVERT: K 148 TYR cc_start: 0.8793 (m-80) cc_final: 0.8443 (m-80) REVERT: K 163 LYS cc_start: 0.8618 (mttt) cc_final: 0.8157 (mttt) REVERT: K 166 VAL cc_start: 0.8920 (t) cc_final: 0.8537 (p) REVERT: K 178 MET cc_start: 0.7866 (ptp) cc_final: 0.7327 (ptp) REVERT: K 180 LEU cc_start: 0.9036 (mt) cc_final: 0.8680 (mm) REVERT: K 192 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8185 (tm-30) REVERT: K 200 LEU cc_start: 0.8343 (tp) cc_final: 0.8139 (tt) REVERT: K 202 GLU cc_start: 0.8698 (mp0) cc_final: 0.8485 (pm20) REVERT: K 217 LYS cc_start: 0.8557 (tmtt) cc_final: 0.8221 (tmtt) REVERT: K 252 LEU cc_start: 0.7824 (tp) cc_final: 0.7571 (tp) outliers start: 122 outliers final: 64 residues processed: 1048 average time/residue: 0.4426 time to fit residues: 691.2921 Evaluate side-chains 1023 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 939 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 VAL 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 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 GLU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 613 HIS Chi-restraints excluded: chain B residue 646 ILE Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 702 THR 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 495 SER Chi-restraints excluded: chain C residue 511 LYS Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 850 LEU Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 186 ILE Chi-restraints excluded: chain K residue 215 LYS Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 242 HIS Chi-restraints excluded: chain K residue 269 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 164 optimal weight: 3.9990 chunk 91 optimal weight: 0.0770 chunk 245 optimal weight: 0.3980 chunk 200 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 295 optimal weight: 0.3980 chunk 319 optimal weight: 2.9990 chunk 263 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 237 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 698 GLN ** C 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 GLN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 HIS ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN F 176 ASN H 847 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 208 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28259 Z= 0.179 Angle : 0.605 16.432 38512 Z= 0.300 Chirality : 0.041 0.253 4285 Planarity : 0.004 0.060 4647 Dihedral : 15.585 175.698 4429 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.78 % Favored : 95.19 % Rotamer: Outliers : 4.75 % Allowed : 16.90 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: 0.76 (0.15), residues: 3186 helix: 1.46 (0.14), residues: 1465 sheet: 0.14 (0.28), residues: 391 loop : -0.39 (0.18), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 342 HIS 0.007 0.001 HIS B 434 PHE 0.021 0.001 PHE D 454 TYR 0.038 0.001 TYR C 533 ARG 0.011 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 973 time to evaluate : 3.227 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8576 (mttt) cc_final: 0.8036 (mttt) REVERT: A 65 MET cc_start: 0.7734 (ptt) cc_final: 0.7223 (ptt) REVERT: A 68 LYS cc_start: 0.7011 (mtmt) cc_final: 0.6758 (tptt) REVERT: A 94 LYS cc_start: 0.7751 (ptpt) cc_final: 0.7227 (ptpt) REVERT: A 124 TYR cc_start: 0.7933 (m-80) cc_final: 0.7696 (m-80) REVERT: A 138 GLU cc_start: 0.8013 (tp30) cc_final: 0.7431 (tp30) REVERT: A 141 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8197 (ptp-110) REVERT: A 153 MET cc_start: 0.7522 (tmm) cc_final: 0.6693 (tmm) REVERT: A 157 LYS cc_start: 0.8886 (tppt) cc_final: 0.8630 (mtmm) REVERT: A 276 MET cc_start: 0.8329 (mmp) cc_final: 0.7753 (mmm) REVERT: A 278 GLU cc_start: 0.8528 (pm20) cc_final: 0.8019 (pm20) REVERT: A 279 GLU cc_start: 0.8743 (tp30) cc_final: 0.8306 (tp30) REVERT: A 282 LYS cc_start: 0.9109 (tttt) cc_final: 0.8568 (ttpp) REVERT: A 305 ASP cc_start: 0.8581 (p0) cc_final: 0.8279 (p0) REVERT: A 321 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 322 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8372 (tppt) REVERT: A 351 VAL cc_start: 0.8974 (t) cc_final: 0.8653 (p) REVERT: A 375 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8190 (ttpt) REVERT: A 379 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8317 (mmmt) REVERT: A 380 MET cc_start: 0.7577 (OUTLIER) cc_final: 0.6876 (ttm) REVERT: A 381 TRP cc_start: 0.8281 (m-10) cc_final: 0.7925 (m-10) REVERT: A 385 ASP cc_start: 0.8220 (p0) cc_final: 0.7912 (p0) REVERT: A 386 ASP cc_start: 0.7660 (t0) cc_final: 0.7448 (t0) REVERT: A 419 ARG cc_start: 0.8507 (ttm170) cc_final: 0.8264 (tpp80) REVERT: A 424 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8092 (tp30) REVERT: A 434 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7641 (mp0) REVERT: A 450 MET cc_start: 0.7487 (ptm) cc_final: 0.6933 (ptm) REVERT: A 453 ARG cc_start: 0.8238 (ptm160) cc_final: 0.7710 (mtm110) REVERT: A 457 ILE cc_start: 0.8665 (tt) cc_final: 0.8347 (tt) REVERT: A 463 LYS cc_start: 0.8560 (mttt) cc_final: 0.8068 (mtmt) REVERT: A 492 ASN cc_start: 0.8065 (t0) cc_final: 0.7550 (t0) REVERT: A 504 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8097 (tttm) REVERT: A 510 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8169 (p) REVERT: A 521 GLU cc_start: 0.8156 (mp0) cc_final: 0.7929 (mp0) REVERT: A 549 LYS cc_start: 0.8017 (mtmt) cc_final: 0.6934 (ttpp) REVERT: A 552 GLU cc_start: 0.7105 (pp20) cc_final: 0.6690 (pp20) REVERT: A 586 GLN cc_start: 0.8047 (tp40) cc_final: 0.7790 (tp-100) REVERT: A 656 ASN cc_start: 0.8068 (m110) cc_final: 0.7798 (m-40) REVERT: A 659 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8066 (p90) REVERT: A 674 THR cc_start: 0.8684 (m) cc_final: 0.8299 (t) REVERT: A 677 GLN cc_start: 0.7505 (mt0) cc_final: 0.7181 (mt0) REVERT: A 683 GLN cc_start: 0.8247 (mm110) cc_final: 0.8017 (mm-40) REVERT: A 711 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8157 (pp30) REVERT: A 715 LYS cc_start: 0.9077 (ptmt) cc_final: 0.8785 (ptmm) REVERT: B 1 MET cc_start: 0.6342 (ppp) cc_final: 0.6071 (ppp) REVERT: B 41 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6449 (tm-30) REVERT: B 42 MET cc_start: 0.7761 (mtp) cc_final: 0.7328 (mtp) REVERT: B 48 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8251 (ttmt) REVERT: B 60 GLN cc_start: 0.8787 (mt0) cc_final: 0.8149 (mt0) REVERT: B 61 ARG cc_start: 0.8393 (mmp80) cc_final: 0.7952 (mmp80) REVERT: B 65 LEU cc_start: 0.7826 (tp) cc_final: 0.7416 (pt) REVERT: B 72 TYR cc_start: 0.7804 (t80) cc_final: 0.7253 (t80) REVERT: B 86 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7830 (tm-30) REVERT: B 133 LYS cc_start: 0.8468 (mttt) cc_final: 0.8093 (tppt) REVERT: B 207 TYR cc_start: 0.8140 (p90) cc_final: 0.7472 (p90) REVERT: B 210 HIS cc_start: 0.8224 (m-70) cc_final: 0.7966 (p-80) REVERT: B 228 LYS cc_start: 0.7875 (ptmt) cc_final: 0.7481 (ptmt) REVERT: B 237 HIS cc_start: 0.8624 (p-80) cc_final: 0.8236 (p-80) REVERT: B 243 CYS cc_start: 0.8348 (m) cc_final: 0.7958 (m) REVERT: B 247 MET cc_start: 0.8107 (mpp) cc_final: 0.7729 (mpp) REVERT: B 258 ARG cc_start: 0.7996 (ttt180) cc_final: 0.7637 (ttt180) REVERT: B 334 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7596 (ttp80) REVERT: B 335 ARG cc_start: 0.8370 (ptt-90) cc_final: 0.8068 (ptt-90) REVERT: B 339 TYR cc_start: 0.8047 (t80) cc_final: 0.6336 (t80) REVERT: B 341 LYS cc_start: 0.9112 (mtmm) cc_final: 0.8766 (mttp) REVERT: B 434 HIS cc_start: 0.5783 (p-80) cc_final: 0.5337 (p-80) REVERT: B 445 LYS cc_start: 0.9159 (mmtt) cc_final: 0.8680 (mmmm) REVERT: B 464 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8038 (mm) REVERT: B 469 LYS cc_start: 0.8679 (ptpp) cc_final: 0.8194 (ptmm) REVERT: B 472 ASP cc_start: 0.7907 (m-30) cc_final: 0.7620 (m-30) REVERT: B 478 MET cc_start: 0.5861 (mmp) cc_final: 0.5487 (mmp) REVERT: B 494 ILE cc_start: 0.9078 (mt) cc_final: 0.8779 (mp) REVERT: B 499 ASN cc_start: 0.8519 (m-40) cc_final: 0.8052 (m-40) REVERT: B 526 GLU cc_start: 0.7644 (pt0) cc_final: 0.7273 (pt0) REVERT: B 570 GLU cc_start: 0.6580 (tm-30) cc_final: 0.6029 (tm-30) REVERT: B 603 LYS cc_start: 0.8715 (ptmm) cc_final: 0.8463 (ptmm) REVERT: B 631 ARG cc_start: 0.7375 (mtp-110) cc_final: 0.7127 (mtp-110) REVERT: B 644 PHE cc_start: 0.8993 (m-80) cc_final: 0.8647 (m-80) REVERT: B 646 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8171 (mm) REVERT: B 655 ASP cc_start: 0.8592 (t0) cc_final: 0.7704 (m-30) REVERT: B 662 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8185 (tm-30) REVERT: B 663 CYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7759 (p) REVERT: B 673 ASP cc_start: 0.7806 (t0) cc_final: 0.7465 (t0) REVERT: B 677 MET cc_start: 0.8050 (mtp) cc_final: 0.7809 (mtp) REVERT: B 682 LYS cc_start: 0.8426 (ttmt) cc_final: 0.7977 (ttmm) REVERT: B 690 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7358 (mtm-85) REVERT: B 711 ASP cc_start: 0.7511 (m-30) cc_final: 0.7014 (m-30) REVERT: B 723 GLN cc_start: 0.7456 (pp30) cc_final: 0.7172 (tp-100) REVERT: C 409 GLN cc_start: 0.8592 (pp30) cc_final: 0.7838 (pp30) REVERT: C 424 SER cc_start: 0.7506 (p) cc_final: 0.7180 (t) REVERT: C 442 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6365 (pm20) REVERT: C 471 LEU cc_start: 0.9368 (mt) cc_final: 0.9107 (tt) REVERT: C 475 PHE cc_start: 0.8760 (t80) cc_final: 0.8396 (t80) REVERT: C 493 MET cc_start: 0.8277 (tpp) cc_final: 0.7442 (tpp) REVERT: C 528 MET cc_start: 0.8938 (mtm) cc_final: 0.8134 (mtm) REVERT: C 529 LEU cc_start: 0.9150 (mt) cc_final: 0.8524 (pp) REVERT: C 533 TYR cc_start: 0.8301 (m-80) cc_final: 0.8023 (m-80) REVERT: C 539 TRP cc_start: 0.8508 (t60) cc_final: 0.7875 (t60) REVERT: C 542 ARG cc_start: 0.7563 (tpm170) cc_final: 0.7119 (tpm170) REVERT: D 20 GLN cc_start: 0.8214 (mt0) cc_final: 0.8003 (mp10) REVERT: D 34 LEU cc_start: 0.8665 (mt) cc_final: 0.8411 (mm) REVERT: D 44 VAL cc_start: 0.9267 (t) cc_final: 0.8990 (m) REVERT: D 47 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7978 (mm-30) REVERT: D 48 LEU cc_start: 0.8714 (mt) cc_final: 0.8387 (mt) REVERT: D 50 SER cc_start: 0.7737 (m) cc_final: 0.6794 (p) REVERT: D 55 TRP cc_start: 0.7302 (m-10) cc_final: 0.6872 (m-90) REVERT: D 57 MET cc_start: 0.8479 (mmp) cc_final: 0.8047 (mmm) REVERT: D 79 PHE cc_start: 0.8080 (m-80) cc_final: 0.7717 (m-80) REVERT: D 81 LYS cc_start: 0.9003 (tttt) cc_final: 0.8651 (ttpp) REVERT: D 85 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7918 (mt-10) REVERT: D 86 SER cc_start: 0.8947 (m) cc_final: 0.8694 (p) REVERT: D 91 SER cc_start: 0.8925 (t) cc_final: 0.8713 (p) REVERT: D 120 ILE cc_start: 0.9094 (mm) cc_final: 0.8796 (tp) REVERT: D 150 LYS cc_start: 0.8441 (tttt) cc_final: 0.7818 (tttt) REVERT: D 151 TYR cc_start: 0.7754 (t80) cc_final: 0.7345 (t80) REVERT: D 154 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8054 (mt-10) REVERT: D 155 ARG cc_start: 0.8380 (mmp80) cc_final: 0.8047 (mmt90) REVERT: D 156 TRP cc_start: 0.8384 (OUTLIER) cc_final: 0.7047 (m-90) REVERT: D 211 GLN cc_start: 0.7845 (mt0) cc_final: 0.7503 (pm20) REVERT: D 213 TRP cc_start: 0.7541 (OUTLIER) cc_final: 0.7229 (t-100) REVERT: D 214 TYR cc_start: 0.7777 (t80) cc_final: 0.7451 (t80) REVERT: D 239 GLN cc_start: 0.9031 (tt0) cc_final: 0.8259 (tm-30) REVERT: D 242 PHE cc_start: 0.8337 (m-10) cc_final: 0.7760 (m-10) REVERT: D 249 TYR cc_start: 0.8282 (m-80) cc_final: 0.7880 (m-80) REVERT: D 254 MET cc_start: 0.5187 (mtt) cc_final: 0.4258 (mtt) REVERT: D 258 LEU cc_start: 0.8631 (mt) cc_final: 0.8383 (tt) REVERT: D 260 ASN cc_start: 0.8900 (m110) cc_final: 0.8510 (p0) REVERT: D 266 ARG cc_start: 0.8660 (ttt180) cc_final: 0.7782 (ttp-170) REVERT: D 270 LEU cc_start: 0.8533 (mt) cc_final: 0.8059 (mm) REVERT: D 271 VAL cc_start: 0.8695 (t) cc_final: 0.8306 (p) REVERT: D 275 LYS cc_start: 0.8293 (pttt) cc_final: 0.7719 (pttt) REVERT: D 316 TYR cc_start: 0.8542 (m-80) cc_final: 0.7569 (m-80) REVERT: D 318 TYR cc_start: 0.8541 (m-10) cc_final: 0.8065 (m-10) REVERT: D 340 ASN cc_start: 0.8630 (p0) cc_final: 0.8157 (p0) REVERT: D 355 ILE cc_start: 0.9009 (mt) cc_final: 0.8777 (mm) REVERT: D 363 GLN cc_start: 0.8611 (mt0) cc_final: 0.8286 (mt0) REVERT: D 366 HIS cc_start: 0.8823 (t70) cc_final: 0.8421 (t70) REVERT: D 369 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7831 (tpp80) REVERT: D 376 MET cc_start: 0.7895 (mtp) cc_final: 0.7521 (mtp) REVERT: D 377 LEU cc_start: 0.8871 (mt) cc_final: 0.8632 (mt) REVERT: D 378 LYS cc_start: 0.8576 (mttt) cc_final: 0.8238 (mttt) REVERT: D 389 ASP cc_start: 0.7998 (m-30) cc_final: 0.7456 (m-30) REVERT: D 408 LEU cc_start: 0.7688 (tp) cc_final: 0.7379 (tp) REVERT: D 412 PHE cc_start: 0.7038 (m-80) cc_final: 0.5803 (m-80) REVERT: D 418 PHE cc_start: 0.8264 (t80) cc_final: 0.7368 (t80) REVERT: D 426 ARG cc_start: 0.8478 (tpp80) cc_final: 0.8187 (tpp80) REVERT: D 438 LYS cc_start: 0.8435 (mttt) cc_final: 0.8091 (mttt) REVERT: E 16 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7449 (mm-30) REVERT: E 19 TRP cc_start: 0.8646 (p90) cc_final: 0.8385 (p90) REVERT: E 20 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: E 35 GLU cc_start: 0.8544 (tt0) cc_final: 0.8132 (tt0) REVERT: E 39 PHE cc_start: 0.8087 (t80) cc_final: 0.7750 (t80) REVERT: E 42 LYS cc_start: 0.8638 (mttt) cc_final: 0.8344 (mptt) REVERT: E 57 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7900 (mtp) REVERT: E 71 MET cc_start: 0.8790 (mmt) cc_final: 0.8437 (mmm) REVERT: E 73 ASP cc_start: 0.8002 (t0) cc_final: 0.6566 (t0) REVERT: E 75 ASP cc_start: 0.7403 (m-30) cc_final: 0.6147 (m-30) REVERT: E 80 ARG cc_start: 0.8376 (mtt180) cc_final: 0.7986 (mtt180) REVERT: E 86 LYS cc_start: 0.8645 (tttt) cc_final: 0.8402 (tttt) REVERT: E 97 ASP cc_start: 0.7878 (t70) cc_final: 0.7654 (t0) REVERT: E 101 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8074 (mm) REVERT: E 102 SER cc_start: 0.8683 (m) cc_final: 0.7958 (m) REVERT: E 112 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7988 (mttt) REVERT: E 125 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7378 (mtt180) REVERT: E 136 ASP cc_start: 0.8027 (m-30) cc_final: 0.7665 (p0) REVERT: E 144 SER cc_start: 0.9015 (t) cc_final: 0.8319 (p) REVERT: E 159 MET cc_start: 0.7956 (mmp) cc_final: 0.7338 (mmp) REVERT: E 166 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6722 (mt-10) REVERT: E 222 ILE cc_start: 0.8452 (mt) cc_final: 0.8206 (mm) REVERT: E 229 LYS cc_start: 0.8173 (tttt) cc_final: 0.7828 (tttt) REVERT: E 251 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7931 (tpp80) REVERT: E 273 MET cc_start: 0.6514 (mmm) cc_final: 0.6032 (mtp) REVERT: E 303 VAL cc_start: 0.8660 (t) cc_final: 0.8059 (p) REVERT: E 304 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7418 (tm-30) REVERT: E 306 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8320 (mmtt) REVERT: E 322 TYR cc_start: 0.7963 (m-10) cc_final: 0.7697 (m-80) REVERT: E 328 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7041 (tp) REVERT: E 329 ASP cc_start: 0.7729 (m-30) cc_final: 0.7401 (p0) REVERT: E 333 GLU cc_start: 0.7479 (tt0) cc_final: 0.7200 (tt0) REVERT: E 355 GLN cc_start: 0.8344 (mt0) cc_final: 0.7623 (mt0) REVERT: E 357 VAL cc_start: 0.7711 (t) cc_final: 0.7348 (m) REVERT: E 370 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7484 (p0) REVERT: E 379 LEU cc_start: 0.9181 (tp) cc_final: 0.8768 (tp) REVERT: F 25 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7068 (tp-100) REVERT: F 28 LYS cc_start: 0.9119 (mttt) cc_final: 0.8672 (mttt) REVERT: F 51 MET cc_start: 0.7901 (mtp) cc_final: 0.7479 (mmm) REVERT: F 52 ASN cc_start: 0.8011 (t0) cc_final: 0.7738 (t0) REVERT: F 55 ASN cc_start: 0.8720 (m110) cc_final: 0.8492 (m110) REVERT: F 56 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7603 (mmtt) REVERT: F 63 HIS cc_start: 0.8321 (t-90) cc_final: 0.7648 (t-90) REVERT: F 68 ARG cc_start: 0.7803 (tpt-90) cc_final: 0.7357 (tpp80) REVERT: F 101 TYR cc_start: 0.7963 (t80) cc_final: 0.7160 (t80) REVERT: F 105 THR cc_start: 0.8370 (m) cc_final: 0.7997 (m) REVERT: F 109 GLU cc_start: 0.8565 (mt-10) cc_final: 0.7974 (mt-10) REVERT: F 111 ILE cc_start: 0.9048 (mt) cc_final: 0.8847 (mm) REVERT: F 117 ASP cc_start: 0.8547 (t70) cc_final: 0.8030 (t70) REVERT: F 139 LYS cc_start: 0.9251 (mttt) cc_final: 0.8941 (mtmt) REVERT: F 147 MET cc_start: 0.8331 (mmm) cc_final: 0.7955 (mmm) REVERT: F 149 LYS cc_start: 0.8066 (mttt) cc_final: 0.7751 (mtmt) REVERT: F 156 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7025 (mt-10) REVERT: F 158 LYS cc_start: 0.8232 (mttt) cc_final: 0.7957 (mttt) REVERT: F 173 GLN cc_start: 0.8140 (mt0) cc_final: 0.7814 (mt0) REVERT: F 185 GLN cc_start: 0.8914 (tt0) cc_final: 0.8676 (tt0) REVERT: F 194 CYS cc_start: 0.8487 (t) cc_final: 0.7950 (t) REVERT: F 195 VAL cc_start: 0.8462 (t) cc_final: 0.8232 (m) REVERT: F 208 ASP cc_start: 0.8055 (t70) cc_final: 0.7638 (t0) REVERT: F 216 LYS cc_start: 0.8974 (tttt) cc_final: 0.8553 (tttt) REVERT: F 227 LEU cc_start: 0.9214 (mt) cc_final: 0.8967 (mm) REVERT: F 237 GLN cc_start: 0.8271 (mt0) cc_final: 0.7533 (mt0) REVERT: F 240 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7487 (mm110) REVERT: F 248 HIS cc_start: 0.4674 (OUTLIER) cc_final: 0.4356 (m-70) REVERT: F 252 ARG cc_start: 0.8719 (mtp180) cc_final: 0.8375 (mtp-110) REVERT: F 281 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8726 (tp) REVERT: G 16 MET cc_start: 0.9014 (mmt) cc_final: 0.8360 (mmm) REVERT: G 36 GLN cc_start: 0.7950 (tp40) cc_final: 0.7116 (tm-30) REVERT: G 42 HIS cc_start: 0.8157 (m90) cc_final: 0.7910 (m90) REVERT: G 43 VAL cc_start: 0.8738 (m) cc_final: 0.8324 (p) REVERT: G 44 PHE cc_start: 0.8093 (t80) cc_final: 0.7700 (t80) REVERT: G 59 GLU cc_start: 0.8475 (tt0) cc_final: 0.8258 (tt0) REVERT: H 862 LYS cc_start: 0.7197 (mmtt) cc_final: 0.6808 (mmtt) REVERT: H 895 GLU cc_start: 0.8216 (tp30) cc_final: 0.7600 (tp30) REVERT: H 899 ILE cc_start: 0.8372 (mm) cc_final: 0.8048 (mm) REVERT: H 900 LEU cc_start: 0.7702 (tp) cc_final: 0.7302 (tp) REVERT: H 912 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7389 (mt-10) REVERT: H 913 LYS cc_start: 0.7176 (mttt) cc_final: 0.6955 (mttt) REVERT: K 103 VAL cc_start: 0.7564 (t) cc_final: 0.7353 (p) REVERT: K 118 MET cc_start: 0.6976 (tpp) cc_final: 0.6376 (tpp) REVERT: K 120 HIS cc_start: 0.8673 (m-70) cc_final: 0.8178 (m-70) REVERT: K 121 PHE cc_start: 0.8488 (m-80) cc_final: 0.7594 (m-80) REVERT: K 123 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6557 (mm) REVERT: K 125 THR cc_start: 0.7764 (m) cc_final: 0.7429 (m) REVERT: K 130 ARG cc_start: 0.7375 (ttt180) cc_final: 0.7163 (ttt180) REVERT: K 136 HIS cc_start: 0.8742 (m90) cc_final: 0.8183 (m90) REVERT: K 138 LEU cc_start: 0.8984 (mt) cc_final: 0.8693 (mm) REVERT: K 141 LYS cc_start: 0.8961 (tttt) cc_final: 0.8617 (tttt) REVERT: K 143 GLU cc_start: 0.8694 (tt0) cc_final: 0.7709 (tm-30) REVERT: K 146 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8466 (tm-30) REVERT: K 163 LYS cc_start: 0.8607 (mttt) cc_final: 0.8106 (mttt) REVERT: K 166 VAL cc_start: 0.8907 (t) cc_final: 0.8574 (p) REVERT: K 168 LYS cc_start: 0.8722 (tptm) cc_final: 0.8462 (tptm) REVERT: K 178 MET cc_start: 0.7624 (ptp) cc_final: 0.7068 (ptp) REVERT: K 192 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8004 (tm-30) REVERT: K 217 LYS cc_start: 0.8573 (tmtt) cc_final: 0.8229 (tmtt) REVERT: K 252 LEU cc_start: 0.7754 (tp) cc_final: 0.7488 (tp) outliers start: 135 outliers final: 70 residues processed: 1041 average time/residue: 0.4360 time to fit residues: 675.6420 Evaluate side-chains 1011 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 922 time to evaluate : 2.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 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 515 SER Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 394 PHE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 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 646 ILE Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 698 GLN 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 479 PHE Chi-restraints excluded: chain C residue 495 SER Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 140 HIS Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 242 HIS Chi-restraints excluded: chain K residue 269 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 292 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 281 optimal weight: 0.3980 chunk 84 optimal weight: 0.0770 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 GLN B 92 ASN B 238 ASN ** B 434 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 ASN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 HIS E 50 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 ASN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN F 179 ASN F 225 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28259 Z= 0.208 Angle : 0.611 11.286 38512 Z= 0.305 Chirality : 0.041 0.291 4285 Planarity : 0.004 0.058 4647 Dihedral : 15.600 176.255 4426 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 4.61 % Allowed : 18.73 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: 0.65 (0.15), residues: 3186 helix: 1.34 (0.14), residues: 1479 sheet: 0.08 (0.28), residues: 386 loop : -0.43 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 511 HIS 0.009 0.001 HIS C 474 PHE 0.021 0.001 PHE D 454 TYR 0.030 0.001 TYR C 533 ARG 0.007 0.001 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 957 time to evaluate : 2.799 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8626 (mttt) cc_final: 0.8118 (mttt) REVERT: A 65 MET cc_start: 0.7737 (ptt) cc_final: 0.7319 (ptt) REVERT: A 68 LYS cc_start: 0.7070 (mtmt) cc_final: 0.6809 (tmtt) REVERT: A 94 LYS cc_start: 0.7819 (ptpt) cc_final: 0.7307 (ptpt) REVERT: A 115 GLU cc_start: 0.7466 (tt0) cc_final: 0.7235 (tt0) REVERT: A 141 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8211 (ptp-110) REVERT: A 150 ASP cc_start: 0.7255 (t0) cc_final: 0.7038 (t0) REVERT: A 275 GLU cc_start: 0.8422 (pm20) cc_final: 0.8123 (pm20) REVERT: A 276 MET cc_start: 0.8381 (mmp) cc_final: 0.7744 (mmm) REVERT: A 278 GLU cc_start: 0.8565 (pm20) cc_final: 0.8165 (pm20) REVERT: A 279 GLU cc_start: 0.8767 (tp30) cc_final: 0.8320 (tp30) REVERT: A 282 LYS cc_start: 0.8972 (tttt) cc_final: 0.8458 (ttpp) REVERT: A 305 ASP cc_start: 0.8554 (p0) cc_final: 0.8264 (p0) REVERT: A 322 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8282 (mtmm) REVERT: A 351 VAL cc_start: 0.9029 (t) cc_final: 0.8709 (p) REVERT: A 379 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8326 (mmmt) REVERT: A 380 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7004 (ttm) REVERT: A 381 TRP cc_start: 0.8319 (m-10) cc_final: 0.7973 (m-10) REVERT: A 385 ASP cc_start: 0.8252 (p0) cc_final: 0.7954 (p0) REVERT: A 386 ASP cc_start: 0.7692 (t0) cc_final: 0.7491 (t0) REVERT: A 434 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7632 (mm-30) REVERT: A 437 LEU cc_start: 0.8866 (tp) cc_final: 0.8586 (tt) REVERT: A 450 MET cc_start: 0.7524 (ptm) cc_final: 0.6988 (ptm) REVERT: A 453 ARG cc_start: 0.8242 (ptm160) cc_final: 0.7737 (mtm110) REVERT: A 457 ILE cc_start: 0.8702 (tt) cc_final: 0.8393 (tt) REVERT: A 463 LYS cc_start: 0.8527 (mttt) cc_final: 0.8117 (mttp) REVERT: A 492 ASN cc_start: 0.8135 (t0) cc_final: 0.7744 (t0) REVERT: A 504 LYS cc_start: 0.8547 (ttpt) cc_final: 0.8082 (tttm) REVERT: A 510 VAL cc_start: 0.8521 (OUTLIER) cc_final: 0.8210 (p) REVERT: A 521 GLU cc_start: 0.8234 (mp0) cc_final: 0.7984 (mp0) REVERT: A 549 LYS cc_start: 0.8078 (mtmt) cc_final: 0.6872 (ttpp) REVERT: A 552 GLU cc_start: 0.7196 (pp20) cc_final: 0.6776 (pp20) REVERT: A 636 GLU cc_start: 0.7734 (tp30) cc_final: 0.7399 (tp30) REVERT: A 656 ASN cc_start: 0.8187 (m110) cc_final: 0.7902 (m-40) REVERT: A 659 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8125 (p90) REVERT: A 674 THR cc_start: 0.8736 (m) cc_final: 0.8349 (t) REVERT: A 677 GLN cc_start: 0.7545 (mt0) cc_final: 0.7181 (mt0) REVERT: A 683 GLN cc_start: 0.8242 (mm110) cc_final: 0.7932 (mm-40) REVERT: A 696 MET cc_start: 0.8165 (tpp) cc_final: 0.7872 (tpp) REVERT: A 697 GLU cc_start: 0.8583 (pm20) cc_final: 0.8306 (pm20) REVERT: A 711 GLN cc_start: 0.8519 (tm-30) cc_final: 0.8224 (pp30) REVERT: A 715 LYS cc_start: 0.9154 (ptmt) cc_final: 0.8852 (ptmm) REVERT: B 20 GLU cc_start: 0.7955 (mp0) cc_final: 0.7581 (mt-10) REVERT: B 30 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8193 (ttm-80) REVERT: B 41 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6319 (tm-30) REVERT: B 42 MET cc_start: 0.7860 (mtp) cc_final: 0.7479 (mtp) REVERT: B 60 GLN cc_start: 0.8867 (mt0) cc_final: 0.8234 (mt0) REVERT: B 61 ARG cc_start: 0.8459 (mmp80) cc_final: 0.8018 (mmp80) REVERT: B 65 LEU cc_start: 0.7873 (tp) cc_final: 0.7442 (pt) REVERT: B 72 TYR cc_start: 0.7754 (t80) cc_final: 0.7129 (t80) REVERT: B 85 GLU cc_start: 0.8417 (pp20) cc_final: 0.7792 (tp30) REVERT: B 86 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7582 (tm-30) REVERT: B 109 LEU cc_start: 0.7852 (mm) cc_final: 0.7616 (mt) REVERT: B 133 LYS cc_start: 0.8474 (mttt) cc_final: 0.8102 (tppt) REVERT: B 186 ARG cc_start: 0.8695 (ptm160) cc_final: 0.8186 (tmm-80) REVERT: B 207 TYR cc_start: 0.8207 (p90) cc_final: 0.7483 (p90) REVERT: B 210 HIS cc_start: 0.8252 (m-70) cc_final: 0.8000 (p-80) REVERT: B 228 LYS cc_start: 0.7927 (ptmt) cc_final: 0.7488 (ptmt) REVERT: B 232 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8702 (p) REVERT: B 237 HIS cc_start: 0.8621 (p-80) cc_final: 0.8215 (p-80) REVERT: B 243 CYS cc_start: 0.8377 (m) cc_final: 0.7945 (m) REVERT: B 247 MET cc_start: 0.8209 (mpp) cc_final: 0.7699 (mpp) REVERT: B 258 ARG cc_start: 0.8024 (ttt180) cc_final: 0.7642 (ttt180) REVERT: B 334 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7651 (ttp80) REVERT: B 335 ARG cc_start: 0.8470 (ptt-90) cc_final: 0.8115 (ptt-90) REVERT: B 339 TYR cc_start: 0.8137 (t80) cc_final: 0.6465 (t80) REVERT: B 341 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8790 (mttp) REVERT: B 434 HIS cc_start: 0.5996 (p-80) cc_final: 0.5445 (p-80) REVERT: B 450 ARG cc_start: 0.7689 (mtp180) cc_final: 0.7309 (ttm-80) REVERT: B 469 LYS cc_start: 0.8709 (ptpp) cc_final: 0.8487 (ptpp) REVERT: B 472 ASP cc_start: 0.7963 (m-30) cc_final: 0.7439 (m-30) REVERT: B 494 ILE cc_start: 0.9088 (mt) cc_final: 0.8787 (mp) REVERT: B 499 ASN cc_start: 0.8552 (m-40) cc_final: 0.8087 (m-40) REVERT: B 526 GLU cc_start: 0.7760 (pt0) cc_final: 0.7202 (pt0) REVERT: B 570 GLU cc_start: 0.6598 (tm-30) cc_final: 0.6013 (tm-30) REVERT: B 633 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8454 (tp) REVERT: B 634 LYS cc_start: 0.7810 (ptpp) cc_final: 0.7371 (mtmm) REVERT: B 655 ASP cc_start: 0.8636 (t0) cc_final: 0.7692 (m-30) REVERT: B 662 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8099 (tm-30) REVERT: B 663 CYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7689 (p) REVERT: B 673 ASP cc_start: 0.7944 (t0) cc_final: 0.7653 (t0) REVERT: B 677 MET cc_start: 0.8089 (mtp) cc_final: 0.7854 (mtp) REVERT: B 682 LYS cc_start: 0.8520 (ttmt) cc_final: 0.8276 (ttmt) REVERT: B 690 ARG cc_start: 0.7923 (mtm110) cc_final: 0.7437 (mtm-85) REVERT: B 711 ASP cc_start: 0.7535 (m-30) cc_final: 0.7152 (m-30) REVERT: B 723 GLN cc_start: 0.7484 (pp30) cc_final: 0.7215 (tp-100) REVERT: C 408 ARG cc_start: 0.8925 (ptm-80) cc_final: 0.8642 (ptm-80) REVERT: C 424 SER cc_start: 0.7579 (p) cc_final: 0.7287 (t) REVERT: C 442 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6354 (pm20) REVERT: C 455 ASN cc_start: 0.7131 (m-40) cc_final: 0.6094 (m-40) REVERT: C 458 GLN cc_start: 0.7643 (pt0) cc_final: 0.7418 (pp30) REVERT: C 470 GLU cc_start: 0.8428 (tp30) cc_final: 0.7092 (tp30) REVERT: C 471 LEU cc_start: 0.9301 (mt) cc_final: 0.9072 (tt) REVERT: C 473 ARG cc_start: 0.8727 (tmt170) cc_final: 0.8019 (tmt170) REVERT: C 474 HIS cc_start: 0.8412 (m90) cc_final: 0.6086 (m90) REVERT: C 475 PHE cc_start: 0.8767 (t80) cc_final: 0.8373 (t80) REVERT: C 493 MET cc_start: 0.8312 (tpp) cc_final: 0.7465 (tpp) REVERT: C 509 GLN cc_start: 0.8560 (pt0) cc_final: 0.8272 (pp30) REVERT: C 528 MET cc_start: 0.8937 (mtm) cc_final: 0.8270 (mtm) REVERT: C 529 LEU cc_start: 0.9151 (mt) cc_final: 0.8947 (mt) REVERT: C 542 ARG cc_start: 0.7561 (tpm170) cc_final: 0.7271 (tpm170) REVERT: D 31 LEU cc_start: 0.8954 (mt) cc_final: 0.8684 (tp) REVERT: D 34 LEU cc_start: 0.8740 (mt) cc_final: 0.8470 (mm) REVERT: D 44 VAL cc_start: 0.9311 (t) cc_final: 0.8998 (m) REVERT: D 47 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7996 (mm-30) REVERT: D 48 LEU cc_start: 0.8735 (mt) cc_final: 0.8441 (mt) REVERT: D 50 SER cc_start: 0.7829 (m) cc_final: 0.7026 (p) REVERT: D 55 TRP cc_start: 0.7182 (m-10) cc_final: 0.6849 (m-90) REVERT: D 79 PHE cc_start: 0.8197 (m-80) cc_final: 0.7817 (m-80) REVERT: D 81 LYS cc_start: 0.8994 (tttt) cc_final: 0.8655 (ttpp) REVERT: D 85 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8011 (mt-10) REVERT: D 86 SER cc_start: 0.8940 (m) cc_final: 0.8722 (p) REVERT: D 120 ILE cc_start: 0.9181 (mm) cc_final: 0.8748 (tp) REVERT: D 150 LYS cc_start: 0.8433 (tttt) cc_final: 0.7787 (tttt) REVERT: D 154 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8172 (mt-10) REVERT: D 156 TRP cc_start: 0.8440 (OUTLIER) cc_final: 0.6769 (m-90) REVERT: D 211 GLN cc_start: 0.7949 (mt0) cc_final: 0.7600 (mt0) REVERT: D 213 TRP cc_start: 0.7730 (OUTLIER) cc_final: 0.7352 (t-100) REVERT: D 217 LEU cc_start: 0.8547 (mm) cc_final: 0.8266 (mm) REVERT: D 239 GLN cc_start: 0.9054 (tt0) cc_final: 0.8190 (tm-30) REVERT: D 242 PHE cc_start: 0.8433 (m-80) cc_final: 0.7926 (m-10) REVERT: D 247 LYS cc_start: 0.7844 (tttt) cc_final: 0.7470 (tttt) REVERT: D 248 ASP cc_start: 0.8273 (p0) cc_final: 0.7804 (t70) REVERT: D 254 MET cc_start: 0.5213 (mtt) cc_final: 0.4371 (mtt) REVERT: D 258 LEU cc_start: 0.8916 (mt) cc_final: 0.8664 (tt) REVERT: D 260 ASN cc_start: 0.8938 (m110) cc_final: 0.8538 (p0) REVERT: D 266 ARG cc_start: 0.8703 (ttt180) cc_final: 0.7930 (ttp-170) REVERT: D 270 LEU cc_start: 0.8510 (mt) cc_final: 0.8232 (mm) REVERT: D 271 VAL cc_start: 0.8717 (t) cc_final: 0.8364 (p) REVERT: D 275 LYS cc_start: 0.8233 (pttt) cc_final: 0.7715 (ptpt) REVERT: D 276 ARG cc_start: 0.7754 (ttt90) cc_final: 0.7449 (tpt-90) REVERT: D 282 TYR cc_start: 0.8053 (m-80) cc_final: 0.7604 (m-10) REVERT: D 340 ASN cc_start: 0.8605 (p0) cc_final: 0.8107 (p0) REVERT: D 363 GLN cc_start: 0.8610 (mt0) cc_final: 0.8301 (mt0) REVERT: D 366 HIS cc_start: 0.8797 (t70) cc_final: 0.8390 (t70) REVERT: D 376 MET cc_start: 0.7882 (mtp) cc_final: 0.7547 (mtp) REVERT: D 377 LEU cc_start: 0.8897 (mt) cc_final: 0.8679 (mt) REVERT: D 378 LYS cc_start: 0.8570 (mttt) cc_final: 0.8228 (mttt) REVERT: D 389 ASP cc_start: 0.8156 (m-30) cc_final: 0.7630 (m-30) REVERT: D 408 LEU cc_start: 0.7644 (tp) cc_final: 0.7344 (tp) REVERT: D 412 PHE cc_start: 0.7094 (m-80) cc_final: 0.5915 (m-80) REVERT: D 418 PHE cc_start: 0.8209 (t80) cc_final: 0.7366 (t80) REVERT: D 426 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8324 (tpp80) REVERT: D 438 LYS cc_start: 0.8438 (mttt) cc_final: 0.8083 (mttt) REVERT: D 450 ASP cc_start: 0.6546 (t0) cc_final: 0.6344 (t0) REVERT: E 16 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7494 (mm-30) REVERT: E 35 GLU cc_start: 0.8528 (tt0) cc_final: 0.8115 (tt0) REVERT: E 39 PHE cc_start: 0.7997 (t80) cc_final: 0.7727 (t80) REVERT: E 57 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7991 (mtp) REVERT: E 66 ASP cc_start: 0.8181 (m-30) cc_final: 0.7907 (m-30) REVERT: E 73 ASP cc_start: 0.8099 (t0) cc_final: 0.6737 (t0) REVERT: E 75 ASP cc_start: 0.7383 (m-30) cc_final: 0.6245 (m-30) REVERT: E 80 ARG cc_start: 0.8457 (mtt180) cc_final: 0.7982 (mtt180) REVERT: E 86 LYS cc_start: 0.8633 (tttt) cc_final: 0.8389 (tttt) REVERT: E 97 ASP cc_start: 0.7893 (t70) cc_final: 0.7666 (t0) REVERT: E 101 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8124 (mm) REVERT: E 102 SER cc_start: 0.8708 (m) cc_final: 0.7502 (t) REVERT: E 112 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7934 (mttt) REVERT: E 125 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7389 (mtt180) REVERT: E 137 MET cc_start: 0.6951 (ppp) cc_final: 0.6635 (tmm) REVERT: E 144 SER cc_start: 0.8967 (t) cc_final: 0.8248 (p) REVERT: E 166 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6736 (mt-10) REVERT: E 213 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7489 (ttp80) REVERT: E 222 ILE cc_start: 0.8459 (mt) cc_final: 0.8219 (mm) REVERT: E 229 LYS cc_start: 0.8180 (tttt) cc_final: 0.7831 (tttt) REVERT: E 251 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.8040 (tpp80) REVERT: E 273 MET cc_start: 0.6689 (mmm) cc_final: 0.6091 (mtp) REVERT: E 306 LYS cc_start: 0.8757 (mmtt) cc_final: 0.8478 (mtpt) REVERT: E 328 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7169 (tp) REVERT: E 329 ASP cc_start: 0.7785 (m-30) cc_final: 0.7411 (p0) REVERT: E 332 GLN cc_start: 0.6731 (mp-120) cc_final: 0.6133 (mp10) REVERT: E 337 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7423 (pt0) REVERT: E 338 GLU cc_start: 0.7860 (mp0) cc_final: 0.7077 (mp0) REVERT: E 343 ARG cc_start: 0.7612 (mmt180) cc_final: 0.7202 (mmt180) REVERT: E 355 GLN cc_start: 0.8400 (mt0) cc_final: 0.7716 (mt0) REVERT: E 357 VAL cc_start: 0.7764 (t) cc_final: 0.7480 (m) REVERT: E 358 TYR cc_start: 0.8247 (m-80) cc_final: 0.8011 (m-80) REVERT: E 370 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7471 (p0) REVERT: E 379 LEU cc_start: 0.9134 (tp) cc_final: 0.8791 (tp) REVERT: F 25 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7123 (tp-100) REVERT: F 28 LYS cc_start: 0.9131 (mttt) cc_final: 0.8728 (mttt) REVERT: F 47 SER cc_start: 0.9021 (m) cc_final: 0.8736 (p) REVERT: F 51 MET cc_start: 0.7912 (mtp) cc_final: 0.7489 (mmm) REVERT: F 56 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7585 (mmtt) REVERT: F 62 SER cc_start: 0.8512 (t) cc_final: 0.8229 (p) REVERT: F 63 HIS cc_start: 0.8504 (t-90) cc_final: 0.7877 (t-90) REVERT: F 65 GLN cc_start: 0.8490 (mm-40) cc_final: 0.7881 (mm-40) REVERT: F 68 ARG cc_start: 0.7845 (tpt-90) cc_final: 0.7447 (tpp80) REVERT: F 101 TYR cc_start: 0.7787 (t80) cc_final: 0.7108 (t80) REVERT: F 104 LEU cc_start: 0.8558 (mp) cc_final: 0.8348 (mt) REVERT: F 105 THR cc_start: 0.8360 (m) cc_final: 0.8038 (m) REVERT: F 109 GLU cc_start: 0.8582 (mt-10) cc_final: 0.7986 (mt-10) REVERT: F 111 ILE cc_start: 0.9067 (mt) cc_final: 0.8864 (mm) REVERT: F 117 ASP cc_start: 0.8516 (t70) cc_final: 0.7976 (t70) REVERT: F 121 LYS cc_start: 0.8467 (mmtt) cc_final: 0.8238 (mmpt) REVERT: F 139 LYS cc_start: 0.9316 (mttt) cc_final: 0.8969 (mtmt) REVERT: F 147 MET cc_start: 0.8257 (mmm) cc_final: 0.7960 (mmm) REVERT: F 149 LYS cc_start: 0.8202 (mttt) cc_final: 0.7839 (mtmt) REVERT: F 156 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7062 (mt-10) REVERT: F 158 LYS cc_start: 0.8256 (mttt) cc_final: 0.7947 (mttt) REVERT: F 173 GLN cc_start: 0.8219 (mt0) cc_final: 0.7921 (mt0) REVERT: F 185 GLN cc_start: 0.8942 (tt0) cc_final: 0.8655 (tt0) REVERT: F 188 ASN cc_start: 0.8438 (t0) cc_final: 0.8232 (t0) REVERT: F 194 CYS cc_start: 0.8485 (t) cc_final: 0.7953 (t) REVERT: F 208 ASP cc_start: 0.8054 (t70) cc_final: 0.7616 (t0) REVERT: F 216 LYS cc_start: 0.8995 (tttt) cc_final: 0.8544 (tttt) REVERT: F 225 GLN cc_start: 0.9167 (tp40) cc_final: 0.8753 (tp40) REVERT: F 229 TRP cc_start: 0.8368 (OUTLIER) cc_final: 0.6971 (t60) REVERT: F 237 GLN cc_start: 0.8269 (mt0) cc_final: 0.7564 (mt0) REVERT: F 240 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7573 (mm110) REVERT: F 251 TYR cc_start: 0.8786 (m-80) cc_final: 0.8202 (m-80) REVERT: F 252 ARG cc_start: 0.8754 (mtp180) cc_final: 0.8350 (ptm160) REVERT: F 281 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8763 (tp) REVERT: G 16 MET cc_start: 0.8958 (mmt) cc_final: 0.8365 (mmm) REVERT: G 36 GLN cc_start: 0.7986 (tp40) cc_final: 0.6997 (tm-30) REVERT: G 42 HIS cc_start: 0.8253 (m90) cc_final: 0.7975 (m90) REVERT: G 43 VAL cc_start: 0.8758 (m) cc_final: 0.8345 (p) REVERT: G 44 PHE cc_start: 0.8289 (t80) cc_final: 0.7908 (t80) REVERT: G 59 GLU cc_start: 0.8440 (tt0) cc_final: 0.8207 (tt0) REVERT: H 862 LYS cc_start: 0.7031 (mmtt) cc_final: 0.6626 (mmtt) REVERT: H 895 GLU cc_start: 0.8233 (tp30) cc_final: 0.7605 (tp30) REVERT: H 899 ILE cc_start: 0.8605 (mm) cc_final: 0.8339 (mm) REVERT: H 909 GLU cc_start: 0.6546 (mp0) cc_final: 0.6290 (mp0) REVERT: H 912 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7411 (mt-10) REVERT: H 913 LYS cc_start: 0.7154 (mttt) cc_final: 0.6948 (mttt) REVERT: K 118 MET cc_start: 0.7046 (tpp) cc_final: 0.6416 (tpp) REVERT: K 120 HIS cc_start: 0.8714 (m-70) cc_final: 0.8254 (m-70) REVERT: K 121 PHE cc_start: 0.8568 (m-80) cc_final: 0.7637 (m-80) REVERT: K 125 THR cc_start: 0.8030 (m) cc_final: 0.7683 (m) REVERT: K 130 ARG cc_start: 0.7364 (ttt180) cc_final: 0.6766 (ptm160) REVERT: K 136 HIS cc_start: 0.8715 (m90) cc_final: 0.8304 (m90) REVERT: K 141 LYS cc_start: 0.8974 (tttt) cc_final: 0.8613 (tttt) REVERT: K 143 GLU cc_start: 0.8701 (tt0) cc_final: 0.7939 (tm-30) REVERT: K 163 LYS cc_start: 0.8548 (mttt) cc_final: 0.8086 (mttt) REVERT: K 166 VAL cc_start: 0.8897 (t) cc_final: 0.8564 (p) REVERT: K 168 LYS cc_start: 0.8666 (tptm) cc_final: 0.8353 (tptm) REVERT: K 178 MET cc_start: 0.7568 (ptp) cc_final: 0.6940 (ptp) REVERT: K 192 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8089 (tm-30) REVERT: K 202 GLU cc_start: 0.8487 (mp0) cc_final: 0.8252 (pm20) REVERT: K 217 LYS cc_start: 0.8587 (tmtt) cc_final: 0.8340 (tmtt) REVERT: K 252 LEU cc_start: 0.7744 (tp) cc_final: 0.7500 (tp) outliers start: 131 outliers final: 77 residues processed: 1023 average time/residue: 0.4447 time to fit residues: 673.1605 Evaluate side-chains 1032 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 937 time to evaluate : 2.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 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 515 SER Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 522 ASN Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 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 678 VAL Chi-restraints excluded: chain B residue 702 THR 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 479 PHE Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 340 ASN Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 240 GLN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 242 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 261 optimal weight: 50.0000 chunk 178 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 129 optimal weight: 20.0000 chunk 268 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 281 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN B 203 ASN B 238 ASN B 328 HIS B 434 HIS B 519 ASN C 458 GLN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN D 264 HIS E 50 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 324 HIS ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 GLN ** F 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN F 176 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 28259 Z= 0.380 Angle : 0.715 13.376 38512 Z= 0.363 Chirality : 0.045 0.258 4285 Planarity : 0.005 0.061 4647 Dihedral : 15.924 178.782 4425 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.06 % Favored : 94.91 % Rotamer: Outliers : 5.32 % Allowed : 19.15 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: 0.19 (0.15), residues: 3186 helix: 0.92 (0.14), residues: 1503 sheet: -0.14 (0.27), residues: 378 loop : -0.64 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 511 HIS 0.008 0.001 HIS E 235 PHE 0.023 0.002 PHE G 66 TYR 0.030 0.002 TYR C 533 ARG 0.021 0.001 ARG D 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 951 time to evaluate : 2.946 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: 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: 0.8701 (mttt) cc_final: 0.8164 (mttt) REVERT: A 65 MET cc_start: 0.7853 (ptt) cc_final: 0.7451 (ptt) REVERT: A 68 LYS cc_start: 0.7284 (mtmt) cc_final: 0.6927 (tmtt) REVERT: A 94 LYS cc_start: 0.8007 (ptpt) cc_final: 0.7478 (ptpt) REVERT: A 115 GLU cc_start: 0.7757 (tt0) cc_final: 0.7543 (tt0) REVERT: A 135 ASP cc_start: 0.8006 (m-30) cc_final: 0.7474 (t0) REVERT: A 146 THR cc_start: 0.7553 (t) cc_final: 0.7276 (t) REVERT: A 150 ASP cc_start: 0.7205 (t0) cc_final: 0.6796 (t0) REVERT: A 195 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8183 (mtt180) REVERT: A 276 MET cc_start: 0.8553 (mmp) cc_final: 0.8003 (mmm) REVERT: A 279 GLU cc_start: 0.8914 (tp30) cc_final: 0.8658 (tp30) REVERT: A 282 LYS cc_start: 0.8953 (tttt) cc_final: 0.8430 (ttpp) REVERT: A 305 ASP cc_start: 0.8590 (p0) cc_final: 0.8284 (p0) REVERT: A 322 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8400 (mppt) REVERT: A 379 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8381 (mmmt) REVERT: A 380 MET cc_start: 0.7746 (ttm) cc_final: 0.7131 (ttm) REVERT: A 381 TRP cc_start: 0.8438 (m-10) cc_final: 0.8066 (m-10) REVERT: A 385 ASP cc_start: 0.8359 (p0) cc_final: 0.8085 (p0) REVERT: A 425 ARG cc_start: 0.7771 (tpp80) cc_final: 0.7432 (tpp80) REVERT: A 434 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7860 (mm-30) REVERT: A 450 MET cc_start: 0.7597 (ptm) cc_final: 0.6911 (ptm) REVERT: A 453 ARG cc_start: 0.8286 (ptm160) cc_final: 0.7727 (ttp-110) REVERT: A 457 ILE cc_start: 0.8687 (tt) cc_final: 0.8395 (tt) REVERT: A 463 LYS cc_start: 0.8621 (mttt) cc_final: 0.8149 (mtmm) REVERT: A 487 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8063 (ttmt) REVERT: A 492 ASN cc_start: 0.8266 (t0) cc_final: 0.7861 (t0) REVERT: A 497 GLN cc_start: 0.8659 (pt0) cc_final: 0.8435 (pt0) REVERT: A 504 LYS cc_start: 0.8457 (ttpt) cc_final: 0.8217 (ttpp) REVERT: A 510 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8313 (p) REVERT: A 525 ILE cc_start: 0.8749 (tp) cc_final: 0.8282 (pt) REVERT: A 549 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7037 (ttpp) REVERT: A 552 GLU cc_start: 0.7419 (pp20) cc_final: 0.6935 (pp20) REVERT: A 569 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8011 (mmmm) REVERT: A 586 GLN cc_start: 0.7964 (tp-100) cc_final: 0.7734 (tp-100) REVERT: A 588 GLU cc_start: 0.8216 (tp30) cc_final: 0.7430 (tp30) REVERT: A 619 GLU cc_start: 0.7173 (mp0) cc_final: 0.6926 (mp0) REVERT: A 636 GLU cc_start: 0.7947 (tp30) cc_final: 0.7740 (tp30) REVERT: A 656 ASN cc_start: 0.8479 (m110) cc_final: 0.8128 (m-40) REVERT: A 659 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7642 (p90) REVERT: A 674 THR cc_start: 0.8963 (m) cc_final: 0.8566 (t) REVERT: A 677 GLN cc_start: 0.7620 (mt0) cc_final: 0.7167 (mt0) REVERT: A 683 GLN cc_start: 0.8196 (mm110) cc_final: 0.7617 (mm-40) REVERT: A 696 MET cc_start: 0.8193 (tpp) cc_final: 0.7877 (tpp) REVERT: A 715 LYS cc_start: 0.9243 (ptmt) cc_final: 0.9018 (ptmm) REVERT: B 1 MET cc_start: 0.6486 (ppp) cc_final: 0.6120 (ppp) REVERT: B 11 TYR cc_start: 0.7869 (p90) cc_final: 0.7357 (p90) REVERT: B 30 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8380 (ttm-80) REVERT: B 42 MET cc_start: 0.7883 (mtp) cc_final: 0.7620 (mtp) REVERT: B 60 GLN cc_start: 0.8983 (mt0) cc_final: 0.8280 (mt0) REVERT: B 61 ARG cc_start: 0.8602 (mmp80) cc_final: 0.8113 (mmp80) REVERT: B 65 LEU cc_start: 0.7940 (tp) cc_final: 0.7545 (pt) REVERT: B 72 TYR cc_start: 0.7728 (t80) cc_final: 0.7235 (t80) REVERT: B 84 ILE cc_start: 0.9126 (mm) cc_final: 0.8715 (tp) REVERT: B 85 GLU cc_start: 0.8495 (pp20) cc_final: 0.7894 (tp30) REVERT: B 86 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 109 LEU cc_start: 0.7876 (mm) cc_final: 0.7668 (mt) REVERT: B 133 LYS cc_start: 0.8655 (mttt) cc_final: 0.8297 (tppt) REVERT: B 207 TYR cc_start: 0.8233 (p90) cc_final: 0.7421 (p90) REVERT: B 228 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7596 (ptmt) REVERT: B 235 GLU cc_start: 0.8392 (tp30) cc_final: 0.7961 (mp0) REVERT: B 243 CYS cc_start: 0.8449 (m) cc_final: 0.7945 (m) REVERT: B 247 MET cc_start: 0.8494 (mpp) cc_final: 0.7806 (mpp) REVERT: B 338 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: B 339 TYR cc_start: 0.8293 (t80) cc_final: 0.7838 (t80) REVERT: B 341 LYS cc_start: 0.9216 (mtmm) cc_final: 0.8891 (mttp) REVERT: B 444 ILE cc_start: 0.9020 (tp) cc_final: 0.8614 (tp) REVERT: B 466 ILE cc_start: 0.8464 (tt) cc_final: 0.8231 (tp) REVERT: B 472 ASP cc_start: 0.7989 (m-30) cc_final: 0.7404 (m-30) REVERT: B 494 ILE cc_start: 0.9047 (mt) cc_final: 0.8763 (mp) REVERT: B 511 ARG cc_start: 0.7975 (mtm180) cc_final: 0.7579 (mtt-85) REVERT: B 513 ASP cc_start: 0.8300 (t0) cc_final: 0.8043 (t0) REVERT: B 526 GLU cc_start: 0.7812 (pt0) cc_final: 0.7231 (pt0) REVERT: B 570 GLU cc_start: 0.6743 (tm-30) cc_final: 0.6300 (tm-30) REVERT: B 603 LYS cc_start: 0.8751 (ptmm) cc_final: 0.8435 (ptmm) REVERT: B 606 GLU cc_start: 0.7391 (pm20) cc_final: 0.6874 (pm20) REVERT: B 633 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8576 (tp) REVERT: B 655 ASP cc_start: 0.8667 (t0) cc_final: 0.7692 (m-30) REVERT: B 657 MET cc_start: 0.8277 (mmm) cc_final: 0.7878 (mmm) REVERT: B 662 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8283 (tm-30) REVERT: B 663 CYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7712 (m) REVERT: B 666 ARG cc_start: 0.7424 (mtp85) cc_final: 0.7078 (mtp85) REVERT: B 672 THR cc_start: 0.9079 (p) cc_final: 0.8746 (t) REVERT: B 677 MET cc_start: 0.8056 (mtp) cc_final: 0.7829 (mtp) REVERT: B 690 ARG cc_start: 0.7954 (mtm110) cc_final: 0.7474 (mtm-85) REVERT: B 707 ASN cc_start: 0.7574 (t0) cc_final: 0.6772 (t0) REVERT: C 402 ASN cc_start: 0.8235 (m110) cc_final: 0.7866 (p0) REVERT: C 412 GLU cc_start: 0.8649 (pp20) cc_final: 0.8336 (pp20) REVERT: C 417 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7590 (mmmt) REVERT: C 424 SER cc_start: 0.7828 (p) cc_final: 0.7528 (t) REVERT: C 442 GLN cc_start: 0.6832 (OUTLIER) cc_final: 0.6529 (pm20) REVERT: C 455 ASN cc_start: 0.7108 (m-40) cc_final: 0.6851 (m-40) REVERT: C 471 LEU cc_start: 0.9314 (mt) cc_final: 0.9093 (tt) REVERT: C 473 ARG cc_start: 0.8845 (tmt170) cc_final: 0.8621 (ttt180) REVERT: C 475 PHE cc_start: 0.8809 (t80) cc_final: 0.8411 (t80) REVERT: C 493 MET cc_start: 0.8337 (tpp) cc_final: 0.7493 (tpp) REVERT: C 528 MET cc_start: 0.8937 (mtm) cc_final: 0.8453 (mtm) REVERT: C 542 ARG cc_start: 0.7621 (tpm170) cc_final: 0.7217 (tpm170) REVERT: D 32 ASP cc_start: 0.8248 (p0) cc_final: 0.8017 (p0) REVERT: D 44 VAL cc_start: 0.9438 (t) cc_final: 0.9038 (p) REVERT: D 47 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8069 (mm-30) REVERT: D 48 LEU cc_start: 0.8867 (mt) cc_final: 0.8545 (mt) REVERT: D 50 SER cc_start: 0.8164 (m) cc_final: 0.7417 (p) REVERT: D 55 TRP cc_start: 0.7517 (m-10) cc_final: 0.7018 (m-90) REVERT: D 79 PHE cc_start: 0.8304 (m-80) cc_final: 0.8064 (m-80) REVERT: D 81 LYS cc_start: 0.9012 (tttt) cc_final: 0.8665 (ttpp) REVERT: D 85 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8031 (mt-10) REVERT: D 86 SER cc_start: 0.8957 (m) cc_final: 0.8678 (p) REVERT: D 150 LYS cc_start: 0.8746 (tttt) cc_final: 0.8088 (tttt) REVERT: D 154 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8295 (mt-10) REVERT: D 213 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.7593 (t-100) REVERT: D 217 LEU cc_start: 0.8610 (mm) cc_final: 0.8327 (mm) REVERT: D 237 LEU cc_start: 0.9280 (tp) cc_final: 0.9007 (tt) REVERT: D 239 GLN cc_start: 0.9086 (tt0) cc_final: 0.8207 (tm-30) REVERT: D 242 PHE cc_start: 0.8542 (m-80) cc_final: 0.8136 (m-10) REVERT: D 247 LYS cc_start: 0.8377 (tttt) cc_final: 0.8034 (tttt) REVERT: D 254 MET cc_start: 0.5548 (mtt) cc_final: 0.4420 (mtt) REVERT: D 258 LEU cc_start: 0.8987 (mt) cc_final: 0.8637 (tt) REVERT: D 261 PHE cc_start: 0.8994 (t80) cc_final: 0.8779 (t80) REVERT: D 266 ARG cc_start: 0.8689 (ttt180) cc_final: 0.7925 (ttp-170) REVERT: D 270 LEU cc_start: 0.8556 (mt) cc_final: 0.8315 (mm) REVERT: D 271 VAL cc_start: 0.8798 (t) cc_final: 0.8422 (p) REVERT: D 276 ARG cc_start: 0.8069 (ttt90) cc_final: 0.7670 (ttt90) REVERT: D 278 SER cc_start: 0.7657 (t) cc_final: 0.7274 (m) REVERT: D 279 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7673 (mmm-85) REVERT: D 289 ASN cc_start: 0.7578 (m-40) cc_final: 0.7147 (m-40) REVERT: D 322 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7484 (mm-30) REVERT: D 333 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6517 (mt-10) REVERT: D 340 ASN cc_start: 0.8521 (p0) cc_final: 0.8189 (p0) REVERT: D 341 MET cc_start: 0.7371 (tpp) cc_final: 0.6984 (tpp) REVERT: D 345 GLN cc_start: 0.8617 (tt0) cc_final: 0.8366 (tt0) REVERT: D 363 GLN cc_start: 0.8630 (mt0) cc_final: 0.8033 (mt0) REVERT: D 366 HIS cc_start: 0.8792 (t70) cc_final: 0.8515 (t70) REVERT: D 376 MET cc_start: 0.8214 (mtp) cc_final: 0.7939 (mtp) REVERT: D 378 LYS cc_start: 0.8655 (mttt) cc_final: 0.8323 (mttt) REVERT: D 389 ASP cc_start: 0.8374 (m-30) cc_final: 0.7877 (m-30) REVERT: D 408 LEU cc_start: 0.7643 (tp) cc_final: 0.7417 (tp) REVERT: D 409 TYR cc_start: 0.7057 (m-80) cc_final: 0.6622 (m-80) REVERT: D 412 PHE cc_start: 0.7175 (m-80) cc_final: 0.5896 (m-80) REVERT: D 418 PHE cc_start: 0.8328 (t80) cc_final: 0.7487 (t80) REVERT: D 426 ARG cc_start: 0.8654 (tpp80) cc_final: 0.8451 (tpp80) REVERT: D 438 LYS cc_start: 0.8551 (mttt) cc_final: 0.8197 (mttt) REVERT: E 16 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7579 (mm-30) REVERT: E 18 THR cc_start: 0.8609 (p) cc_final: 0.8383 (p) REVERT: E 20 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7843 (mm-30) REVERT: E 35 GLU cc_start: 0.8608 (tt0) cc_final: 0.8320 (tt0) REVERT: E 36 ASP cc_start: 0.8631 (t0) cc_final: 0.8384 (t0) REVERT: E 39 PHE cc_start: 0.8112 (t80) cc_final: 0.7722 (t80) REVERT: E 40 LYS cc_start: 0.8640 (mmtm) cc_final: 0.8428 (mmtm) REVERT: E 57 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8114 (mtp) REVERT: E 66 ASP cc_start: 0.8193 (m-30) cc_final: 0.7900 (m-30) REVERT: E 71 MET cc_start: 0.8892 (mmt) cc_final: 0.8612 (mmm) REVERT: E 73 ASP cc_start: 0.8160 (t0) cc_final: 0.7273 (t0) REVERT: E 74 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8440 (mp10) REVERT: E 75 ASP cc_start: 0.7540 (m-30) cc_final: 0.6419 (m-30) REVERT: E 80 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8243 (mtt180) REVERT: E 86 LYS cc_start: 0.8551 (tttt) cc_final: 0.8292 (tttt) REVERT: E 94 GLU cc_start: 0.8021 (tp30) cc_final: 0.7436 (mp0) REVERT: E 97 ASP cc_start: 0.8027 (t70) cc_final: 0.7800 (t0) REVERT: E 101 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8221 (mm) REVERT: E 102 SER cc_start: 0.8643 (m) cc_final: 0.8272 (p) REVERT: E 112 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8175 (mttt) REVERT: E 125 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7407 (mtt180) REVERT: E 166 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6862 (mt-10) REVERT: E 222 ILE cc_start: 0.8459 (mt) cc_final: 0.8198 (mm) REVERT: E 229 LYS cc_start: 0.8186 (tttt) cc_final: 0.7896 (tttt) REVERT: E 251 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.8133 (tpp80) REVERT: E 303 VAL cc_start: 0.8831 (p) cc_final: 0.8436 (m) REVERT: E 306 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8476 (mmtt) REVERT: E 328 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7390 (tp) REVERT: E 332 GLN cc_start: 0.6992 (mp-120) cc_final: 0.6330 (mp10) REVERT: E 337 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7450 (pt0) REVERT: E 338 GLU cc_start: 0.7825 (mp0) cc_final: 0.6977 (mp0) REVERT: E 343 ARG cc_start: 0.7758 (mmt180) cc_final: 0.7549 (mmt180) REVERT: E 355 GLN cc_start: 0.8515 (mt0) cc_final: 0.7862 (mt0) REVERT: E 357 VAL cc_start: 0.7830 (t) cc_final: 0.7493 (m) REVERT: E 365 ASN cc_start: 0.8100 (m-40) cc_final: 0.7604 (m-40) REVERT: E 379 LEU cc_start: 0.9115 (tp) cc_final: 0.8891 (tp) REVERT: E 381 CYS cc_start: 0.8413 (t) cc_final: 0.7831 (t) REVERT: F 47 SER cc_start: 0.9139 (m) cc_final: 0.8862 (p) REVERT: F 51 MET cc_start: 0.7952 (mtp) cc_final: 0.7652 (mmm) REVERT: F 56 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7643 (mmtt) REVERT: F 63 HIS cc_start: 0.8687 (t-90) cc_final: 0.8174 (t-90) REVERT: F 65 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8316 (mm-40) REVERT: F 101 TYR cc_start: 0.7878 (t80) cc_final: 0.7222 (t80) REVERT: F 105 THR cc_start: 0.8491 (m) cc_final: 0.8160 (m) REVERT: F 109 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7937 (mt-10) REVERT: F 117 ASP cc_start: 0.8496 (t70) cc_final: 0.8075 (t70) REVERT: F 121 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8199 (mmpt) REVERT: F 139 LYS cc_start: 0.9373 (mttt) cc_final: 0.9057 (mtmt) REVERT: F 147 MET cc_start: 0.8329 (mmm) cc_final: 0.8018 (mmm) REVERT: F 156 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7053 (mt-10) REVERT: F 158 LYS cc_start: 0.8274 (mttt) cc_final: 0.8010 (mttt) REVERT: F 173 GLN cc_start: 0.8351 (mt0) cc_final: 0.8076 (mt0) REVERT: F 185 GLN cc_start: 0.8978 (tt0) cc_final: 0.8688 (tt0) REVERT: F 194 CYS cc_start: 0.8533 (t) cc_final: 0.8082 (t) REVERT: F 195 VAL cc_start: 0.9041 (m) cc_final: 0.8739 (p) REVERT: F 208 ASP cc_start: 0.8102 (t70) cc_final: 0.7669 (t0) REVERT: F 216 LYS cc_start: 0.9017 (tttt) cc_final: 0.8658 (tttt) REVERT: F 225 GLN cc_start: 0.9236 (tp40) cc_final: 0.8899 (tp40) REVERT: F 228 LEU cc_start: 0.9235 (mt) cc_final: 0.8921 (mt) REVERT: F 229 TRP cc_start: 0.8539 (OUTLIER) cc_final: 0.7070 (t60) REVERT: F 237 GLN cc_start: 0.8244 (mt0) cc_final: 0.7667 (mt0) REVERT: F 251 TYR cc_start: 0.8844 (m-80) cc_final: 0.8307 (m-80) REVERT: F 252 ARG cc_start: 0.8744 (mtp180) cc_final: 0.8535 (mtp180) REVERT: F 281 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8829 (tp) REVERT: G 12 CYS cc_start: 0.9136 (p) cc_final: 0.8502 (p) REVERT: G 16 MET cc_start: 0.8971 (mmt) cc_final: 0.8295 (mmm) REVERT: G 36 GLN cc_start: 0.8579 (tp40) cc_final: 0.7279 (tm-30) REVERT: G 43 VAL cc_start: 0.8626 (m) cc_final: 0.8244 (p) REVERT: G 44 PHE cc_start: 0.8748 (t80) cc_final: 0.8268 (t80) REVERT: G 55 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8124 (tm-30) REVERT: G 56 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8267 (tpp80) REVERT: H 862 LYS cc_start: 0.7244 (mmtt) cc_final: 0.6824 (mmtt) REVERT: H 895 GLU cc_start: 0.8128 (tp30) cc_final: 0.7583 (tp30) REVERT: H 909 GLU cc_start: 0.6738 (mp0) cc_final: 0.6530 (mp0) REVERT: H 912 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7387 (mt-10) REVERT: H 913 LYS cc_start: 0.7310 (mttt) cc_final: 0.7085 (mttt) REVERT: K 116 TYR cc_start: 0.8435 (t80) cc_final: 0.8012 (t80) REVERT: K 118 MET cc_start: 0.7151 (tpp) cc_final: 0.6574 (tpp) REVERT: K 120 HIS cc_start: 0.8710 (m-70) cc_final: 0.8244 (m-70) REVERT: K 121 PHE cc_start: 0.8570 (m-80) cc_final: 0.7507 (m-80) REVERT: K 125 THR cc_start: 0.8222 (m) cc_final: 0.7924 (m) REVERT: K 130 ARG cc_start: 0.7420 (ttt180) cc_final: 0.7121 (ptm160) REVERT: K 136 HIS cc_start: 0.8593 (m90) cc_final: 0.8366 (m90) REVERT: K 141 LYS cc_start: 0.9002 (tttt) cc_final: 0.8621 (tttt) REVERT: K 143 GLU cc_start: 0.8635 (tt0) cc_final: 0.7997 (tm-30) REVERT: K 163 LYS cc_start: 0.8505 (mttt) cc_final: 0.8087 (mttt) REVERT: K 166 VAL cc_start: 0.8865 (t) cc_final: 0.8563 (p) REVERT: K 168 LYS cc_start: 0.8605 (tptm) cc_final: 0.8262 (tptm) REVERT: K 177 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: K 178 MET cc_start: 0.7654 (ptp) cc_final: 0.7093 (ptp) REVERT: K 188 LYS cc_start: 0.8945 (tppp) cc_final: 0.8633 (mmmm) REVERT: K 190 SER cc_start: 0.9270 (t) cc_final: 0.8986 (p) REVERT: K 192 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8066 (mt-10) REVERT: K 213 LYS cc_start: 0.8182 (tptt) cc_final: 0.7632 (tptt) REVERT: K 217 LYS cc_start: 0.8678 (tmtt) cc_final: 0.8337 (tmtt) REVERT: K 252 LEU cc_start: 0.7887 (tp) cc_final: 0.7557 (tp) outliers start: 151 outliers final: 104 residues processed: 1026 average time/residue: 0.4497 time to fit residues: 683.2436 Evaluate side-chains 1033 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 914 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 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 512 CYS Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 598 HIS Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain B residue 519 ASN Chi-restraints excluded: chain B residue 522 ASN 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 633 LEU Chi-restraints excluded: chain B residue 663 CYS Chi-restraints excluded: chain B residue 678 VAL Chi-restraints excluded: chain B residue 702 THR 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 495 SER Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain F residue 37 CYS Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 250 ASP Chi-restraints excluded: chain F residue 260 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain H residue 849 LYS Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 242 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 105 optimal weight: 0.8980 chunk 282 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 314 optimal weight: 0.4980 chunk 261 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 539 ASN A 625 GLN ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 ASN B 519 ASN B 723 GLN C 458 GLN ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN D 202 GLN ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN F 145 HIS F 176 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 28259 Z= 0.205 Angle : 0.656 13.866 38512 Z= 0.324 Chirality : 0.042 0.310 4285 Planarity : 0.004 0.059 4647 Dihedral : 15.763 176.083 4420 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.38 % Rotamer: Outliers : 4.61 % Allowed : 21.68 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: 0.32 (0.15), residues: 3186 helix: 1.05 (0.14), residues: 1494 sheet: -0.17 (0.27), residues: 392 loop : -0.56 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 421 HIS 0.007 0.001 HIS C 524 PHE 0.044 0.001 PHE J 162 TYR 0.039 0.001 TYR C 533 ARG 0.007 0.001 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 934 time to evaluate : 2.883 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8644 (mttt) cc_final: 0.8106 (mttt) REVERT: A 65 MET cc_start: 0.7925 (ptt) cc_final: 0.7474 (ptt) REVERT: A 68 LYS cc_start: 0.7196 (mtmt) cc_final: 0.6928 (tptt) REVERT: A 94 LYS cc_start: 0.7899 (ptpt) cc_final: 0.7392 (ptpt) REVERT: A 115 GLU cc_start: 0.7601 (tt0) cc_final: 0.7392 (tt0) REVERT: A 135 ASP cc_start: 0.7943 (m-30) cc_final: 0.7461 (t0) REVERT: A 146 THR cc_start: 0.7285 (t) cc_final: 0.7009 (t) REVERT: A 150 ASP cc_start: 0.7317 (t0) cc_final: 0.6897 (t0) REVERT: A 153 MET cc_start: 0.8122 (mmm) cc_final: 0.7770 (mmm) REVERT: A 195 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8152 (mtt90) REVERT: A 276 MET cc_start: 0.8450 (mmp) cc_final: 0.7924 (mmm) REVERT: A 282 LYS cc_start: 0.8903 (tttt) cc_final: 0.8383 (ttpp) REVERT: A 283 ARG cc_start: 0.7776 (tpt90) cc_final: 0.7558 (tpt90) REVERT: A 305 ASP cc_start: 0.8570 (p0) cc_final: 0.8265 (p0) REVERT: A 322 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8456 (tppt) REVERT: A 351 VAL cc_start: 0.9144 (t) cc_final: 0.8845 (p) REVERT: A 373 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8110 (mm-40) REVERT: A 375 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8125 (ttpt) REVERT: A 379 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8281 (mmmt) REVERT: A 380 MET cc_start: 0.7724 (ttm) cc_final: 0.7070 (ttm) REVERT: A 381 TRP cc_start: 0.8346 (m-10) cc_final: 0.7951 (m-10) REVERT: A 385 ASP cc_start: 0.8341 (p0) cc_final: 0.8011 (p0) REVERT: A 392 PHE cc_start: 0.8232 (t80) cc_final: 0.7367 (t80) REVERT: A 412 MET cc_start: 0.6321 (ttt) cc_final: 0.5970 (ttt) REVERT: A 415 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7843 (m-70) REVERT: A 434 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7543 (mp0) REVERT: A 437 LEU cc_start: 0.8851 (tp) cc_final: 0.8609 (tt) REVERT: A 450 MET cc_start: 0.7594 (ptm) cc_final: 0.6955 (ptm) REVERT: A 453 ARG cc_start: 0.8217 (ptm160) cc_final: 0.7735 (mtm110) REVERT: A 457 ILE cc_start: 0.8648 (tt) cc_final: 0.8393 (tt) REVERT: A 463 LYS cc_start: 0.8586 (mttt) cc_final: 0.8062 (mtmm) REVERT: A 487 LYS cc_start: 0.8626 (ttmt) cc_final: 0.8233 (ttmt) REVERT: A 488 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7913 (mt) REVERT: A 492 ASN cc_start: 0.8286 (t0) cc_final: 0.7888 (t0) REVERT: A 504 LYS cc_start: 0.8460 (ttpt) cc_final: 0.8222 (ttpp) REVERT: A 510 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 525 ILE cc_start: 0.8722 (tp) cc_final: 0.8197 (pt) REVERT: A 549 LYS cc_start: 0.8196 (mtmt) cc_final: 0.6966 (ttpp) REVERT: A 552 GLU cc_start: 0.7354 (pp20) cc_final: 0.6918 (pp20) REVERT: A 586 GLN cc_start: 0.7962 (tp-100) cc_final: 0.7656 (tp-100) REVERT: A 619 GLU cc_start: 0.7175 (mp0) cc_final: 0.6856 (mp0) REVERT: A 621 ASN cc_start: 0.8604 (m-40) cc_final: 0.8398 (m-40) REVERT: A 636 GLU cc_start: 0.7973 (tp30) cc_final: 0.7570 (tp30) REVERT: A 656 ASN cc_start: 0.8418 (m110) cc_final: 0.8066 (m-40) REVERT: A 659 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8058 (p90) REVERT: A 674 THR cc_start: 0.8844 (m) cc_final: 0.8440 (t) REVERT: A 677 GLN cc_start: 0.7559 (mt0) cc_final: 0.7102 (mt0) REVERT: A 683 GLN cc_start: 0.8209 (mm110) cc_final: 0.7902 (mm-40) REVERT: A 715 LYS cc_start: 0.9208 (ptmt) cc_final: 0.8922 (ptmm) REVERT: B 1 MET cc_start: 0.6523 (ppp) cc_final: 0.6203 (ppp) REVERT: B 11 TYR cc_start: 0.7803 (p90) cc_final: 0.7293 (p90) REVERT: B 20 GLU cc_start: 0.7895 (mp0) cc_final: 0.7658 (mt-10) REVERT: B 30 ARG cc_start: 0.8624 (ttm-80) cc_final: 0.8361 (ttm-80) REVERT: B 41 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6338 (tm-30) REVERT: B 42 MET cc_start: 0.7916 (mtp) cc_final: 0.7504 (mtp) REVERT: B 48 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8137 (ttmm) REVERT: B 60 GLN cc_start: 0.8963 (mt0) cc_final: 0.8485 (mt0) REVERT: B 65 LEU cc_start: 0.7884 (tp) cc_final: 0.7444 (pt) REVERT: B 72 TYR cc_start: 0.7807 (t80) cc_final: 0.7465 (t80) REVERT: B 84 ILE cc_start: 0.9150 (mm) cc_final: 0.8747 (tp) REVERT: B 85 GLU cc_start: 0.8544 (pp20) cc_final: 0.7900 (tp30) REVERT: B 86 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 109 LEU cc_start: 0.7861 (mm) cc_final: 0.7408 (mt) REVERT: B 133 LYS cc_start: 0.8573 (mttt) cc_final: 0.8193 (tppt) REVERT: B 207 TYR cc_start: 0.8171 (p90) cc_final: 0.7409 (p90) REVERT: B 211 TYR cc_start: 0.7745 (m-10) cc_final: 0.7489 (m-80) REVERT: B 228 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7654 (ptmt) REVERT: B 233 PHE cc_start: 0.8302 (m-10) cc_final: 0.8083 (m-80) REVERT: B 235 GLU cc_start: 0.8305 (tp30) cc_final: 0.7930 (mp0) REVERT: B 243 CYS cc_start: 0.8377 (m) cc_final: 0.8125 (m) REVERT: B 247 MET cc_start: 0.8517 (mpp) cc_final: 0.8159 (mpp) REVERT: B 258 ARG cc_start: 0.8014 (ttt180) cc_final: 0.6929 (tpp80) REVERT: B 268 LYS cc_start: 0.8483 (tptp) cc_final: 0.8280 (tptp) REVERT: B 339 TYR cc_start: 0.8269 (t80) cc_final: 0.7720 (t80) REVERT: B 341 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8862 (mttt) REVERT: B 434 HIS cc_start: 0.6077 (OUTLIER) cc_final: 0.5530 (p90) REVERT: B 445 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8746 (mmmm) REVERT: B 450 ARG cc_start: 0.7706 (mtp180) cc_final: 0.7281 (ttm-80) REVERT: B 466 ILE cc_start: 0.8493 (tt) cc_final: 0.8154 (tp) REVERT: B 472 ASP cc_start: 0.7858 (m-30) cc_final: 0.7393 (m-30) REVERT: B 493 MET cc_start: 0.8195 (ptt) cc_final: 0.7809 (ptp) REVERT: B 494 ILE cc_start: 0.9045 (mt) cc_final: 0.8745 (mp) REVERT: B 508 PHE cc_start: 0.8301 (t80) cc_final: 0.6407 (t80) REVERT: B 511 ARG cc_start: 0.7922 (mtm180) cc_final: 0.7543 (mtt-85) REVERT: B 513 ASP cc_start: 0.8282 (t0) cc_final: 0.8065 (t0) REVERT: B 570 GLU cc_start: 0.6653 (tm-30) cc_final: 0.6194 (tm-30) REVERT: B 603 LYS cc_start: 0.8715 (ptmm) cc_final: 0.8371 (tmtt) REVERT: B 642 ASP cc_start: 0.7385 (p0) cc_final: 0.7035 (p0) REVERT: B 655 ASP cc_start: 0.8660 (t0) cc_final: 0.7674 (m-30) REVERT: B 663 CYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7825 (p) REVERT: B 672 THR cc_start: 0.9061 (p) cc_final: 0.8743 (t) REVERT: B 682 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8271 (tppt) REVERT: B 690 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7131 (mtm-85) REVERT: B 707 ASN cc_start: 0.7478 (t0) cc_final: 0.6395 (t0) REVERT: C 412 GLU cc_start: 0.8673 (pp20) cc_final: 0.8303 (pp20) REVERT: C 440 LEU cc_start: 0.8699 (mm) cc_final: 0.8459 (mp) REVERT: C 442 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.6479 (pm20) REVERT: C 471 LEU cc_start: 0.9283 (mt) cc_final: 0.9069 (tt) REVERT: C 473 ARG cc_start: 0.8802 (tmt170) cc_final: 0.8236 (tmt170) REVERT: C 475 PHE cc_start: 0.8823 (t80) cc_final: 0.8457 (t80) REVERT: C 493 MET cc_start: 0.8326 (tpp) cc_final: 0.7530 (tpp) REVERT: C 528 MET cc_start: 0.8944 (mtm) cc_final: 0.8567 (mtm) REVERT: C 539 TRP cc_start: 0.8544 (t60) cc_final: 0.7937 (t60) REVERT: D 31 LEU cc_start: 0.9106 (mt) cc_final: 0.8881 (tp) REVERT: D 44 VAL cc_start: 0.9403 (t) cc_final: 0.8967 (p) REVERT: D 47 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7966 (mm-30) REVERT: D 48 LEU cc_start: 0.8783 (mt) cc_final: 0.8398 (mt) REVERT: D 50 SER cc_start: 0.7961 (m) cc_final: 0.7230 (p) REVERT: D 55 TRP cc_start: 0.7445 (m-10) cc_final: 0.7081 (m-90) REVERT: D 81 LYS cc_start: 0.9004 (tttt) cc_final: 0.8680 (ttpp) REVERT: D 85 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8071 (mt-10) REVERT: D 86 SER cc_start: 0.8997 (m) cc_final: 0.8732 (p) REVERT: D 150 LYS cc_start: 0.8714 (tttt) cc_final: 0.8059 (tttt) REVERT: D 154 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8235 (mt-10) REVERT: D 155 ARG cc_start: 0.8387 (mmm-85) cc_final: 0.7634 (mmt90) REVERT: D 213 TRP cc_start: 0.8042 (OUTLIER) cc_final: 0.7516 (t-100) REVERT: D 217 LEU cc_start: 0.8560 (mm) cc_final: 0.8191 (mm) REVERT: D 237 LEU cc_start: 0.9224 (tp) cc_final: 0.8950 (tt) REVERT: D 239 GLN cc_start: 0.9007 (tt0) cc_final: 0.8150 (tm-30) REVERT: D 242 PHE cc_start: 0.8518 (m-80) cc_final: 0.8179 (m-10) REVERT: D 247 LYS cc_start: 0.8428 (tttt) cc_final: 0.7994 (tttt) REVERT: D 248 ASP cc_start: 0.8396 (p0) cc_final: 0.8127 (t70) REVERT: D 254 MET cc_start: 0.5578 (mtt) cc_final: 0.4640 (mtt) REVERT: D 258 LEU cc_start: 0.9004 (mt) cc_final: 0.8677 (tt) REVERT: D 260 ASN cc_start: 0.9119 (m110) cc_final: 0.8781 (p0) REVERT: D 261 PHE cc_start: 0.8949 (t80) cc_final: 0.8691 (t80) REVERT: D 266 ARG cc_start: 0.8611 (ttt180) cc_final: 0.7712 (ttp-170) REVERT: D 270 LEU cc_start: 0.8528 (mt) cc_final: 0.8302 (mm) REVERT: D 271 VAL cc_start: 0.8656 (t) cc_final: 0.8208 (p) REVERT: D 275 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8373 (mtmm) REVERT: D 278 SER cc_start: 0.7153 (t) cc_final: 0.6802 (p) REVERT: D 289 ASN cc_start: 0.7450 (m-40) cc_final: 0.6969 (m-40) REVERT: D 322 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7412 (mm-30) REVERT: D 333 GLU cc_start: 0.6676 (mt-10) cc_final: 0.6377 (mt-10) REVERT: D 340 ASN cc_start: 0.8524 (p0) cc_final: 0.7940 (p0) REVERT: D 345 GLN cc_start: 0.8538 (tt0) cc_final: 0.8326 (tt0) REVERT: D 363 GLN cc_start: 0.8532 (mt0) cc_final: 0.8084 (mt0) REVERT: D 366 HIS cc_start: 0.8731 (t70) cc_final: 0.8475 (t70) REVERT: D 376 MET cc_start: 0.8114 (mtp) cc_final: 0.7829 (mtp) REVERT: D 378 LYS cc_start: 0.8632 (mttt) cc_final: 0.8295 (mttt) REVERT: D 389 ASP cc_start: 0.8308 (m-30) cc_final: 0.7790 (m-30) REVERT: D 408 LEU cc_start: 0.7669 (tp) cc_final: 0.7431 (tp) REVERT: D 409 TYR cc_start: 0.6951 (m-80) cc_final: 0.6528 (m-80) REVERT: D 412 PHE cc_start: 0.7284 (m-80) cc_final: 0.6136 (m-80) REVERT: D 418 PHE cc_start: 0.8277 (t80) cc_final: 0.7424 (t80) REVERT: D 438 LYS cc_start: 0.8481 (mttt) cc_final: 0.8130 (mttt) REVERT: E 16 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7536 (mm-30) REVERT: E 20 GLU cc_start: 0.8052 (mp0) cc_final: 0.7836 (mm-30) REVERT: E 35 GLU cc_start: 0.8626 (tt0) cc_final: 0.8226 (tt0) REVERT: E 39 PHE cc_start: 0.7981 (t80) cc_final: 0.7409 (t80) REVERT: E 57 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7868 (mtp) REVERT: E 66 ASP cc_start: 0.8095 (m-30) cc_final: 0.7852 (m-30) REVERT: E 71 MET cc_start: 0.8861 (mmt) cc_final: 0.8543 (mmm) REVERT: E 72 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7609 (mm-30) REVERT: E 73 ASP cc_start: 0.8225 (t0) cc_final: 0.7195 (t0) REVERT: E 74 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8466 (mp10) REVERT: E 75 ASP cc_start: 0.7516 (m-30) cc_final: 0.6412 (m-30) REVERT: E 80 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8072 (mtt180) REVERT: E 86 LYS cc_start: 0.8566 (tttt) cc_final: 0.8315 (tttt) REVERT: E 94 GLU cc_start: 0.7991 (tp30) cc_final: 0.7434 (mp0) REVERT: E 97 ASP cc_start: 0.7932 (t70) cc_final: 0.7726 (t0) REVERT: E 101 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8150 (mm) REVERT: E 102 SER cc_start: 0.8553 (m) cc_final: 0.8107 (p) REVERT: E 125 ARG cc_start: 0.7658 (mtt180) cc_final: 0.7362 (mtt180) REVERT: E 144 SER cc_start: 0.8912 (t) cc_final: 0.8473 (p) REVERT: E 166 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6712 (mt-10) REVERT: E 222 ILE cc_start: 0.8431 (mt) cc_final: 0.8159 (mm) REVERT: E 229 LYS cc_start: 0.8191 (tttt) cc_final: 0.7883 (tttt) REVERT: E 251 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.8102 (tpp80) REVERT: E 303 VAL cc_start: 0.8830 (p) cc_final: 0.8422 (m) REVERT: E 306 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8532 (mmtt) REVERT: E 328 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7437 (tp) REVERT: E 332 GLN cc_start: 0.7021 (mp-120) cc_final: 0.6367 (mp10) REVERT: E 337 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7401 (pt0) REVERT: E 338 GLU cc_start: 0.7830 (mp0) cc_final: 0.7092 (mp0) REVERT: E 343 ARG cc_start: 0.7536 (mmt180) cc_final: 0.7322 (mmt180) REVERT: E 355 GLN cc_start: 0.8500 (mt0) cc_final: 0.7772 (mt0) REVERT: E 357 VAL cc_start: 0.7812 (t) cc_final: 0.7445 (m) REVERT: E 365 ASN cc_start: 0.8006 (m-40) cc_final: 0.7528 (m-40) REVERT: E 379 LEU cc_start: 0.9117 (tp) cc_final: 0.8911 (tp) REVERT: E 381 CYS cc_start: 0.8360 (t) cc_final: 0.7855 (t) REVERT: F 25 GLN cc_start: 0.8386 (tp40) cc_final: 0.7258 (tp40) REVERT: F 28 LYS cc_start: 0.9210 (mttt) cc_final: 0.8765 (mttt) REVERT: F 47 SER cc_start: 0.9058 (m) cc_final: 0.8733 (p) REVERT: F 56 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7600 (mmtt) REVERT: F 63 HIS cc_start: 0.8621 (t-90) cc_final: 0.8171 (t-90) REVERT: F 65 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8312 (mm-40) REVERT: F 68 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7397 (tpp80) REVERT: F 101 TYR cc_start: 0.7762 (t80) cc_final: 0.7284 (t80) REVERT: F 105 THR cc_start: 0.8452 (m) cc_final: 0.8103 (m) REVERT: F 109 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7945 (mt-10) REVERT: F 117 ASP cc_start: 0.8536 (t70) cc_final: 0.7895 (t70) REVERT: F 121 LYS cc_start: 0.8491 (mmtt) cc_final: 0.8179 (mmpt) REVERT: F 147 MET cc_start: 0.8334 (mmm) cc_final: 0.7945 (mmm) REVERT: F 156 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7042 (mt-10) REVERT: F 158 LYS cc_start: 0.8287 (mttt) cc_final: 0.7967 (mttt) REVERT: F 173 GLN cc_start: 0.8233 (mt0) cc_final: 0.7945 (mt0) REVERT: F 185 GLN cc_start: 0.9014 (tt0) cc_final: 0.8693 (tt0) REVERT: F 194 CYS cc_start: 0.8501 (t) cc_final: 0.8058 (t) REVERT: F 195 VAL cc_start: 0.8925 (m) cc_final: 0.8588 (p) REVERT: F 208 ASP cc_start: 0.8049 (t70) cc_final: 0.7587 (t0) REVERT: F 216 LYS cc_start: 0.8979 (tttt) cc_final: 0.8619 (tttt) REVERT: F 222 SER cc_start: 0.9195 (m) cc_final: 0.8906 (m) REVERT: F 225 GLN cc_start: 0.9175 (tp40) cc_final: 0.8631 (tp40) REVERT: F 228 LEU cc_start: 0.9212 (mt) cc_final: 0.8842 (mt) REVERT: F 229 TRP cc_start: 0.8549 (OUTLIER) cc_final: 0.7125 (t60) REVERT: F 237 GLN cc_start: 0.8284 (mt0) cc_final: 0.7554 (mt0) REVERT: F 251 TYR cc_start: 0.8818 (m-80) cc_final: 0.8254 (m-80) REVERT: F 281 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8827 (tp) REVERT: G 12 CYS cc_start: 0.9152 (p) cc_final: 0.8456 (p) REVERT: G 16 MET cc_start: 0.8964 (mmt) cc_final: 0.8211 (mmm) REVERT: G 36 GLN cc_start: 0.8429 (tp40) cc_final: 0.7275 (tm-30) REVERT: G 43 VAL cc_start: 0.8616 (m) cc_final: 0.8259 (p) REVERT: G 44 PHE cc_start: 0.8782 (t80) cc_final: 0.8262 (t80) REVERT: G 55 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8104 (tm-30) REVERT: G 56 ARG cc_start: 0.8489 (tpp80) cc_final: 0.8254 (tpp80) REVERT: H 862 LYS cc_start: 0.7110 (mmtt) cc_final: 0.6643 (mmtt) REVERT: H 895 GLU cc_start: 0.8151 (tp30) cc_final: 0.7552 (tp30) REVERT: H 909 GLU cc_start: 0.6765 (mp0) cc_final: 0.6482 (mp0) REVERT: H 912 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7383 (mt-10) REVERT: H 913 LYS cc_start: 0.7370 (mttt) cc_final: 0.7132 (mttt) REVERT: K 113 MET cc_start: 0.7857 (mmt) cc_final: 0.7605 (mmt) REVERT: K 116 TYR cc_start: 0.8406 (t80) cc_final: 0.8060 (t80) REVERT: K 118 MET cc_start: 0.6898 (tpp) cc_final: 0.6323 (tpp) REVERT: K 120 HIS cc_start: 0.8688 (m-70) cc_final: 0.8168 (m-70) REVERT: K 121 PHE cc_start: 0.8560 (m-80) cc_final: 0.7449 (m-80) REVERT: K 125 THR cc_start: 0.8239 (m) cc_final: 0.7975 (m) REVERT: K 141 LYS cc_start: 0.8992 (tttt) cc_final: 0.8606 (tttt) REVERT: K 143 GLU cc_start: 0.8580 (tt0) cc_final: 0.7892 (tm-30) REVERT: K 151 LYS cc_start: 0.7898 (mttm) cc_final: 0.7677 (mttt) REVERT: K 159 GLU cc_start: 0.7907 (tp30) cc_final: 0.7591 (tp30) REVERT: K 163 LYS cc_start: 0.8441 (mttt) cc_final: 0.8040 (mttt) REVERT: K 166 VAL cc_start: 0.8937 (t) cc_final: 0.8628 (p) REVERT: K 168 LYS cc_start: 0.8576 (tptm) cc_final: 0.8200 (tptm) REVERT: K 178 MET cc_start: 0.7665 (ptp) cc_final: 0.7023 (ptp) REVERT: K 190 SER cc_start: 0.9284 (t) cc_final: 0.8893 (p) REVERT: K 192 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8231 (tm-30) REVERT: K 202 GLU cc_start: 0.8644 (mp0) cc_final: 0.8388 (pm20) REVERT: K 213 LYS cc_start: 0.8151 (tptt) cc_final: 0.7598 (tptt) REVERT: K 217 LYS cc_start: 0.8701 (tmtt) cc_final: 0.8327 (tmtt) REVERT: K 252 LEU cc_start: 0.7848 (tp) cc_final: 0.7517 (tp) REVERT: K 263 MET cc_start: 0.5624 (ptt) cc_final: 0.5186 (ppp) outliers start: 131 outliers final: 87 residues processed: 1001 average time/residue: 0.4655 time to fit residues: 699.7834 Evaluate side-chains 1020 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 919 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 LEU 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 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 505 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 586 GLU 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 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 479 PHE Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 242 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 303 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 229 optimal weight: 0.3980 chunk 177 optimal weight: 0.9980 chunk 264 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 313 optimal weight: 0.0020 chunk 196 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN A 625 GLN B 203 ASN ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN B 723 GLN C 402 ASN ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 ASN F 176 ASN K 119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 28259 Z= 0.202 Angle : 0.671 13.756 38512 Z= 0.331 Chirality : 0.042 0.272 4285 Planarity : 0.004 0.086 4647 Dihedral : 15.696 175.281 4417 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.00 % Favored : 94.97 % Rotamer: Outliers : 4.40 % Allowed : 22.88 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: 0.31 (0.15), residues: 3186 helix: 1.05 (0.14), residues: 1493 sheet: -0.25 (0.27), residues: 393 loop : -0.55 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 421 HIS 0.008 0.001 HIS C 524 PHE 0.040 0.001 PHE J 162 TYR 0.041 0.001 TYR C 533 ARG 0.018 0.001 ARG A 317 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 941 time to evaluate : 3.205 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8655 (mttt) cc_final: 0.8144 (mttt) REVERT: A 65 MET cc_start: 0.7939 (ptt) cc_final: 0.7482 (ptt) REVERT: A 68 LYS cc_start: 0.7166 (mtmt) cc_final: 0.6839 (tptt) REVERT: A 94 LYS cc_start: 0.7883 (ptpt) cc_final: 0.7390 (ptpt) REVERT: A 115 GLU cc_start: 0.7534 (tt0) cc_final: 0.7280 (tt0) REVERT: A 135 ASP cc_start: 0.7936 (m-30) cc_final: 0.7466 (t0) REVERT: A 146 THR cc_start: 0.7340 (t) cc_final: 0.7076 (t) REVERT: A 154 GLN cc_start: 0.7466 (mp10) cc_final: 0.7033 (pm20) REVERT: A 157 LYS cc_start: 0.8711 (mtmm) cc_final: 0.8415 (pttm) REVERT: A 195 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8127 (mtt90) REVERT: A 276 MET cc_start: 0.8421 (mmp) cc_final: 0.8221 (mmp) REVERT: A 282 LYS cc_start: 0.8913 (tttt) cc_final: 0.8410 (ttpp) REVERT: A 305 ASP cc_start: 0.8565 (p0) cc_final: 0.8252 (p0) REVERT: A 322 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8297 (mtmm) REVERT: A 325 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7180 (mtt-85) REVERT: A 351 VAL cc_start: 0.9097 (t) cc_final: 0.8822 (p) REVERT: A 373 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8147 (mm-40) REVERT: A 379 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8252 (mmmt) REVERT: A 380 MET cc_start: 0.7741 (ttm) cc_final: 0.7458 (ttm) REVERT: A 381 TRP cc_start: 0.8358 (m-10) cc_final: 0.8039 (m-10) REVERT: A 385 ASP cc_start: 0.8445 (p0) cc_final: 0.8143 (p0) REVERT: A 392 PHE cc_start: 0.8188 (t80) cc_final: 0.7272 (t80) REVERT: A 412 MET cc_start: 0.6537 (ttt) cc_final: 0.6236 (ttt) REVERT: A 415 HIS cc_start: 0.8105 (OUTLIER) cc_final: 0.7704 (m-70) REVERT: A 434 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7547 (mp0) REVERT: A 437 LEU cc_start: 0.8723 (tp) cc_final: 0.8514 (tt) REVERT: A 450 MET cc_start: 0.7488 (ptm) cc_final: 0.6898 (ptm) REVERT: A 453 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7744 (mtm110) REVERT: A 457 ILE cc_start: 0.8664 (tt) cc_final: 0.8379 (tt) REVERT: A 463 LYS cc_start: 0.8615 (mttt) cc_final: 0.8109 (mtmm) REVERT: A 487 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8181 (ttmt) REVERT: A 497 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8341 (tm-30) REVERT: A 510 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8294 (p) REVERT: A 520 ARG cc_start: 0.8417 (mmm160) cc_final: 0.8092 (mmm160) REVERT: A 525 ILE cc_start: 0.8753 (tp) cc_final: 0.8253 (pt) REVERT: A 531 ILE cc_start: 0.8243 (mm) cc_final: 0.7987 (tp) REVERT: A 549 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7243 (mtpp) REVERT: A 552 GLU cc_start: 0.7362 (pp20) cc_final: 0.6932 (pp20) REVERT: A 571 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.7976 (t80) REVERT: A 586 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7714 (tp-100) REVERT: A 619 GLU cc_start: 0.7294 (mp0) cc_final: 0.6968 (mp0) REVERT: A 636 GLU cc_start: 0.7970 (tp30) cc_final: 0.7550 (tp30) REVERT: A 656 ASN cc_start: 0.8386 (m110) cc_final: 0.8013 (m-40) REVERT: A 659 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8108 (p90) REVERT: A 674 THR cc_start: 0.8819 (m) cc_final: 0.8423 (t) REVERT: A 677 GLN cc_start: 0.7567 (mt0) cc_final: 0.7121 (mt0) REVERT: B 1 MET cc_start: 0.6484 (ppp) cc_final: 0.6131 (ppp) REVERT: B 30 ARG cc_start: 0.8647 (ttm-80) cc_final: 0.8388 (ttm-80) REVERT: B 41 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6324 (tm-30) REVERT: B 42 MET cc_start: 0.7946 (mtp) cc_final: 0.7522 (mtp) REVERT: B 60 GLN cc_start: 0.8945 (mt0) cc_final: 0.8395 (mt0) REVERT: B 61 ARG cc_start: 0.8416 (mmp80) cc_final: 0.8087 (mmp80) REVERT: B 65 LEU cc_start: 0.7836 (tp) cc_final: 0.7376 (pt) REVERT: B 72 TYR cc_start: 0.7810 (t80) cc_final: 0.7466 (t80) REVERT: B 84 ILE cc_start: 0.9129 (mm) cc_final: 0.8736 (tp) REVERT: B 85 GLU cc_start: 0.8542 (pp20) cc_final: 0.7897 (tp30) REVERT: B 86 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7981 (tm-30) REVERT: B 133 LYS cc_start: 0.8566 (mttt) cc_final: 0.8184 (tppt) REVERT: B 162 ASP cc_start: 0.8796 (t0) cc_final: 0.8262 (m-30) REVERT: B 196 ARG cc_start: 0.8495 (ptp-170) cc_final: 0.7693 (ptp-170) REVERT: B 207 TYR cc_start: 0.8171 (p90) cc_final: 0.7369 (p90) REVERT: B 228 LYS cc_start: 0.8230 (ptmt) cc_final: 0.7669 (ptmt) REVERT: B 235 GLU cc_start: 0.8327 (tp30) cc_final: 0.7977 (mp0) REVERT: B 243 CYS cc_start: 0.8366 (m) cc_final: 0.7863 (m) REVERT: B 247 MET cc_start: 0.8514 (mpp) cc_final: 0.7769 (mpp) REVERT: B 339 TYR cc_start: 0.8281 (t80) cc_final: 0.7823 (t80) REVERT: B 341 LYS cc_start: 0.9194 (mtmm) cc_final: 0.8897 (mttp) REVERT: B 434 HIS cc_start: 0.6185 (OUTLIER) cc_final: 0.5618 (p90) REVERT: B 438 MET cc_start: 0.7691 (mtm) cc_final: 0.6946 (mtm) REVERT: B 450 ARG cc_start: 0.7643 (mtp180) cc_final: 0.7198 (ttm-80) REVERT: B 469 LYS cc_start: 0.9066 (ptpp) cc_final: 0.8858 (ptpp) REVERT: B 472 ASP cc_start: 0.7832 (m-30) cc_final: 0.7243 (m-30) REVERT: B 493 MET cc_start: 0.8184 (ptt) cc_final: 0.7797 (ptp) REVERT: B 494 ILE cc_start: 0.9033 (mt) cc_final: 0.8749 (mp) REVERT: B 508 PHE cc_start: 0.8317 (t80) cc_final: 0.6488 (t80) REVERT: B 511 ARG cc_start: 0.7892 (mtm180) cc_final: 0.7533 (mtt-85) REVERT: B 513 ASP cc_start: 0.8187 (t0) cc_final: 0.7974 (t0) REVERT: B 570 GLU cc_start: 0.6627 (tm-30) cc_final: 0.6097 (tm-30) REVERT: B 603 LYS cc_start: 0.8750 (ptmm) cc_final: 0.8393 (tmtt) REVERT: B 634 LYS cc_start: 0.7996 (ptpp) cc_final: 0.7547 (mtmm) REVERT: B 642 ASP cc_start: 0.7345 (p0) cc_final: 0.6984 (p0) REVERT: B 655 ASP cc_start: 0.8673 (t0) cc_final: 0.7676 (m-30) REVERT: B 662 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8277 (tm-30) REVERT: B 663 CYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7760 (p) REVERT: B 672 THR cc_start: 0.9062 (p) cc_final: 0.8736 (t) REVERT: B 690 ARG cc_start: 0.7945 (mtm110) cc_final: 0.7129 (mtm-85) REVERT: B 707 ASN cc_start: 0.7354 (t0) cc_final: 0.6608 (t0) REVERT: C 402 ASN cc_start: 0.8239 (m110) cc_final: 0.7833 (p0) REVERT: C 412 GLU cc_start: 0.8608 (pp20) cc_final: 0.8308 (pp20) REVERT: C 442 GLN cc_start: 0.6722 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: C 471 LEU cc_start: 0.9294 (mt) cc_final: 0.9078 (tt) REVERT: C 473 ARG cc_start: 0.8799 (tmt170) cc_final: 0.8232 (tmt170) REVERT: C 475 PHE cc_start: 0.8821 (t80) cc_final: 0.8442 (t80) REVERT: C 493 MET cc_start: 0.8329 (tpp) cc_final: 0.7527 (tpp) REVERT: C 528 MET cc_start: 0.8927 (mtm) cc_final: 0.8212 (mtm) REVERT: C 539 TRP cc_start: 0.8459 (t60) cc_final: 0.7881 (t60) REVERT: D 32 ASP cc_start: 0.8307 (p0) cc_final: 0.8037 (p0) REVERT: D 44 VAL cc_start: 0.9405 (t) cc_final: 0.8958 (p) REVERT: D 47 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7972 (mm-30) REVERT: D 48 LEU cc_start: 0.8758 (mt) cc_final: 0.8387 (mt) REVERT: D 50 SER cc_start: 0.7916 (m) cc_final: 0.7229 (p) REVERT: D 55 TRP cc_start: 0.7474 (m-10) cc_final: 0.7210 (m-90) REVERT: D 79 PHE cc_start: 0.8313 (m-80) cc_final: 0.8032 (m-10) REVERT: D 86 SER cc_start: 0.9005 (m) cc_final: 0.8748 (p) REVERT: D 150 LYS cc_start: 0.8738 (tttt) cc_final: 0.8078 (tttt) REVERT: D 154 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8297 (mt-10) REVERT: D 177 GLN cc_start: 0.8292 (mp10) cc_final: 0.7594 (pm20) REVERT: D 186 LYS cc_start: 0.8717 (pttt) cc_final: 0.8391 (pttt) REVERT: D 213 TRP cc_start: 0.8005 (OUTLIER) cc_final: 0.7548 (t-100) REVERT: D 217 LEU cc_start: 0.8554 (mm) cc_final: 0.8259 (mt) REVERT: D 237 LEU cc_start: 0.9238 (tp) cc_final: 0.8983 (tt) REVERT: D 239 GLN cc_start: 0.8995 (tt0) cc_final: 0.8159 (tm-30) REVERT: D 242 PHE cc_start: 0.8472 (m-80) cc_final: 0.8129 (m-10) REVERT: D 247 LYS cc_start: 0.8499 (tttt) cc_final: 0.8149 (tttt) REVERT: D 254 MET cc_start: 0.5455 (mtt) cc_final: 0.4608 (mtt) REVERT: D 258 LEU cc_start: 0.9039 (mt) cc_final: 0.8736 (tt) REVERT: D 260 ASN cc_start: 0.9166 (m110) cc_final: 0.8871 (p0) REVERT: D 261 PHE cc_start: 0.8932 (t80) cc_final: 0.8611 (t80) REVERT: D 266 ARG cc_start: 0.8573 (ttt180) cc_final: 0.8095 (ttp-170) REVERT: D 270 LEU cc_start: 0.8507 (mt) cc_final: 0.8288 (mm) REVERT: D 271 VAL cc_start: 0.8643 (t) cc_final: 0.8199 (p) REVERT: D 289 ASN cc_start: 0.7379 (m-40) cc_final: 0.6924 (m-40) REVERT: D 322 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7369 (mm-30) REVERT: D 340 ASN cc_start: 0.8443 (p0) cc_final: 0.8029 (p0) REVERT: D 345 GLN cc_start: 0.8506 (tt0) cc_final: 0.8254 (tt0) REVERT: D 363 GLN cc_start: 0.8383 (mt0) cc_final: 0.7968 (mt0) REVERT: D 366 HIS cc_start: 0.8719 (t70) cc_final: 0.8499 (t70) REVERT: D 376 MET cc_start: 0.8157 (mtp) cc_final: 0.7881 (mtp) REVERT: D 378 LYS cc_start: 0.8608 (mttt) cc_final: 0.8245 (mttt) REVERT: D 389 ASP cc_start: 0.8297 (m-30) cc_final: 0.7767 (m-30) REVERT: D 408 LEU cc_start: 0.7660 (tp) cc_final: 0.7434 (tp) REVERT: D 409 TYR cc_start: 0.6936 (m-80) cc_final: 0.6270 (m-80) REVERT: D 412 PHE cc_start: 0.7285 (m-80) cc_final: 0.5418 (m-80) REVERT: D 418 PHE cc_start: 0.8270 (t80) cc_final: 0.7232 (t80) REVERT: D 438 LYS cc_start: 0.8475 (mttt) cc_final: 0.8116 (mttt) REVERT: E 35 GLU cc_start: 0.8621 (tt0) cc_final: 0.8213 (tt0) REVERT: E 39 PHE cc_start: 0.7947 (t80) cc_final: 0.7408 (t80) REVERT: E 40 LYS cc_start: 0.8370 (mmtm) cc_final: 0.8155 (mmtm) REVERT: E 57 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7900 (mtp) REVERT: E 66 ASP cc_start: 0.8089 (m-30) cc_final: 0.7845 (m-30) REVERT: E 71 MET cc_start: 0.8851 (mmt) cc_final: 0.8546 (mmm) REVERT: E 72 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7583 (mm-30) REVERT: E 73 ASP cc_start: 0.8241 (t0) cc_final: 0.7325 (t0) REVERT: E 74 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8470 (mp10) REVERT: E 75 ASP cc_start: 0.7466 (m-30) cc_final: 0.6471 (m-30) REVERT: E 80 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8065 (mtt180) REVERT: E 86 LYS cc_start: 0.8568 (tttt) cc_final: 0.8330 (tttt) REVERT: E 94 GLU cc_start: 0.7955 (tp30) cc_final: 0.7401 (mp0) REVERT: E 101 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8134 (mm) REVERT: E 102 SER cc_start: 0.8541 (m) cc_final: 0.8091 (p) REVERT: E 125 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7359 (mtt180) REVERT: E 144 SER cc_start: 0.8937 (t) cc_final: 0.8474 (p) REVERT: E 166 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6725 (mt-10) REVERT: E 222 ILE cc_start: 0.8408 (mt) cc_final: 0.8155 (mm) REVERT: E 229 LYS cc_start: 0.8168 (tttt) cc_final: 0.7859 (tttt) REVERT: E 295 ARG cc_start: 0.7999 (mmt180) cc_final: 0.7560 (mmm160) REVERT: E 303 VAL cc_start: 0.8900 (p) cc_final: 0.8530 (m) REVERT: E 328 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7443 (tp) REVERT: E 332 GLN cc_start: 0.7066 (mp-120) cc_final: 0.6376 (mp10) REVERT: E 337 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7415 (pt0) REVERT: E 338 GLU cc_start: 0.7754 (mp0) cc_final: 0.7010 (mp0) REVERT: E 343 ARG cc_start: 0.7504 (mmt180) cc_final: 0.7278 (mmt180) REVERT: E 355 GLN cc_start: 0.8506 (mt0) cc_final: 0.7775 (mt0) REVERT: E 357 VAL cc_start: 0.7782 (t) cc_final: 0.7400 (m) REVERT: E 365 ASN cc_start: 0.7969 (m-40) cc_final: 0.7513 (m-40) REVERT: E 379 LEU cc_start: 0.9132 (tp) cc_final: 0.8923 (tp) REVERT: E 381 CYS cc_start: 0.8547 (t) cc_final: 0.7960 (t) REVERT: F 25 GLN cc_start: 0.8410 (tp40) cc_final: 0.7221 (tp40) REVERT: F 28 LYS cc_start: 0.9220 (mttt) cc_final: 0.8774 (mttt) REVERT: F 47 SER cc_start: 0.9069 (m) cc_final: 0.8753 (p) REVERT: F 51 MET cc_start: 0.7874 (mtp) cc_final: 0.7629 (mmm) REVERT: F 56 LYS cc_start: 0.8010 (mmtt) cc_final: 0.7577 (mmtt) REVERT: F 63 HIS cc_start: 0.8632 (t-90) cc_final: 0.8147 (t-90) REVERT: F 65 GLN cc_start: 0.8575 (mm-40) cc_final: 0.8269 (mm-40) REVERT: F 68 ARG cc_start: 0.7899 (tpp80) cc_final: 0.7227 (tpp80) REVERT: F 101 TYR cc_start: 0.7759 (t80) cc_final: 0.7281 (t80) REVERT: F 105 THR cc_start: 0.8504 (m) cc_final: 0.8069 (m) REVERT: F 109 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7857 (mt-10) REVERT: F 117 ASP cc_start: 0.8530 (t70) cc_final: 0.7871 (t70) REVERT: F 121 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8193 (mmpt) REVERT: F 139 LYS cc_start: 0.9260 (mttt) cc_final: 0.8792 (mtmt) REVERT: F 147 MET cc_start: 0.8362 (mmm) cc_final: 0.7947 (mmm) REVERT: F 156 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7094 (mt-10) REVERT: F 158 LYS cc_start: 0.8219 (mttt) cc_final: 0.7899 (mttt) REVERT: F 173 GLN cc_start: 0.8232 (mt0) cc_final: 0.7940 (mt0) REVERT: F 185 GLN cc_start: 0.9007 (tt0) cc_final: 0.8690 (tt0) REVERT: F 194 CYS cc_start: 0.8462 (t) cc_final: 0.8026 (t) REVERT: F 195 VAL cc_start: 0.8927 (m) cc_final: 0.8579 (p) REVERT: F 208 ASP cc_start: 0.8055 (t70) cc_final: 0.7589 (t0) REVERT: F 216 LYS cc_start: 0.8976 (tttt) cc_final: 0.8621 (tttt) REVERT: F 222 SER cc_start: 0.9244 (m) cc_final: 0.8963 (m) REVERT: F 225 GLN cc_start: 0.9061 (tp40) cc_final: 0.8725 (tp40) REVERT: F 228 LEU cc_start: 0.9215 (mt) cc_final: 0.8915 (mt) REVERT: F 229 TRP cc_start: 0.8545 (OUTLIER) cc_final: 0.7027 (t60) REVERT: F 237 GLN cc_start: 0.8304 (mt0) cc_final: 0.7535 (mt0) REVERT: F 251 TYR cc_start: 0.8842 (m-80) cc_final: 0.8302 (m-80) REVERT: F 252 ARG cc_start: 0.8678 (mtp180) cc_final: 0.8461 (mtp-110) REVERT: F 281 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8818 (tp) REVERT: G 12 CYS cc_start: 0.9132 (p) cc_final: 0.8472 (p) REVERT: G 16 MET cc_start: 0.8936 (mmt) cc_final: 0.8475 (mmm) REVERT: G 43 VAL cc_start: 0.8621 (m) cc_final: 0.8284 (p) REVERT: G 44 PHE cc_start: 0.8765 (t80) cc_final: 0.8303 (t80) REVERT: G 55 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8135 (tm-30) REVERT: G 56 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8226 (tpp80) REVERT: H 859 GLU cc_start: 0.7990 (tt0) cc_final: 0.7650 (tp30) REVERT: H 895 GLU cc_start: 0.8168 (tp30) cc_final: 0.7562 (tp30) REVERT: H 900 LEU cc_start: 0.7766 (mp) cc_final: 0.7452 (mp) REVERT: H 912 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7391 (mt-10) REVERT: H 913 LYS cc_start: 0.7387 (mttt) cc_final: 0.7142 (mttt) REVERT: K 116 TYR cc_start: 0.8464 (t80) cc_final: 0.8159 (t80) REVERT: K 118 MET cc_start: 0.6998 (tpp) cc_final: 0.6410 (tpp) REVERT: K 120 HIS cc_start: 0.8685 (m-70) cc_final: 0.8219 (m-70) REVERT: K 121 PHE cc_start: 0.8536 (m-80) cc_final: 0.7457 (m-80) REVERT: K 141 LYS cc_start: 0.8964 (tttt) cc_final: 0.8591 (tttt) REVERT: K 143 GLU cc_start: 0.8545 (tt0) cc_final: 0.8057 (tt0) REVERT: K 151 LYS cc_start: 0.7832 (mttm) cc_final: 0.7615 (mttt) REVERT: K 159 GLU cc_start: 0.7931 (tp30) cc_final: 0.7726 (tp30) REVERT: K 163 LYS cc_start: 0.8428 (mttt) cc_final: 0.8001 (mttt) REVERT: K 166 VAL cc_start: 0.8935 (t) cc_final: 0.8640 (p) REVERT: K 168 LYS cc_start: 0.8562 (tptm) cc_final: 0.8289 (tptm) REVERT: K 178 MET cc_start: 0.7597 (ptp) cc_final: 0.6931 (ptp) REVERT: K 211 ARG cc_start: 0.8690 (mmt180) cc_final: 0.8276 (mmt-90) REVERT: K 213 LYS cc_start: 0.8207 (tptt) cc_final: 0.7768 (tptt) REVERT: K 215 LYS cc_start: 0.8835 (mtmm) cc_final: 0.8490 (mtmt) REVERT: K 217 LYS cc_start: 0.8728 (tmtt) cc_final: 0.8339 (tmtt) REVERT: K 263 MET cc_start: 0.5616 (ptt) cc_final: 0.5225 (ppp) outliers start: 125 outliers final: 90 residues processed: 1006 average time/residue: 0.4472 time to fit residues: 667.1548 Evaluate side-chains 1025 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 920 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 497 GLN 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 602 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 GLU 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 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 479 PHE Chi-restraints excluded: chain C residue 494 LYS Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 117 ASN Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain H residue 849 LYS Chi-restraints excluded: chain H residue 899 ILE Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 200 LEU Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 242 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 193 optimal weight: 10.0000 chunk 125 optimal weight: 0.0970 chunk 187 optimal weight: 4.9990 chunk 94 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 199 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 chunk 154 optimal weight: 0.4980 chunk 29 optimal weight: 0.0170 chunk 246 optimal weight: 0.9980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 726 GLN ** C 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 379 GLN E 50 HIS E 74 GLN ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN F 188 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28259 Z= 0.190 Angle : 0.676 13.733 38512 Z= 0.332 Chirality : 0.042 0.286 4285 Planarity : 0.004 0.058 4647 Dihedral : 15.622 174.158 4417 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 3.52 % Allowed : 24.71 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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: 0.27 (0.15), residues: 3186 helix: 1.02 (0.14), residues: 1484 sheet: -0.32 (0.27), residues: 396 loop : -0.55 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 421 HIS 0.008 0.001 HIS C 524 PHE 0.039 0.001 PHE J 162 TYR 0.044 0.001 TYR C 533 ARG 0.009 0.000 ARG H 860 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 951 time to evaluate : 3.128 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8633 (mttt) cc_final: 0.8228 (mttt) REVERT: A 65 MET cc_start: 0.7924 (ptt) cc_final: 0.7461 (ptt) REVERT: A 68 LYS cc_start: 0.7195 (mtmt) cc_final: 0.6907 (tptt) REVERT: A 94 LYS cc_start: 0.7853 (ptpt) cc_final: 0.7357 (ptpt) REVERT: A 115 GLU cc_start: 0.7510 (tt0) cc_final: 0.7247 (tt0) REVERT: A 135 ASP cc_start: 0.7939 (m-30) cc_final: 0.7471 (t0) REVERT: A 146 THR cc_start: 0.7166 (t) cc_final: 0.6914 (t) REVERT: A 150 ASP cc_start: 0.7086 (t0) cc_final: 0.6720 (t0) REVERT: A 157 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8306 (pttm) REVERT: A 195 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8015 (mtt90) REVERT: A 276 MET cc_start: 0.8363 (mmp) cc_final: 0.8093 (mmp) REVERT: A 282 LYS cc_start: 0.8947 (tttt) cc_final: 0.8440 (ttpp) REVERT: A 305 ASP cc_start: 0.8553 (p0) cc_final: 0.8242 (p0) REVERT: A 322 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8290 (mppt) REVERT: A 325 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7145 (mtt-85) REVERT: A 351 VAL cc_start: 0.9047 (t) cc_final: 0.8744 (p) REVERT: A 373 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8130 (mm110) REVERT: A 379 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8225 (mmmt) REVERT: A 380 MET cc_start: 0.7791 (ttm) cc_final: 0.7499 (ttm) REVERT: A 381 TRP cc_start: 0.8323 (m-10) cc_final: 0.8038 (m-10) REVERT: A 385 ASP cc_start: 0.8449 (p0) cc_final: 0.8097 (p0) REVERT: A 392 PHE cc_start: 0.8157 (t80) cc_final: 0.7252 (t80) REVERT: A 415 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7512 (m-70) REVERT: A 424 GLU cc_start: 0.8570 (tp30) cc_final: 0.8363 (tm-30) REVERT: A 434 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7536 (mp0) REVERT: A 450 MET cc_start: 0.7502 (ptm) cc_final: 0.6916 (ptm) REVERT: A 453 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7728 (mtm110) REVERT: A 457 ILE cc_start: 0.8705 (tt) cc_final: 0.8421 (tt) REVERT: A 463 LYS cc_start: 0.8587 (mttt) cc_final: 0.8088 (mtmm) REVERT: A 487 LYS cc_start: 0.8566 (ttmt) cc_final: 0.8062 (ttmt) REVERT: A 504 LYS cc_start: 0.8405 (ttpt) cc_final: 0.7910 (tttm) REVERT: A 510 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8303 (p) REVERT: A 520 ARG cc_start: 0.8405 (mmm160) cc_final: 0.8130 (mmm160) REVERT: A 525 ILE cc_start: 0.8719 (tp) cc_final: 0.8178 (pt) REVERT: A 531 ILE cc_start: 0.8218 (mm) cc_final: 0.8010 (tp) REVERT: A 549 LYS cc_start: 0.8204 (mtmt) cc_final: 0.6928 (ttpp) REVERT: A 552 GLU cc_start: 0.7435 (pp20) cc_final: 0.6960 (pp20) REVERT: A 571 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8063 (t80) REVERT: A 586 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7691 (tp-100) REVERT: A 619 GLU cc_start: 0.7288 (mp0) cc_final: 0.6946 (mp0) REVERT: A 636 GLU cc_start: 0.7932 (tp30) cc_final: 0.7498 (tp30) REVERT: A 656 ASN cc_start: 0.8346 (m110) cc_final: 0.7988 (m-40) REVERT: A 659 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8097 (p90) REVERT: A 674 THR cc_start: 0.8744 (m) cc_final: 0.8357 (t) REVERT: A 677 GLN cc_start: 0.7560 (mt0) cc_final: 0.7095 (mt0) REVERT: A 683 GLN cc_start: 0.8207 (mm-40) cc_final: 0.7791 (mm-40) REVERT: B 1 MET cc_start: 0.6580 (ppp) cc_final: 0.6277 (ppp) REVERT: B 11 TYR cc_start: 0.7558 (p90) cc_final: 0.7177 (p90) REVERT: B 14 TYR cc_start: 0.8192 (m-80) cc_final: 0.7771 (m-80) REVERT: B 30 ARG cc_start: 0.8630 (ttm-80) cc_final: 0.8373 (ttm-80) REVERT: B 41 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6296 (tm-30) REVERT: B 42 MET cc_start: 0.7931 (mtp) cc_final: 0.7549 (mtp) REVERT: B 60 GLN cc_start: 0.8941 (mt0) cc_final: 0.8612 (mt0) REVERT: B 61 ARG cc_start: 0.8415 (mmp80) cc_final: 0.8057 (mmp80) REVERT: B 65 LEU cc_start: 0.7865 (tp) cc_final: 0.7399 (pt) REVERT: B 72 TYR cc_start: 0.7822 (t80) cc_final: 0.7503 (t80) REVERT: B 84 ILE cc_start: 0.9110 (mm) cc_final: 0.8732 (tp) REVERT: B 85 GLU cc_start: 0.8537 (pp20) cc_final: 0.7889 (tp30) REVERT: B 86 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7974 (tm-30) REVERT: B 133 LYS cc_start: 0.8562 (mttt) cc_final: 0.8269 (mmmt) REVERT: B 162 ASP cc_start: 0.8745 (t0) cc_final: 0.8200 (m-30) REVERT: B 207 TYR cc_start: 0.8226 (p90) cc_final: 0.7429 (p90) REVERT: B 228 LYS cc_start: 0.8136 (ptmt) cc_final: 0.7739 (ptmt) REVERT: B 235 GLU cc_start: 0.8289 (tp30) cc_final: 0.7965 (mp0) REVERT: B 243 CYS cc_start: 0.8281 (m) cc_final: 0.7775 (m) REVERT: B 247 MET cc_start: 0.8523 (mpp) cc_final: 0.7793 (mpp) REVERT: B 339 TYR cc_start: 0.8291 (t80) cc_final: 0.7792 (t80) REVERT: B 341 LYS cc_start: 0.9182 (mtmm) cc_final: 0.8885 (mttp) REVERT: B 358 LEU cc_start: 0.7472 (pp) cc_final: 0.6789 (pp) REVERT: B 434 HIS cc_start: 0.6085 (OUTLIER) cc_final: 0.5487 (p90) REVERT: B 438 MET cc_start: 0.7665 (mtm) cc_final: 0.6870 (mtm) REVERT: B 450 ARG cc_start: 0.7637 (mtp180) cc_final: 0.7220 (ttm-80) REVERT: B 469 LYS cc_start: 0.9022 (ptpp) cc_final: 0.8784 (ptpp) REVERT: B 472 ASP cc_start: 0.7801 (m-30) cc_final: 0.7189 (m-30) REVERT: B 493 MET cc_start: 0.8179 (ptt) cc_final: 0.7811 (ptp) REVERT: B 494 ILE cc_start: 0.9031 (mt) cc_final: 0.8747 (mp) REVERT: B 508 PHE cc_start: 0.8315 (t80) cc_final: 0.6537 (t80) REVERT: B 511 ARG cc_start: 0.7884 (mtm180) cc_final: 0.7573 (mtt-85) REVERT: B 543 GLN cc_start: 0.8516 (mp10) cc_final: 0.8224 (pm20) REVERT: B 545 MET cc_start: 0.8476 (ttm) cc_final: 0.8156 (tpp) REVERT: B 570 GLU cc_start: 0.6607 (tm-30) cc_final: 0.6031 (tm-30) REVERT: B 603 LYS cc_start: 0.8688 (ptmm) cc_final: 0.8341 (tmtt) REVERT: B 634 LYS cc_start: 0.7975 (ptpp) cc_final: 0.7499 (mtmm) REVERT: B 642 ASP cc_start: 0.7326 (p0) cc_final: 0.6968 (p0) REVERT: B 655 ASP cc_start: 0.8693 (t0) cc_final: 0.8297 (t0) REVERT: B 662 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8252 (tm-30) REVERT: B 663 CYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7703 (p) REVERT: B 672 THR cc_start: 0.9055 (p) cc_final: 0.8731 (t) REVERT: B 690 ARG cc_start: 0.7932 (mtm110) cc_final: 0.7092 (mtm-85) REVERT: C 402 ASN cc_start: 0.8265 (m110) cc_final: 0.7851 (p0) REVERT: C 412 GLU cc_start: 0.8550 (pp20) cc_final: 0.8285 (pp20) REVERT: C 442 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6370 (pm20) REVERT: C 471 LEU cc_start: 0.9302 (mt) cc_final: 0.9081 (tt) REVERT: C 473 ARG cc_start: 0.8763 (tmt170) cc_final: 0.8186 (tmt170) REVERT: C 475 PHE cc_start: 0.8803 (t80) cc_final: 0.8414 (t80) REVERT: C 493 MET cc_start: 0.8301 (tpp) cc_final: 0.7513 (tpp) REVERT: C 528 MET cc_start: 0.8934 (mtm) cc_final: 0.8196 (mtm) REVERT: C 539 TRP cc_start: 0.8445 (t60) cc_final: 0.7912 (t60) REVERT: D 32 ASP cc_start: 0.8316 (p0) cc_final: 0.8057 (p0) REVERT: D 44 VAL cc_start: 0.9393 (t) cc_final: 0.9132 (p) REVERT: D 47 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7941 (mm-30) REVERT: D 50 SER cc_start: 0.7816 (m) cc_final: 0.7141 (p) REVERT: D 55 TRP cc_start: 0.7441 (m-10) cc_final: 0.7212 (m-90) REVERT: D 79 PHE cc_start: 0.8336 (m-80) cc_final: 0.8058 (m-10) REVERT: D 86 SER cc_start: 0.9021 (m) cc_final: 0.8755 (p) REVERT: D 90 LEU cc_start: 0.9085 (tp) cc_final: 0.8863 (tp) REVERT: D 123 LEU cc_start: 0.8926 (mm) cc_final: 0.8557 (tp) REVERT: D 150 LYS cc_start: 0.8702 (tttt) cc_final: 0.8050 (tttt) REVERT: D 154 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8264 (mt-10) REVERT: D 186 LYS cc_start: 0.8605 (pttt) cc_final: 0.8247 (pttt) REVERT: D 202 GLN cc_start: 0.8363 (mt0) cc_final: 0.8014 (mm-40) REVERT: D 213 TRP cc_start: 0.7974 (OUTLIER) cc_final: 0.7550 (t-100) REVERT: D 217 LEU cc_start: 0.8539 (mm) cc_final: 0.8212 (mt) REVERT: D 237 LEU cc_start: 0.9206 (tp) cc_final: 0.8945 (tt) REVERT: D 239 GLN cc_start: 0.8940 (tt0) cc_final: 0.8144 (tm-30) REVERT: D 242 PHE cc_start: 0.8371 (m-80) cc_final: 0.8127 (m-10) REVERT: D 247 LYS cc_start: 0.8482 (tttt) cc_final: 0.8054 (tttt) REVERT: D 254 MET cc_start: 0.5566 (mtt) cc_final: 0.4923 (mtt) REVERT: D 258 LEU cc_start: 0.9017 (mt) cc_final: 0.8781 (tt) REVERT: D 260 ASN cc_start: 0.9073 (m110) cc_final: 0.8743 (p0) REVERT: D 261 PHE cc_start: 0.8926 (t80) cc_final: 0.8613 (t80) REVERT: D 266 ARG cc_start: 0.8542 (ttt180) cc_final: 0.7939 (ttp-170) REVERT: D 270 LEU cc_start: 0.8438 (mt) cc_final: 0.8229 (tp) REVERT: D 279 ARG cc_start: 0.8079 (mmm-85) cc_final: 0.7876 (mmm-85) REVERT: D 284 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8462 (p) REVERT: D 289 ASN cc_start: 0.7486 (m-40) cc_final: 0.7065 (m-40) REVERT: D 322 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7334 (mm-30) REVERT: D 340 ASN cc_start: 0.8431 (p0) cc_final: 0.7979 (p0) REVERT: D 366 HIS cc_start: 0.8696 (t70) cc_final: 0.8483 (t70) REVERT: D 376 MET cc_start: 0.8094 (mtp) cc_final: 0.7865 (mtp) REVERT: D 378 LYS cc_start: 0.8497 (mttt) cc_final: 0.8160 (mttt) REVERT: D 389 ASP cc_start: 0.8231 (m-30) cc_final: 0.7742 (m-30) REVERT: D 408 LEU cc_start: 0.7702 (tp) cc_final: 0.7496 (tp) REVERT: D 409 TYR cc_start: 0.6944 (m-80) cc_final: 0.6207 (m-80) REVERT: D 412 PHE cc_start: 0.7198 (m-80) cc_final: 0.5319 (m-80) REVERT: D 418 PHE cc_start: 0.8190 (t80) cc_final: 0.7661 (t80) REVERT: D 438 LYS cc_start: 0.8475 (mttt) cc_final: 0.8106 (mttt) REVERT: D 441 MET cc_start: 0.7316 (ptm) cc_final: 0.6945 (ptm) REVERT: E 20 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: E 35 GLU cc_start: 0.8595 (tt0) cc_final: 0.8183 (tt0) REVERT: E 39 PHE cc_start: 0.7862 (t80) cc_final: 0.7407 (t80) REVERT: E 57 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7854 (mtp) REVERT: E 66 ASP cc_start: 0.8066 (m-30) cc_final: 0.7819 (m-30) REVERT: E 71 MET cc_start: 0.8819 (mmt) cc_final: 0.8533 (mmm) REVERT: E 72 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7625 (mm-30) REVERT: E 73 ASP cc_start: 0.8230 (t0) cc_final: 0.7304 (t0) REVERT: E 74 GLN cc_start: 0.8776 (mm110) cc_final: 0.8476 (mp10) REVERT: E 75 ASP cc_start: 0.7436 (m-30) cc_final: 0.6379 (m-30) REVERT: E 80 ARG cc_start: 0.8552 (mtt180) cc_final: 0.8080 (mtt180) REVERT: E 86 LYS cc_start: 0.8569 (tttt) cc_final: 0.8357 (tttt) REVERT: E 94 GLU cc_start: 0.8066 (tp30) cc_final: 0.7438 (mp0) REVERT: E 101 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8090 (mm) REVERT: E 102 SER cc_start: 0.8547 (m) cc_final: 0.7357 (t) REVERT: E 125 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7330 (mtt180) REVERT: E 144 SER cc_start: 0.8946 (t) cc_final: 0.8478 (p) REVERT: E 166 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6753 (mt-10) REVERT: E 170 ILE cc_start: 0.8750 (mt) cc_final: 0.8252 (mm) REVERT: E 222 ILE cc_start: 0.8396 (mt) cc_final: 0.8168 (mm) REVERT: E 229 LYS cc_start: 0.8167 (tttt) cc_final: 0.7863 (tttt) REVERT: E 295 ARG cc_start: 0.7973 (mmt180) cc_final: 0.7522 (mmm160) REVERT: E 303 VAL cc_start: 0.9034 (p) cc_final: 0.8711 (m) REVERT: E 328 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7441 (tp) REVERT: E 332 GLN cc_start: 0.7037 (mp-120) cc_final: 0.6396 (mp10) REVERT: E 337 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7493 (pt0) REVERT: E 338 GLU cc_start: 0.7796 (mp0) cc_final: 0.7118 (mp0) REVERT: E 343 ARG cc_start: 0.7466 (mmt180) cc_final: 0.7240 (mmt180) REVERT: E 355 GLN cc_start: 0.8510 (mt0) cc_final: 0.7768 (mt0) REVERT: E 365 ASN cc_start: 0.7969 (m-40) cc_final: 0.7509 (m-40) REVERT: E 379 LEU cc_start: 0.9147 (tp) cc_final: 0.8924 (tp) REVERT: E 381 CYS cc_start: 0.8561 (t) cc_final: 0.7886 (t) REVERT: F 25 GLN cc_start: 0.8392 (tp40) cc_final: 0.7220 (tp40) REVERT: F 28 LYS cc_start: 0.9195 (mttt) cc_final: 0.8772 (mttt) REVERT: F 47 SER cc_start: 0.9063 (m) cc_final: 0.8758 (p) REVERT: F 56 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7527 (mmtt) REVERT: F 63 HIS cc_start: 0.8600 (t-90) cc_final: 0.8127 (t-90) REVERT: F 65 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8273 (mm-40) REVERT: F 68 ARG cc_start: 0.7918 (tpp80) cc_final: 0.7246 (tpp80) REVERT: F 101 TYR cc_start: 0.7624 (t80) cc_final: 0.7129 (t80) REVERT: F 105 THR cc_start: 0.8538 (m) cc_final: 0.8075 (m) REVERT: F 109 GLU cc_start: 0.8457 (mt-10) cc_final: 0.7844 (mt-10) REVERT: F 114 GLU cc_start: 0.8869 (tp30) cc_final: 0.8423 (tp30) REVERT: F 117 ASP cc_start: 0.8510 (t70) cc_final: 0.7849 (t70) REVERT: F 121 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8184 (mmpt) REVERT: F 139 LYS cc_start: 0.9272 (mttt) cc_final: 0.8707 (mtmt) REVERT: F 147 MET cc_start: 0.8363 (mmm) cc_final: 0.8027 (mmm) REVERT: F 156 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7137 (mt-10) REVERT: F 158 LYS cc_start: 0.8212 (mttt) cc_final: 0.7889 (mttt) REVERT: F 173 GLN cc_start: 0.8213 (mt0) cc_final: 0.7889 (mt0) REVERT: F 185 GLN cc_start: 0.8979 (tt0) cc_final: 0.8744 (tt0) REVERT: F 194 CYS cc_start: 0.8445 (t) cc_final: 0.8010 (t) REVERT: F 195 VAL cc_start: 0.8895 (m) cc_final: 0.8530 (p) REVERT: F 208 ASP cc_start: 0.8043 (t70) cc_final: 0.7574 (t0) REVERT: F 216 LYS cc_start: 0.8963 (tttt) cc_final: 0.8613 (tttt) REVERT: F 222 SER cc_start: 0.9260 (m) cc_final: 0.8963 (m) REVERT: F 225 GLN cc_start: 0.9039 (tp40) cc_final: 0.8688 (tp40) REVERT: F 228 LEU cc_start: 0.9207 (mt) cc_final: 0.8848 (mt) REVERT: F 229 TRP cc_start: 0.8531 (OUTLIER) cc_final: 0.6971 (t60) REVERT: F 237 GLN cc_start: 0.8309 (mt0) cc_final: 0.7538 (mt0) REVERT: F 251 TYR cc_start: 0.8793 (m-80) cc_final: 0.8237 (m-80) REVERT: F 252 ARG cc_start: 0.8665 (mtp180) cc_final: 0.8166 (mtm110) REVERT: F 281 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8813 (tp) REVERT: G 12 CYS cc_start: 0.9019 (p) cc_final: 0.8413 (p) REVERT: G 16 MET cc_start: 0.9024 (mmt) cc_final: 0.8563 (mmt) REVERT: G 43 VAL cc_start: 0.8761 (m) cc_final: 0.8386 (p) REVERT: G 44 PHE cc_start: 0.8693 (t80) cc_final: 0.8260 (t80) REVERT: H 818 LYS cc_start: 0.4096 (ptpt) cc_final: 0.3694 (mmtm) REVERT: H 862 LYS cc_start: 0.7093 (mmtt) cc_final: 0.6646 (mmtt) REVERT: H 895 GLU cc_start: 0.8192 (tp30) cc_final: 0.7587 (tp30) REVERT: H 900 LEU cc_start: 0.7682 (mp) cc_final: 0.7413 (mp) REVERT: H 909 GLU cc_start: 0.6662 (mp0) cc_final: 0.6101 (mp0) REVERT: H 912 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7378 (mt-10) REVERT: H 913 LYS cc_start: 0.7352 (mttt) cc_final: 0.7092 (mttt) REVERT: K 116 TYR cc_start: 0.8482 (t80) cc_final: 0.8187 (t80) REVERT: K 118 MET cc_start: 0.6964 (tpp) cc_final: 0.6384 (tpp) REVERT: K 120 HIS cc_start: 0.8677 (m-70) cc_final: 0.8246 (m-70) REVERT: K 121 PHE cc_start: 0.8480 (m-80) cc_final: 0.7520 (m-80) REVERT: K 141 LYS cc_start: 0.8977 (tttt) cc_final: 0.8599 (tttt) REVERT: K 143 GLU cc_start: 0.8522 (tt0) cc_final: 0.8049 (tt0) REVERT: K 148 TYR cc_start: 0.8623 (m-80) cc_final: 0.8390 (m-80) REVERT: K 159 GLU cc_start: 0.8006 (tp30) cc_final: 0.7798 (tp30) REVERT: K 163 LYS cc_start: 0.8375 (mttt) cc_final: 0.7987 (mttt) REVERT: K 166 VAL cc_start: 0.8921 (t) cc_final: 0.8612 (p) REVERT: K 168 LYS cc_start: 0.8575 (tptm) cc_final: 0.8298 (tptm) REVERT: K 178 MET cc_start: 0.7586 (ptp) cc_final: 0.6855 (ptp) REVERT: K 213 LYS cc_start: 0.8244 (tptt) cc_final: 0.7853 (tptt) REVERT: K 215 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8518 (ptpt) REVERT: K 217 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8343 (tmtt) REVERT: K 263 MET cc_start: 0.5439 (ptt) cc_final: 0.5198 (ppp) outliers start: 100 outliers final: 75 residues processed: 1002 average time/residue: 0.4435 time to fit residues: 658.7716 Evaluate side-chains 1016 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 925 time to evaluate : 2.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 483 LEU 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 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 GLU 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 705 ASN Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 379 GLN Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 187 LYS Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 242 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 284 optimal weight: 0.0770 chunk 300 optimal weight: 2.9990 chunk 273 optimal weight: 0.0000 chunk 291 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 276 optimal weight: 8.9990 chunk 290 optimal weight: 0.0870 overall best weight: 1.0324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN B 210 HIS ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 GLN E 50 HIS E 293 GLN ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN F 179 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28259 Z= 0.256 Angle : 0.714 14.228 38512 Z= 0.352 Chirality : 0.043 0.268 4285 Planarity : 0.004 0.085 4647 Dihedral : 15.687 175.162 4417 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 3.91 % Allowed : 24.32 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % 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 (0.15), residues: 3186 helix: 0.96 (0.14), residues: 1498 sheet: -0.34 (0.27), residues: 388 loop : -0.65 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 421 HIS 0.008 0.001 HIS C 524 PHE 0.036 0.002 PHE J 162 TYR 0.040 0.001 TYR C 533 ARG 0.009 0.001 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 947 time to evaluate : 3.035 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8685 (mttt) cc_final: 0.8242 (mttt) REVERT: A 65 MET cc_start: 0.7960 (ptt) cc_final: 0.7627 (ptt) REVERT: A 68 LYS cc_start: 0.7375 (mtmt) cc_final: 0.6876 (tptt) REVERT: A 94 LYS cc_start: 0.7934 (ptpt) cc_final: 0.7437 (ptpt) REVERT: A 115 GLU cc_start: 0.7544 (tt0) cc_final: 0.7275 (tt0) REVERT: A 135 ASP cc_start: 0.7945 (m-30) cc_final: 0.7479 (t0) REVERT: A 150 ASP cc_start: 0.7065 (t0) cc_final: 0.6623 (t0) REVERT: A 157 LYS cc_start: 0.8701 (mtmm) cc_final: 0.8394 (pttt) REVERT: A 195 ARG cc_start: 0.8512 (mtm-85) cc_final: 0.8183 (mtt90) REVERT: A 276 MET cc_start: 0.8435 (mmp) cc_final: 0.8216 (mmp) REVERT: A 282 LYS cc_start: 0.8929 (tttt) cc_final: 0.8443 (ttpp) REVERT: A 288 GLU cc_start: 0.8333 (mp0) cc_final: 0.8046 (pm20) REVERT: A 305 ASP cc_start: 0.8572 (p0) cc_final: 0.8254 (p0) REVERT: A 322 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8335 (mppt) REVERT: A 325 ARG cc_start: 0.7851 (ttm-80) cc_final: 0.7264 (mtt-85) REVERT: A 373 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8198 (mm-40) REVERT: A 379 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8254 (mmmt) REVERT: A 380 MET cc_start: 0.7794 (ttm) cc_final: 0.7519 (ttm) REVERT: A 381 TRP cc_start: 0.8368 (m-10) cc_final: 0.8147 (m-10) REVERT: A 385 ASP cc_start: 0.8452 (p0) cc_final: 0.8124 (p0) REVERT: A 392 PHE cc_start: 0.8079 (t80) cc_final: 0.7359 (t80) REVERT: A 412 MET cc_start: 0.6416 (ttt) cc_final: 0.6093 (ttt) REVERT: A 415 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.7627 (m-70) REVERT: A 424 GLU cc_start: 0.8588 (tp30) cc_final: 0.8374 (tm-30) REVERT: A 434 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7569 (mp0) REVERT: A 450 MET cc_start: 0.7485 (ptm) cc_final: 0.6832 (ptm) REVERT: A 453 ARG cc_start: 0.8210 (ptm160) cc_final: 0.7647 (ttp-110) REVERT: A 457 ILE cc_start: 0.8732 (tt) cc_final: 0.8457 (tt) REVERT: A 463 LYS cc_start: 0.8623 (mttt) cc_final: 0.8023 (mtmm) REVERT: A 478 VAL cc_start: 0.9060 (t) cc_final: 0.8851 (m) REVERT: A 487 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8083 (ttmt) REVERT: A 504 LYS cc_start: 0.8453 (ttpt) cc_final: 0.7848 (tttm) REVERT: A 510 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8311 (p) REVERT: A 520 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8175 (mmm160) REVERT: A 525 ILE cc_start: 0.8737 (tp) cc_final: 0.8277 (pt) REVERT: A 549 LYS cc_start: 0.8254 (mtmt) cc_final: 0.7348 (mtpp) REVERT: A 552 GLU cc_start: 0.7451 (pp20) cc_final: 0.7011 (pp20) REVERT: A 571 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.8047 (t80) REVERT: A 586 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7680 (tp-100) REVERT: A 619 GLU cc_start: 0.7323 (mp0) cc_final: 0.6967 (mp0) REVERT: A 636 GLU cc_start: 0.8004 (tp30) cc_final: 0.7568 (tp30) REVERT: A 656 ASN cc_start: 0.8433 (m110) cc_final: 0.8074 (m-40) REVERT: A 659 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8100 (p90) REVERT: A 674 THR cc_start: 0.8839 (m) cc_final: 0.8432 (t) REVERT: A 677 GLN cc_start: 0.7606 (mt0) cc_final: 0.7128 (mt0) REVERT: A 683 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7983 (mm-40) REVERT: B 1 MET cc_start: 0.6660 (ppp) cc_final: 0.6333 (ppp) REVERT: B 11 TYR cc_start: 0.7590 (p90) cc_final: 0.7245 (p90) REVERT: B 14 TYR cc_start: 0.8166 (m-80) cc_final: 0.7778 (m-80) REVERT: B 30 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8353 (ttm-80) REVERT: B 41 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6340 (tm-30) REVERT: B 42 MET cc_start: 0.7991 (mtp) cc_final: 0.7536 (mtp) REVERT: B 60 GLN cc_start: 0.8970 (mt0) cc_final: 0.8389 (mt0) REVERT: B 61 ARG cc_start: 0.8483 (mmp80) cc_final: 0.8164 (mmp80) REVERT: B 65 LEU cc_start: 0.7890 (tp) cc_final: 0.7484 (pt) REVERT: B 72 TYR cc_start: 0.7860 (t80) cc_final: 0.7474 (t80) REVERT: B 84 ILE cc_start: 0.9139 (mm) cc_final: 0.8764 (tp) REVERT: B 85 GLU cc_start: 0.8546 (pp20) cc_final: 0.7913 (tp30) REVERT: B 86 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 133 LYS cc_start: 0.8563 (mttt) cc_final: 0.8276 (mmmt) REVERT: B 196 ARG cc_start: 0.8280 (ptp-170) cc_final: 0.7431 (ptp-170) REVERT: B 207 TYR cc_start: 0.8199 (p90) cc_final: 0.7428 (p90) REVERT: B 228 LYS cc_start: 0.8192 (ptmt) cc_final: 0.7722 (ptmt) REVERT: B 235 GLU cc_start: 0.8375 (tp30) cc_final: 0.8027 (mp0) REVERT: B 243 CYS cc_start: 0.8328 (m) cc_final: 0.8065 (m) REVERT: B 247 MET cc_start: 0.8526 (mpp) cc_final: 0.8162 (mpp) REVERT: B 258 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7717 (ttt180) REVERT: B 339 TYR cc_start: 0.8271 (t80) cc_final: 0.7640 (t80) REVERT: B 434 HIS cc_start: 0.6178 (OUTLIER) cc_final: 0.5593 (p90) REVERT: B 438 MET cc_start: 0.7778 (mtm) cc_final: 0.6899 (mtm) REVERT: B 450 ARG cc_start: 0.7709 (mtp180) cc_final: 0.7290 (ttm-80) REVERT: B 469 LYS cc_start: 0.9073 (ptpp) cc_final: 0.8856 (ptpp) REVERT: B 472 ASP cc_start: 0.7817 (m-30) cc_final: 0.7223 (m-30) REVERT: B 493 MET cc_start: 0.8182 (ptt) cc_final: 0.7797 (ptp) REVERT: B 494 ILE cc_start: 0.9028 (mt) cc_final: 0.8742 (mp) REVERT: B 508 PHE cc_start: 0.8392 (t80) cc_final: 0.6691 (t80) REVERT: B 511 ARG cc_start: 0.7924 (mtm180) cc_final: 0.7586 (mtt-85) REVERT: B 545 MET cc_start: 0.8627 (ttm) cc_final: 0.8357 (tpp) REVERT: B 570 GLU cc_start: 0.6681 (tm-30) cc_final: 0.6125 (tm-30) REVERT: B 634 LYS cc_start: 0.8061 (ptpp) cc_final: 0.7574 (mtmm) REVERT: B 642 ASP cc_start: 0.7376 (p0) cc_final: 0.7131 (p0) REVERT: B 662 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8328 (tm-30) REVERT: B 663 CYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7750 (p) REVERT: B 672 THR cc_start: 0.9077 (p) cc_final: 0.8743 (t) REVERT: B 690 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7169 (mtm-85) REVERT: C 442 GLN cc_start: 0.6808 (OUTLIER) cc_final: 0.6526 (pm20) REVERT: C 471 LEU cc_start: 0.9305 (mt) cc_final: 0.9091 (tt) REVERT: C 473 ARG cc_start: 0.8793 (tmt170) cc_final: 0.8220 (tmt170) REVERT: C 475 PHE cc_start: 0.8815 (t80) cc_final: 0.8437 (t80) REVERT: C 493 MET cc_start: 0.8333 (tpp) cc_final: 0.7511 (tpp) REVERT: C 528 MET cc_start: 0.8991 (mtm) cc_final: 0.8694 (mtm) REVERT: C 539 TRP cc_start: 0.8429 (t60) cc_final: 0.7978 (t60) REVERT: D 47 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7998 (mm-30) REVERT: D 50 SER cc_start: 0.7949 (m) cc_final: 0.7272 (p) REVERT: D 55 TRP cc_start: 0.7468 (m-10) cc_final: 0.7235 (m-90) REVERT: D 79 PHE cc_start: 0.8376 (m-80) cc_final: 0.8103 (m-10) REVERT: D 86 SER cc_start: 0.9015 (m) cc_final: 0.8743 (p) REVERT: D 150 LYS cc_start: 0.8748 (tttt) cc_final: 0.8093 (tttt) REVERT: D 154 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8094 (mt-10) REVERT: D 185 MET cc_start: 0.8031 (mpp) cc_final: 0.7660 (mpp) REVERT: D 186 LYS cc_start: 0.8610 (pttt) cc_final: 0.8264 (pttt) REVERT: D 213 TRP cc_start: 0.8012 (OUTLIER) cc_final: 0.7669 (t-100) REVERT: D 217 LEU cc_start: 0.8581 (mm) cc_final: 0.8307 (mt) REVERT: D 237 LEU cc_start: 0.9222 (tp) cc_final: 0.8978 (tt) REVERT: D 239 GLN cc_start: 0.8968 (tt0) cc_final: 0.8192 (tm-30) REVERT: D 247 LYS cc_start: 0.8431 (tttt) cc_final: 0.8040 (tttt) REVERT: D 254 MET cc_start: 0.5774 (mtt) cc_final: 0.4997 (mtt) REVERT: D 258 LEU cc_start: 0.9012 (mt) cc_final: 0.8784 (tt) REVERT: D 260 ASN cc_start: 0.9077 (m110) cc_final: 0.8807 (p0) REVERT: D 261 PHE cc_start: 0.8917 (t80) cc_final: 0.8612 (t80) REVERT: D 266 ARG cc_start: 0.8600 (ttt180) cc_final: 0.7918 (ttt180) REVERT: D 270 LEU cc_start: 0.8446 (mt) cc_final: 0.8235 (tp) REVERT: D 279 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.7855 (mmm-85) REVERT: D 285 ARG cc_start: 0.6981 (ttt180) cc_final: 0.6600 (ttt180) REVERT: D 289 ASN cc_start: 0.7565 (m-40) cc_final: 0.7183 (m-40) REVERT: D 322 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7391 (mm-30) REVERT: D 341 MET cc_start: 0.7584 (tpp) cc_final: 0.7290 (tpp) REVERT: D 363 GLN cc_start: 0.8384 (mt0) cc_final: 0.8019 (mt0) REVERT: D 369 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7359 (tpp80) REVERT: D 376 MET cc_start: 0.8266 (mtp) cc_final: 0.8048 (mtp) REVERT: D 378 LYS cc_start: 0.8647 (mttt) cc_final: 0.8291 (mttt) REVERT: D 389 ASP cc_start: 0.8284 (m-30) cc_final: 0.7813 (m-30) REVERT: D 408 LEU cc_start: 0.7742 (tp) cc_final: 0.7536 (tp) REVERT: D 409 TYR cc_start: 0.6994 (m-80) cc_final: 0.6269 (m-80) REVERT: D 412 PHE cc_start: 0.7308 (m-80) cc_final: 0.5416 (m-80) REVERT: D 418 PHE cc_start: 0.8246 (t80) cc_final: 0.7736 (t80) REVERT: D 438 LYS cc_start: 0.8540 (mttt) cc_final: 0.8164 (mttt) REVERT: D 441 MET cc_start: 0.7387 (ptm) cc_final: 0.6960 (ptm) REVERT: E 35 GLU cc_start: 0.8567 (tt0) cc_final: 0.8165 (tt0) REVERT: E 39 PHE cc_start: 0.7922 (t80) cc_final: 0.7324 (t80) REVERT: E 57 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7954 (mtp) REVERT: E 66 ASP cc_start: 0.8094 (m-30) cc_final: 0.7769 (m-30) REVERT: E 72 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7772 (mm-30) REVERT: E 73 ASP cc_start: 0.8207 (t0) cc_final: 0.7028 (t0) REVERT: E 75 ASP cc_start: 0.7454 (m-30) cc_final: 0.6415 (m-30) REVERT: E 80 ARG cc_start: 0.8586 (mtt180) cc_final: 0.8093 (mtt180) REVERT: E 86 LYS cc_start: 0.8557 (tttt) cc_final: 0.8331 (tttt) REVERT: E 94 GLU cc_start: 0.8018 (tp30) cc_final: 0.7410 (mp0) REVERT: E 101 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8159 (mm) REVERT: E 102 SER cc_start: 0.8548 (m) cc_final: 0.8122 (p) REVERT: E 125 ARG cc_start: 0.7638 (mtt180) cc_final: 0.7344 (mtt180) REVERT: E 166 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6777 (mt-10) REVERT: E 170 ILE cc_start: 0.8741 (mt) cc_final: 0.8227 (mm) REVERT: E 222 ILE cc_start: 0.8414 (mt) cc_final: 0.8183 (mm) REVERT: E 229 LYS cc_start: 0.8180 (tttt) cc_final: 0.7872 (tttt) REVERT: E 273 MET cc_start: 0.7345 (tpp) cc_final: 0.6858 (ttm) REVERT: E 295 ARG cc_start: 0.7900 (mmt180) cc_final: 0.7432 (mmm-85) REVERT: E 303 VAL cc_start: 0.9079 (p) cc_final: 0.8751 (m) REVERT: E 328 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7573 (tp) REVERT: E 331 PHE cc_start: 0.8347 (m-10) cc_final: 0.8105 (m-80) REVERT: E 332 GLN cc_start: 0.7156 (mp-120) cc_final: 0.6461 (mp10) REVERT: E 337 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7509 (pt0) REVERT: E 338 GLU cc_start: 0.7789 (mp0) cc_final: 0.7082 (mp0) REVERT: E 355 GLN cc_start: 0.8540 (mt0) cc_final: 0.7778 (mt0) REVERT: E 357 VAL cc_start: 0.7971 (t) cc_final: 0.7571 (m) REVERT: E 365 ASN cc_start: 0.7977 (m-40) cc_final: 0.7529 (m-40) REVERT: E 379 LEU cc_start: 0.9113 (tp) cc_final: 0.8905 (tp) REVERT: E 381 CYS cc_start: 0.8482 (t) cc_final: 0.7882 (t) REVERT: F 25 GLN cc_start: 0.8522 (tp40) cc_final: 0.7336 (tp40) REVERT: F 28 LYS cc_start: 0.9230 (mttt) cc_final: 0.8818 (mttt) REVERT: F 47 SER cc_start: 0.9111 (m) cc_final: 0.8833 (p) REVERT: F 56 LYS cc_start: 0.8010 (mmtt) cc_final: 0.7559 (mmtt) REVERT: F 63 HIS cc_start: 0.8620 (t-90) cc_final: 0.8200 (t-90) REVERT: F 65 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8306 (mm-40) REVERT: F 68 ARG cc_start: 0.8025 (tpp80) cc_final: 0.7140 (tpp80) REVERT: F 101 TYR cc_start: 0.7505 (t80) cc_final: 0.7186 (t80) REVERT: F 105 THR cc_start: 0.8574 (m) cc_final: 0.8104 (m) REVERT: F 109 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7852 (mt-10) REVERT: F 114 GLU cc_start: 0.8802 (tp30) cc_final: 0.7840 (tp30) REVERT: F 117 ASP cc_start: 0.8485 (t70) cc_final: 0.7776 (t70) REVERT: F 121 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8223 (mmpt) REVERT: F 139 LYS cc_start: 0.9342 (mttt) cc_final: 0.8779 (mtmt) REVERT: F 147 MET cc_start: 0.8349 (mmm) cc_final: 0.8030 (mmm) REVERT: F 156 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7168 (mt-10) REVERT: F 158 LYS cc_start: 0.8177 (mttt) cc_final: 0.7866 (mttt) REVERT: F 173 GLN cc_start: 0.8275 (mt0) cc_final: 0.7951 (mt0) REVERT: F 185 GLN cc_start: 0.8995 (tt0) cc_final: 0.8679 (tt0) REVERT: F 194 CYS cc_start: 0.8434 (t) cc_final: 0.7988 (t) REVERT: F 195 VAL cc_start: 0.8942 (m) cc_final: 0.8585 (p) REVERT: F 208 ASP cc_start: 0.8075 (t70) cc_final: 0.7621 (t0) REVERT: F 216 LYS cc_start: 0.8995 (tttt) cc_final: 0.8642 (tttt) REVERT: F 222 SER cc_start: 0.9238 (m) cc_final: 0.8961 (m) REVERT: F 225 GLN cc_start: 0.9063 (tp40) cc_final: 0.8757 (tp40) REVERT: F 228 LEU cc_start: 0.9224 (mt) cc_final: 0.8936 (mt) REVERT: F 229 TRP cc_start: 0.8589 (OUTLIER) cc_final: 0.7073 (t60) REVERT: F 237 GLN cc_start: 0.8274 (mt0) cc_final: 0.7559 (mt0) REVERT: F 251 TYR cc_start: 0.8870 (m-80) cc_final: 0.8351 (m-80) REVERT: F 281 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8814 (tp) REVERT: G 12 CYS cc_start: 0.9116 (p) cc_final: 0.8450 (p) REVERT: G 43 VAL cc_start: 0.8649 (m) cc_final: 0.8262 (p) REVERT: G 44 PHE cc_start: 0.8713 (t80) cc_final: 0.8337 (t80) REVERT: G 55 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8239 (tm-30) REVERT: H 895 GLU cc_start: 0.8166 (tp30) cc_final: 0.7596 (tp30) REVERT: H 900 LEU cc_start: 0.7747 (mp) cc_final: 0.7485 (mp) REVERT: H 909 GLU cc_start: 0.6727 (mp0) cc_final: 0.6195 (mp0) REVERT: H 912 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7391 (mt-10) REVERT: H 913 LYS cc_start: 0.7412 (mttt) cc_final: 0.7130 (mttt) REVERT: K 116 TYR cc_start: 0.8446 (t80) cc_final: 0.8172 (t80) REVERT: K 118 MET cc_start: 0.7101 (tpp) cc_final: 0.6533 (tpp) REVERT: K 120 HIS cc_start: 0.8704 (m-70) cc_final: 0.8203 (m-70) REVERT: K 121 PHE cc_start: 0.8472 (m-80) cc_final: 0.7475 (m-80) REVERT: K 141 LYS cc_start: 0.8971 (tttt) cc_final: 0.8592 (tttt) REVERT: K 143 GLU cc_start: 0.8512 (tt0) cc_final: 0.8060 (tt0) REVERT: K 163 LYS cc_start: 0.8405 (mttt) cc_final: 0.7999 (mttt) REVERT: K 166 VAL cc_start: 0.8930 (t) cc_final: 0.8632 (p) REVERT: K 168 LYS cc_start: 0.8564 (tptm) cc_final: 0.8283 (tptm) REVERT: K 178 MET cc_start: 0.7605 (ptp) cc_final: 0.6877 (ptp) REVERT: K 180 LEU cc_start: 0.8878 (mt) cc_final: 0.8646 (mm) REVERT: K 192 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8345 (mm-30) REVERT: K 213 LYS cc_start: 0.8242 (tptt) cc_final: 0.7902 (tptt) REVERT: K 215 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8524 (ptpt) REVERT: K 217 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8428 (tmtt) REVERT: K 263 MET cc_start: 0.5689 (ptt) cc_final: 0.5410 (ppp) outliers start: 111 outliers final: 87 residues processed: 1001 average time/residue: 0.4489 time to fit residues: 667.1358 Evaluate side-chains 1040 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 939 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 415 HIS 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 602 ILE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 GLU 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 705 ASN Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 244 THR Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 178 ASP Chi-restraints excluded: chain E residue 256 GLN Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 128 HIS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 142 CYS Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 31 LYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain K residue 115 SER Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 204 LYS Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 227 ARG Chi-restraints excluded: chain K residue 242 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 191 optimal weight: 1.9990 chunk 308 optimal weight: 0.5980 chunk 188 optimal weight: 0.8980 chunk 146 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 323 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 chunk 257 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 GLN A 709 GLN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 GLN ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN F 179 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28259 Z= 0.221 Angle : 0.731 13.696 38512 Z= 0.358 Chirality : 0.043 0.195 4285 Planarity : 0.004 0.080 4647 Dihedral : 15.662 174.367 4417 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.18 % Favored : 94.78 % Rotamer: Outliers : 3.45 % Allowed : 25.55 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.09 (0.15), residues: 3186 helix: 0.91 (0.14), residues: 1495 sheet: -0.34 (0.27), residues: 382 loop : -0.74 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 421 HIS 0.008 0.001 HIS C 524 PHE 0.035 0.001 PHE J 162 TYR 0.058 0.001 TYR K 148 ARG 0.007 0.001 ARG H 860 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6372 Ramachandran restraints generated. 3186 Oldfield, 0 Emsley, 3186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 955 time to evaluate : 2.981 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8696 (mttt) cc_final: 0.8214 (mttt) REVERT: A 65 MET cc_start: 0.8018 (ptt) cc_final: 0.7643 (ptt) REVERT: A 68 LYS cc_start: 0.7371 (mtmt) cc_final: 0.6871 (tptt) REVERT: A 94 LYS cc_start: 0.7910 (ptpt) cc_final: 0.7416 (ptpt) REVERT: A 115 GLU cc_start: 0.7513 (tt0) cc_final: 0.7313 (tt0) REVERT: A 135 ASP cc_start: 0.7941 (m-30) cc_final: 0.7511 (t0) REVERT: A 150 ASP cc_start: 0.7052 (t0) cc_final: 0.6606 (t0) REVERT: A 157 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8372 (pttt) REVERT: A 195 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8186 (mtt90) REVERT: A 276 MET cc_start: 0.8429 (mmp) cc_final: 0.8168 (mmp) REVERT: A 279 GLU cc_start: 0.8803 (tp30) cc_final: 0.8476 (tp30) REVERT: A 282 LYS cc_start: 0.8917 (tttt) cc_final: 0.8441 (ttpp) REVERT: A 294 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7028 (mm-30) REVERT: A 305 ASP cc_start: 0.8557 (p0) cc_final: 0.8248 (p0) REVERT: A 322 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8327 (mppt) REVERT: A 325 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7223 (mtt-85) REVERT: A 351 VAL cc_start: 0.9146 (t) cc_final: 0.8880 (p) REVERT: A 373 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8204 (mm-40) REVERT: A 379 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8245 (mmmt) REVERT: A 380 MET cc_start: 0.7796 (ttm) cc_final: 0.7509 (ttm) REVERT: A 381 TRP cc_start: 0.8338 (m-10) cc_final: 0.8056 (m-10) REVERT: A 385 ASP cc_start: 0.8449 (p0) cc_final: 0.8137 (p0) REVERT: A 392 PHE cc_start: 0.8028 (t80) cc_final: 0.7280 (t80) REVERT: A 412 MET cc_start: 0.6045 (ttt) cc_final: 0.5845 (ttt) REVERT: A 415 HIS cc_start: 0.7954 (OUTLIER) cc_final: 0.7551 (m-70) REVERT: A 434 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7562 (mp0) REVERT: A 450 MET cc_start: 0.7593 (ptm) cc_final: 0.6932 (ptm) REVERT: A 453 ARG cc_start: 0.8201 (ptm160) cc_final: 0.7635 (ttp-110) REVERT: A 457 ILE cc_start: 0.8727 (tt) cc_final: 0.8425 (tt) REVERT: A 463 LYS cc_start: 0.8628 (mttt) cc_final: 0.8028 (mtmm) REVERT: A 478 VAL cc_start: 0.9069 (t) cc_final: 0.8847 (m) REVERT: A 487 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8047 (ttmt) REVERT: A 494 MET cc_start: 0.8746 (mmm) cc_final: 0.8482 (mmm) REVERT: A 497 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8279 (tt0) REVERT: A 504 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7808 (tttt) REVERT: A 510 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8333 (p) REVERT: A 520 ARG cc_start: 0.8477 (mmm160) cc_final: 0.8191 (mmm160) REVERT: A 525 ILE cc_start: 0.8699 (tp) cc_final: 0.8216 (pt) REVERT: A 541 PHE cc_start: 0.8996 (t80) cc_final: 0.8698 (t80) REVERT: A 549 LYS cc_start: 0.8240 (mtmt) cc_final: 0.7299 (mtpp) REVERT: A 552 GLU cc_start: 0.7457 (pp20) cc_final: 0.7026 (pp20) REVERT: A 553 ARG cc_start: 0.7932 (mtm-85) cc_final: 0.7624 (mtm-85) REVERT: A 571 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.8045 (t80) REVERT: A 586 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7635 (tp-100) REVERT: A 619 GLU cc_start: 0.7313 (mp0) cc_final: 0.6948 (mp0) REVERT: A 636 GLU cc_start: 0.7978 (tp30) cc_final: 0.7541 (tp30) REVERT: A 656 ASN cc_start: 0.8431 (m110) cc_final: 0.8059 (m-40) REVERT: A 659 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8133 (p90) REVERT: A 674 THR cc_start: 0.8820 (m) cc_final: 0.8426 (t) REVERT: A 677 GLN cc_start: 0.7579 (mt0) cc_final: 0.7115 (mt0) REVERT: A 683 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7771 (mm-40) REVERT: B 1 MET cc_start: 0.6651 (ppp) cc_final: 0.6342 (ppp) REVERT: B 11 TYR cc_start: 0.7612 (p90) cc_final: 0.7267 (p90) REVERT: B 14 TYR cc_start: 0.8184 (m-80) cc_final: 0.7814 (m-80) REVERT: B 30 ARG cc_start: 0.8606 (ttm-80) cc_final: 0.8361 (ttm-80) REVERT: B 41 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6287 (tm-30) REVERT: B 42 MET cc_start: 0.7990 (mtp) cc_final: 0.7501 (mtp) REVERT: B 48 LYS cc_start: 0.8411 (ttmt) cc_final: 0.7968 (ttmm) REVERT: B 60 GLN cc_start: 0.8972 (mt0) cc_final: 0.8633 (mt0) REVERT: B 65 LEU cc_start: 0.7870 (tp) cc_final: 0.7415 (pt) REVERT: B 72 TYR cc_start: 0.7861 (t80) cc_final: 0.7498 (t80) REVERT: B 84 ILE cc_start: 0.9149 (mm) cc_final: 0.8899 (tp) REVERT: B 85 GLU cc_start: 0.8563 (pp20) cc_final: 0.7956 (tp30) REVERT: B 86 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 133 LYS cc_start: 0.8556 (mttt) cc_final: 0.8269 (mmmt) REVERT: B 196 ARG cc_start: 0.8217 (ptp-170) cc_final: 0.7327 (ptp-170) REVERT: B 207 TYR cc_start: 0.8196 (p90) cc_final: 0.7421 (p90) REVERT: B 228 LYS cc_start: 0.8185 (ptmt) cc_final: 0.7725 (ptmt) REVERT: B 235 GLU cc_start: 0.8338 (tp30) cc_final: 0.7999 (mp0) REVERT: B 243 CYS cc_start: 0.8307 (m) cc_final: 0.8045 (m) REVERT: B 247 MET cc_start: 0.8530 (mpp) cc_final: 0.8160 (mpp) REVERT: B 258 ARG cc_start: 0.8004 (ttt180) cc_final: 0.7709 (ttt180) REVERT: B 268 LYS cc_start: 0.8419 (tptp) cc_final: 0.8193 (tptp) REVERT: B 339 TYR cc_start: 0.8166 (t80) cc_final: 0.6868 (t80) REVERT: B 341 LYS cc_start: 0.9256 (mtmm) cc_final: 0.9044 (mttt) REVERT: B 434 HIS cc_start: 0.6101 (OUTLIER) cc_final: 0.5592 (p90) REVERT: B 435 PHE cc_start: 0.8249 (t80) cc_final: 0.7859 (t80) REVERT: B 438 MET cc_start: 0.7767 (mtm) cc_final: 0.6858 (mtm) REVERT: B 445 LYS cc_start: 0.9296 (mmtt) cc_final: 0.8705 (mmmm) REVERT: B 450 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7215 (ttm-80) REVERT: B 469 LYS cc_start: 0.9067 (ptpp) cc_final: 0.8721 (ptpp) REVERT: B 472 ASP cc_start: 0.7811 (m-30) cc_final: 0.7324 (m-30) REVERT: B 493 MET cc_start: 0.8192 (ptt) cc_final: 0.7819 (ptp) REVERT: B 494 ILE cc_start: 0.9037 (mt) cc_final: 0.8738 (mp) REVERT: B 508 PHE cc_start: 0.8388 (t80) cc_final: 0.6647 (t80) REVERT: B 511 ARG cc_start: 0.7893 (mtm180) cc_final: 0.7601 (mtt-85) REVERT: B 545 MET cc_start: 0.8569 (ttm) cc_final: 0.8285 (tpp) REVERT: B 570 GLU cc_start: 0.6691 (tm-30) cc_final: 0.6138 (tm-30) REVERT: B 603 LYS cc_start: 0.8634 (ptmm) cc_final: 0.8418 (tmtt) REVERT: B 642 ASP cc_start: 0.7365 (p0) cc_final: 0.7122 (p0) REVERT: B 647 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.8138 (mmm-85) REVERT: B 662 GLN cc_start: 0.8520 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 663 CYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7731 (p) REVERT: B 672 THR cc_start: 0.9073 (p) cc_final: 0.8736 (t) REVERT: B 690 ARG cc_start: 0.7949 (mtm110) cc_final: 0.7166 (mtm-85) REVERT: C 402 ASN cc_start: 0.8254 (m110) cc_final: 0.7957 (p0) REVERT: C 442 GLN cc_start: 0.6693 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: C 471 LEU cc_start: 0.9314 (mt) cc_final: 0.9111 (tt) REVERT: C 473 ARG cc_start: 0.8773 (tmt170) cc_final: 0.8193 (tmt170) REVERT: C 475 PHE cc_start: 0.8795 (t80) cc_final: 0.8443 (t80) REVERT: C 493 MET cc_start: 0.8324 (tpp) cc_final: 0.7568 (tpp) REVERT: C 528 MET cc_start: 0.8965 (mtm) cc_final: 0.8659 (mtm) REVERT: C 539 TRP cc_start: 0.8442 (t60) cc_final: 0.7961 (t60) REVERT: D 47 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7998 (mm-30) REVERT: D 50 SER cc_start: 0.7861 (m) cc_final: 0.7208 (p) REVERT: D 55 TRP cc_start: 0.7479 (m-10) cc_final: 0.7270 (m-90) REVERT: D 79 PHE cc_start: 0.8384 (m-80) cc_final: 0.8107 (m-10) REVERT: D 86 SER cc_start: 0.9005 (m) cc_final: 0.8741 (p) REVERT: D 150 LYS cc_start: 0.8752 (tttt) cc_final: 0.8087 (tttt) REVERT: D 151 TYR cc_start: 0.8361 (t80) cc_final: 0.8079 (t80) REVERT: D 154 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8093 (mt-10) REVERT: D 155 ARG cc_start: 0.8805 (mmm-85) cc_final: 0.8310 (mmm-85) REVERT: D 185 MET cc_start: 0.8134 (mpp) cc_final: 0.7789 (mpp) REVERT: D 186 LYS cc_start: 0.8579 (pttt) cc_final: 0.8218 (pttt) REVERT: D 202 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8134 (mm-40) REVERT: D 213 TRP cc_start: 0.8011 (OUTLIER) cc_final: 0.7682 (t-100) REVERT: D 214 TYR cc_start: 0.8262 (t80) cc_final: 0.7982 (t80) REVERT: D 217 LEU cc_start: 0.8587 (mm) cc_final: 0.8306 (mt) REVERT: D 237 LEU cc_start: 0.9214 (tp) cc_final: 0.8988 (tt) REVERT: D 239 GLN cc_start: 0.8935 (tt0) cc_final: 0.8167 (tm-30) REVERT: D 242 PHE cc_start: 0.8483 (m-10) cc_final: 0.7774 (m-10) REVERT: D 247 LYS cc_start: 0.8576 (tttt) cc_final: 0.8070 (tttt) REVERT: D 249 TYR cc_start: 0.8190 (m-80) cc_final: 0.7265 (m-80) REVERT: D 254 MET cc_start: 0.5921 (mtt) cc_final: 0.5486 (mtm) REVERT: D 260 ASN cc_start: 0.9075 (m110) cc_final: 0.8801 (p0) REVERT: D 266 ARG cc_start: 0.8561 (ttt180) cc_final: 0.7873 (ttt180) REVERT: D 275 LYS cc_start: 0.8675 (mtmm) cc_final: 0.7808 (mtmt) REVERT: D 279 ARG cc_start: 0.8106 (mmm-85) cc_final: 0.7853 (mmm-85) REVERT: D 284 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.8511 (p) REVERT: D 285 ARG cc_start: 0.7098 (ttt180) cc_final: 0.6788 (ttt180) REVERT: D 289 ASN cc_start: 0.7543 (m-40) cc_final: 0.7198 (m-40) REVERT: D 316 TYR cc_start: 0.8754 (m-80) cc_final: 0.7895 (m-10) REVERT: D 322 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7363 (mm-30) REVERT: D 333 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6382 (mt-10) REVERT: D 336 TYR cc_start: 0.8711 (m-80) cc_final: 0.8488 (m-80) REVERT: D 341 MET cc_start: 0.7567 (tpp) cc_final: 0.7232 (tpp) REVERT: D 378 LYS cc_start: 0.8603 (mttt) cc_final: 0.8252 (mttt) REVERT: D 389 ASP cc_start: 0.8313 (m-30) cc_final: 0.7793 (m-30) REVERT: D 390 GLN cc_start: 0.8361 (tp-100) cc_final: 0.7770 (mm-40) REVERT: D 409 TYR cc_start: 0.6925 (m-80) cc_final: 0.6197 (m-80) REVERT: D 412 PHE cc_start: 0.7463 (m-80) cc_final: 0.5461 (m-80) REVERT: D 418 PHE cc_start: 0.8227 (t80) cc_final: 0.7723 (t80) REVERT: D 438 LYS cc_start: 0.8525 (mttt) cc_final: 0.8150 (mttt) REVERT: D 441 MET cc_start: 0.7384 (ptm) cc_final: 0.6906 (ptm) REVERT: E 35 GLU cc_start: 0.8627 (tt0) cc_final: 0.8222 (tt0) REVERT: E 39 PHE cc_start: 0.7914 (t80) cc_final: 0.7427 (t80) REVERT: E 57 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7878 (mtp) REVERT: E 66 ASP cc_start: 0.8077 (m-30) cc_final: 0.7728 (m-30) REVERT: E 71 MET cc_start: 0.8779 (mmt) cc_final: 0.8508 (mmm) REVERT: E 72 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7674 (mm-30) REVERT: E 73 ASP cc_start: 0.8194 (t0) cc_final: 0.7671 (t0) REVERT: E 74 GLN cc_start: 0.8789 (mm-40) cc_final: 0.8511 (mp10) REVERT: E 80 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8161 (mtt180) REVERT: E 94 GLU cc_start: 0.8013 (tp30) cc_final: 0.7401 (mp0) REVERT: E 101 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.8116 (mm) REVERT: E 102 SER cc_start: 0.8510 (m) cc_final: 0.8096 (p) REVERT: E 110 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7854 (mtpp) REVERT: E 125 ARG cc_start: 0.7612 (mtt180) cc_final: 0.7315 (mtt180) REVERT: E 144 SER cc_start: 0.8937 (t) cc_final: 0.8498 (p) REVERT: E 153 MET cc_start: 0.7995 (tpp) cc_final: 0.7462 (mtt) REVERT: E 166 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6767 (mt-10) REVERT: E 170 ILE cc_start: 0.8765 (mt) cc_final: 0.8159 (mm) REVERT: E 213 ARG cc_start: 0.7999 (ttp80) cc_final: 0.7540 (ttp80) REVERT: E 222 ILE cc_start: 0.8393 (mt) cc_final: 0.8161 (mm) REVERT: E 229 LYS cc_start: 0.8178 (tttt) cc_final: 0.7867 (tttt) REVERT: E 273 MET cc_start: 0.7306 (tpp) cc_final: 0.6828 (ttm) REVERT: E 295 ARG cc_start: 0.7887 (mmt180) cc_final: 0.7418 (mmm-85) REVERT: E 303 VAL cc_start: 0.9103 (p) cc_final: 0.8764 (m) REVERT: E 328 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7575 (tp) REVERT: E 329 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7155 (p0) REVERT: E 338 GLU cc_start: 0.7788 (mp0) cc_final: 0.7571 (mp0) REVERT: E 355 GLN cc_start: 0.8536 (mt0) cc_final: 0.7796 (mt0) REVERT: E 357 VAL cc_start: 0.7943 (t) cc_final: 0.7544 (m) REVERT: E 365 ASN cc_start: 0.8020 (m-40) cc_final: 0.7560 (m-40) REVERT: E 370 ASP cc_start: 0.8163 (m-30) cc_final: 0.7730 (p0) REVERT: E 381 CYS cc_start: 0.8461 (t) cc_final: 0.7911 (t) REVERT: F 25 GLN cc_start: 0.8532 (tp40) cc_final: 0.7294 (tp40) REVERT: F 28 LYS cc_start: 0.9232 (mttt) cc_final: 0.8834 (mttt) REVERT: F 47 SER cc_start: 0.9084 (m) cc_final: 0.8800 (p) REVERT: F 56 LYS cc_start: 0.8000 (mmtt) cc_final: 0.7540 (mmtt) REVERT: F 63 HIS cc_start: 0.8600 (t-90) cc_final: 0.8169 (t-90) REVERT: F 65 GLN cc_start: 0.8587 (mm-40) cc_final: 0.8276 (mm-40) REVERT: F 68 ARG cc_start: 0.8059 (tpp80) cc_final: 0.7284 (tpp80) REVERT: F 101 TYR cc_start: 0.7554 (t80) cc_final: 0.6781 (t80) REVERT: F 105 THR cc_start: 0.8552 (m) cc_final: 0.8119 (m) REVERT: F 109 GLU cc_start: 0.8485 (mt-10) cc_final: 0.7826 (mt-10) REVERT: F 114 GLU cc_start: 0.8786 (tp30) cc_final: 0.7861 (tp30) REVERT: F 117 ASP cc_start: 0.8558 (t70) cc_final: 0.7945 (t70) REVERT: F 121 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8204 (mmpt) REVERT: F 139 LYS cc_start: 0.9332 (mttt) cc_final: 0.8844 (mtmt) REVERT: F 147 MET cc_start: 0.8372 (mmm) cc_final: 0.7998 (mmm) REVERT: F 156 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7196 (mt-10) REVERT: F 158 LYS cc_start: 0.8161 (mttt) cc_final: 0.7853 (mttt) REVERT: F 173 GLN cc_start: 0.8225 (mt0) cc_final: 0.7938 (mt0) REVERT: F 185 GLN cc_start: 0.8981 (tt0) cc_final: 0.8753 (tt0) REVERT: F 194 CYS cc_start: 0.8455 (t) cc_final: 0.7983 (t) REVERT: F 195 VAL cc_start: 0.8944 (m) cc_final: 0.8574 (p) REVERT: F 208 ASP cc_start: 0.8064 (t70) cc_final: 0.7595 (t0) REVERT: F 216 LYS cc_start: 0.8975 (tttt) cc_final: 0.8548 (ttmt) REVERT: F 222 SER cc_start: 0.9243 (m) cc_final: 0.8950 (m) REVERT: F 225 GLN cc_start: 0.9055 (tp40) cc_final: 0.8742 (tp40) REVERT: F 228 LEU cc_start: 0.9221 (mt) cc_final: 0.8877 (mt) REVERT: F 229 TRP cc_start: 0.8611 (OUTLIER) cc_final: 0.7109 (t60) REVERT: F 237 GLN cc_start: 0.8259 (mt0) cc_final: 0.7542 (mt0) REVERT: F 251 TYR cc_start: 0.8845 (m-80) cc_final: 0.8334 (m-80) REVERT: F 281 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8807 (tp) REVERT: G 6 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7510 (mppt) REVERT: G 12 CYS cc_start: 0.9124 (p) cc_final: 0.8448 (p) REVERT: G 43 VAL cc_start: 0.8761 (m) cc_final: 0.8393 (p) REVERT: G 44 PHE cc_start: 0.8696 (t80) cc_final: 0.8319 (t80) REVERT: H 895 GLU cc_start: 0.8174 (tp30) cc_final: 0.7595 (tp30) REVERT: H 900 LEU cc_start: 0.7723 (mp) cc_final: 0.7457 (mp) REVERT: H 909 GLU cc_start: 0.6637 (mp0) cc_final: 0.6117 (mp0) REVERT: H 912 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7409 (mt-10) REVERT: H 913 LYS cc_start: 0.7408 (mttt) cc_final: 0.7123 (mttt) REVERT: K 106 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8686 (mm-30) REVERT: K 113 MET cc_start: 0.7348 (mmp) cc_final: 0.7116 (mmp) REVERT: K 116 TYR cc_start: 0.8440 (t80) cc_final: 0.8159 (t80) REVERT: K 118 MET cc_start: 0.7105 (tpp) cc_final: 0.6518 (tpp) REVERT: K 120 HIS cc_start: 0.8682 (m-70) cc_final: 0.8148 (m-70) REVERT: K 121 PHE cc_start: 0.8474 (m-80) cc_final: 0.7685 (m-80) REVERT: K 141 LYS cc_start: 0.8964 (tttt) cc_final: 0.8584 (tttt) REVERT: K 143 GLU cc_start: 0.8471 (tt0) cc_final: 0.8033 (tt0) REVERT: K 163 LYS cc_start: 0.8358 (mttt) cc_final: 0.7654 (mttt) REVERT: K 166 VAL cc_start: 0.8930 (t) cc_final: 0.8637 (p) REVERT: K 168 LYS cc_start: 0.8574 (tptm) cc_final: 0.8300 (tptm) REVERT: K 178 MET cc_start: 0.7645 (ptp) cc_final: 0.6918 (ptp) REVERT: K 180 LEU cc_start: 0.8944 (mt) cc_final: 0.8719 (mm) REVERT: K 192 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8325 (mm-30) REVERT: K 213 LYS cc_start: 0.8244 (tptt) cc_final: 0.7902 (tptt) REVERT: K 215 LYS cc_start: 0.8935 (mtmm) cc_final: 0.8571 (ptpt) REVERT: K 217 LYS cc_start: 0.8716 (tmtt) cc_final: 0.8330 (tmtt) REVERT: K 263 MET cc_start: 0.5620 (ptt) cc_final: 0.5382 (ppp) outliers start: 98 outliers final: 73 residues processed: 1002 average time/residue: 0.4458 time to fit residues: 666.4843 Evaluate side-chains 1023 residues out of total 2843 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 934 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 415 HIS 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 608 SER Chi-restraints excluded: chain A residue 658 PHE Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 384 HIS Chi-restraints excluded: chain B residue 399 LEU Chi-restraints excluded: chain B residue 434 HIS Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 500 ASP Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 586 GLU 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 705 ASN Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 442 GLN Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 465 TYR Chi-restraints excluded: chain C residue 479 PHE Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 213 TRP Chi-restraints excluded: chain D residue 215 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 407 VAL Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 20 GLU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 101 ILE Chi-restraints excluded: chain E residue 133 LYS Chi-restraints excluded: chain E residue 157 LYS Chi-restraints excluded: chain E residue 171 PHE Chi-restraints excluded: chain E residue 178 ASP 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 111 ILE Chi-restraints excluded: chain F residue 119 MET Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 192 ASP Chi-restraints excluded: chain F residue 229 TRP Chi-restraints excluded: chain F residue 234 ASP Chi-restraints excluded: chain F residue 248 HIS Chi-restraints excluded: chain F residue 258 HIS Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain G residue 6 LYS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain H residue 849 LYS Chi-restraints excluded: chain J residue 26 THR Chi-restraints excluded: chain J residue 63 GLU Chi-restraints excluded: chain J residue 168 LYS Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 227 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 204 optimal weight: 0.8980 chunk 274 optimal weight: 20.0000 chunk 78 optimal weight: 0.0970 chunk 237 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 258 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 265 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 ASN ** B 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 GLN ** D 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 HIS E 74 GLN E 293 GLN ** E 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 176 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.143790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.107960 restraints weight = 98558.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.112354 restraints weight = 37473.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.115105 restraints weight = 19866.222| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28259 Z= 0.225 Angle : 0.740 13.457 38512 Z= 0.363 Chirality : 0.043 0.194 4285 Planarity : 0.004 0.073 4647 Dihedral : 15.638 174.236 4414 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.28 % Favored : 94.69 % Rotamer: Outliers : 3.59 % Allowed : 26.12 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3186 helix: 0.91 (0.14), residues: 1494 sheet: -0.39 (0.27), residues: 380 loop : -0.76 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 421 HIS 0.008 0.001 HIS C 524 PHE 0.040 0.002 PHE D 454 TYR 0.040 0.001 TYR C 533 ARG 0.014 0.001 ARG F 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10010.82 seconds wall clock time: 177 minutes 44.55 seconds (10664.55 seconds total)