Starting phenix.real_space_refine on Mon Aug 25 14:59:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euf_28613/08_2025/8euf_28613_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euf_28613/08_2025/8euf_28613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8euf_28613/08_2025/8euf_28613_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euf_28613/08_2025/8euf_28613_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8euf_28613/08_2025/8euf_28613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euf_28613/08_2025/8euf_28613.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 95 5.16 5 C 18062 2.51 5 N 4947 2.21 5 O 5591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28707 Number of models: 1 Model: "" Number of chains: 16 Chain: "Q" Number of atoms: 3409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3409 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 398} Chain breaks: 5 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 3536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3536 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1025 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3353 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 3354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3354 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 248 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.28, per 1000 atoms: 0.22 Number of scatterers: 28707 At special positions: 0 Unit cell: (132.765, 195.39, 153.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 95 16.00 P 12 15.00 O 5591 8.00 N 4947 7.00 C 18062 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.4 microseconds 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 35 sheets defined 44.2% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'Q' and resid 957 through 972 Processing helix chain 'Q' and resid 974 through 985 Processing helix chain 'Q' and resid 1000 through 1013 Processing helix chain 'Q' and resid 1013 through 1018 removed outlier: 3.507A pdb=" N PHE Q1017 " --> pdb=" O HIS Q1013 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 3.724A pdb=" N TYR Q1090 " --> pdb=" O PRO Q1086 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1101 through 1111 Processing helix chain 'Q' and resid 1121 through 1133 Processing helix chain 'Q' and resid 1138 through 1145 Processing helix chain 'Q' and resid 1147 through 1154 Processing helix chain 'Q' and resid 1169 through 1178 Processing helix chain 'Q' and resid 1185 through 1190 Processing helix chain 'Q' and resid 1193 through 1201 Processing helix chain 'Q' and resid 1202 through 1206 removed outlier: 3.619A pdb=" N CYS Q1205 " --> pdb=" O TYR Q1202 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE Q1206 " --> pdb=" O LEU Q1203 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1202 through 1206' Processing helix chain 'Q' and resid 1226 through 1238 removed outlier: 4.043A pdb=" N THR Q1230 " --> pdb=" O SER Q1226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1290 through 1298 removed outlier: 3.623A pdb=" N ILE Q1295 " --> pdb=" O MET Q1291 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR Q1296 " --> pdb=" O ASP Q1292 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER Q1298 " --> pdb=" O PHE Q1294 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1298 through 1311 Processing helix chain 'Q' and resid 1325 through 1335 removed outlier: 3.716A pdb=" N ASP Q1329 " --> pdb=" O THR Q1325 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1357 through 1363 Processing helix chain 'Q' and resid 1397 through 1405 Processing helix chain 'Q' and resid 1427 through 1435 removed outlier: 4.220A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 95 Processing helix chain 'R' and resid 107 through 122 Processing helix chain 'R' and resid 143 through 159 removed outlier: 4.077A pdb=" N THR R 157 " --> pdb=" O ILE R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 216 through 231 removed outlier: 3.561A pdb=" N TYR R 231 " --> pdb=" O MET R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 250 Processing helix chain 'R' and resid 256 through 264 removed outlier: 3.830A pdb=" N ASP R 260 " --> pdb=" O ASN R 256 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE R 261 " --> pdb=" O TYR R 257 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU R 262 " --> pdb=" O ASP R 258 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS R 263 " --> pdb=" O GLU R 259 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 274 removed outlier: 3.550A pdb=" N ASP R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 589 through 597 Processing helix chain 'R' and resid 605 through 610 Processing helix chain 'R' and resid 619 through 624 removed outlier: 3.714A pdb=" N VAL R 624 " --> pdb=" O ARG R 620 " (cutoff:3.500A) Processing helix chain 'R' and resid 625 through 626 No H-bonds generated for 'chain 'R' and resid 625 through 626' Processing helix chain 'R' and resid 627 through 632 removed outlier: 3.728A pdb=" N MET R 630 " --> pdb=" O GLN R 627 " (cutoff:3.500A) Processing helix chain 'R' and resid 637 through 649 removed outlier: 3.616A pdb=" N LYS R 649 " --> pdb=" O ILE R 645 " (cutoff:3.500A) Processing helix chain 'R' and resid 658 through 667 Processing helix chain 'R' and resid 672 through 677 removed outlier: 3.511A pdb=" N ALA R 675 " --> pdb=" O GLY R 672 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL R 677 " --> pdb=" O ASN R 674 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 672 through 677' Processing helix chain 'R' and resid 679 through 692 removed outlier: 3.642A pdb=" N ARG R 683 " --> pdb=" O GLY R 679 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE R 691 " --> pdb=" O GLU R 687 " (cutoff:3.500A) Processing helix chain 'R' and resid 708 through 720 removed outlier: 3.734A pdb=" N LYS R 712 " --> pdb=" O LEU R 708 " (cutoff:3.500A) Processing helix chain 'R' and resid 720 through 728 removed outlier: 4.383A pdb=" N LYS R 726 " --> pdb=" O GLU R 722 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR R 727 " --> pdb=" O GLN R 723 " (cutoff:3.500A) Processing helix chain 'R' and resid 730 through 738 Processing helix chain 'S' and resid 29 through 39 Processing helix chain 'S' and resid 62 through 83 removed outlier: 3.982A pdb=" N LYS S 83 " --> pdb=" O THR S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 151 through 159 removed outlier: 4.045A pdb=" N LEU S 158 " --> pdb=" O GLU S 154 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG S 159 " --> pdb=" O TYR S 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.818A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.563A pdb=" N TYR T 111 " --> pdb=" O SER T 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 108 through 111' Processing helix chain 'T' and resid 116 through 128 Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 249 through 256 Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.613A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 313 through 316 Processing helix chain 'T' and resid 317 through 328 Processing helix chain 'T' and resid 362 through 366 Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 418 removed outlier: 3.848A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) Processing helix chain 'T' and resid 418 through 429 removed outlier: 3.708A pdb=" N CYS T 422 " --> pdb=" O LEU T 418 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 removed outlier: 3.540A pdb=" N VAL T 439 " --> pdb=" O VAL T 435 " (cutoff:3.500A) Processing helix chain 'T' and resid 448 through 459 removed outlier: 3.507A pdb=" N THR T 458 " --> pdb=" O LYS T 454 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 64 removed outlier: 3.530A pdb=" N GLY U 64 " --> pdb=" O MET U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 93 removed outlier: 4.412A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.613A pdb=" N ILE U 176 " --> pdb=" O GLY U 172 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 249 Processing helix chain 'U' and resid 255 through 260 Processing helix chain 'U' and resid 266 through 284 removed outlier: 3.829A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 301 Processing helix chain 'U' and resid 302 through 313 removed outlier: 3.536A pdb=" N LEU U 313 " --> pdb=" O ILE U 309 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 343 Processing helix chain 'U' and resid 344 through 350 Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.846A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.521A pdb=" N VAL U 423 " --> pdb=" O GLU U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 443 removed outlier: 3.613A pdb=" N ASN U 443 " --> pdb=" O TYR U 439 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.668A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 Processing helix chain 'V' and resid 108 through 111 Processing helix chain 'V' and resid 116 through 129 removed outlier: 3.806A pdb=" N ILE V 129 " --> pdb=" O PHE V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 182 through 192 Processing helix chain 'V' and resid 249 through 258 Processing helix chain 'V' and resid 264 through 273 removed outlier: 3.995A pdb=" N LEU V 272 " --> pdb=" O MET V 268 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.610A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 312 through 316 Processing helix chain 'V' and resid 317 through 328 removed outlier: 3.543A pdb=" N PHE V 321 " --> pdb=" O ASP V 317 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 360 through 367 removed outlier: 3.703A pdb=" N ASP V 365 " --> pdb=" O PRO V 361 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 417 removed outlier: 3.521A pdb=" N ALA V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 429 Processing helix chain 'V' and resid 435 through 446 removed outlier: 3.591A pdb=" N VAL V 439 " --> pdb=" O VAL V 435 " (cutoff:3.500A) Processing helix chain 'V' and resid 448 through 458 removed outlier: 3.568A pdb=" N SER V 452 " --> pdb=" O ASP V 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.557A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 92 Processing helix chain 'W' and resid 104 through 106 No H-bonds generated for 'chain 'W' and resid 104 through 106' Processing helix chain 'W' and resid 112 through 125 removed outlier: 3.575A pdb=" N ILE W 125 " --> pdb=" O PHE W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 172 through 181 removed outlier: 3.712A pdb=" N LYS W 181 " --> pdb=" O ASP W 177 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 250 removed outlier: 3.898A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.668A pdb=" N ALA W 256 " --> pdb=" O GLN W 252 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.730A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 298 through 301 Processing helix chain 'W' and resid 302 through 313 Processing helix chain 'W' and resid 340 through 343 Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.645A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.758A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 Processing helix chain 'W' and resid 432 through 443 removed outlier: 3.590A pdb=" N ASN W 443 " --> pdb=" O TYR W 439 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.688A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 Processing helix chain 'X' and resid 108 through 111 removed outlier: 3.731A pdb=" N TYR X 111 " --> pdb=" O SER X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 108 through 111' Processing helix chain 'X' and resid 116 through 128 Processing helix chain 'X' and resid 185 through 192 Processing helix chain 'X' and resid 249 through 258 removed outlier: 3.645A pdb=" N ARG X 258 " --> pdb=" O VAL X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 273 Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.736A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 316 Processing helix chain 'X' and resid 317 through 329 Processing helix chain 'X' and resid 360 through 367 Processing helix chain 'X' and resid 376 through 392 Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 418 removed outlier: 3.520A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 418 through 428 Processing helix chain 'X' and resid 435 through 446 removed outlier: 3.534A pdb=" N VAL X 439 " --> pdb=" O VAL X 435 " (cutoff:3.500A) Processing helix chain 'X' and resid 448 through 459 Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 80 through 93 Processing helix chain 'Y' and resid 104 through 106 No H-bonds generated for 'chain 'Y' and resid 104 through 106' Processing helix chain 'Y' and resid 112 through 124 Processing helix chain 'Y' and resid 172 through 182 Processing helix chain 'Y' and resid 207 through 209 No H-bonds generated for 'chain 'Y' and resid 207 through 209' Processing helix chain 'Y' and resid 241 through 250 removed outlier: 3.932A pdb=" N ARG Y 250 " --> pdb=" O VAL Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 260 removed outlier: 3.624A pdb=" N GLY Y 260 " --> pdb=" O ALA Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 266 through 284 removed outlier: 3.592A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 312 Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 3.730A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL Y 405 " --> pdb=" O ASN Y 401 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.635A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 443 removed outlier: 3.851A pdb=" N ASN Y 443 " --> pdb=" O TYR Y 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 950 through 951 removed outlier: 7.314A pdb=" N ILE Q 950 " --> pdb=" O ARG Q1421 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR Q1420 " --> pdb=" O VAL Q1389 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG Q1317 " --> pdb=" O ILE Q1390 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 5.988A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'Q' and resid 1071 through 1073 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 1071 through 1073 current: chain 'V' and resid 163 through 171 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 177 through 181 current: chain 'V' and resid 209 through 215 removed outlier: 6.101A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 5.944A pdb=" N TYR Q1083 " --> pdb=" O GLU Q1222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'R' and resid 61 through 63 removed outlier: 7.148A pdb=" N ILE R 40 " --> pdb=" O LEU R 135 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N THR R 137 " --> pdb=" O ILE R 40 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ILE R 42 " --> pdb=" O THR R 137 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR R 164 " --> pdb=" O ILE R 134 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLY R 166 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 184 through 189 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 203 through 204 current: chain 'R' and resid 700 through 701 Processing sheet with id=AA7, first strand: chain 'R' and resid 277 through 278 Processing sheet with id=AA8, first strand: chain 'S' and resid 125 through 126 removed outlier: 3.622A pdb=" N TYR S 125 " --> pdb=" O TYR S 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB1, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.273A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE T 75 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N SER T 340 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU T 77 " --> pdb=" O SER T 340 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 129 through 143 removed outlier: 4.034A pdb=" N GLY T 142 " --> pdb=" O ILE T 200 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 146 through 150 removed outlier: 3.801A pdb=" N GLU T 146 " --> pdb=" O GLY T 169 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AB5, first strand: chain 'T' and resid 394 through 395 removed outlier: 7.509A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AB7, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.263A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU U 293 " --> pdb=" O MET U 322 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ALA U 324 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE U 295 " --> pdb=" O ALA U 324 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 126 through 146 removed outlier: 7.046A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ILE U 145 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N GLN U 155 " --> pdb=" O ILE U 145 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 171 current: chain 'U' and resid 198 through 204 Processing sheet with id=AB9, first strand: chain 'U' and resid 330 through 331 Processing sheet with id=AC1, first strand: chain 'V' and resid 44 through 45 removed outlier: 3.716A pdb=" N GLU V 45 " --> pdb=" O PHE V 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.898A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER V 340 " --> pdb=" O LEU V 77 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=AC4, first strand: chain 'V' and resid 394 through 395 removed outlier: 8.107A pdb=" N GLN V 394 " --> pdb=" O ILE V 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC6, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.347A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 126 through 147 removed outlier: 5.052A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 171 current: chain 'W' and resid 198 through 204 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 198 through 204 current: chain 'X' and resid 162 through 172 removed outlier: 3.696A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 180 current: chain 'X' and resid 213 through 215 removed outlier: 5.892A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 229 through 230 current: chain 'Z' and resid 315 through 318 Processing sheet with id=AC8, first strand: chain 'W' and resid 330 through 331 Processing sheet with id=AC9, first strand: chain 'X' and resid 44 through 45 Processing sheet with id=AD1, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.441A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU X 308 " --> pdb=" O VAL X 337 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA X 339 " --> pdb=" O LEU X 308 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ILE X 310 " --> pdb=" O ALA X 339 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ILE X 75 " --> pdb=" O LEU X 338 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N SER X 340 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU X 77 " --> pdb=" O SER X 340 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'X' and resid 344 through 346 Processing sheet with id=AD3, first strand: chain 'X' and resid 394 through 395 removed outlier: 7.605A pdb=" N GLN X 394 " --> pdb=" O ILE X 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'Y' and resid 40 through 41 removed outlier: 3.516A pdb=" N SER Y 41 " --> pdb=" O MET Y 44 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.426A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ASP Y 296 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE Y 101 " --> pdb=" O ASP Y 296 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU Y 293 " --> pdb=" O MET Y 322 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA Y 324 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE Y 295 " --> pdb=" O ALA Y 324 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 236 through 240 Processing sheet with id=AD7, first strand: chain 'Y' and resid 133 through 146 removed outlier: 6.745A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE Y 145 " --> pdb=" O GLN Y 155 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLN Y 155 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE Y 160 " --> pdb=" O THR Y 167 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 171 current: chain 'Y' and resid 203 through 205 removed outlier: 5.511A pdb=" N ARG Y 204 " --> pdb=" O VAL Y 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Y' and resid 330 through 331 1098 hydrogen bonds defined for protein. 3198 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.87 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6213 1.33 - 1.45: 6082 1.45 - 1.58: 16655 1.58 - 1.70: 23 1.70 - 1.83: 166 Bond restraints: 29139 Sorted by residual: bond pdb=" N PRO R 20 " pdb=" CD PRO R 20 " ideal model delta sigma weight residual 1.473 1.379 0.094 1.40e-02 5.10e+03 4.53e+01 bond pdb=" C PRO R 19 " pdb=" O PRO R 19 " ideal model delta sigma weight residual 1.240 1.202 0.038 1.12e-02 7.97e+03 1.15e+01 bond pdb=" N LEU R 21 " pdb=" CA LEU R 21 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.14e+00 bond pdb=" N ARG R 22 " pdb=" CA ARG R 22 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.14e-02 7.69e+03 7.69e+00 bond pdb=" N ILE Q1428 " pdb=" CA ILE Q1428 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.17e-02 7.31e+03 7.46e+00 ... (remaining 29134 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.66: 38941 3.66 - 7.32: 413 7.32 - 10.98: 53 10.98 - 14.65: 14 14.65 - 18.31: 4 Bond angle restraints: 39425 Sorted by residual: angle pdb=" CA PRO Q1182 " pdb=" N PRO Q1182 " pdb=" CD PRO Q1182 " ideal model delta sigma weight residual 112.00 100.35 11.65 1.40e+00 5.10e-01 6.92e+01 angle pdb=" CA PRO R 20 " pdb=" N PRO R 20 " pdb=" CD PRO R 20 " ideal model delta sigma weight residual 112.00 123.09 -11.09 1.40e+00 5.10e-01 6.28e+01 angle pdb=" CA PRO Q1014 " pdb=" N PRO Q1014 " pdb=" CD PRO Q1014 " ideal model delta sigma weight residual 112.00 101.01 10.99 1.40e+00 5.10e-01 6.17e+01 angle pdb=" N PRO R 20 " pdb=" CA PRO R 20 " pdb=" CB PRO R 20 " ideal model delta sigma weight residual 103.15 95.82 7.33 9.70e-01 1.06e+00 5.71e+01 angle pdb=" CA PRO S 56 " pdb=" N PRO S 56 " pdb=" CD PRO S 56 " ideal model delta sigma weight residual 112.00 102.29 9.71 1.40e+00 5.10e-01 4.81e+01 ... (remaining 39420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.25: 17194 33.25 - 66.49: 650 66.49 - 99.74: 47 99.74 - 132.98: 7 132.98 - 166.22: 3 Dihedral angle restraints: 17901 sinusoidal: 7315 harmonic: 10586 Sorted by residual: dihedral pdb=" C5' ADP X 501 " pdb=" O5' ADP X 501 " pdb=" PA ADP X 501 " pdb=" O2A ADP X 501 " ideal model delta sinusoidal sigma weight residual 300.00 133.78 166.22 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' ADP Y 501 " pdb=" O5' ADP Y 501 " pdb=" PA ADP Y 501 " pdb=" O2A ADP Y 501 " ideal model delta sinusoidal sigma weight residual -60.00 102.88 -162.88 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O1B ADP X 501 " pdb=" O3A ADP X 501 " pdb=" PB ADP X 501 " pdb=" PA ADP X 501 " ideal model delta sinusoidal sigma weight residual 300.00 157.56 142.44 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 17898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 4116 0.091 - 0.182: 472 0.182 - 0.272: 35 0.272 - 0.363: 1 0.363 - 0.454: 2 Chirality restraints: 4626 Sorted by residual: chirality pdb=" CG LEU R 122 " pdb=" CB LEU R 122 " pdb=" CD1 LEU R 122 " pdb=" CD2 LEU R 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CB ILE X 304 " pdb=" CA ILE X 304 " pdb=" CG1 ILE X 304 " pdb=" CG2 ILE X 304 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CB ILE R 205 " pdb=" CA ILE R 205 " pdb=" CG1 ILE R 205 " pdb=" CG2 ILE R 205 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 4623 not shown) Planarity restraints: 5049 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS S 55 " -0.120 5.00e-02 4.00e+02 1.74e-01 4.84e+01 pdb=" N PRO S 56 " 0.301 5.00e-02 4.00e+02 pdb=" CA PRO S 56 " -0.098 5.00e-02 4.00e+02 pdb=" CD PRO S 56 " -0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS Q1013 " -0.111 5.00e-02 4.00e+02 1.60e-01 4.11e+01 pdb=" N PRO Q1014 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO Q1014 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO Q1014 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 586 " 0.040 2.00e-02 2.50e+03 3.87e-02 3.75e+01 pdb=" CG TRP R 586 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 TRP R 586 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP R 586 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 586 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 586 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 586 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 586 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 586 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP R 586 " -0.005 2.00e-02 2.50e+03 ... (remaining 5046 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 2994 2.74 - 3.28: 27814 3.28 - 3.82: 48662 3.82 - 4.36: 56079 4.36 - 4.90: 96753 Nonbonded interactions: 232302 Sorted by model distance: nonbonded pdb=" OG SER X 164 " pdb=" OE2 GLU Z 314 " model vdw 2.206 3.040 nonbonded pdb=" O THR W 262 " pdb=" OG1 THR W 262 " model vdw 2.263 3.040 nonbonded pdb=" O TRP R 108 " pdb=" OG1 THR R 111 " model vdw 2.274 3.040 nonbonded pdb=" O GLU T 409 " pdb=" OG SER Y 457 " model vdw 2.276 3.040 nonbonded pdb=" O SER R 188 " pdb=" OG1 THR R 194 " model vdw 2.277 3.040 ... (remaining 232297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'T' and resid 22 through 501) selection = (chain 'V' and (resid 22 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 154 or (resid 161 through 163 and \ (name N or name CA or name C or name O or name CB )) or resid 164 through 501)) selection = (chain 'X' and (resid 22 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 154 or (resid 161 through 163 and \ (name N or name CA or name C or name O or name CB )) or resid 164 through 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 210 or resid 221 through 501)) selection = (chain 'Y' and (resid 18 through 210 or resid 221 through 459 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 28.660 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 0.128 29139 Z= 0.269 Angle : 1.025 18.306 39425 Z= 0.544 Chirality : 0.057 0.454 4626 Planarity : 0.008 0.174 5049 Dihedral : 16.916 166.225 11065 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.03 % Allowed : 19.15 % Favored : 80.82 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.12), residues: 3626 helix: -1.56 (0.11), residues: 1515 sheet: -0.13 (0.21), residues: 596 loop : -1.24 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.038 0.001 ARG U 350 TYR 0.051 0.003 TYR X 462 PHE 0.033 0.002 PHE R 28 TRP 0.103 0.005 TRP R 586 HIS 0.008 0.002 HIS Q1013 Details of bonding type rmsd covalent geometry : bond 0.00604 (29139) covalent geometry : angle 1.02461 (39425) hydrogen bonds : bond 0.16490 ( 1098) hydrogen bonds : angle 6.75022 ( 3198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1309 time to evaluate : 1.140 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: Q 1008 ARG cc_start: 0.8530 (tpp80) cc_final: 0.7701 (tpp80) REVERT: Q 1027 SER cc_start: 0.8709 (m) cc_final: 0.8294 (p) REVERT: Q 1108 LEU cc_start: 0.8031 (tt) cc_final: 0.7829 (tp) REVERT: Q 1112 LYS cc_start: 0.8894 (mttp) cc_final: 0.8326 (ttmm) REVERT: Q 1123 GLU cc_start: 0.7669 (mp0) cc_final: 0.7467 (mp0) REVERT: Q 1127 PHE cc_start: 0.8555 (t80) cc_final: 0.8348 (t80) REVERT: Q 1134 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7786 (mm-30) REVERT: Q 1142 ARG cc_start: 0.8030 (mtm-85) cc_final: 0.7670 (mtm-85) REVERT: Q 1148 LEU cc_start: 0.8301 (tt) cc_final: 0.7677 (mt) REVERT: Q 1150 LYS cc_start: 0.8553 (tttm) cc_final: 0.7594 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7050 (mp0) cc_final: 0.6595 (mp0) REVERT: Q 1170 ILE cc_start: 0.7672 (mm) cc_final: 0.7079 (tp) REVERT: Q 1173 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7135 (mp0) REVERT: Q 1195 LYS cc_start: 0.7978 (tppt) cc_final: 0.7163 (tppt) REVERT: Q 1222 GLU cc_start: 0.7610 (tm-30) cc_final: 0.6517 (tm-30) REVERT: Q 1230 THR cc_start: 0.8563 (m) cc_final: 0.7978 (p) REVERT: Q 1231 ASN cc_start: 0.8455 (t0) cc_final: 0.8197 (m-40) REVERT: Q 1234 ASN cc_start: 0.8373 (t0) cc_final: 0.8148 (m-40) REVERT: Q 1235 ASN cc_start: 0.8478 (t0) cc_final: 0.8220 (t0) REVERT: Q 1239 ASP cc_start: 0.8298 (t70) cc_final: 0.7986 (t70) REVERT: Q 1241 LEU cc_start: 0.8913 (tp) cc_final: 0.8563 (tp) REVERT: Q 1243 SER cc_start: 0.8566 (m) cc_final: 0.8155 (p) REVERT: Q 1248 ASP cc_start: 0.6661 (t70) cc_final: 0.6365 (t0) REVERT: Q 1256 ASN cc_start: 0.8288 (m-40) cc_final: 0.8008 (m-40) REVERT: Q 1267 ASP cc_start: 0.8422 (m-30) cc_final: 0.8093 (m-30) REVERT: Q 1293 ARG cc_start: 0.7417 (mmm-85) cc_final: 0.6827 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.7968 (mt) cc_final: 0.7693 (mm) REVERT: Q 1302 ARG cc_start: 0.7910 (ttt180) cc_final: 0.7452 (mtp85) REVERT: Q 1331 MET cc_start: 0.7992 (tpp) cc_final: 0.7778 (tpp) REVERT: R 17 ASP cc_start: 0.7227 (m-30) cc_final: 0.6958 (m-30) REVERT: R 29 ASP cc_start: 0.7611 (p0) cc_final: 0.7317 (m-30) REVERT: R 54 VAL cc_start: 0.8973 (t) cc_final: 0.8567 (m) REVERT: R 55 ASN cc_start: 0.8540 (p0) cc_final: 0.8288 (p0) REVERT: R 97 ARG cc_start: 0.7442 (mmt-90) cc_final: 0.7221 (mmt-90) REVERT: R 136 LEU cc_start: 0.7630 (tp) cc_final: 0.7404 (tp) REVERT: R 150 TRP cc_start: 0.8698 (m100) cc_final: 0.8279 (m100) REVERT: R 182 LYS cc_start: 0.8615 (mmmm) cc_final: 0.8321 (mmmm) REVERT: R 192 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6222 (mt-10) REVERT: R 218 GLN cc_start: 0.8006 (mp10) cc_final: 0.7766 (mp10) REVERT: R 242 GLN cc_start: 0.8199 (mt0) cc_final: 0.7564 (mt0) REVERT: R 252 TYR cc_start: 0.8266 (p90) cc_final: 0.7638 (p90) REVERT: R 262 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7742 (mm-30) REVERT: R 591 LEU cc_start: 0.8839 (mt) cc_final: 0.8484 (mt) REVERT: R 592 HIS cc_start: 0.8286 (t-90) cc_final: 0.7379 (t-90) REVERT: R 599 ARG cc_start: 0.8196 (tpp-160) cc_final: 0.7848 (tpp-160) REVERT: R 606 ILE cc_start: 0.8623 (tp) cc_final: 0.7911 (tp) REVERT: R 610 HIS cc_start: 0.7945 (m90) cc_final: 0.7542 (m90) REVERT: R 612 MET cc_start: 0.7523 (tpp) cc_final: 0.7035 (tpp) REVERT: R 620 ARG cc_start: 0.7867 (ttt180) cc_final: 0.7492 (mmm-85) REVERT: R 630 MET cc_start: 0.6984 (mtm) cc_final: 0.6742 (mtm) REVERT: R 643 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7084 (mm-30) REVERT: R 648 LYS cc_start: 0.7905 (mttp) cc_final: 0.7660 (mtpp) REVERT: R 659 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8242 (tp-100) REVERT: R 661 SER cc_start: 0.8621 (m) cc_final: 0.8231 (p) REVERT: R 663 ASP cc_start: 0.8335 (m-30) cc_final: 0.7585 (m-30) REVERT: R 664 MET cc_start: 0.8477 (mtm) cc_final: 0.8139 (mtp) REVERT: R 681 LYS cc_start: 0.8810 (tptt) cc_final: 0.8328 (tptt) REVERT: R 685 VAL cc_start: 0.8967 (p) cc_final: 0.8608 (m) REVERT: R 686 LYS cc_start: 0.8802 (ttmt) cc_final: 0.8445 (ttmt) REVERT: R 705 ASP cc_start: 0.8618 (t70) cc_final: 0.8232 (t0) REVERT: R 717 LEU cc_start: 0.8569 (tp) cc_final: 0.8245 (tp) REVERT: R 721 GLU cc_start: 0.8423 (tm-30) cc_final: 0.7371 (tm-30) REVERT: R 724 TYR cc_start: 0.8601 (t80) cc_final: 0.7543 (t80) REVERT: R 725 ARG cc_start: 0.8650 (mmt180) cc_final: 0.8169 (mmp80) REVERT: R 728 VAL cc_start: 0.8829 (t) cc_final: 0.8525 (m) REVERT: R 747 LEU cc_start: 0.7867 (pt) cc_final: 0.6800 (tp) REVERT: S 68 SER cc_start: 0.8259 (m) cc_final: 0.8052 (p) REVERT: S 73 ARG cc_start: 0.8473 (ttp-110) cc_final: 0.8168 (tmm-80) REVERT: S 77 LEU cc_start: 0.8843 (mt) cc_final: 0.8632 (mt) REVERT: S 110 ARG cc_start: 0.7531 (ptt180) cc_final: 0.7292 (ptt-90) REVERT: S 122 LYS cc_start: 0.8264 (mmmm) cc_final: 0.7714 (mtpp) REVERT: S 140 TYR cc_start: 0.8670 (t80) cc_final: 0.8027 (t80) REVERT: S 145 LYS cc_start: 0.8459 (tppp) cc_final: 0.8035 (tppp) REVERT: T 49 VAL cc_start: 0.8431 (p) cc_final: 0.8202 (m) REVERT: T 64 LEU cc_start: 0.8422 (tt) cc_final: 0.8147 (tp) REVERT: T 94 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7773 (tm-30) REVERT: T 95 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7949 (tp30) REVERT: T 119 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6708 (tm-30) REVERT: T 177 LYS cc_start: 0.8190 (tttt) cc_final: 0.7581 (mtpp) REVERT: T 178 THR cc_start: 0.8888 (m) cc_final: 0.8661 (t) REVERT: T 186 TYR cc_start: 0.8118 (t80) cc_final: 0.7914 (t80) REVERT: T 193 LYS cc_start: 0.8284 (mmmt) cc_final: 0.7876 (mmmt) REVERT: T 223 ASP cc_start: 0.7517 (m-30) cc_final: 0.4724 (m-30) REVERT: T 229 TYR cc_start: 0.8652 (m-80) cc_final: 0.8359 (m-80) REVERT: T 240 LYS cc_start: 0.8292 (ttmt) cc_final: 0.8043 (ttmt) REVERT: T 244 VAL cc_start: 0.8820 (m) cc_final: 0.8497 (p) REVERT: T 251 ASP cc_start: 0.7872 (m-30) cc_final: 0.7470 (m-30) REVERT: T 268 MET cc_start: 0.7683 (tpt) cc_final: 0.7452 (tpt) REVERT: T 269 MET cc_start: 0.7196 (mtt) cc_final: 0.6900 (mtt) REVERT: T 282 GLU cc_start: 0.8165 (tt0) cc_final: 0.7909 (tt0) REVERT: T 294 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8406 (ttpp) REVERT: T 295 TYR cc_start: 0.8463 (m-80) cc_final: 0.7844 (m-80) REVERT: T 323 TYR cc_start: 0.8525 (t80) cc_final: 0.8051 (t80) REVERT: T 325 ASN cc_start: 0.8361 (t0) cc_final: 0.7873 (t0) REVERT: T 381 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.8009 (ttm-80) REVERT: T 382 THR cc_start: 0.8397 (p) cc_final: 0.8157 (m) REVERT: T 385 GLU cc_start: 0.8174 (pt0) cc_final: 0.7575 (pp20) REVERT: T 395 VAL cc_start: 0.7956 (t) cc_final: 0.7639 (p) REVERT: T 405 THR cc_start: 0.7967 (m) cc_final: 0.7636 (p) REVERT: T 419 LEU cc_start: 0.8516 (mm) cc_final: 0.8188 (mp) REVERT: T 431 ARG cc_start: 0.7610 (mtm180) cc_final: 0.6900 (mtm180) REVERT: T 450 LYS cc_start: 0.8723 (mttm) cc_final: 0.8249 (mtmm) REVERT: T 454 LYS cc_start: 0.8446 (tptp) cc_final: 0.8208 (ttpp) REVERT: U 73 VAL cc_start: 0.8858 (m) cc_final: 0.8429 (p) REVERT: U 81 LYS cc_start: 0.8480 (mtmm) cc_final: 0.8202 (mtmm) REVERT: U 86 MET cc_start: 0.8132 (mmm) cc_final: 0.7475 (mmm) REVERT: U 110 GLU cc_start: 0.7882 (pp20) cc_final: 0.7507 (pp20) REVERT: U 111 LEU cc_start: 0.8636 (mt) cc_final: 0.8401 (mt) REVERT: U 123 LYS cc_start: 0.8365 (mttt) cc_final: 0.7929 (mttp) REVERT: U 129 ILE cc_start: 0.8428 (mt) cc_final: 0.8121 (mm) REVERT: U 130 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7934 (mtmm) REVERT: U 134 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7295 (mm-30) REVERT: U 161 LYS cc_start: 0.8512 (ptmm) cc_final: 0.8009 (ptmm) REVERT: U 164 ASP cc_start: 0.7637 (t70) cc_final: 0.7345 (t0) REVERT: U 175 MET cc_start: 0.7747 (tpp) cc_final: 0.7502 (tpp) REVERT: U 180 THR cc_start: 0.8579 (m) cc_final: 0.8338 (p) REVERT: U 183 LYS cc_start: 0.8828 (mttm) cc_final: 0.8617 (mttp) REVERT: U 193 ASP cc_start: 0.8021 (t0) cc_final: 0.7612 (t70) REVERT: U 194 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8174 (ttpp) REVERT: U 198 LYS cc_start: 0.8550 (tttm) cc_final: 0.8126 (tttm) REVERT: U 199 ILE cc_start: 0.8093 (mp) cc_final: 0.7702 (mt) REVERT: U 221 PHE cc_start: 0.7240 (m-80) cc_final: 0.6722 (m-80) REVERT: U 223 GLN cc_start: 0.7059 (pp30) cc_final: 0.6521 (pp30) REVERT: U 248 ASN cc_start: 0.8488 (t0) cc_final: 0.8133 (t0) REVERT: U 254 PHE cc_start: 0.8174 (p90) cc_final: 0.7702 (p90) REVERT: U 258 PHE cc_start: 0.8638 (m-80) cc_final: 0.7892 (m-80) REVERT: U 272 GLN cc_start: 0.7908 (tp40) cc_final: 0.7379 (tp40) REVERT: U 276 LYS cc_start: 0.8834 (tptt) cc_final: 0.8336 (tptm) REVERT: U 279 GLU cc_start: 0.7822 (pt0) cc_final: 0.7569 (pt0) REVERT: U 310 ASN cc_start: 0.8225 (m-40) cc_final: 0.7876 (m-40) REVERT: U 313 LEU cc_start: 0.8717 (mt) cc_final: 0.8353 (mp) REVERT: U 321 VAL cc_start: 0.8776 (t) cc_final: 0.8490 (p) REVERT: U 331 LYS cc_start: 0.8573 (pttm) cc_final: 0.8367 (pptt) REVERT: U 338 LYS cc_start: 0.8723 (mttt) cc_final: 0.8328 (mtpp) REVERT: U 339 SER cc_start: 0.8839 (m) cc_final: 0.8392 (p) REVERT: U 349 ASP cc_start: 0.8492 (t0) cc_final: 0.8018 (m-30) REVERT: U 365 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8388 (tttp) REVERT: U 376 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7729 (mm-30) REVERT: U 398 TYR cc_start: 0.8820 (t80) cc_final: 0.8596 (t80) REVERT: U 400 SER cc_start: 0.8157 (t) cc_final: 0.7817 (m) REVERT: U 404 SER cc_start: 0.8748 (t) cc_final: 0.8448 (p) REVERT: U 413 ARG cc_start: 0.7485 (mtm110) cc_final: 0.7061 (ptt180) REVERT: U 419 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6900 (mt-10) REVERT: U 428 LEU cc_start: 0.8405 (tp) cc_final: 0.7940 (pp) REVERT: U 438 LYS cc_start: 0.8385 (mtpp) cc_final: 0.8123 (mtpp) REVERT: V 30 ILE cc_start: 0.8307 (mt) cc_final: 0.8017 (mp) REVERT: V 31 LYS cc_start: 0.7838 (mmpt) cc_final: 0.7487 (mmtt) REVERT: V 37 GLU cc_start: 0.7628 (pm20) cc_final: 0.7065 (mp0) REVERT: V 52 ILE cc_start: 0.8297 (mp) cc_final: 0.7950 (mm) REVERT: V 55 ARG cc_start: 0.7787 (mtm180) cc_final: 0.7134 (mtt180) REVERT: V 68 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7801 (mtmm) REVERT: V 95 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7403 (mt-10) REVERT: V 100 VAL cc_start: 0.8862 (t) cc_final: 0.8482 (p) REVERT: V 109 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8057 (tt0) REVERT: V 114 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7429 (mt-10) REVERT: V 134 LYS cc_start: 0.8333 (mttp) cc_final: 0.7992 (ptpp) REVERT: V 136 THR cc_start: 0.8005 (p) cc_final: 0.7789 (t) REVERT: V 144 VAL cc_start: 0.8313 (t) cc_final: 0.7879 (m) REVERT: V 148 THR cc_start: 0.8859 (t) cc_final: 0.8519 (p) REVERT: V 167 ILE cc_start: 0.8584 (mt) cc_final: 0.8289 (mp) REVERT: V 180 ARG cc_start: 0.7817 (ttm-80) cc_final: 0.7520 (tpt-90) REVERT: V 186 TYR cc_start: 0.8438 (t80) cc_final: 0.8098 (t80) REVERT: V 187 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7481 (mt-10) REVERT: V 203 GLU cc_start: 0.7535 (tt0) cc_final: 0.7210 (tt0) REVERT: V 218 TYR cc_start: 0.8395 (m-80) cc_final: 0.8142 (m-80) REVERT: V 221 GLU cc_start: 0.7640 (pm20) cc_final: 0.7368 (tm-30) REVERT: V 222 PHE cc_start: 0.8016 (m-80) cc_final: 0.7569 (m-10) REVERT: V 253 ASP cc_start: 0.7329 (m-30) cc_final: 0.7029 (m-30) REVERT: V 254 VAL cc_start: 0.8681 (t) cc_final: 0.8410 (m) REVERT: V 274 LYS cc_start: 0.8319 (tttp) cc_final: 0.8104 (tttp) REVERT: V 287 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7615 (mm-30) REVERT: V 290 LYS cc_start: 0.8292 (mtpp) cc_final: 0.7947 (mtpp) REVERT: V 294 LYS cc_start: 0.8519 (tppt) cc_final: 0.8305 (tppt) REVERT: V 302 GLU cc_start: 0.8045 (pt0) cc_final: 0.7516 (pm20) REVERT: V 314 ASN cc_start: 0.8882 (p0) cc_final: 0.8419 (p0) REVERT: V 318 ILE cc_start: 0.8612 (tp) cc_final: 0.8295 (tt) REVERT: V 325 ASN cc_start: 0.8154 (t0) cc_final: 0.7850 (t0) REVERT: V 326 LYS cc_start: 0.8285 (tmmt) cc_final: 0.8050 (tttt) REVERT: V 329 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7297 (mt-10) REVERT: V 379 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8288 (mt-10) REVERT: V 385 GLU cc_start: 0.8112 (tt0) cc_final: 0.7727 (pp20) REVERT: V 403 LEU cc_start: 0.8573 (mt) cc_final: 0.8222 (mp) REVERT: V 418 LEU cc_start: 0.8873 (tp) cc_final: 0.8545 (tp) REVERT: V 427 GLN cc_start: 0.8111 (pt0) cc_final: 0.7868 (pt0) REVERT: V 432 LYS cc_start: 0.7426 (tptt) cc_final: 0.7056 (tptt) REVERT: V 437 ASN cc_start: 0.8119 (m-40) cc_final: 0.7904 (m-40) REVERT: V 439 VAL cc_start: 0.8174 (p) cc_final: 0.7908 (t) REVERT: V 440 ASN cc_start: 0.7583 (m-40) cc_final: 0.7088 (m-40) REVERT: V 450 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7058 (mttm) REVERT: V 453 THR cc_start: 0.8448 (m) cc_final: 0.8048 (p) REVERT: V 454 LYS cc_start: 0.8620 (mptt) cc_final: 0.8140 (mmtt) REVERT: W 26 ILE cc_start: 0.8718 (mt) cc_final: 0.8478 (mm) REVERT: W 81 LYS cc_start: 0.8716 (mtmm) cc_final: 0.8477 (ptpp) REVERT: W 86 MET cc_start: 0.7029 (mmm) cc_final: 0.6694 (mmm) REVERT: W 90 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8229 (mm-40) REVERT: W 105 GLU cc_start: 0.7778 (mp0) cc_final: 0.7462 (mp0) REVERT: W 109 LEU cc_start: 0.8588 (mt) cc_final: 0.8249 (mt) REVERT: W 113 LYS cc_start: 0.8502 (mttp) cc_final: 0.8204 (mttp) REVERT: W 115 GLU cc_start: 0.7891 (tp30) cc_final: 0.7407 (mm-30) REVERT: W 133 THR cc_start: 0.8122 (m) cc_final: 0.7783 (p) REVERT: W 146 ASP cc_start: 0.7735 (m-30) cc_final: 0.7260 (m-30) REVERT: W 147 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7664 (ptm160) REVERT: W 157 LYS cc_start: 0.8439 (mttm) cc_final: 0.8108 (mttm) REVERT: W 158 LEU cc_start: 0.8525 (tt) cc_final: 0.8057 (tp) REVERT: W 159 THR cc_start: 0.8356 (m) cc_final: 0.7890 (p) REVERT: W 160 ILE cc_start: 0.8785 (tt) cc_final: 0.8559 (mm) REVERT: W 188 ASP cc_start: 0.7381 (m-30) cc_final: 0.6668 (m-30) REVERT: W 191 SER cc_start: 0.7897 (t) cc_final: 0.6886 (p) REVERT: W 200 THR cc_start: 0.7947 (m) cc_final: 0.6854 (p) REVERT: W 231 LYS cc_start: 0.8098 (mttm) cc_final: 0.7884 (mmmm) REVERT: W 246 VAL cc_start: 0.8507 (t) cc_final: 0.8232 (m) REVERT: W 264 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6442 (mt-10) REVERT: W 267 SER cc_start: 0.8231 (p) cc_final: 0.7880 (m) REVERT: W 271 ASP cc_start: 0.7573 (m-30) cc_final: 0.7212 (m-30) REVERT: W 272 GLN cc_start: 0.8259 (mt0) cc_final: 0.7974 (mt0) REVERT: W 281 LYS cc_start: 0.8822 (tttm) cc_final: 0.8304 (tppt) REVERT: W 302 ASP cc_start: 0.8428 (t0) cc_final: 0.7734 (t70) REVERT: W 304 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7851 (mt-10) REVERT: W 306 PHE cc_start: 0.8358 (m-80) cc_final: 0.7826 (m-80) REVERT: W 310 ASN cc_start: 0.8041 (m-40) cc_final: 0.7625 (m-40) REVERT: W 315 ASP cc_start: 0.8417 (t0) cc_final: 0.8040 (t0) REVERT: W 339 SER cc_start: 0.8246 (m) cc_final: 0.7993 (p) REVERT: W 341 HIS cc_start: 0.8190 (m-70) cc_final: 0.7835 (m-70) REVERT: W 371 ARG cc_start: 0.8225 (mmm160) cc_final: 0.7632 (mmm160) REVERT: W 373 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7823 (mm-40) REVERT: W 375 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7002 (mt-10) REVERT: W 389 LYS cc_start: 0.8614 (tppt) cc_final: 0.7987 (tppt) REVERT: W 390 THR cc_start: 0.8220 (m) cc_final: 0.8003 (p) REVERT: W 393 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7727 (mt-10) REVERT: W 424 LYS cc_start: 0.8439 (mtmm) cc_final: 0.7984 (mmmm) REVERT: W 430 PHE cc_start: 0.7597 (m-80) cc_final: 0.7239 (m-10) REVERT: W 437 VAL cc_start: 0.8813 (t) cc_final: 0.8602 (t) REVERT: W 440 VAL cc_start: 0.8553 (t) cc_final: 0.8217 (p) REVERT: W 448 ILE cc_start: 0.7870 (mt) cc_final: 0.7597 (mp) REVERT: X 33 LEU cc_start: 0.8535 (mt) cc_final: 0.8060 (mm) REVERT: X 88 LEU cc_start: 0.8663 (mt) cc_final: 0.8233 (tt) REVERT: X 95 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7793 (mm-30) REVERT: X 99 LYS cc_start: 0.7736 (pttm) cc_final: 0.7104 (ptpp) REVERT: X 116 LYS cc_start: 0.8293 (pttt) cc_final: 0.8039 (ptpp) REVERT: X 119 GLU cc_start: 0.7589 (tp30) cc_final: 0.7080 (tp30) REVERT: X 123 GLU cc_start: 0.8158 (pt0) cc_final: 0.7416 (pp20) REVERT: X 141 GLU cc_start: 0.7404 (pm20) cc_final: 0.6834 (pm20) REVERT: X 185 ILE cc_start: 0.7590 (tp) cc_final: 0.7360 (tp) REVERT: X 188 SER cc_start: 0.8138 (m) cc_final: 0.7774 (p) REVERT: X 189 ILE cc_start: 0.9186 (mm) cc_final: 0.8912 (mt) REVERT: X 190 GLN cc_start: 0.8071 (mt0) cc_final: 0.7835 (mt0) REVERT: X 191 ARG cc_start: 0.7326 (ttp-110) cc_final: 0.6792 (ttp-110) REVERT: X 198 ASP cc_start: 0.7059 (m-30) cc_final: 0.6199 (m-30) REVERT: X 201 TYR cc_start: 0.7076 (t80) cc_final: 0.6842 (t80) REVERT: X 211 ARG cc_start: 0.7951 (ttt-90) cc_final: 0.6783 (ttt-90) REVERT: X 212 VAL cc_start: 0.8673 (t) cc_final: 0.8369 (m) REVERT: X 229 TYR cc_start: 0.7485 (m-80) cc_final: 0.7025 (m-80) REVERT: X 239 LYS cc_start: 0.7993 (ptpt) cc_final: 0.7668 (ptpp) REVERT: X 277 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8127 (mtmt) REVERT: X 282 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6231 (tp30) REVERT: X 286 GLN cc_start: 0.7982 (tp-100) cc_final: 0.7607 (mm-40) REVERT: X 289 ASN cc_start: 0.8279 (m-40) cc_final: 0.8062 (m-40) REVERT: X 290 LYS cc_start: 0.8355 (tppt) cc_final: 0.7975 (tppt) REVERT: X 291 VAL cc_start: 0.8873 (p) cc_final: 0.8571 (m) REVERT: X 292 VAL cc_start: 0.8823 (t) cc_final: 0.8591 (p) REVERT: X 315 MET cc_start: 0.7699 (mtp) cc_final: 0.7496 (mtp) REVERT: X 328 LEU cc_start: 0.8470 (mt) cc_final: 0.8216 (mm) REVERT: X 341 ASN cc_start: 0.8578 (p0) cc_final: 0.8065 (p0) REVERT: X 344 MET cc_start: 0.7810 (mmm) cc_final: 0.7543 (mmt) REVERT: X 365 ASP cc_start: 0.8256 (t0) cc_final: 0.7910 (t0) REVERT: X 377 LYS cc_start: 0.8035 (ttpp) cc_final: 0.7482 (ttpp) REVERT: X 378 ASP cc_start: 0.7912 (p0) cc_final: 0.7255 (t70) REVERT: X 380 ILE cc_start: 0.8562 (mt) cc_final: 0.8344 (tt) REVERT: X 385 GLU cc_start: 0.8188 (pp20) cc_final: 0.7776 (pp20) REVERT: X 391 GLU cc_start: 0.8601 (tt0) cc_final: 0.7613 (tp30) REVERT: X 392 ARG cc_start: 0.8591 (mtm110) cc_final: 0.8283 (mpp80) REVERT: X 401 ASP cc_start: 0.8061 (m-30) cc_final: 0.7724 (m-30) REVERT: X 402 LEU cc_start: 0.8620 (tp) cc_final: 0.8303 (tt) REVERT: X 409 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7288 (mp0) REVERT: X 414 TYR cc_start: 0.8426 (t80) cc_final: 0.8070 (t80) REVERT: X 424 ILE cc_start: 0.8932 (mm) cc_final: 0.8720 (mm) REVERT: X 432 LYS cc_start: 0.8144 (tttt) cc_final: 0.7866 (tmtt) REVERT: X 443 LYS cc_start: 0.8456 (tmmt) cc_final: 0.8015 (ttmt) REVERT: X 446 PHE cc_start: 0.8293 (m-80) cc_final: 0.8074 (m-10) REVERT: X 448 ASP cc_start: 0.8280 (t0) cc_final: 0.7812 (t70) REVERT: X 454 LYS cc_start: 0.8708 (tmmt) cc_final: 0.8056 (tmmt) REVERT: X 458 THR cc_start: 0.8829 (m) cc_final: 0.8410 (t) REVERT: Y 52 ARG cc_start: 0.8482 (ttt90) cc_final: 0.8240 (tpt170) REVERT: Y 59 LYS cc_start: 0.8290 (mmmt) cc_final: 0.8082 (tptp) REVERT: Y 78 SER cc_start: 0.8267 (t) cc_final: 0.7893 (m) REVERT: Y 94 LYS cc_start: 0.7807 (tptm) cc_final: 0.7545 (tptm) REVERT: Y 105 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7491 (mm-30) REVERT: Y 136 ILE cc_start: 0.8582 (mt) cc_final: 0.8350 (tp) REVERT: Y 164 ASP cc_start: 0.8105 (m-30) cc_final: 0.7820 (m-30) REVERT: Y 166 GLU cc_start: 0.6524 (tm-30) cc_final: 0.6206 (tm-30) REVERT: Y 173 ASN cc_start: 0.7660 (p0) cc_final: 0.6571 (m-40) REVERT: Y 175 MET cc_start: 0.9064 (tpp) cc_final: 0.8221 (tpp) REVERT: Y 185 LEU cc_start: 0.7554 (mt) cc_final: 0.7261 (mt) REVERT: Y 213 ASP cc_start: 0.8039 (t0) cc_final: 0.7816 (t0) REVERT: Y 254 PHE cc_start: 0.8103 (p90) cc_final: 0.7824 (p90) REVERT: Y 271 ASP cc_start: 0.8111 (t0) cc_final: 0.7682 (t0) REVERT: Y 272 GLN cc_start: 0.8329 (mt0) cc_final: 0.8076 (tt0) REVERT: Y 273 ILE cc_start: 0.8624 (mt) cc_final: 0.8309 (tt) REVERT: Y 274 ASN cc_start: 0.8312 (m-40) cc_final: 0.7929 (m110) REVERT: Y 277 VAL cc_start: 0.8361 (t) cc_final: 0.8092 (p) REVERT: Y 279 GLU cc_start: 0.7686 (pp20) cc_final: 0.7284 (pp20) REVERT: Y 296 ASP cc_start: 0.8311 (t0) cc_final: 0.8060 (t70) REVERT: Y 310 ASN cc_start: 0.8042 (m-40) cc_final: 0.7487 (m-40) REVERT: Y 320 ILE cc_start: 0.8637 (mm) cc_final: 0.8191 (tp) REVERT: Y 333 ARG cc_start: 0.8374 (mtp-110) cc_final: 0.8045 (mtm180) REVERT: Y 349 ASP cc_start: 0.8026 (t0) cc_final: 0.7665 (t0) REVERT: Y 370 ILE cc_start: 0.9075 (mt) cc_final: 0.8647 (tt) REVERT: Y 374 GLU cc_start: 0.8072 (tp30) cc_final: 0.6932 (mm-30) REVERT: Y 384 LEU cc_start: 0.8803 (tp) cc_final: 0.8549 (tt) REVERT: Y 389 LYS cc_start: 0.8632 (ttpt) cc_final: 0.7927 (mmmm) REVERT: Y 393 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7562 (mt-10) REVERT: Y 405 VAL cc_start: 0.8767 (m) cc_final: 0.8322 (p) REVERT: Y 407 GLN cc_start: 0.8389 (tt0) cc_final: 0.8055 (tp40) REVERT: Y 411 MET cc_start: 0.8435 (mtp) cc_final: 0.8130 (mtp) REVERT: Y 412 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8581 (mmmt) REVERT: Y 419 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7772 (mm-30) REVERT: Y 420 VAL cc_start: 0.8950 (m) cc_final: 0.8246 (p) REVERT: Y 424 LYS cc_start: 0.8421 (mtmm) cc_final: 0.8177 (mtmm) REVERT: Y 427 TYR cc_start: 0.8394 (t80) cc_final: 0.7872 (t80) REVERT: Y 441 GLN cc_start: 0.8355 (mm110) cc_final: 0.7807 (mt0) REVERT: Y 444 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7079 (mp0) REVERT: Y 453 ASN cc_start: 0.8094 (m110) cc_final: 0.7821 (m110) REVERT: Y 456 ILE cc_start: 0.8654 (mt) cc_final: 0.8126 (mt) REVERT: Z 310 ARG cc_start: 0.7706 (mtt-85) cc_final: 0.7019 (mtp85) outliers start: 1 outliers final: 0 residues processed: 1309 average time/residue: 0.2025 time to fit residues: 398.4793 Evaluate side-chains 1161 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1161 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.5980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 960 GLN Q1207 GLN ** Q1228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN R 635 GLN T 27 HIS T 29 HIS T 124 ASN T 205 ASN T 289 ASN T 437 ASN U 62 GLN U 63 ASN U 119 GLN U 401 ASN V 263 GLN V 341 ASN W 63 ASN W 144 GLN W 248 ASN W 299 HIS W 401 ASN W 443 ASN W 446 GLN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 256 ASN X 331 ASN X 440 ASN Y 23 HIS Y 119 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.126578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.107645 restraints weight = 57788.044| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 3.32 r_work: 0.3332 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29139 Z= 0.239 Angle : 0.707 19.669 39425 Z= 0.362 Chirality : 0.047 0.290 4626 Planarity : 0.006 0.108 5049 Dihedral : 8.386 164.398 4012 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.73 % Allowed : 21.58 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.13), residues: 3626 helix: -0.05 (0.12), residues: 1538 sheet: -0.05 (0.21), residues: 594 loop : -0.89 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 55 TYR 0.029 0.002 TYR T 201 PHE 0.026 0.002 PHE X 102 TRP 0.016 0.002 TRP Q1361 HIS 0.008 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00490 (29139) covalent geometry : angle 0.70665 (39425) hydrogen bonds : bond 0.04565 ( 1098) hydrogen bonds : angle 4.84896 ( 3198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 1216 time to evaluate : 1.105 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: Q 960 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8070 (mm110) REVERT: Q 1005 MET cc_start: 0.6684 (mmp) cc_final: 0.6043 (mmp) REVERT: Q 1023 ASP cc_start: 0.7560 (t0) cc_final: 0.7075 (t0) REVERT: Q 1027 SER cc_start: 0.8856 (m) cc_final: 0.8338 (p) REVERT: Q 1112 LYS cc_start: 0.8868 (mttp) cc_final: 0.8189 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8657 (m) cc_final: 0.8115 (t) REVERT: Q 1127 PHE cc_start: 0.8808 (t80) cc_final: 0.8594 (t80) REVERT: Q 1134 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8269 (mm-30) REVERT: Q 1142 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.8010 (mtm-85) REVERT: Q 1148 LEU cc_start: 0.8685 (tt) cc_final: 0.8076 (mp) REVERT: Q 1150 LYS cc_start: 0.8656 (tttm) cc_final: 0.7918 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: Q 1170 ILE cc_start: 0.8128 (mm) cc_final: 0.7601 (tp) REVERT: Q 1173 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7146 (mp0) REVERT: Q 1195 LYS cc_start: 0.8362 (tppt) cc_final: 0.7592 (tppt) REVERT: Q 1208 ARG cc_start: 0.8679 (ttm170) cc_final: 0.8091 (mtp85) REVERT: Q 1230 THR cc_start: 0.8869 (m) cc_final: 0.8505 (p) REVERT: Q 1231 ASN cc_start: 0.8670 (t0) cc_final: 0.8388 (t0) REVERT: Q 1247 SER cc_start: 0.8721 (p) cc_final: 0.8512 (t) REVERT: Q 1248 ASP cc_start: 0.7348 (t70) cc_final: 0.6706 (t0) REVERT: Q 1256 ASN cc_start: 0.8415 (m-40) cc_final: 0.8155 (m-40) REVERT: Q 1261 LYS cc_start: 0.8650 (mttt) cc_final: 0.8290 (mtmm) REVERT: Q 1267 ASP cc_start: 0.8534 (m-30) cc_final: 0.8147 (m-30) REVERT: Q 1280 LYS cc_start: 0.8713 (pttm) cc_final: 0.8445 (pttt) REVERT: Q 1291 MET cc_start: 0.7753 (tpp) cc_final: 0.7533 (tpt) REVERT: Q 1293 ARG cc_start: 0.7712 (mmm-85) cc_final: 0.6969 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8388 (mt) cc_final: 0.8019 (mm) REVERT: Q 1302 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7433 (mtp85) REVERT: Q 1331 MET cc_start: 0.7881 (tpp) cc_final: 0.7424 (tpp) REVERT: Q 1337 TYR cc_start: 0.6852 (t80) cc_final: 0.6618 (t80) REVERT: R 17 ASP cc_start: 0.7233 (m-30) cc_final: 0.6952 (m-30) REVERT: R 55 ASN cc_start: 0.8493 (p0) cc_final: 0.8217 (p0) REVERT: R 208 ASP cc_start: 0.8062 (t0) cc_final: 0.7789 (t0) REVERT: R 218 GLN cc_start: 0.8141 (mp10) cc_final: 0.7854 (mp10) REVERT: R 230 LYS cc_start: 0.8903 (tttt) cc_final: 0.8586 (tttt) REVERT: R 252 TYR cc_start: 0.8311 (p90) cc_final: 0.8081 (p90) REVERT: R 260 ASP cc_start: 0.7753 (m-30) cc_final: 0.7525 (p0) REVERT: R 262 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7937 (mm-30) REVERT: R 592 HIS cc_start: 0.8265 (t-90) cc_final: 0.7574 (t-90) REVERT: R 627 GLN cc_start: 0.8434 (pt0) cc_final: 0.8105 (pt0) REVERT: R 640 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7862 (mt-10) REVERT: R 643 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7126 (mm-30) REVERT: R 647 LEU cc_start: 0.8367 (mp) cc_final: 0.8029 (mp) REVERT: R 659 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8222 (tp-100) REVERT: R 661 SER cc_start: 0.8520 (m) cc_final: 0.8199 (p) REVERT: R 663 ASP cc_start: 0.8398 (m-30) cc_final: 0.7992 (m-30) REVERT: R 664 MET cc_start: 0.8747 (mtm) cc_final: 0.8490 (mtp) REVERT: R 681 LYS cc_start: 0.8936 (tptt) cc_final: 0.8618 (tptt) REVERT: R 721 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7876 (tp30) REVERT: R 724 TYR cc_start: 0.8291 (t80) cc_final: 0.7745 (t80) REVERT: R 728 VAL cc_start: 0.8905 (t) cc_final: 0.8697 (m) REVERT: S 65 GLN cc_start: 0.7565 (tp-100) cc_final: 0.7165 (tp-100) REVERT: S 100 TYR cc_start: 0.7832 (t80) cc_final: 0.7625 (t80) REVERT: S 110 ARG cc_start: 0.7932 (ptt180) cc_final: 0.7592 (mtm-85) REVERT: S 122 LYS cc_start: 0.8349 (mmmm) cc_final: 0.7823 (mtpp) REVERT: S 140 TYR cc_start: 0.8751 (t80) cc_final: 0.8056 (t80) REVERT: S 145 LYS cc_start: 0.8657 (tppp) cc_final: 0.8211 (tppp) REVERT: T 49 VAL cc_start: 0.8540 (p) cc_final: 0.8173 (m) REVERT: T 56 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7813 (mt-10) REVERT: T 92 ILE cc_start: 0.8887 (mt) cc_final: 0.8648 (mp) REVERT: T 95 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8309 (mm-30) REVERT: T 108 SER cc_start: 0.8791 (m) cc_final: 0.8501 (m) REVERT: T 134 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7868 (mmmt) REVERT: T 165 HIS cc_start: 0.8004 (p-80) cc_final: 0.7660 (p-80) REVERT: T 177 LYS cc_start: 0.8542 (tttt) cc_final: 0.8053 (mtpp) REVERT: T 178 THR cc_start: 0.8995 (m) cc_final: 0.8723 (t) REVERT: T 193 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8016 (mmmt) REVERT: T 223 ASP cc_start: 0.7005 (m-30) cc_final: 0.6428 (m-30) REVERT: T 229 TYR cc_start: 0.8706 (m-80) cc_final: 0.8001 (m-80) REVERT: T 240 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8133 (ttmt) REVERT: T 251 ASP cc_start: 0.8142 (m-30) cc_final: 0.7837 (m-30) REVERT: T 274 LYS cc_start: 0.8531 (mmtt) cc_final: 0.8282 (mmtm) REVERT: T 279 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7476 (pt0) REVERT: T 295 TYR cc_start: 0.8669 (m-80) cc_final: 0.8111 (m-80) REVERT: T 323 TYR cc_start: 0.8473 (t80) cc_final: 0.8064 (t80) REVERT: T 381 ARG cc_start: 0.8738 (ttt-90) cc_final: 0.8345 (ttm-80) REVERT: T 382 THR cc_start: 0.8635 (p) cc_final: 0.8321 (m) REVERT: T 385 GLU cc_start: 0.8548 (pt0) cc_final: 0.7898 (pp20) REVERT: T 395 VAL cc_start: 0.8329 (t) cc_final: 0.7999 (p) REVERT: T 401 ASP cc_start: 0.8542 (m-30) cc_final: 0.7972 (m-30) REVERT: T 413 ARG cc_start: 0.7753 (mtp180) cc_final: 0.6721 (mtm-85) REVERT: T 417 GLN cc_start: 0.8322 (mt0) cc_final: 0.7989 (mt0) REVERT: T 419 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8315 (mp) REVERT: T 431 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7377 (mtm180) REVERT: T 436 VAL cc_start: 0.8862 (m) cc_final: 0.8605 (p) REVERT: T 438 ASP cc_start: 0.8323 (m-30) cc_final: 0.7353 (m-30) REVERT: T 448 ASP cc_start: 0.7509 (p0) cc_final: 0.7095 (p0) REVERT: U 29 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7441 (mp) REVERT: U 38 ARG cc_start: 0.8073 (mtt90) cc_final: 0.7846 (mtt180) REVERT: U 42 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7728 (mt-10) REVERT: U 45 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7691 (p) REVERT: U 73 VAL cc_start: 0.8749 (OUTLIER) cc_final: 0.8524 (m) REVERT: U 86 MET cc_start: 0.8190 (mmm) cc_final: 0.7619 (mmm) REVERT: U 90 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8171 (mm110) REVERT: U 94 LYS cc_start: 0.8771 (tppt) cc_final: 0.8337 (tptp) REVERT: U 110 GLU cc_start: 0.7924 (pp20) cc_final: 0.7607 (pp20) REVERT: U 123 LYS cc_start: 0.8319 (mttt) cc_final: 0.7994 (mttp) REVERT: U 128 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8472 (ttmm) REVERT: U 161 LYS cc_start: 0.8668 (ptmm) cc_final: 0.8079 (ptmm) REVERT: U 164 ASP cc_start: 0.7916 (t70) cc_final: 0.7699 (t70) REVERT: U 176 ILE cc_start: 0.8272 (mt) cc_final: 0.8064 (mt) REVERT: U 180 THR cc_start: 0.8567 (m) cc_final: 0.8285 (p) REVERT: U 193 ASP cc_start: 0.7982 (t0) cc_final: 0.7718 (t0) REVERT: U 194 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8201 (ttpp) REVERT: U 198 LYS cc_start: 0.8607 (tttm) cc_final: 0.8211 (tttm) REVERT: U 221 PHE cc_start: 0.7357 (m-80) cc_final: 0.7000 (m-80) REVERT: U 223 GLN cc_start: 0.7157 (pp30) cc_final: 0.6513 (pp30) REVERT: U 254 PHE cc_start: 0.8126 (p90) cc_final: 0.7901 (p90) REVERT: U 272 GLN cc_start: 0.8056 (tp40) cc_final: 0.7541 (tp40) REVERT: U 276 LYS cc_start: 0.8910 (tptt) cc_final: 0.8488 (tptm) REVERT: U 281 LYS cc_start: 0.8925 (tttm) cc_final: 0.8491 (ttmm) REVERT: U 310 ASN cc_start: 0.8213 (m-40) cc_final: 0.7936 (m110) REVERT: U 313 LEU cc_start: 0.8845 (mt) cc_final: 0.8606 (mp) REVERT: U 338 LYS cc_start: 0.8890 (mttt) cc_final: 0.8643 (mtpp) REVERT: U 339 SER cc_start: 0.8880 (m) cc_final: 0.8568 (t) REVERT: U 349 ASP cc_start: 0.8691 (t0) cc_final: 0.8214 (m-30) REVERT: U 365 LYS cc_start: 0.8796 (ttpt) cc_final: 0.8451 (ttmt) REVERT: U 373 GLN cc_start: 0.8814 (tm-30) cc_final: 0.7860 (tm-30) REVERT: U 374 GLU cc_start: 0.7884 (tt0) cc_final: 0.7534 (tp30) REVERT: U 376 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7972 (mm-30) REVERT: U 398 TYR cc_start: 0.8564 (t80) cc_final: 0.8359 (t80) REVERT: U 399 SER cc_start: 0.8381 (m) cc_final: 0.8012 (p) REVERT: U 400 SER cc_start: 0.8205 (t) cc_final: 0.7765 (m) REVERT: U 407 GLN cc_start: 0.8439 (tt0) cc_final: 0.7858 (tt0) REVERT: U 411 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7034 (mpt) REVERT: U 419 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7096 (mm-30) REVERT: U 428 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8238 (pp) REVERT: U 444 GLU cc_start: 0.8130 (tp30) cc_final: 0.7545 (tp30) REVERT: V 30 ILE cc_start: 0.8506 (mt) cc_final: 0.8152 (mt) REVERT: V 31 LYS cc_start: 0.8043 (mmpt) cc_final: 0.7632 (mmtm) REVERT: V 37 GLU cc_start: 0.8173 (pm20) cc_final: 0.7636 (mp0) REVERT: V 52 ILE cc_start: 0.8587 (mp) cc_final: 0.8181 (mm) REVERT: V 56 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7702 (mt-10) REVERT: V 95 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7822 (mt-10) REVERT: V 99 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8386 (mtpp) REVERT: V 109 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8077 (tt0) REVERT: V 114 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7460 (mt-10) REVERT: V 132 ARG cc_start: 0.8190 (tpp80) cc_final: 0.7654 (ttm-80) REVERT: V 144 VAL cc_start: 0.8429 (t) cc_final: 0.8074 (m) REVERT: V 148 THR cc_start: 0.8826 (t) cc_final: 0.8588 (p) REVERT: V 167 ILE cc_start: 0.8652 (mt) cc_final: 0.8256 (mp) REVERT: V 180 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7049 (ttm-80) REVERT: V 187 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7716 (mt-10) REVERT: V 192 GLU cc_start: 0.7327 (tp30) cc_final: 0.7077 (tp30) REVERT: V 203 GLU cc_start: 0.8019 (tt0) cc_final: 0.7502 (tt0) REVERT: V 218 TYR cc_start: 0.8641 (m-80) cc_final: 0.8269 (m-80) REVERT: V 222 PHE cc_start: 0.8409 (m-80) cc_final: 0.8057 (m-10) REVERT: V 239 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7757 (mttt) REVERT: V 253 ASP cc_start: 0.7514 (m-30) cc_final: 0.7222 (m-30) REVERT: V 264 ASP cc_start: 0.7776 (p0) cc_final: 0.7548 (p0) REVERT: V 286 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8106 (mm-40) REVERT: V 290 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8281 (mtpp) REVERT: V 292 VAL cc_start: 0.8605 (t) cc_final: 0.8319 (m) REVERT: V 294 LYS cc_start: 0.8649 (tppt) cc_final: 0.8442 (tppt) REVERT: V 302 GLU cc_start: 0.8032 (pt0) cc_final: 0.7433 (pm20) REVERT: V 318 ILE cc_start: 0.8643 (tp) cc_final: 0.8372 (tt) REVERT: V 325 ASN cc_start: 0.8470 (t0) cc_final: 0.7697 (t0) REVERT: V 326 LYS cc_start: 0.8549 (tmmt) cc_final: 0.8341 (tttt) REVERT: V 329 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7228 (mt-10) REVERT: V 344 MET cc_start: 0.8690 (mmt) cc_final: 0.8381 (mmm) REVERT: V 367 LEU cc_start: 0.8388 (mt) cc_final: 0.8172 (mm) REVERT: V 379 GLU cc_start: 0.8641 (mt-10) cc_final: 0.8272 (mt-10) REVERT: V 403 LEU cc_start: 0.8725 (mt) cc_final: 0.8401 (mm) REVERT: V 418 LEU cc_start: 0.8899 (tp) cc_final: 0.8626 (tp) REVERT: V 432 LYS cc_start: 0.7348 (tptt) cc_final: 0.7104 (tptt) REVERT: V 439 VAL cc_start: 0.8211 (p) cc_final: 0.7963 (t) REVERT: V 440 ASN cc_start: 0.7876 (m-40) cc_final: 0.7326 (m-40) REVERT: V 443 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8316 (pttm) REVERT: V 450 LYS cc_start: 0.8109 (mtmt) cc_final: 0.7637 (mttt) REVERT: V 453 THR cc_start: 0.8731 (m) cc_final: 0.8412 (p) REVERT: V 454 LYS cc_start: 0.8765 (mptt) cc_final: 0.8325 (mmtt) REVERT: W 26 ILE cc_start: 0.8770 (mt) cc_final: 0.8552 (mm) REVERT: W 42 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7943 (mt-10) REVERT: W 86 MET cc_start: 0.7754 (mmm) cc_final: 0.7383 (mmm) REVERT: W 109 LEU cc_start: 0.8532 (mt) cc_final: 0.8327 (mt) REVERT: W 113 LYS cc_start: 0.8666 (mttp) cc_final: 0.8464 (mttp) REVERT: W 154 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8302 (mtpt) REVERT: W 157 LYS cc_start: 0.8369 (mttm) cc_final: 0.8028 (mttp) REVERT: W 158 LEU cc_start: 0.8480 (tt) cc_final: 0.8276 (tt) REVERT: W 159 THR cc_start: 0.8037 (m) cc_final: 0.7636 (p) REVERT: W 185 LEU cc_start: 0.8166 (mt) cc_final: 0.7895 (mt) REVERT: W 188 ASP cc_start: 0.7493 (m-30) cc_final: 0.7120 (m-30) REVERT: W 191 SER cc_start: 0.8453 (t) cc_final: 0.7921 (p) REVERT: W 192 ILE cc_start: 0.8205 (mm) cc_final: 0.7985 (mt) REVERT: W 198 LYS cc_start: 0.8282 (mmmt) cc_final: 0.7928 (tppt) REVERT: W 229 LEU cc_start: 0.8678 (tp) cc_final: 0.8456 (tp) REVERT: W 231 LYS cc_start: 0.8350 (mttm) cc_final: 0.8092 (mmmm) REVERT: W 246 VAL cc_start: 0.8644 (t) cc_final: 0.8348 (m) REVERT: W 261 ASP cc_start: 0.8188 (t0) cc_final: 0.7715 (t0) REVERT: W 264 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6702 (mt-10) REVERT: W 267 SER cc_start: 0.8530 (p) cc_final: 0.8221 (m) REVERT: W 271 ASP cc_start: 0.7968 (m-30) cc_final: 0.7664 (m-30) REVERT: W 275 THR cc_start: 0.8855 (t) cc_final: 0.8633 (p) REVERT: W 281 LYS cc_start: 0.8806 (tttm) cc_final: 0.8452 (tppt) REVERT: W 300 MET cc_start: 0.8677 (mmm) cc_final: 0.8448 (mmm) REVERT: W 362 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7973 (mm-40) REVERT: W 367 ILE cc_start: 0.8750 (mt) cc_final: 0.8369 (tt) REVERT: W 375 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7642 (mt-10) REVERT: W 386 LEU cc_start: 0.8500 (tp) cc_final: 0.8191 (tt) REVERT: W 393 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7987 (mm-30) REVERT: W 413 ARG cc_start: 0.7970 (ttp-170) cc_final: 0.7749 (ttp-170) REVERT: W 438 LYS cc_start: 0.8917 (pttt) cc_final: 0.8690 (pttt) REVERT: W 440 VAL cc_start: 0.9049 (t) cc_final: 0.8691 (t) REVERT: X 33 LEU cc_start: 0.8673 (mt) cc_final: 0.8332 (mm) REVERT: X 88 LEU cc_start: 0.8684 (mt) cc_final: 0.8312 (tt) REVERT: X 95 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8363 (mm-30) REVERT: X 99 LYS cc_start: 0.7706 (pttm) cc_final: 0.6888 (ptpp) REVERT: X 106 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7874 (p) REVERT: X 123 GLU cc_start: 0.8358 (pt0) cc_final: 0.7936 (tt0) REVERT: X 125 PHE cc_start: 0.8178 (m-80) cc_final: 0.7920 (t80) REVERT: X 141 GLU cc_start: 0.7669 (pm20) cc_final: 0.7061 (pm20) REVERT: X 188 SER cc_start: 0.8227 (m) cc_final: 0.7932 (p) REVERT: X 189 ILE cc_start: 0.9282 (mm) cc_final: 0.8999 (mm) REVERT: X 191 ARG cc_start: 0.7576 (ttp-110) cc_final: 0.7143 (ttp-110) REVERT: X 198 ASP cc_start: 0.7537 (m-30) cc_final: 0.6317 (m-30) REVERT: X 201 TYR cc_start: 0.7233 (t80) cc_final: 0.6872 (t80) REVERT: X 211 ARG cc_start: 0.8300 (ttt-90) cc_final: 0.7599 (ttt-90) REVERT: X 212 VAL cc_start: 0.8730 (t) cc_final: 0.8442 (m) REVERT: X 239 LYS cc_start: 0.8383 (ptpt) cc_final: 0.8067 (ptpp) REVERT: X 245 GLN cc_start: 0.8064 (tp40) cc_final: 0.7793 (tp40) REVERT: X 251 ASP cc_start: 0.8028 (m-30) cc_final: 0.7651 (m-30) REVERT: X 263 GLN cc_start: 0.7268 (tm-30) cc_final: 0.6706 (tm-30) REVERT: X 272 LEU cc_start: 0.8958 (tt) cc_final: 0.8653 (tp) REVERT: X 274 LYS cc_start: 0.7979 (tmmt) cc_final: 0.7718 (ttmt) REVERT: X 277 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8398 (mtmt) REVERT: X 282 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7123 (tp30) REVERT: X 285 ARG cc_start: 0.8342 (mtt90) cc_final: 0.7871 (mtm-85) REVERT: X 289 ASN cc_start: 0.8656 (m-40) cc_final: 0.8401 (m-40) REVERT: X 290 LYS cc_start: 0.8489 (tppt) cc_final: 0.7886 (tppt) REVERT: X 292 VAL cc_start: 0.9108 (t) cc_final: 0.8883 (m) REVERT: X 311 ASP cc_start: 0.7654 (m-30) cc_final: 0.7244 (m-30) REVERT: X 325 ASN cc_start: 0.8738 (m-40) cc_final: 0.8358 (m-40) REVERT: X 328 LEU cc_start: 0.8684 (mt) cc_final: 0.8371 (mm) REVERT: X 341 ASN cc_start: 0.8727 (p0) cc_final: 0.8501 (p0) REVERT: X 344 MET cc_start: 0.8248 (mmm) cc_final: 0.7645 (mpp) REVERT: X 345 THR cc_start: 0.8140 (t) cc_final: 0.7601 (p) REVERT: X 362 ASP cc_start: 0.7678 (p0) cc_final: 0.7380 (p0) REVERT: X 363 LEU cc_start: 0.8287 (tp) cc_final: 0.8076 (tp) REVERT: X 376 ASP cc_start: 0.7793 (m-30) cc_final: 0.7574 (m-30) REVERT: X 378 ASP cc_start: 0.7863 (p0) cc_final: 0.7387 (t0) REVERT: X 385 GLU cc_start: 0.8373 (pp20) cc_final: 0.8047 (pp20) REVERT: X 391 GLU cc_start: 0.8585 (tt0) cc_final: 0.7911 (tp30) REVERT: X 392 ARG cc_start: 0.8647 (mtm110) cc_final: 0.8408 (mpp80) REVERT: X 401 ASP cc_start: 0.8357 (m-30) cc_final: 0.8039 (m-30) REVERT: X 402 LEU cc_start: 0.8815 (tp) cc_final: 0.8563 (tt) REVERT: X 406 MET cc_start: 0.8321 (mtp) cc_final: 0.8057 (mtp) REVERT: X 409 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7773 (mm-30) REVERT: X 443 LYS cc_start: 0.8528 (tmmt) cc_final: 0.8212 (ttmm) REVERT: X 447 LEU cc_start: 0.8796 (mp) cc_final: 0.8497 (mt) REVERT: X 448 ASP cc_start: 0.8140 (t0) cc_final: 0.7827 (t70) REVERT: X 450 LYS cc_start: 0.9081 (ttpt) cc_final: 0.8881 (mtpp) REVERT: X 454 LYS cc_start: 0.8640 (tmmt) cc_final: 0.7499 (tmmt) REVERT: X 458 THR cc_start: 0.8540 (m) cc_final: 0.7782 (p) REVERT: Y 59 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8216 (tptp) REVERT: Y 66 ILE cc_start: 0.8824 (mp) cc_final: 0.8535 (mm) REVERT: Y 78 SER cc_start: 0.8437 (t) cc_final: 0.8103 (m) REVERT: Y 105 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7538 (mp0) REVERT: Y 136 ILE cc_start: 0.8567 (mt) cc_final: 0.8137 (tp) REVERT: Y 162 THR cc_start: 0.8594 (p) cc_final: 0.8202 (t) REVERT: Y 164 ASP cc_start: 0.8228 (m-30) cc_final: 0.7990 (m-30) REVERT: Y 166 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6241 (tm-30) REVERT: Y 171 LEU cc_start: 0.8259 (mp) cc_final: 0.8029 (mm) REVERT: Y 173 ASN cc_start: 0.7953 (p0) cc_final: 0.6863 (m-40) REVERT: Y 175 MET cc_start: 0.8883 (tpp) cc_final: 0.8227 (tpp) REVERT: Y 192 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8637 (mm) REVERT: Y 193 ASP cc_start: 0.8444 (t70) cc_final: 0.8169 (t70) REVERT: Y 229 LEU cc_start: 0.8593 (tp) cc_final: 0.8335 (tp) REVERT: Y 243 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7864 (mt-10) REVERT: Y 254 PHE cc_start: 0.7983 (p90) cc_final: 0.7694 (p90) REVERT: Y 271 ASP cc_start: 0.8456 (t0) cc_final: 0.8068 (t0) REVERT: Y 272 GLN cc_start: 0.8535 (mt0) cc_final: 0.8286 (tt0) REVERT: Y 273 ILE cc_start: 0.8732 (mt) cc_final: 0.8386 (mt) REVERT: Y 274 ASN cc_start: 0.8705 (m-40) cc_final: 0.8304 (m-40) REVERT: Y 277 VAL cc_start: 0.8652 (t) cc_final: 0.8423 (p) REVERT: Y 310 ASN cc_start: 0.8121 (m-40) cc_final: 0.7670 (m-40) REVERT: Y 322 MET cc_start: 0.8495 (mtp) cc_final: 0.8189 (mtm) REVERT: Y 327 ARG cc_start: 0.7982 (ttm-80) cc_final: 0.7630 (ttm-80) REVERT: Y 349 ASP cc_start: 0.8303 (t0) cc_final: 0.8065 (t0) REVERT: Y 370 ILE cc_start: 0.9067 (mt) cc_final: 0.8744 (mt) REVERT: Y 375 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7948 (tt0) REVERT: Y 389 LYS cc_start: 0.8906 (ttpt) cc_final: 0.8263 (mmmm) REVERT: Y 393 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7909 (mt-10) REVERT: Y 405 VAL cc_start: 0.8967 (m) cc_final: 0.8764 (p) REVERT: Y 407 GLN cc_start: 0.8434 (tt0) cc_final: 0.8197 (tp40) REVERT: Y 412 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8766 (tptm) REVERT: Y 420 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8355 (p) REVERT: Y 424 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8219 (mtmm) REVERT: Y 441 GLN cc_start: 0.8501 (mm110) cc_final: 0.8188 (mt0) REVERT: Y 456 ILE cc_start: 0.8787 (mt) cc_final: 0.8342 (mt) REVERT: Z 310 ARG cc_start: 0.8141 (mtt-85) cc_final: 0.7505 (mmm-85) REVERT: Z 316 LEU cc_start: 0.8445 (mt) cc_final: 0.8234 (mm) outliers start: 118 outliers final: 51 residues processed: 1277 average time/residue: 0.1951 time to fit residues: 378.4868 Evaluate side-chains 1217 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1152 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 960 GLN Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1270 LYS Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain R residue 22 ARG Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 638 ILE Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 699 THR Chi-restraints excluded: chain R residue 743 LYS Chi-restraints excluded: chain S residue 71 ASN Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 419 LEU Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 307 VAL Chi-restraints excluded: chain V residue 335 VAL Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 63 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 364 ILE Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 340 SER Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 167 THR Chi-restraints excluded: chain Y residue 192 ILE Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 368 LEU Chi-restraints excluded: chain Y residue 399 SER Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 445 SER Chi-restraints excluded: chain Z residue 294 VAL Chi-restraints excluded: chain Z residue 302 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 194 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 329 optimal weight: 10.0000 chunk 277 optimal weight: 6.9990 chunk 359 optimal weight: 0.9990 chunk 111 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 300 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1228 HIS ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q1342 HIS ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 175 ASN R 242 GLN ** R 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 613 HIS ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 HIS T 29 HIS T 205 ASN T 289 ASN T 417 GLN U 119 GLN V 190 GLN V 263 GLN V 341 ASN V 417 GLN W 36 GLN W 90 GLN W 144 GLN W 155 GLN W 248 ASN W 373 GLN W 443 ASN W 446 GLN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.120536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.101905 restraints weight = 57589.104| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.20 r_work: 0.3309 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29139 Z= 0.270 Angle : 0.712 17.001 39425 Z= 0.365 Chirality : 0.048 0.406 4626 Planarity : 0.005 0.084 5049 Dihedral : 8.217 143.934 4012 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.27 % Allowed : 23.29 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.13), residues: 3626 helix: 0.26 (0.13), residues: 1543 sheet: -0.10 (0.21), residues: 568 loop : -0.91 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 69 TYR 0.030 0.002 TYR R 737 PHE 0.027 0.002 PHE R 594 TRP 0.014 0.002 TRP Q1361 HIS 0.009 0.002 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00547 (29139) covalent geometry : angle 0.71163 (39425) hydrogen bonds : bond 0.04773 ( 1098) hydrogen bonds : angle 4.90319 ( 3198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1173 time to evaluate : 0.911 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: Q 960 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8128 (mm-40) REVERT: Q 1005 MET cc_start: 0.6686 (mmp) cc_final: 0.5993 (mmp) REVERT: Q 1023 ASP cc_start: 0.7729 (t0) cc_final: 0.7270 (t0) REVERT: Q 1027 SER cc_start: 0.8812 (m) cc_final: 0.8284 (p) REVERT: Q 1112 LYS cc_start: 0.8840 (mttp) cc_final: 0.8339 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8095 (t) REVERT: Q 1127 PHE cc_start: 0.8840 (t80) cc_final: 0.8618 (t80) REVERT: Q 1142 ARG cc_start: 0.8306 (mtm-85) cc_final: 0.7995 (mtm-85) REVERT: Q 1150 LYS cc_start: 0.8652 (tttm) cc_final: 0.7809 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: Q 1170 ILE cc_start: 0.8355 (mm) cc_final: 0.7917 (tp) REVERT: Q 1173 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7280 (mp0) REVERT: Q 1195 LYS cc_start: 0.8319 (tppt) cc_final: 0.7602 (tppt) REVERT: Q 1208 ARG cc_start: 0.8728 (ttm170) cc_final: 0.8214 (mtp85) REVERT: Q 1230 THR cc_start: 0.8833 (m) cc_final: 0.8374 (p) REVERT: Q 1231 ASN cc_start: 0.8614 (t0) cc_final: 0.8309 (t0) REVERT: Q 1234 ASN cc_start: 0.8481 (m-40) cc_final: 0.8234 (m-40) REVERT: Q 1248 ASP cc_start: 0.7505 (t70) cc_final: 0.6988 (t0) REVERT: Q 1256 ASN cc_start: 0.8414 (m-40) cc_final: 0.8180 (m-40) REVERT: Q 1261 LYS cc_start: 0.8733 (mttt) cc_final: 0.8505 (mtmt) REVERT: Q 1267 ASP cc_start: 0.8584 (m-30) cc_final: 0.8209 (m-30) REVERT: Q 1276 GLU cc_start: 0.8118 (tp30) cc_final: 0.7848 (tp30) REVERT: Q 1293 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.6914 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8395 (mt) cc_final: 0.8109 (mm) REVERT: Q 1302 ARG cc_start: 0.8063 (ttt180) cc_final: 0.7543 (mtp-110) REVERT: Q 1331 MET cc_start: 0.7852 (tpp) cc_final: 0.7485 (tpp) REVERT: Q 1334 TYR cc_start: 0.8038 (p90) cc_final: 0.7675 (p90) REVERT: Q 1337 TYR cc_start: 0.6916 (t80) cc_final: 0.6704 (t80) REVERT: R 35 ASN cc_start: 0.8769 (t0) cc_final: 0.8286 (t0) REVERT: R 55 ASN cc_start: 0.8433 (p0) cc_final: 0.8079 (p0) REVERT: R 63 PHE cc_start: 0.7294 (m-80) cc_final: 0.6804 (m-80) REVERT: R 155 PHE cc_start: 0.7246 (m-10) cc_final: 0.6888 (m-10) REVERT: R 183 THR cc_start: 0.7353 (m) cc_final: 0.6725 (t) REVERT: R 208 ASP cc_start: 0.8067 (t0) cc_final: 0.7805 (t0) REVERT: R 211 ARG cc_start: 0.7553 (ttp-110) cc_final: 0.7050 (ttp-110) REVERT: R 214 TRP cc_start: 0.7601 (t-100) cc_final: 0.6847 (t-100) REVERT: R 242 GLN cc_start: 0.8277 (mt0) cc_final: 0.7696 (mt0) REVERT: R 260 ASP cc_start: 0.7967 (m-30) cc_final: 0.7625 (p0) REVERT: R 262 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8043 (mm-30) REVERT: R 592 HIS cc_start: 0.8194 (t-90) cc_final: 0.7545 (t-90) REVERT: R 612 MET cc_start: 0.6506 (tpp) cc_final: 0.6131 (tpp) REVERT: R 627 GLN cc_start: 0.8487 (pt0) cc_final: 0.8284 (pt0) REVERT: R 640 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: R 643 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7565 (mm-30) REVERT: R 647 LEU cc_start: 0.8497 (mp) cc_final: 0.8143 (mp) REVERT: R 659 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8163 (tp-100) REVERT: R 663 ASP cc_start: 0.8174 (m-30) cc_final: 0.7816 (m-30) REVERT: R 664 MET cc_start: 0.8752 (mtm) cc_final: 0.8506 (mtp) REVERT: R 681 LYS cc_start: 0.8925 (tptt) cc_final: 0.8619 (tptt) REVERT: R 699 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7702 (p) REVERT: R 722 GLU cc_start: 0.8192 (pp20) cc_final: 0.7601 (pp20) REVERT: R 723 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7697 (mm-40) REVERT: R 724 TYR cc_start: 0.8247 (t80) cc_final: 0.7743 (t80) REVERT: R 725 ARG cc_start: 0.8635 (mmt180) cc_final: 0.8233 (tpp80) REVERT: R 726 LYS cc_start: 0.8471 (tptp) cc_final: 0.8201 (tptp) REVERT: R 728 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8702 (m) REVERT: R 729 ILE cc_start: 0.6780 (OUTLIER) cc_final: 0.6546 (tp) REVERT: R 743 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.7048 (mtmm) REVERT: S 100 TYR cc_start: 0.7912 (t80) cc_final: 0.7559 (t80) REVERT: S 110 ARG cc_start: 0.8138 (ptt180) cc_final: 0.7548 (mtm180) REVERT: S 122 LYS cc_start: 0.8406 (mmmm) cc_final: 0.8025 (mtpp) REVERT: S 140 TYR cc_start: 0.8666 (t80) cc_final: 0.8212 (t80) REVERT: S 145 LYS cc_start: 0.8748 (tppp) cc_final: 0.8366 (tppp) REVERT: T 49 VAL cc_start: 0.8533 (p) cc_final: 0.8203 (m) REVERT: T 56 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7885 (mm-30) REVERT: T 70 MET cc_start: 0.7760 (mmm) cc_final: 0.6440 (mmm) REVERT: T 92 ILE cc_start: 0.8921 (mt) cc_final: 0.8631 (mp) REVERT: T 95 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8241 (mm-30) REVERT: T 108 SER cc_start: 0.8779 (m) cc_final: 0.8564 (m) REVERT: T 134 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7970 (mmmt) REVERT: T 177 LYS cc_start: 0.8528 (tttt) cc_final: 0.8022 (mtpp) REVERT: T 178 THR cc_start: 0.9008 (m) cc_final: 0.8720 (t) REVERT: T 193 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8148 (mmmt) REVERT: T 224 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8497 (tp) REVERT: T 240 LYS cc_start: 0.8389 (ttmt) cc_final: 0.8175 (ttmt) REVERT: T 251 ASP cc_start: 0.8210 (m-30) cc_final: 0.7906 (m-30) REVERT: T 273 LEU cc_start: 0.7744 (tp) cc_final: 0.7495 (tt) REVERT: T 274 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8240 (mmtm) REVERT: T 279 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: T 295 TYR cc_start: 0.8665 (m-80) cc_final: 0.8104 (m-80) REVERT: T 371 ARG cc_start: 0.8087 (mtp-110) cc_final: 0.7633 (ptm160) REVERT: T 381 ARG cc_start: 0.8706 (ttt-90) cc_final: 0.8339 (ttm-80) REVERT: T 385 GLU cc_start: 0.8492 (pt0) cc_final: 0.7857 (pp20) REVERT: T 395 VAL cc_start: 0.8540 (t) cc_final: 0.8208 (p) REVERT: T 401 ASP cc_start: 0.8488 (m-30) cc_final: 0.7713 (m-30) REVERT: T 413 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7146 (mtm-85) REVERT: T 417 GLN cc_start: 0.8269 (mt0) cc_final: 0.8026 (mt0) REVERT: T 424 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8041 (mt) REVERT: T 431 ARG cc_start: 0.7915 (mtm180) cc_final: 0.7531 (mtm180) REVERT: T 438 ASP cc_start: 0.8383 (m-30) cc_final: 0.7462 (m-30) REVERT: T 448 ASP cc_start: 0.7646 (p0) cc_final: 0.7201 (p0) REVERT: T 456 LEU cc_start: 0.8911 (tp) cc_final: 0.8337 (mt) REVERT: T 457 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8016 (mt-10) REVERT: U 45 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7912 (p) REVERT: U 73 VAL cc_start: 0.8793 (m) cc_final: 0.8262 (p) REVERT: U 86 MET cc_start: 0.8150 (mmm) cc_final: 0.7679 (mmm) REVERT: U 94 LYS cc_start: 0.8845 (tppt) cc_final: 0.8407 (tptp) REVERT: U 104 SER cc_start: 0.8546 (m) cc_final: 0.8259 (t) REVERT: U 105 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7307 (mt-10) REVERT: U 110 GLU cc_start: 0.7902 (pp20) cc_final: 0.7571 (pp20) REVERT: U 123 LYS cc_start: 0.8345 (mttt) cc_final: 0.8119 (mttp) REVERT: U 128 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8474 (ttmm) REVERT: U 132 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7498 (mt-10) REVERT: U 139 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6319 (tp30) REVERT: U 161 LYS cc_start: 0.8723 (ptmm) cc_final: 0.8127 (ptmm) REVERT: U 164 ASP cc_start: 0.8045 (t70) cc_final: 0.7769 (t70) REVERT: U 175 MET cc_start: 0.8044 (tpp) cc_final: 0.7833 (tpp) REVERT: U 193 ASP cc_start: 0.7943 (t0) cc_final: 0.7560 (t0) REVERT: U 198 LYS cc_start: 0.8495 (tttm) cc_final: 0.8162 (tttm) REVERT: U 221 PHE cc_start: 0.7539 (m-80) cc_final: 0.7029 (m-80) REVERT: U 265 ILE cc_start: 0.8846 (mp) cc_final: 0.8616 (mm) REVERT: U 272 GLN cc_start: 0.8088 (tp40) cc_final: 0.7606 (tp40) REVERT: U 276 LYS cc_start: 0.8978 (tptt) cc_final: 0.8539 (tptm) REVERT: U 281 LYS cc_start: 0.8981 (tttm) cc_final: 0.8585 (ttmm) REVERT: U 310 ASN cc_start: 0.8250 (m-40) cc_final: 0.8008 (m110) REVERT: U 313 LEU cc_start: 0.8838 (mt) cc_final: 0.8580 (mp) REVERT: U 338 LYS cc_start: 0.8878 (mttt) cc_final: 0.8630 (mtpp) REVERT: U 339 SER cc_start: 0.8850 (m) cc_final: 0.8557 (t) REVERT: U 349 ASP cc_start: 0.8673 (t0) cc_final: 0.8271 (m-30) REVERT: U 351 SER cc_start: 0.8507 (t) cc_final: 0.8297 (p) REVERT: U 365 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8526 (ttmt) REVERT: U 374 GLU cc_start: 0.7873 (tt0) cc_final: 0.7556 (tt0) REVERT: U 376 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7881 (mm-30) REVERT: U 378 GLU cc_start: 0.7354 (mp0) cc_final: 0.7140 (mp0) REVERT: U 399 SER cc_start: 0.8399 (m) cc_final: 0.8058 (p) REVERT: U 400 SER cc_start: 0.8277 (t) cc_final: 0.7797 (m) REVERT: U 411 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7159 (mpt) REVERT: U 424 LYS cc_start: 0.8330 (mmtt) cc_final: 0.8016 (mmtt) REVERT: U 428 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8358 (pp) REVERT: U 444 GLU cc_start: 0.8165 (tp30) cc_final: 0.7588 (tp30) REVERT: V 30 ILE cc_start: 0.8682 (mt) cc_final: 0.8443 (mm) REVERT: V 31 LYS cc_start: 0.8218 (mmpt) cc_final: 0.7901 (mmtt) REVERT: V 37 GLU cc_start: 0.8214 (pm20) cc_final: 0.7656 (mp0) REVERT: V 52 ILE cc_start: 0.8717 (mp) cc_final: 0.8365 (mm) REVERT: V 56 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7757 (mt-10) REVERT: V 95 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7859 (mt-10) REVERT: V 99 LYS cc_start: 0.8721 (mtpt) cc_final: 0.8390 (mtpp) REVERT: V 109 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8072 (tt0) REVERT: V 114 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7368 (mt-10) REVERT: V 132 ARG cc_start: 0.8303 (tpp80) cc_final: 0.7648 (tpp80) REVERT: V 144 VAL cc_start: 0.8569 (t) cc_final: 0.8166 (m) REVERT: V 187 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7701 (mt-10) REVERT: V 192 GLU cc_start: 0.7269 (tp30) cc_final: 0.7027 (tp30) REVERT: V 203 GLU cc_start: 0.8028 (tt0) cc_final: 0.7760 (tt0) REVERT: V 218 TYR cc_start: 0.8662 (m-80) cc_final: 0.8234 (m-80) REVERT: V 222 PHE cc_start: 0.8397 (m-80) cc_final: 0.8143 (m-10) REVERT: V 239 LYS cc_start: 0.8303 (mtpt) cc_final: 0.8012 (mtmm) REVERT: V 253 ASP cc_start: 0.7500 (m-30) cc_final: 0.7207 (m-30) REVERT: V 268 MET cc_start: 0.8162 (mmm) cc_final: 0.7603 (mmm) REVERT: V 282 GLU cc_start: 0.8153 (pp20) cc_final: 0.7597 (pp20) REVERT: V 302 GLU cc_start: 0.8049 (pt0) cc_final: 0.7716 (pm20) REVERT: V 318 ILE cc_start: 0.8696 (tp) cc_final: 0.8452 (tt) REVERT: V 325 ASN cc_start: 0.8451 (t0) cc_final: 0.7688 (t0) REVERT: V 326 LYS cc_start: 0.8592 (tmmt) cc_final: 0.8353 (tttt) REVERT: V 329 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7219 (mm-30) REVERT: V 367 LEU cc_start: 0.8439 (mt) cc_final: 0.8231 (mm) REVERT: V 373 LEU cc_start: 0.8574 (mm) cc_final: 0.8340 (mp) REVERT: V 379 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8277 (mt-10) REVERT: V 403 LEU cc_start: 0.8796 (mt) cc_final: 0.8446 (mm) REVERT: V 418 LEU cc_start: 0.8929 (tp) cc_final: 0.8697 (tp) REVERT: V 439 VAL cc_start: 0.8191 (p) cc_final: 0.7867 (t) REVERT: V 440 ASN cc_start: 0.7896 (m-40) cc_final: 0.7218 (m-40) REVERT: V 443 LYS cc_start: 0.8570 (mtpt) cc_final: 0.8328 (mtmt) REVERT: V 450 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7608 (mttt) REVERT: V 453 THR cc_start: 0.8820 (m) cc_final: 0.8485 (p) REVERT: V 454 LYS cc_start: 0.8762 (mptt) cc_final: 0.8332 (mmtt) REVERT: W 86 MET cc_start: 0.7876 (mmm) cc_final: 0.7536 (mmm) REVERT: W 113 LYS cc_start: 0.8684 (mttp) cc_final: 0.8460 (mtmm) REVERT: W 136 ILE cc_start: 0.8689 (mp) cc_final: 0.8457 (mp) REVERT: W 159 THR cc_start: 0.8032 (m) cc_final: 0.7674 (p) REVERT: W 185 LEU cc_start: 0.8149 (mt) cc_final: 0.7766 (mt) REVERT: W 188 ASP cc_start: 0.7603 (m-30) cc_final: 0.7130 (m-30) REVERT: W 191 SER cc_start: 0.8701 (t) cc_final: 0.8222 (p) REVERT: W 229 LEU cc_start: 0.8593 (tp) cc_final: 0.8331 (tp) REVERT: W 231 LYS cc_start: 0.8442 (mttm) cc_final: 0.8216 (mmmm) REVERT: W 261 ASP cc_start: 0.8185 (t0) cc_final: 0.7412 (t0) REVERT: W 264 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6814 (mt-10) REVERT: W 271 ASP cc_start: 0.7926 (m-30) cc_final: 0.7721 (m-30) REVERT: W 281 LYS cc_start: 0.8790 (tttm) cc_final: 0.8441 (tppt) REVERT: W 306 PHE cc_start: 0.8319 (m-80) cc_final: 0.7966 (m-80) REVERT: W 310 ASN cc_start: 0.8136 (m-40) cc_final: 0.7734 (m-40) REVERT: W 365 LYS cc_start: 0.9000 (tmmt) cc_final: 0.8674 (tmmt) REVERT: W 367 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8255 (tt) REVERT: W 386 LEU cc_start: 0.8498 (tp) cc_final: 0.8283 (tt) REVERT: W 393 GLU cc_start: 0.8257 (mt-10) cc_final: 0.8003 (mm-30) REVERT: W 424 LYS cc_start: 0.8660 (ptpt) cc_final: 0.8392 (ptpt) REVERT: W 450 ASP cc_start: 0.7726 (m-30) cc_final: 0.7513 (m-30) REVERT: X 95 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8194 (mm-30) REVERT: X 123 GLU cc_start: 0.8312 (pt0) cc_final: 0.7959 (tt0) REVERT: X 141 GLU cc_start: 0.7585 (pm20) cc_final: 0.7370 (pm20) REVERT: X 186 TYR cc_start: 0.8468 (t80) cc_final: 0.8209 (t80) REVERT: X 189 ILE cc_start: 0.9185 (mm) cc_final: 0.8934 (mt) REVERT: X 198 ASP cc_start: 0.7446 (m-30) cc_final: 0.7099 (m-30) REVERT: X 201 TYR cc_start: 0.7104 (t80) cc_final: 0.6809 (t80) REVERT: X 212 VAL cc_start: 0.8722 (t) cc_final: 0.8506 (m) REVERT: X 239 LYS cc_start: 0.8454 (ptpt) cc_final: 0.8175 (ptpt) REVERT: X 245 GLN cc_start: 0.8139 (tp40) cc_final: 0.7802 (tp40) REVERT: X 251 ASP cc_start: 0.7975 (m-30) cc_final: 0.7582 (m-30) REVERT: X 263 GLN cc_start: 0.7300 (tm-30) cc_final: 0.6635 (tm-30) REVERT: X 268 MET cc_start: 0.8433 (mtt) cc_final: 0.8196 (mtp) REVERT: X 272 LEU cc_start: 0.8927 (tt) cc_final: 0.8687 (tp) REVERT: X 274 LYS cc_start: 0.8097 (tmmt) cc_final: 0.7734 (ttpt) REVERT: X 285 ARG cc_start: 0.8246 (mtt90) cc_final: 0.7801 (mtm-85) REVERT: X 303 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7767 (tp) REVERT: X 312 GLU cc_start: 0.7689 (mp0) cc_final: 0.7472 (pm20) REVERT: X 315 MET cc_start: 0.8329 (mtp) cc_final: 0.8022 (mtp) REVERT: X 325 ASN cc_start: 0.8770 (m-40) cc_final: 0.8474 (m-40) REVERT: X 328 LEU cc_start: 0.8794 (mt) cc_final: 0.8504 (mm) REVERT: X 344 MET cc_start: 0.8125 (mmm) cc_final: 0.7842 (mmm) REVERT: X 345 THR cc_start: 0.8275 (t) cc_final: 0.7851 (p) REVERT: X 378 ASP cc_start: 0.7814 (p0) cc_final: 0.7462 (t0) REVERT: X 385 GLU cc_start: 0.8402 (pp20) cc_final: 0.8089 (pp20) REVERT: X 392 ARG cc_start: 0.8629 (mtm110) cc_final: 0.8411 (mpp80) REVERT: X 401 ASP cc_start: 0.8408 (m-30) cc_final: 0.8076 (m-30) REVERT: X 406 MET cc_start: 0.8299 (mtp) cc_final: 0.7896 (mtp) REVERT: X 409 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7853 (mm-30) REVERT: X 417 GLN cc_start: 0.8165 (mt0) cc_final: 0.7896 (mt0) REVERT: X 431 ARG cc_start: 0.7806 (ttp-110) cc_final: 0.7401 (ttp-110) REVERT: X 443 LYS cc_start: 0.8541 (tmmt) cc_final: 0.8242 (ttmt) REVERT: X 448 ASP cc_start: 0.8074 (t0) cc_final: 0.7865 (t70) REVERT: X 454 LYS cc_start: 0.8426 (tmmt) cc_final: 0.7952 (tmmt) REVERT: Y 52 ARG cc_start: 0.8588 (tpt170) cc_final: 0.8320 (tpt170) REVERT: Y 59 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8312 (tptp) REVERT: Y 66 ILE cc_start: 0.8816 (mp) cc_final: 0.8475 (mp) REVERT: Y 78 SER cc_start: 0.8473 (t) cc_final: 0.8156 (m) REVERT: Y 105 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7551 (mp0) REVERT: Y 130 LYS cc_start: 0.7931 (ttmm) cc_final: 0.7726 (mtmm) REVERT: Y 136 ILE cc_start: 0.8568 (mt) cc_final: 0.8075 (tp) REVERT: Y 164 ASP cc_start: 0.8258 (m-30) cc_final: 0.8003 (m-30) REVERT: Y 166 GLU cc_start: 0.6714 (tm-30) cc_final: 0.6398 (tm-30) REVERT: Y 171 LEU cc_start: 0.8332 (mp) cc_final: 0.8101 (mm) REVERT: Y 173 ASN cc_start: 0.8007 (p0) cc_final: 0.7754 (p0) REVERT: Y 174 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8409 (mmtm) REVERT: Y 175 MET cc_start: 0.8868 (tpp) cc_final: 0.8202 (tpp) REVERT: Y 192 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8718 (mm) REVERT: Y 237 HIS cc_start: 0.7871 (m170) cc_final: 0.7670 (m170) REVERT: Y 266 ARG cc_start: 0.7715 (mtm110) cc_final: 0.6416 (mtm110) REVERT: Y 271 ASP cc_start: 0.8453 (t0) cc_final: 0.8068 (t0) REVERT: Y 272 GLN cc_start: 0.8503 (mt0) cc_final: 0.8286 (tt0) REVERT: Y 273 ILE cc_start: 0.8719 (mt) cc_final: 0.8386 (mt) REVERT: Y 274 ASN cc_start: 0.8708 (m-40) cc_final: 0.8288 (m-40) REVERT: Y 277 VAL cc_start: 0.8656 (t) cc_final: 0.8394 (p) REVERT: Y 287 GLU cc_start: 0.7952 (pm20) cc_final: 0.7732 (pm20) REVERT: Y 310 ASN cc_start: 0.8108 (m-40) cc_final: 0.7650 (m-40) REVERT: Y 322 MET cc_start: 0.8470 (mtp) cc_final: 0.8247 (mtt) REVERT: Y 327 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7591 (ttm-80) REVERT: Y 338 LYS cc_start: 0.8715 (mtpp) cc_final: 0.8477 (mttm) REVERT: Y 339 SER cc_start: 0.8777 (t) cc_final: 0.8358 (p) REVERT: Y 370 ILE cc_start: 0.9030 (mt) cc_final: 0.8801 (mt) REVERT: Y 375 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7894 (tt0) REVERT: Y 384 LEU cc_start: 0.8994 (tp) cc_final: 0.8696 (tt) REVERT: Y 389 LYS cc_start: 0.8902 (ttpt) cc_final: 0.8383 (mmmm) REVERT: Y 390 THR cc_start: 0.8864 (p) cc_final: 0.8516 (p) REVERT: Y 393 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8079 (mt-10) REVERT: Y 401 ASN cc_start: 0.8893 (m-40) cc_final: 0.8666 (m110) REVERT: Y 407 GLN cc_start: 0.8680 (tt0) cc_final: 0.8419 (tp40) REVERT: Y 424 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8325 (mtmm) REVERT: Y 427 TYR cc_start: 0.8336 (t80) cc_final: 0.7613 (t80) REVERT: Y 441 GLN cc_start: 0.8523 (mm110) cc_final: 0.8222 (mt0) REVERT: Y 455 GLN cc_start: 0.8131 (tt0) cc_final: 0.7841 (mt0) REVERT: Y 456 ILE cc_start: 0.8832 (mt) cc_final: 0.8380 (mt) REVERT: Z 310 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7427 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7731 (ttm110) cc_final: 0.7291 (ttm110) REVERT: Z 316 LEU cc_start: 0.8548 (mt) cc_final: 0.8314 (mm) outliers start: 135 outliers final: 64 residues processed: 1235 average time/residue: 0.1959 time to fit residues: 367.9521 Evaluate side-chains 1211 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1130 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1125 CYS Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1270 LYS Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1309 VAL Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 165 PHE Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 638 ILE Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 699 THR Chi-restraints excluded: chain R residue 728 VAL Chi-restraints excluded: chain R residue 729 ILE Chi-restraints excluded: chain R residue 743 LYS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 329 GLU Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 347 VAL Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 424 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 282 GLU Chi-restraints excluded: chain U residue 335 THR Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 335 VAL Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 133 THR Chi-restraints excluded: chain W residue 134 GLU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 364 ILE Chi-restraints excluded: chain W residue 367 ILE Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 171 LYS Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 303 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 340 SER Chi-restraints excluded: chain X residue 430 ASN Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 113 LYS Chi-restraints excluded: chain Y residue 167 THR Chi-restraints excluded: chain Y residue 192 ILE Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Z residue 294 VAL Chi-restraints excluded: chain Z residue 305 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 55 optimal weight: 0.8980 chunk 270 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 chunk 343 optimal weight: 2.9990 chunk 262 optimal weight: 0.6980 chunk 278 optimal weight: 0.0570 chunk 350 optimal weight: 0.9980 chunk 263 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 chunk 315 optimal weight: 2.9990 chunk 226 optimal weight: 0.8980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 960 GLN Q1110 ASN Q1228 HIS ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 224 ASN ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 HIS T 29 HIS T 124 ASN U 237 HIS V 341 ASN W 63 ASN W 90 GLN W 144 GLN X 27 HIS ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 190 GLN X 289 ASN X 440 ASN Y 407 GLN Y 453 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.127625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.108712 restraints weight = 56884.275| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.30 r_work: 0.3349 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29139 Z= 0.132 Angle : 0.640 16.734 39425 Z= 0.316 Chirality : 0.045 0.233 4626 Planarity : 0.005 0.072 5049 Dihedral : 7.778 140.419 4012 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.11 % Allowed : 24.59 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.14), residues: 3626 helix: 0.66 (0.13), residues: 1534 sheet: -0.07 (0.21), residues: 576 loop : -0.73 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 266 TYR 0.027 0.002 TYR R 734 PHE 0.022 0.001 PHE Y 254 TRP 0.021 0.002 TRP R 108 HIS 0.016 0.001 HIS R 613 Details of bonding type rmsd covalent geometry : bond 0.00291 (29139) covalent geometry : angle 0.63989 (39425) hydrogen bonds : bond 0.03615 ( 1098) hydrogen bonds : angle 4.50778 ( 3198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1150 time to evaluate : 0.956 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: Q 960 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7992 (mm110) REVERT: Q 1005 MET cc_start: 0.6679 (mmp) cc_final: 0.5942 (mmp) REVERT: Q 1023 ASP cc_start: 0.7728 (t0) cc_final: 0.7270 (t0) REVERT: Q 1027 SER cc_start: 0.8745 (m) cc_final: 0.8281 (p) REVERT: Q 1102 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.8038 (m) REVERT: Q 1112 LYS cc_start: 0.8797 (mttp) cc_final: 0.8271 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8651 (m) cc_final: 0.8187 (t) REVERT: Q 1127 PHE cc_start: 0.8792 (t80) cc_final: 0.8576 (t80) REVERT: Q 1150 LYS cc_start: 0.8585 (tttm) cc_final: 0.7715 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: Q 1173 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7165 (mp0) REVERT: Q 1180 ASN cc_start: 0.7572 (m110) cc_final: 0.7323 (m-40) REVERT: Q 1195 LYS cc_start: 0.8254 (tppt) cc_final: 0.7486 (tppt) REVERT: Q 1208 ARG cc_start: 0.8725 (ttm170) cc_final: 0.7717 (mtp180) REVERT: Q 1230 THR cc_start: 0.8733 (m) cc_final: 0.8283 (p) REVERT: Q 1231 ASN cc_start: 0.8553 (t0) cc_final: 0.8260 (t0) REVERT: Q 1234 ASN cc_start: 0.8443 (m-40) cc_final: 0.8182 (m-40) REVERT: Q 1242 ILE cc_start: 0.9187 (tp) cc_final: 0.8768 (tt) REVERT: Q 1248 ASP cc_start: 0.7443 (t70) cc_final: 0.6841 (t0) REVERT: Q 1256 ASN cc_start: 0.8424 (m-40) cc_final: 0.8189 (m-40) REVERT: Q 1261 LYS cc_start: 0.8697 (mttt) cc_final: 0.8444 (mttt) REVERT: Q 1266 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7776 (tm-30) REVERT: Q 1267 ASP cc_start: 0.8551 (m-30) cc_final: 0.7840 (m-30) REVERT: Q 1276 GLU cc_start: 0.8185 (tp30) cc_final: 0.7934 (tp30) REVERT: Q 1293 ARG cc_start: 0.7676 (mmm-85) cc_final: 0.6814 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8351 (mt) cc_final: 0.7997 (mm) REVERT: Q 1302 ARG cc_start: 0.8010 (ttt180) cc_final: 0.7499 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8584 (m-30) cc_final: 0.8299 (m-30) REVERT: Q 1331 MET cc_start: 0.7886 (tpp) cc_final: 0.7422 (tpp) REVERT: Q 1334 TYR cc_start: 0.7993 (p90) cc_final: 0.7657 (p90) REVERT: Q 1335 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7691 (mp) REVERT: R 35 ASN cc_start: 0.8792 (t0) cc_final: 0.8277 (t0) REVERT: R 55 ASN cc_start: 0.8424 (p0) cc_final: 0.8054 (p0) REVERT: R 70 PHE cc_start: 0.7565 (t80) cc_final: 0.7267 (t80) REVERT: R 110 LEU cc_start: 0.8181 (mp) cc_final: 0.7976 (mp) REVERT: R 155 PHE cc_start: 0.7390 (m-10) cc_final: 0.7166 (m-10) REVERT: R 183 THR cc_start: 0.7288 (m) cc_final: 0.6716 (t) REVERT: R 211 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.6959 (ttp80) REVERT: R 214 TRP cc_start: 0.7468 (t-100) cc_final: 0.6925 (t-100) REVERT: R 227 MET cc_start: 0.8357 (mmp) cc_final: 0.8146 (mmp) REVERT: R 230 LYS cc_start: 0.8889 (tttt) cc_final: 0.8533 (tttt) REVERT: R 244 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: R 251 CYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6957 (m) REVERT: R 260 ASP cc_start: 0.7851 (m-30) cc_final: 0.7560 (p0) REVERT: R 262 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8086 (mm-30) REVERT: R 592 HIS cc_start: 0.8132 (t-90) cc_final: 0.7436 (t-90) REVERT: R 609 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.7246 (mp10) REVERT: R 612 MET cc_start: 0.6653 (tpp) cc_final: 0.6193 (tpp) REVERT: R 627 GLN cc_start: 0.8480 (pt0) cc_final: 0.8227 (pt0) REVERT: R 640 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.6886 (mm-30) REVERT: R 643 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7452 (mm-30) REVERT: R 647 LEU cc_start: 0.8426 (mp) cc_final: 0.8065 (mp) REVERT: R 659 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8084 (tp-100) REVERT: R 663 ASP cc_start: 0.8170 (m-30) cc_final: 0.7784 (m-30) REVERT: R 664 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8413 (mtp) REVERT: R 699 THR cc_start: 0.8023 (m) cc_final: 0.7687 (p) REVERT: R 722 GLU cc_start: 0.8415 (pp20) cc_final: 0.7230 (pp20) REVERT: R 723 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7452 (mm-40) REVERT: R 724 TYR cc_start: 0.8142 (t80) cc_final: 0.7650 (t80) REVERT: R 726 LYS cc_start: 0.8473 (tptp) cc_final: 0.8100 (tptp) REVERT: R 728 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8605 (m) REVERT: R 729 ILE cc_start: 0.6530 (OUTLIER) cc_final: 0.6285 (tp) REVERT: S 73 ARG cc_start: 0.8435 (tmm-80) cc_final: 0.7964 (tmm-80) REVERT: S 100 TYR cc_start: 0.7945 (t80) cc_final: 0.7629 (t80) REVERT: S 110 ARG cc_start: 0.8144 (ptt180) cc_final: 0.7439 (mtm-85) REVERT: S 122 LYS cc_start: 0.8396 (mmmm) cc_final: 0.8020 (mtpp) REVERT: S 140 TYR cc_start: 0.8596 (t80) cc_final: 0.8155 (t80) REVERT: S 145 LYS cc_start: 0.8686 (tppp) cc_final: 0.8287 (tppp) REVERT: T 49 VAL cc_start: 0.8395 (p) cc_final: 0.8022 (m) REVERT: T 56 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7778 (mm-30) REVERT: T 95 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8157 (mm-30) REVERT: T 177 LYS cc_start: 0.8503 (tttt) cc_final: 0.8108 (mtpp) REVERT: T 178 THR cc_start: 0.8979 (m) cc_final: 0.8705 (t) REVERT: T 193 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8050 (mmmt) REVERT: T 218 TYR cc_start: 0.7720 (m-80) cc_final: 0.7144 (m-10) REVERT: T 224 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8481 (tp) REVERT: T 229 TYR cc_start: 0.8595 (m-80) cc_final: 0.7684 (m-80) REVERT: T 251 ASP cc_start: 0.8149 (m-30) cc_final: 0.7826 (m-30) REVERT: T 273 LEU cc_start: 0.7706 (tp) cc_final: 0.7505 (tt) REVERT: T 274 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8246 (mmtm) REVERT: T 279 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7408 (pt0) REVERT: T 295 TYR cc_start: 0.8603 (m-80) cc_final: 0.8049 (m-80) REVERT: T 371 ARG cc_start: 0.7957 (mtp-110) cc_final: 0.7412 (ptm-80) REVERT: T 381 ARG cc_start: 0.8708 (ttt-90) cc_final: 0.8235 (ttm-80) REVERT: T 382 THR cc_start: 0.8583 (p) cc_final: 0.8348 (m) REVERT: T 385 GLU cc_start: 0.8508 (pt0) cc_final: 0.7803 (pp20) REVERT: T 395 VAL cc_start: 0.8491 (t) cc_final: 0.8273 (t) REVERT: T 396 GLU cc_start: 0.7363 (pt0) cc_final: 0.7111 (pt0) REVERT: T 401 ASP cc_start: 0.8486 (m-30) cc_final: 0.7656 (m-30) REVERT: T 409 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: T 413 ARG cc_start: 0.7736 (mtp180) cc_final: 0.6441 (mtm-85) REVERT: T 414 TYR cc_start: 0.8025 (t80) cc_final: 0.7601 (t80) REVERT: T 417 GLN cc_start: 0.8242 (mt0) cc_final: 0.7851 (mt0) REVERT: T 431 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7361 (mtm180) REVERT: T 434 ILE cc_start: 0.7693 (mt) cc_final: 0.7129 (mt) REVERT: T 439 VAL cc_start: 0.8882 (t) cc_final: 0.8676 (t) REVERT: T 448 ASP cc_start: 0.7605 (p0) cc_final: 0.7261 (p0) REVERT: T 457 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8049 (mt-10) REVERT: U 38 ARG cc_start: 0.8171 (mtt90) cc_final: 0.7588 (mpt180) REVERT: U 81 LYS cc_start: 0.8678 (mtmm) cc_final: 0.8215 (mtmm) REVERT: U 86 MET cc_start: 0.8060 (mmm) cc_final: 0.7585 (mmm) REVERT: U 94 LYS cc_start: 0.8810 (tppt) cc_final: 0.8388 (tptp) REVERT: U 104 SER cc_start: 0.8536 (m) cc_final: 0.8162 (t) REVERT: U 110 GLU cc_start: 0.7905 (pp20) cc_final: 0.7567 (pp20) REVERT: U 123 LYS cc_start: 0.8259 (mttt) cc_final: 0.7965 (mttp) REVERT: U 128 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8445 (ttmm) REVERT: U 132 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7710 (mt-10) REVERT: U 139 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6303 (tp30) REVERT: U 161 LYS cc_start: 0.8646 (ptmm) cc_final: 0.7484 (ptmm) REVERT: U 164 ASP cc_start: 0.7979 (t70) cc_final: 0.7683 (t70) REVERT: U 166 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7132 (tp30) REVERT: U 182 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7833 (tm-30) REVERT: U 193 ASP cc_start: 0.7919 (t0) cc_final: 0.7540 (t0) REVERT: U 198 LYS cc_start: 0.8554 (tttm) cc_final: 0.8207 (tttm) REVERT: U 221 PHE cc_start: 0.7404 (m-80) cc_final: 0.7171 (m-80) REVERT: U 272 GLN cc_start: 0.8017 (tp40) cc_final: 0.7505 (tp40) REVERT: U 276 LYS cc_start: 0.8951 (tptt) cc_final: 0.8488 (tptm) REVERT: U 281 LYS cc_start: 0.8927 (tttm) cc_final: 0.8514 (ttmm) REVERT: U 300 MET cc_start: 0.8543 (mmm) cc_final: 0.8092 (mmp) REVERT: U 313 LEU cc_start: 0.8830 (mt) cc_final: 0.8562 (mp) REVERT: U 338 LYS cc_start: 0.8874 (mttt) cc_final: 0.8616 (mtpp) REVERT: U 339 SER cc_start: 0.8830 (m) cc_final: 0.8515 (t) REVERT: U 349 ASP cc_start: 0.8703 (t0) cc_final: 0.8255 (m-30) REVERT: U 362 GLN cc_start: 0.8157 (tp40) cc_final: 0.7919 (tp-100) REVERT: U 365 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8484 (ttmt) REVERT: U 376 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7969 (mm-30) REVERT: U 393 GLU cc_start: 0.7561 (pp20) cc_final: 0.7332 (pp20) REVERT: U 399 SER cc_start: 0.8385 (m) cc_final: 0.8141 (p) REVERT: U 400 SER cc_start: 0.8257 (t) cc_final: 0.7821 (m) REVERT: U 411 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7131 (mpt) REVERT: U 419 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7047 (mm-30) REVERT: U 424 LYS cc_start: 0.8274 (mmtt) cc_final: 0.7959 (mmtt) REVERT: U 428 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8335 (pp) REVERT: U 444 GLU cc_start: 0.8199 (tp30) cc_final: 0.7629 (tp30) REVERT: V 30 ILE cc_start: 0.8530 (mt) cc_final: 0.8269 (mp) REVERT: V 31 LYS cc_start: 0.8103 (mmpt) cc_final: 0.7683 (mmtm) REVERT: V 35 LEU cc_start: 0.8454 (mm) cc_final: 0.7581 (mm) REVERT: V 37 GLU cc_start: 0.8211 (pm20) cc_final: 0.7647 (mp0) REVERT: V 52 ILE cc_start: 0.8625 (mp) cc_final: 0.8179 (mm) REVERT: V 56 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7347 (mm-30) REVERT: V 69 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7605 (mtmm) REVERT: V 95 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7785 (mt-10) REVERT: V 99 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8397 (mtpp) REVERT: V 109 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8068 (tt0) REVERT: V 127 ARG cc_start: 0.8236 (ttp-170) cc_final: 0.7840 (ttm110) REVERT: V 132 ARG cc_start: 0.8315 (tpp80) cc_final: 0.8048 (tpp80) REVERT: V 135 GLU cc_start: 0.7545 (tp30) cc_final: 0.7285 (tp30) REVERT: V 144 VAL cc_start: 0.8504 (t) cc_final: 0.8062 (m) REVERT: V 148 THR cc_start: 0.8885 (t) cc_final: 0.8674 (p) REVERT: V 180 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7638 (tpt-90) REVERT: V 187 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7637 (mt-10) REVERT: V 192 GLU cc_start: 0.7340 (tp30) cc_final: 0.7054 (tp30) REVERT: V 201 TYR cc_start: 0.8396 (t80) cc_final: 0.8105 (t80) REVERT: V 203 GLU cc_start: 0.7986 (tt0) cc_final: 0.7474 (tt0) REVERT: V 218 TYR cc_start: 0.8618 (m-80) cc_final: 0.8184 (m-80) REVERT: V 222 PHE cc_start: 0.8383 (m-80) cc_final: 0.8103 (m-10) REVERT: V 253 ASP cc_start: 0.7485 (m-30) cc_final: 0.7195 (m-30) REVERT: V 254 VAL cc_start: 0.8708 (t) cc_final: 0.8424 (m) REVERT: V 268 MET cc_start: 0.8055 (mmm) cc_final: 0.7369 (mmm) REVERT: V 286 GLN cc_start: 0.8273 (mm-40) cc_final: 0.7847 (mp10) REVERT: V 302 GLU cc_start: 0.8080 (pt0) cc_final: 0.7489 (pm20) REVERT: V 318 ILE cc_start: 0.8614 (tp) cc_final: 0.8398 (tt) REVERT: V 325 ASN cc_start: 0.8381 (t0) cc_final: 0.7552 (t0) REVERT: V 326 LYS cc_start: 0.8537 (tmmt) cc_final: 0.8322 (tttt) REVERT: V 329 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7120 (mm-30) REVERT: V 365 ASP cc_start: 0.7837 (m-30) cc_final: 0.7349 (t0) REVERT: V 367 LEU cc_start: 0.8401 (mt) cc_final: 0.8155 (mm) REVERT: V 379 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8177 (mt-10) REVERT: V 403 LEU cc_start: 0.8794 (mt) cc_final: 0.8450 (mm) REVERT: V 418 LEU cc_start: 0.8915 (tp) cc_final: 0.8519 (tt) REVERT: V 440 ASN cc_start: 0.7826 (m-40) cc_final: 0.7006 (m-40) REVERT: V 443 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8202 (mtmt) REVERT: V 450 LYS cc_start: 0.8090 (mtmt) cc_final: 0.7627 (ptpt) REVERT: V 453 THR cc_start: 0.8761 (m) cc_final: 0.8413 (p) REVERT: V 454 LYS cc_start: 0.8767 (mptt) cc_final: 0.8303 (mmtt) REVERT: W 44 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7449 (ttp) REVERT: W 45 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8335 (p) REVERT: W 66 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8507 (mm) REVERT: W 86 MET cc_start: 0.7702 (mmm) cc_final: 0.7391 (mmm) REVERT: W 113 LYS cc_start: 0.8619 (mttp) cc_final: 0.8203 (mtpp) REVERT: W 136 ILE cc_start: 0.8688 (mp) cc_final: 0.8460 (mp) REVERT: W 157 LYS cc_start: 0.8352 (mttm) cc_final: 0.7997 (mttp) REVERT: W 158 LEU cc_start: 0.8447 (tt) cc_final: 0.8111 (tp) REVERT: W 167 THR cc_start: 0.8838 (t) cc_final: 0.8632 (m) REVERT: W 185 LEU cc_start: 0.8137 (mt) cc_final: 0.7717 (mt) REVERT: W 188 ASP cc_start: 0.7577 (m-30) cc_final: 0.7028 (m-30) REVERT: W 191 SER cc_start: 0.8685 (t) cc_final: 0.8154 (m) REVERT: W 229 LEU cc_start: 0.8583 (tp) cc_final: 0.8314 (tp) REVERT: W 231 LYS cc_start: 0.8469 (mttm) cc_final: 0.8185 (mmmm) REVERT: W 246 VAL cc_start: 0.8500 (p) cc_final: 0.8233 (m) REVERT: W 264 GLU cc_start: 0.7321 (mt-10) cc_final: 0.6603 (mt-10) REVERT: W 271 ASP cc_start: 0.7886 (m-30) cc_final: 0.7652 (m-30) REVERT: W 281 LYS cc_start: 0.8760 (tttm) cc_final: 0.8468 (tppt) REVERT: W 306 PHE cc_start: 0.8284 (m-80) cc_final: 0.7907 (m-80) REVERT: W 310 ASN cc_start: 0.8052 (m-40) cc_final: 0.7678 (m-40) REVERT: W 365 LYS cc_start: 0.8960 (tmmt) cc_final: 0.8697 (tmmt) REVERT: W 367 ILE cc_start: 0.8610 (mt) cc_final: 0.8230 (tt) REVERT: W 373 GLN cc_start: 0.8519 (mp10) cc_final: 0.8180 (mt0) REVERT: W 375 GLU cc_start: 0.8351 (tp30) cc_final: 0.8030 (tp30) REVERT: W 376 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7690 (tp30) REVERT: W 386 LEU cc_start: 0.8489 (tp) cc_final: 0.8257 (tt) REVERT: W 389 LYS cc_start: 0.8791 (tppt) cc_final: 0.7654 (tppt) REVERT: W 393 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7896 (mm-30) REVERT: W 438 LYS cc_start: 0.9019 (pttt) cc_final: 0.8705 (pttt) REVERT: X 99 LYS cc_start: 0.7625 (pttm) cc_final: 0.7290 (mtmm) REVERT: X 123 GLU cc_start: 0.8280 (pt0) cc_final: 0.7852 (tt0) REVERT: X 125 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7913 (t80) REVERT: X 141 GLU cc_start: 0.7452 (pm20) cc_final: 0.6749 (pm20) REVERT: X 186 TYR cc_start: 0.8490 (t80) cc_final: 0.8287 (t80) REVERT: X 189 ILE cc_start: 0.9188 (mm) cc_final: 0.8917 (mm) REVERT: X 190 GLN cc_start: 0.8483 (mt0) cc_final: 0.8216 (mt0) REVERT: X 198 ASP cc_start: 0.7540 (m-30) cc_final: 0.7157 (m-30) REVERT: X 201 TYR cc_start: 0.7122 (t80) cc_final: 0.6699 (t80) REVERT: X 211 ARG cc_start: 0.8214 (ttt-90) cc_final: 0.7829 (ttt-90) REVERT: X 212 VAL cc_start: 0.8633 (t) cc_final: 0.8310 (m) REVERT: X 228 GLU cc_start: 0.7514 (pm20) cc_final: 0.7224 (pm20) REVERT: X 239 LYS cc_start: 0.8494 (ptpt) cc_final: 0.8022 (ptpp) REVERT: X 245 GLN cc_start: 0.8071 (tp40) cc_final: 0.7728 (tp40) REVERT: X 251 ASP cc_start: 0.7914 (m-30) cc_final: 0.7541 (m-30) REVERT: X 263 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6624 (tm-30) REVERT: X 272 LEU cc_start: 0.8905 (tt) cc_final: 0.8665 (tp) REVERT: X 277 LYS cc_start: 0.8730 (ttmm) cc_final: 0.8461 (mtmt) REVERT: X 285 ARG cc_start: 0.8271 (mtt90) cc_final: 0.7917 (mtm-85) REVERT: X 291 VAL cc_start: 0.8982 (p) cc_final: 0.8777 (m) REVERT: X 313 VAL cc_start: 0.8059 (OUTLIER) cc_final: 0.7518 (t) REVERT: X 325 ASN cc_start: 0.8680 (m-40) cc_final: 0.8273 (m-40) REVERT: X 328 LEU cc_start: 0.8769 (mt) cc_final: 0.8478 (mm) REVERT: X 345 THR cc_start: 0.8257 (t) cc_final: 0.7762 (p) REVERT: X 362 ASP cc_start: 0.7641 (p0) cc_final: 0.7293 (p0) REVERT: X 377 LYS cc_start: 0.8535 (mmmm) cc_final: 0.8251 (mmmm) REVERT: X 378 ASP cc_start: 0.7694 (p0) cc_final: 0.7401 (t0) REVERT: X 385 GLU cc_start: 0.8358 (pp20) cc_final: 0.8019 (pp20) REVERT: X 391 GLU cc_start: 0.8543 (tt0) cc_final: 0.7964 (tp30) REVERT: X 401 ASP cc_start: 0.8367 (m-30) cc_final: 0.8093 (m-30) REVERT: X 406 MET cc_start: 0.8026 (mtp) cc_final: 0.7814 (mtp) REVERT: X 417 GLN cc_start: 0.8127 (mt0) cc_final: 0.7917 (mt0) REVERT: X 443 LYS cc_start: 0.8429 (tmmt) cc_final: 0.8049 (ttmm) REVERT: X 450 LYS cc_start: 0.9082 (ttpt) cc_final: 0.8877 (mtmm) REVERT: X 454 LYS cc_start: 0.8421 (tmmt) cc_final: 0.8007 (tmmt) REVERT: Y 59 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8251 (tptp) REVERT: Y 66 ILE cc_start: 0.8792 (mp) cc_final: 0.8592 (mp) REVERT: Y 122 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7830 (mmm-85) REVERT: Y 130 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7741 (mtmm) REVERT: Y 136 ILE cc_start: 0.8498 (mt) cc_final: 0.8154 (mm) REVERT: Y 164 ASP cc_start: 0.8199 (m-30) cc_final: 0.7920 (m-30) REVERT: Y 166 GLU cc_start: 0.6643 (tm-30) cc_final: 0.6288 (tm-30) REVERT: Y 171 LEU cc_start: 0.8403 (mp) cc_final: 0.8175 (mm) REVERT: Y 173 ASN cc_start: 0.7983 (p0) cc_final: 0.7100 (m-40) REVERT: Y 174 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8332 (mmtm) REVERT: Y 175 MET cc_start: 0.8889 (tpp) cc_final: 0.8314 (tpp) REVERT: Y 182 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7101 (tm-30) REVERT: Y 208 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7690 (mmm-85) REVERT: Y 237 HIS cc_start: 0.7919 (m170) cc_final: 0.7696 (m170) REVERT: Y 271 ASP cc_start: 0.8406 (t0) cc_final: 0.8017 (t0) REVERT: Y 272 GLN cc_start: 0.8546 (mt0) cc_final: 0.8262 (tt0) REVERT: Y 274 ASN cc_start: 0.8689 (m-40) cc_final: 0.8346 (m-40) REVERT: Y 277 VAL cc_start: 0.8602 (t) cc_final: 0.8322 (p) REVERT: Y 304 GLU cc_start: 0.7902 (mp0) cc_final: 0.7662 (mt-10) REVERT: Y 310 ASN cc_start: 0.8023 (m-40) cc_final: 0.7661 (m-40) REVERT: Y 316 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7532 (tp30) REVERT: Y 327 ARG cc_start: 0.7905 (ttm-80) cc_final: 0.7568 (ttm-80) REVERT: Y 370 ILE cc_start: 0.9029 (mt) cc_final: 0.8786 (mt) REVERT: Y 384 LEU cc_start: 0.8948 (tp) cc_final: 0.8653 (tt) REVERT: Y 389 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8339 (mmmm) REVERT: Y 393 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8084 (mt-10) REVERT: Y 407 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8212 (tp40) REVERT: Y 412 LYS cc_start: 0.9039 (tptm) cc_final: 0.8697 (tptm) REVERT: Y 422 ASP cc_start: 0.7911 (m-30) cc_final: 0.7597 (t0) REVERT: Y 424 LYS cc_start: 0.8556 (mtmm) cc_final: 0.8322 (mtmm) REVERT: Y 427 TYR cc_start: 0.8268 (t80) cc_final: 0.7582 (t80) REVERT: Y 441 GLN cc_start: 0.8524 (mm110) cc_final: 0.8082 (mt0) REVERT: Y 444 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7007 (tp30) REVERT: Y 456 ILE cc_start: 0.8839 (mt) cc_final: 0.8409 (mt) REVERT: Z 310 ARG cc_start: 0.8151 (mtt-85) cc_final: 0.7472 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7290 (ttm110) outliers start: 130 outliers final: 66 residues processed: 1210 average time/residue: 0.1921 time to fit residues: 351.9460 Evaluate side-chains 1235 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1143 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 960 GLN Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1270 LYS Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1335 LEU Chi-restraints excluded: chain Q residue 1430 GLU Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 165 PHE Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 664 MET Chi-restraints excluded: chain R residue 728 VAL Chi-restraints excluded: chain R residue 729 ILE Chi-restraints excluded: chain R residue 742 ILE Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 142 LEU Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 406 MET Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 331 LYS Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 335 VAL Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain V residue 428 THR Chi-restraints excluded: chain V residue 441 GLU Chi-restraints excluded: chain V residue 455 ILE Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 44 MET Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 304 ILE Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 340 SER Chi-restraints excluded: chain X residue 412 LEU Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 430 ASN Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 368 LEU Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 257 optimal weight: 0.9980 chunk 153 optimal weight: 0.9990 chunk 319 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 321 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 312 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 313 optimal weight: 0.9990 chunk 190 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1180 ASN Q1204 ASN Q1228 HIS ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 609 GLN T 27 HIS T 29 HIS T 417 GLN V 289 ASN V 341 ASN W 119 GLN X 51 GLN ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 286 GLN X 440 ASN ** Y 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 453 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.126547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107769 restraints weight = 57255.186| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.28 r_work: 0.3331 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29139 Z= 0.165 Angle : 0.653 17.327 39425 Z= 0.324 Chirality : 0.045 0.209 4626 Planarity : 0.005 0.066 5049 Dihedral : 7.652 138.641 4012 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.56 % Allowed : 25.44 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.14), residues: 3626 helix: 0.78 (0.13), residues: 1535 sheet: -0.12 (0.21), residues: 577 loop : -0.71 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 34 TYR 0.021 0.002 TYR R 737 PHE 0.026 0.001 PHE Y 254 TRP 0.018 0.002 TRP R 108 HIS 0.005 0.001 HIS Q1228 Details of bonding type rmsd covalent geometry : bond 0.00354 (29139) covalent geometry : angle 0.65312 (39425) hydrogen bonds : bond 0.03819 ( 1098) hydrogen bonds : angle 4.52344 ( 3198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1154 time to evaluate : 0.973 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: Q 960 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8052 (mm-40) REVERT: Q 1005 MET cc_start: 0.6724 (mmp) cc_final: 0.6000 (mmp) REVERT: Q 1023 ASP cc_start: 0.7794 (t0) cc_final: 0.7339 (t0) REVERT: Q 1027 SER cc_start: 0.8761 (m) cc_final: 0.8220 (p) REVERT: Q 1102 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8041 (m) REVERT: Q 1112 LYS cc_start: 0.8817 (mttp) cc_final: 0.8311 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8661 (m) cc_final: 0.8202 (t) REVERT: Q 1150 LYS cc_start: 0.8577 (tttm) cc_final: 0.7729 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6775 (mp0) REVERT: Q 1173 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7133 (mp0) REVERT: Q 1186 VAL cc_start: 0.9010 (p) cc_final: 0.8708 (t) REVERT: Q 1195 LYS cc_start: 0.8230 (tppt) cc_final: 0.7464 (tppt) REVERT: Q 1208 ARG cc_start: 0.8713 (ttm170) cc_final: 0.7706 (mtp180) REVERT: Q 1222 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7411 (tm-30) REVERT: Q 1230 THR cc_start: 0.8783 (m) cc_final: 0.8340 (p) REVERT: Q 1231 ASN cc_start: 0.8584 (t0) cc_final: 0.8299 (t0) REVERT: Q 1234 ASN cc_start: 0.8513 (m-40) cc_final: 0.8276 (m-40) REVERT: Q 1242 ILE cc_start: 0.9179 (tp) cc_final: 0.8670 (tt) REVERT: Q 1248 ASP cc_start: 0.7424 (t70) cc_final: 0.6919 (t0) REVERT: Q 1256 ASN cc_start: 0.8432 (m-40) cc_final: 0.8216 (m-40) REVERT: Q 1266 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7863 (tm-30) REVERT: Q 1267 ASP cc_start: 0.8571 (m-30) cc_final: 0.7869 (m-30) REVERT: Q 1276 GLU cc_start: 0.8272 (tp30) cc_final: 0.8060 (tp30) REVERT: Q 1291 MET cc_start: 0.7995 (tpt) cc_final: 0.7739 (tpp) REVERT: Q 1293 ARG cc_start: 0.7646 (mmm-85) cc_final: 0.6810 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8359 (mt) cc_final: 0.8035 (mm) REVERT: Q 1302 ARG cc_start: 0.8030 (ttt180) cc_final: 0.7532 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8582 (m-30) cc_final: 0.8283 (m-30) REVERT: Q 1317 ARG cc_start: 0.8062 (ptm160) cc_final: 0.7823 (ptm160) REVERT: Q 1331 MET cc_start: 0.7864 (tpp) cc_final: 0.7350 (tpp) REVERT: Q 1334 TYR cc_start: 0.7931 (p90) cc_final: 0.7448 (p90) REVERT: Q 1335 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7761 (mp) REVERT: Q 1421 ARG cc_start: 0.7513 (mtt90) cc_final: 0.6869 (mtt90) REVERT: R 21 LEU cc_start: 0.6927 (tp) cc_final: 0.6598 (tp) REVERT: R 35 ASN cc_start: 0.8833 (t0) cc_final: 0.8310 (t0) REVERT: R 55 ASN cc_start: 0.8455 (p0) cc_final: 0.8086 (p0) REVERT: R 70 PHE cc_start: 0.7487 (t80) cc_final: 0.7180 (t80) REVERT: R 144 GLN cc_start: 0.7596 (pm20) cc_final: 0.6814 (pm20) REVERT: R 155 PHE cc_start: 0.7428 (m-10) cc_final: 0.7142 (m-10) REVERT: R 182 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8086 (mmmm) REVERT: R 183 THR cc_start: 0.7362 (m) cc_final: 0.6828 (t) REVERT: R 218 GLN cc_start: 0.7992 (mp10) cc_final: 0.7430 (mp10) REVERT: R 230 LYS cc_start: 0.8897 (tttt) cc_final: 0.8509 (ttpt) REVERT: R 242 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: R 244 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: R 251 CYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7086 (m) REVERT: R 260 ASP cc_start: 0.7874 (m-30) cc_final: 0.7578 (p0) REVERT: R 262 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8120 (mm-30) REVERT: R 592 HIS cc_start: 0.8183 (t-90) cc_final: 0.7516 (t-90) REVERT: R 593 LEU cc_start: 0.8720 (mm) cc_final: 0.8470 (mm) REVERT: R 609 GLN cc_start: 0.7849 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: R 612 MET cc_start: 0.6725 (tpp) cc_final: 0.6302 (tpp) REVERT: R 627 GLN cc_start: 0.8496 (pt0) cc_final: 0.8239 (pt0) REVERT: R 640 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7204 (tp30) REVERT: R 643 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7481 (mm-30) REVERT: R 647 LEU cc_start: 0.8462 (mp) cc_final: 0.8086 (mp) REVERT: R 659 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8171 (tp-100) REVERT: R 663 ASP cc_start: 0.8159 (m-30) cc_final: 0.7833 (m-30) REVERT: R 664 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8398 (mtp) REVERT: R 681 LYS cc_start: 0.8987 (tttt) cc_final: 0.8761 (tptt) REVERT: R 699 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7722 (p) REVERT: R 721 GLU cc_start: 0.8067 (tp30) cc_final: 0.7771 (tp30) REVERT: R 722 GLU cc_start: 0.8330 (pp20) cc_final: 0.7442 (pp20) REVERT: R 723 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7477 (mm-40) REVERT: R 724 TYR cc_start: 0.8264 (t80) cc_final: 0.7733 (t80) REVERT: R 726 LYS cc_start: 0.8499 (tptp) cc_final: 0.8114 (tptp) REVERT: R 728 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8614 (m) REVERT: R 747 LEU cc_start: 0.7689 (pt) cc_final: 0.7463 (pt) REVERT: S 110 ARG cc_start: 0.8199 (ptt180) cc_final: 0.7612 (mtm180) REVERT: S 114 LYS cc_start: 0.8455 (mttt) cc_final: 0.8201 (mttt) REVERT: S 122 LYS cc_start: 0.8404 (mmmm) cc_final: 0.8014 (mtpp) REVERT: S 140 TYR cc_start: 0.8603 (t80) cc_final: 0.8132 (t80) REVERT: S 145 LYS cc_start: 0.8715 (tppp) cc_final: 0.8326 (tppp) REVERT: T 49 VAL cc_start: 0.8330 (p) cc_final: 0.8002 (m) REVERT: T 56 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7856 (mt-10) REVERT: T 95 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8285 (mm-30) REVERT: T 177 LYS cc_start: 0.8506 (tttt) cc_final: 0.8107 (mtpp) REVERT: T 178 THR cc_start: 0.8984 (m) cc_final: 0.8692 (t) REVERT: T 193 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8096 (mmmt) REVERT: T 224 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8442 (tp) REVERT: T 251 ASP cc_start: 0.8205 (m-30) cc_final: 0.7880 (m-30) REVERT: T 273 LEU cc_start: 0.7772 (tp) cc_final: 0.7554 (tt) REVERT: T 279 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7425 (pt0) REVERT: T 295 TYR cc_start: 0.8610 (m-80) cc_final: 0.8102 (m-80) REVERT: T 371 ARG cc_start: 0.8016 (mtp-110) cc_final: 0.7392 (ptm-80) REVERT: T 381 ARG cc_start: 0.8739 (ttt-90) cc_final: 0.8244 (ttm-80) REVERT: T 382 THR cc_start: 0.8607 (p) cc_final: 0.8116 (p) REVERT: T 385 GLU cc_start: 0.8510 (pt0) cc_final: 0.7802 (pp20) REVERT: T 395 VAL cc_start: 0.8549 (t) cc_final: 0.8328 (t) REVERT: T 396 GLU cc_start: 0.7369 (pt0) cc_final: 0.7141 (pt0) REVERT: T 401 ASP cc_start: 0.8486 (m-30) cc_final: 0.7657 (m-30) REVERT: T 409 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7611 (mt-10) REVERT: T 414 TYR cc_start: 0.8037 (t80) cc_final: 0.7733 (t80) REVERT: T 417 GLN cc_start: 0.8271 (mt0) cc_final: 0.7969 (mt0) REVERT: T 419 LEU cc_start: 0.8640 (mm) cc_final: 0.8337 (mp) REVERT: T 424 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7920 (mt) REVERT: T 431 ARG cc_start: 0.7855 (mtm180) cc_final: 0.7379 (mtm180) REVERT: T 434 ILE cc_start: 0.7692 (mt) cc_final: 0.7061 (mt) REVERT: T 439 VAL cc_start: 0.8917 (t) cc_final: 0.8713 (t) REVERT: T 448 ASP cc_start: 0.7679 (p0) cc_final: 0.7323 (p0) REVERT: T 457 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8102 (mm-30) REVERT: U 38 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7693 (mtt180) REVERT: U 86 MET cc_start: 0.8095 (mmm) cc_final: 0.7610 (mmm) REVERT: U 94 LYS cc_start: 0.8840 (tppt) cc_final: 0.8423 (tptp) REVERT: U 104 SER cc_start: 0.8549 (m) cc_final: 0.8215 (t) REVERT: U 105 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7147 (mt-10) REVERT: U 110 GLU cc_start: 0.7967 (pp20) cc_final: 0.7641 (pp20) REVERT: U 123 LYS cc_start: 0.8248 (mttt) cc_final: 0.7945 (mttp) REVERT: U 128 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8442 (ttmm) REVERT: U 139 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: U 161 LYS cc_start: 0.8633 (ptmm) cc_final: 0.7466 (ptmm) REVERT: U 164 ASP cc_start: 0.7927 (t70) cc_final: 0.7635 (t70) REVERT: U 166 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7131 (tp30) REVERT: U 182 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7776 (tm-30) REVERT: U 193 ASP cc_start: 0.7970 (t0) cc_final: 0.7464 (t70) REVERT: U 198 LYS cc_start: 0.8582 (tttm) cc_final: 0.8229 (tttm) REVERT: U 221 PHE cc_start: 0.7447 (m-80) cc_final: 0.7186 (m-80) REVERT: U 272 GLN cc_start: 0.8053 (tp40) cc_final: 0.7540 (tp40) REVERT: U 276 LYS cc_start: 0.8942 (tptt) cc_final: 0.8489 (tptm) REVERT: U 281 LYS cc_start: 0.8956 (tttm) cc_final: 0.8531 (ttmm) REVERT: U 306 PHE cc_start: 0.8314 (m-10) cc_final: 0.8013 (m-10) REVERT: U 313 LEU cc_start: 0.8829 (mt) cc_final: 0.8588 (mp) REVERT: U 338 LYS cc_start: 0.8899 (mttt) cc_final: 0.8661 (ttmm) REVERT: U 339 SER cc_start: 0.8867 (m) cc_final: 0.8557 (t) REVERT: U 349 ASP cc_start: 0.8697 (t0) cc_final: 0.8226 (m-30) REVERT: U 365 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8514 (ttmt) REVERT: U 374 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7758 (tm-30) REVERT: U 376 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7972 (mm-30) REVERT: U 378 GLU cc_start: 0.7369 (mp0) cc_final: 0.7134 (mp0) REVERT: U 393 GLU cc_start: 0.7618 (pp20) cc_final: 0.7345 (pp20) REVERT: U 399 SER cc_start: 0.8414 (m) cc_final: 0.8153 (p) REVERT: U 400 SER cc_start: 0.8261 (t) cc_final: 0.7813 (m) REVERT: U 411 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7177 (mpt) REVERT: U 412 LYS cc_start: 0.8831 (tppt) cc_final: 0.8576 (tppt) REVERT: U 419 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6993 (mm-30) REVERT: U 424 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7972 (mmtt) REVERT: U 428 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8363 (pp) REVERT: U 444 GLU cc_start: 0.8255 (tp30) cc_final: 0.7685 (tp30) REVERT: V 30 ILE cc_start: 0.8552 (mt) cc_final: 0.8283 (mp) REVERT: V 31 LYS cc_start: 0.8138 (mmpt) cc_final: 0.7703 (mmtm) REVERT: V 35 LEU cc_start: 0.8466 (mm) cc_final: 0.7622 (mm) REVERT: V 37 GLU cc_start: 0.8235 (pm20) cc_final: 0.7685 (mp0) REVERT: V 52 ILE cc_start: 0.8637 (mp) cc_final: 0.8217 (mm) REVERT: V 56 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7393 (mm-30) REVERT: V 69 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7626 (mtmm) REVERT: V 95 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7787 (mt-10) REVERT: V 99 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8383 (mtpp) REVERT: V 109 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8071 (tt0) REVERT: V 132 ARG cc_start: 0.8337 (tpp80) cc_final: 0.8024 (tpp80) REVERT: V 141 GLU cc_start: 0.7608 (pm20) cc_final: 0.7308 (pm20) REVERT: V 144 VAL cc_start: 0.8531 (t) cc_final: 0.8092 (m) REVERT: V 148 THR cc_start: 0.8854 (t) cc_final: 0.8643 (p) REVERT: V 187 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7646 (mt-10) REVERT: V 194 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.7916 (t) REVERT: V 201 TYR cc_start: 0.8388 (t80) cc_final: 0.8128 (t80) REVERT: V 203 GLU cc_start: 0.8010 (tt0) cc_final: 0.7743 (tt0) REVERT: V 218 TYR cc_start: 0.8677 (m-80) cc_final: 0.8201 (m-80) REVERT: V 222 PHE cc_start: 0.8375 (m-80) cc_final: 0.8122 (m-10) REVERT: V 239 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8112 (mttt) REVERT: V 253 ASP cc_start: 0.7477 (m-30) cc_final: 0.7205 (m-30) REVERT: V 254 VAL cc_start: 0.8694 (t) cc_final: 0.8408 (m) REVERT: V 263 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8393 (mm-40) REVERT: V 264 ASP cc_start: 0.7715 (p0) cc_final: 0.7470 (p0) REVERT: V 302 GLU cc_start: 0.8123 (pt0) cc_final: 0.7484 (pm20) REVERT: V 311 ASP cc_start: 0.8269 (t0) cc_final: 0.8040 (t0) REVERT: V 318 ILE cc_start: 0.8638 (tp) cc_final: 0.8409 (tt) REVERT: V 325 ASN cc_start: 0.8388 (t0) cc_final: 0.7568 (t0) REVERT: V 326 LYS cc_start: 0.8557 (tmmt) cc_final: 0.8296 (tttt) REVERT: V 329 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7125 (mm-30) REVERT: V 344 MET cc_start: 0.8800 (mmt) cc_final: 0.8560 (mmm) REVERT: V 365 ASP cc_start: 0.7860 (m-30) cc_final: 0.7411 (t70) REVERT: V 367 LEU cc_start: 0.8400 (mt) cc_final: 0.8136 (mm) REVERT: V 371 ARG cc_start: 0.8362 (ttp80) cc_final: 0.7949 (ttt180) REVERT: V 379 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8219 (mt-10) REVERT: V 403 LEU cc_start: 0.8837 (mt) cc_final: 0.8477 (mm) REVERT: V 440 ASN cc_start: 0.7851 (m-40) cc_final: 0.7023 (m-40) REVERT: V 443 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8204 (mtmt) REVERT: V 450 LYS cc_start: 0.8095 (mtmt) cc_final: 0.7522 (mttt) REVERT: V 453 THR cc_start: 0.8780 (m) cc_final: 0.8426 (p) REVERT: V 454 LYS cc_start: 0.8831 (mptt) cc_final: 0.8382 (mmtt) REVERT: W 45 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8284 (p) REVERT: W 66 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8514 (mm) REVERT: W 86 MET cc_start: 0.7791 (mmm) cc_final: 0.7476 (mmm) REVERT: W 105 GLU cc_start: 0.7983 (mp0) cc_final: 0.7769 (mp0) REVERT: W 113 LYS cc_start: 0.8625 (mttp) cc_final: 0.8250 (mtpt) REVERT: W 135 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7881 (mm) REVERT: W 136 ILE cc_start: 0.8702 (mp) cc_final: 0.8487 (mp) REVERT: W 142 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: W 157 LYS cc_start: 0.8213 (mttm) cc_final: 0.7869 (mttp) REVERT: W 159 THR cc_start: 0.8329 (m) cc_final: 0.7764 (p) REVERT: W 185 LEU cc_start: 0.8097 (mt) cc_final: 0.7655 (mt) REVERT: W 188 ASP cc_start: 0.7621 (m-30) cc_final: 0.7027 (m-30) REVERT: W 191 SER cc_start: 0.8737 (t) cc_final: 0.7921 (m) REVERT: W 200 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.7660 (p) REVERT: W 229 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8268 (tp) REVERT: W 231 LYS cc_start: 0.8473 (mttm) cc_final: 0.8186 (mmmm) REVERT: W 264 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6710 (mt-10) REVERT: W 271 ASP cc_start: 0.7896 (m-30) cc_final: 0.7677 (m-30) REVERT: W 273 ILE cc_start: 0.8845 (tp) cc_final: 0.8637 (tp) REVERT: W 281 LYS cc_start: 0.8787 (tttm) cc_final: 0.8420 (tppt) REVERT: W 306 PHE cc_start: 0.8314 (m-80) cc_final: 0.7919 (m-80) REVERT: W 310 ASN cc_start: 0.7953 (m-40) cc_final: 0.7676 (m-40) REVERT: W 365 LYS cc_start: 0.8943 (tmmt) cc_final: 0.8694 (tmmt) REVERT: W 367 ILE cc_start: 0.8631 (mt) cc_final: 0.8258 (tt) REVERT: W 373 GLN cc_start: 0.8542 (mp10) cc_final: 0.8258 (mt0) REVERT: W 375 GLU cc_start: 0.8359 (tp30) cc_final: 0.7956 (tp30) REVERT: W 376 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: W 386 LEU cc_start: 0.8520 (tp) cc_final: 0.8290 (tt) REVERT: W 389 LYS cc_start: 0.8806 (tppt) cc_final: 0.7671 (tppt) REVERT: W 393 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7926 (mm-30) REVERT: W 424 LYS cc_start: 0.8615 (ptpt) cc_final: 0.8320 (ptpt) REVERT: W 438 LYS cc_start: 0.9063 (pttt) cc_final: 0.8774 (pttt) REVERT: X 95 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8188 (mt-10) REVERT: X 123 GLU cc_start: 0.8276 (pt0) cc_final: 0.7877 (tt0) REVERT: X 125 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7913 (t80) REVERT: X 141 GLU cc_start: 0.7339 (pm20) cc_final: 0.6943 (pm20) REVERT: X 177 LYS cc_start: 0.8425 (pttm) cc_final: 0.8147 (pttm) REVERT: X 186 TYR cc_start: 0.8521 (t80) cc_final: 0.8294 (t80) REVERT: X 189 ILE cc_start: 0.9183 (mm) cc_final: 0.8917 (mm) REVERT: X 201 TYR cc_start: 0.7117 (t80) cc_final: 0.6687 (t80) REVERT: X 211 ARG cc_start: 0.8321 (ttt-90) cc_final: 0.7911 (ttt-90) REVERT: X 212 VAL cc_start: 0.8683 (t) cc_final: 0.8363 (t) REVERT: X 228 GLU cc_start: 0.7582 (pm20) cc_final: 0.7237 (pm20) REVERT: X 239 LYS cc_start: 0.8536 (ptpt) cc_final: 0.8093 (ptpp) REVERT: X 245 GLN cc_start: 0.8151 (tp40) cc_final: 0.7833 (tp40) REVERT: X 251 ASP cc_start: 0.7925 (m-30) cc_final: 0.7542 (m-30) REVERT: X 263 GLN cc_start: 0.7186 (tm-30) cc_final: 0.6528 (tm-30) REVERT: X 271 GLN cc_start: 0.8359 (tp40) cc_final: 0.8089 (tp40) REVERT: X 272 LEU cc_start: 0.8940 (tt) cc_final: 0.8694 (tp) REVERT: X 277 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8471 (mtmt) REVERT: X 285 ARG cc_start: 0.8338 (mtt90) cc_final: 0.8081 (mtt-85) REVERT: X 298 GLN cc_start: 0.8134 (mt0) cc_final: 0.7919 (mp10) REVERT: X 303 LEU cc_start: 0.8335 (tp) cc_final: 0.7846 (pt) REVERT: X 313 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7600 (t) REVERT: X 325 ASN cc_start: 0.8685 (m-40) cc_final: 0.8409 (m-40) REVERT: X 328 LEU cc_start: 0.8791 (mt) cc_final: 0.8508 (mm) REVERT: X 377 LYS cc_start: 0.8572 (mmmm) cc_final: 0.8248 (mmmm) REVERT: X 378 ASP cc_start: 0.7707 (p0) cc_final: 0.7438 (t70) REVERT: X 385 GLU cc_start: 0.8423 (pp20) cc_final: 0.8081 (pp20) REVERT: X 401 ASP cc_start: 0.8371 (m-30) cc_final: 0.8120 (m-30) REVERT: X 417 GLN cc_start: 0.8111 (mt0) cc_final: 0.7839 (mt0) REVERT: X 431 ARG cc_start: 0.7729 (ttp-110) cc_final: 0.7451 (ttp-110) REVERT: X 441 GLU cc_start: 0.7889 (tp30) cc_final: 0.7582 (tp30) REVERT: X 443 LYS cc_start: 0.8440 (tmmt) cc_final: 0.8092 (ttmm) REVERT: X 454 LYS cc_start: 0.8444 (tmmt) cc_final: 0.8045 (tmmt) REVERT: Y 59 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8276 (tptp) REVERT: Y 66 ILE cc_start: 0.8809 (mp) cc_final: 0.8521 (mp) REVERT: Y 111 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7701 (tp) REVERT: Y 113 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7772 (mtmm) REVERT: Y 122 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7850 (mmm-85) REVERT: Y 128 LYS cc_start: 0.8537 (ttpp) cc_final: 0.8186 (ttpp) REVERT: Y 130 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7761 (mtmm) REVERT: Y 164 ASP cc_start: 0.8221 (m-30) cc_final: 0.7936 (m-30) REVERT: Y 166 GLU cc_start: 0.6703 (tm-30) cc_final: 0.6328 (tm-30) REVERT: Y 171 LEU cc_start: 0.8421 (mp) cc_final: 0.8210 (mm) REVERT: Y 173 ASN cc_start: 0.7992 (p0) cc_final: 0.7179 (m-40) REVERT: Y 174 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8371 (mmtm) REVERT: Y 175 MET cc_start: 0.8881 (tpp) cc_final: 0.8269 (tpp) REVERT: Y 182 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7133 (tm-30) REVERT: Y 194 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8300 (mmmt) REVERT: Y 208 ARG cc_start: 0.8013 (mmm-85) cc_final: 0.7479 (mmm-85) REVERT: Y 266 ARG cc_start: 0.7771 (mtm110) cc_final: 0.7469 (mtm110) REVERT: Y 271 ASP cc_start: 0.8392 (t0) cc_final: 0.8040 (t0) REVERT: Y 272 GLN cc_start: 0.8525 (mt0) cc_final: 0.8278 (tt0) REVERT: Y 274 ASN cc_start: 0.8702 (m-40) cc_final: 0.8400 (m-40) REVERT: Y 277 VAL cc_start: 0.8631 (t) cc_final: 0.8373 (p) REVERT: Y 287 GLU cc_start: 0.7585 (pm20) cc_final: 0.7330 (pm20) REVERT: Y 310 ASN cc_start: 0.8086 (m-40) cc_final: 0.7733 (m-40) REVERT: Y 327 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7548 (ttm-80) REVERT: Y 339 SER cc_start: 0.8770 (t) cc_final: 0.8379 (p) REVERT: Y 370 ILE cc_start: 0.9003 (mt) cc_final: 0.8768 (mt) REVERT: Y 373 GLN cc_start: 0.8732 (tt0) cc_final: 0.8503 (mm-40) REVERT: Y 374 GLU cc_start: 0.7987 (tp30) cc_final: 0.7735 (mm-30) REVERT: Y 384 LEU cc_start: 0.8989 (tp) cc_final: 0.8695 (tt) REVERT: Y 389 LYS cc_start: 0.8936 (ttpt) cc_final: 0.8443 (mmmm) REVERT: Y 393 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8106 (mt-10) REVERT: Y 412 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8750 (tptm) REVERT: Y 422 ASP cc_start: 0.7978 (m-30) cc_final: 0.7638 (t0) REVERT: Y 424 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8325 (mtmm) REVERT: Y 427 TYR cc_start: 0.8290 (t80) cc_final: 0.7613 (t80) REVERT: Y 444 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7058 (tm-30) REVERT: Y 456 ILE cc_start: 0.8860 (mt) cc_final: 0.8465 (mt) REVERT: Z 310 ARG cc_start: 0.8214 (mtt-85) cc_final: 0.7548 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7715 (ttm110) cc_final: 0.7404 (ttm110) outliers start: 144 outliers final: 75 residues processed: 1220 average time/residue: 0.2028 time to fit residues: 376.4406 Evaluate side-chains 1239 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1131 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1073 LEU Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1179 ARG Chi-restraints excluded: chain Q residue 1270 LYS Chi-restraints excluded: chain Q residue 1335 LEU Chi-restraints excluded: chain Q residue 1389 VAL Chi-restraints excluded: chain Q residue 1430 GLU Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 165 PHE Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 664 MET Chi-restraints excluded: chain R residue 699 THR Chi-restraints excluded: chain R residue 728 VAL Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 265 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 406 MET Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 424 ILE Chi-restraints excluded: chain T residue 436 VAL Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 331 LYS Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 300 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 393 LEU Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain V residue 441 GLU Chi-restraints excluded: chain V residue 455 ILE Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 44 MET Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 142 GLU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 229 LEU Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 230 VAL Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 340 SER Chi-restraints excluded: chain X residue 412 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 430 ASN Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 113 LYS Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 368 LEU Chi-restraints excluded: chain Y residue 377 VAL Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 412 LYS Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 449 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 154 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 15 optimal weight: 0.0010 chunk 64 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 219 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 313 optimal weight: 0.2980 chunk 304 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 960 GLN Q1204 ASN Q1228 HIS ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN T 27 HIS T 29 HIS T 437 ASN U 446 GLN V 289 ASN V 341 ASN V 394 GLN W 90 GLN ** W 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 440 ASN Y 401 ASN Y 407 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 453 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.127549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108695 restraints weight = 57040.214| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.28 r_work: 0.3339 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29139 Z= 0.137 Angle : 0.648 17.250 39425 Z= 0.317 Chirality : 0.044 0.210 4626 Planarity : 0.005 0.060 5049 Dihedral : 7.436 134.413 4012 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.65 % Allowed : 26.42 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.14), residues: 3626 helix: 0.91 (0.13), residues: 1536 sheet: -0.15 (0.21), residues: 596 loop : -0.61 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG S 34 TYR 0.024 0.001 TYR Q1198 PHE 0.029 0.001 PHE Y 254 TRP 0.015 0.002 TRP R 108 HIS 0.004 0.001 HIS W 341 Details of bonding type rmsd covalent geometry : bond 0.00301 (29139) covalent geometry : angle 0.64825 (39425) hydrogen bonds : bond 0.03553 ( 1098) hydrogen bonds : angle 4.39579 ( 3198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1152 time to evaluate : 1.057 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: Q 1005 MET cc_start: 0.6813 (mmp) cc_final: 0.6094 (mmp) REVERT: Q 1023 ASP cc_start: 0.7817 (t0) cc_final: 0.7353 (t0) REVERT: Q 1027 SER cc_start: 0.8727 (m) cc_final: 0.8189 (p) REVERT: Q 1081 ILE cc_start: 0.8932 (mt) cc_final: 0.8615 (tt) REVERT: Q 1087 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8296 (ttm-80) REVERT: Q 1102 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.8064 (m) REVERT: Q 1112 LYS cc_start: 0.8818 (mttp) cc_final: 0.8291 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8626 (m) cc_final: 0.8154 (t) REVERT: Q 1150 LYS cc_start: 0.8551 (tttm) cc_final: 0.7724 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: Q 1173 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7154 (mp0) REVERT: Q 1186 VAL cc_start: 0.9016 (p) cc_final: 0.8811 (t) REVERT: Q 1195 LYS cc_start: 0.8209 (tppt) cc_final: 0.7441 (tppt) REVERT: Q 1204 ASN cc_start: 0.7942 (OUTLIER) cc_final: 0.7248 (p0) REVERT: Q 1208 ARG cc_start: 0.8715 (ttm170) cc_final: 0.7703 (mtp180) REVERT: Q 1222 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7448 (tm-30) REVERT: Q 1230 THR cc_start: 0.8753 (m) cc_final: 0.8383 (p) REVERT: Q 1231 ASN cc_start: 0.8614 (t0) cc_final: 0.8334 (t0) REVERT: Q 1234 ASN cc_start: 0.8492 (m-40) cc_final: 0.8273 (m-40) REVERT: Q 1242 ILE cc_start: 0.9112 (tp) cc_final: 0.8833 (tt) REVERT: Q 1248 ASP cc_start: 0.7400 (t70) cc_final: 0.6932 (t0) REVERT: Q 1256 ASN cc_start: 0.8448 (m-40) cc_final: 0.8239 (m-40) REVERT: Q 1266 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7890 (tm-30) REVERT: Q 1267 ASP cc_start: 0.8563 (m-30) cc_final: 0.7864 (m-30) REVERT: Q 1276 GLU cc_start: 0.8294 (tp30) cc_final: 0.8048 (tp30) REVERT: Q 1291 MET cc_start: 0.8016 (tpt) cc_final: 0.7760 (tpp) REVERT: Q 1293 ARG cc_start: 0.7602 (mmm-85) cc_final: 0.6772 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8316 (mt) cc_final: 0.8026 (mm) REVERT: Q 1302 ARG cc_start: 0.8023 (ttt180) cc_final: 0.7487 (mtp-110) REVERT: Q 1317 ARG cc_start: 0.8139 (ptm160) cc_final: 0.7880 (ptm160) REVERT: Q 1331 MET cc_start: 0.7876 (tpp) cc_final: 0.7371 (tpp) REVERT: Q 1334 TYR cc_start: 0.7935 (p90) cc_final: 0.7396 (p90) REVERT: Q 1335 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7767 (mp) REVERT: Q 1421 ARG cc_start: 0.7435 (mtt90) cc_final: 0.6838 (mtt90) REVERT: R 21 LEU cc_start: 0.6908 (tp) cc_final: 0.6572 (tp) REVERT: R 35 ASN cc_start: 0.8839 (t0) cc_final: 0.8516 (m-40) REVERT: R 55 ASN cc_start: 0.8428 (p0) cc_final: 0.8072 (p0) REVERT: R 70 PHE cc_start: 0.7537 (t80) cc_final: 0.7251 (t80) REVERT: R 154 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7656 (mm) REVERT: R 155 PHE cc_start: 0.7412 (m-10) cc_final: 0.7023 (m-10) REVERT: R 156 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: R 182 LYS cc_start: 0.8392 (mmmm) cc_final: 0.8043 (mmmm) REVERT: R 183 THR cc_start: 0.7361 (m) cc_final: 0.6827 (t) REVERT: R 211 ARG cc_start: 0.7622 (ttp80) cc_final: 0.7035 (ttp80) REVERT: R 218 GLN cc_start: 0.7969 (mp10) cc_final: 0.7454 (mp10) REVERT: R 242 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: R 251 CYS cc_start: 0.7322 (OUTLIER) cc_final: 0.7027 (m) REVERT: R 260 ASP cc_start: 0.7837 (m-30) cc_final: 0.7561 (p0) REVERT: R 262 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8118 (mm-30) REVERT: R 592 HIS cc_start: 0.8169 (t-90) cc_final: 0.7467 (t-90) REVERT: R 593 LEU cc_start: 0.8684 (mm) cc_final: 0.8473 (mm) REVERT: R 599 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8042 (tpp-160) REVERT: R 609 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: R 612 MET cc_start: 0.6798 (tpp) cc_final: 0.6475 (tpp) REVERT: R 627 GLN cc_start: 0.8472 (pt0) cc_final: 0.8062 (pt0) REVERT: R 642 SER cc_start: 0.8743 (m) cc_final: 0.8264 (p) REVERT: R 643 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7425 (mm-30) REVERT: R 645 ILE cc_start: 0.9150 (mt) cc_final: 0.8783 (tt) REVERT: R 647 LEU cc_start: 0.8493 (mp) cc_final: 0.8128 (mp) REVERT: R 659 GLN cc_start: 0.8449 (tp-100) cc_final: 0.8141 (tp-100) REVERT: R 663 ASP cc_start: 0.8138 (m-30) cc_final: 0.7769 (m-30) REVERT: R 664 MET cc_start: 0.8716 (mtm) cc_final: 0.8441 (mtp) REVERT: R 699 THR cc_start: 0.8108 (OUTLIER) cc_final: 0.7752 (p) REVERT: R 721 GLU cc_start: 0.8058 (tp30) cc_final: 0.7685 (tp30) REVERT: R 722 GLU cc_start: 0.8331 (pp20) cc_final: 0.7557 (pp20) REVERT: R 723 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7734 (mm-40) REVERT: R 724 TYR cc_start: 0.8217 (t80) cc_final: 0.7732 (t80) REVERT: R 726 LYS cc_start: 0.8382 (tptp) cc_final: 0.8041 (tptp) REVERT: R 728 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8619 (m) REVERT: S 73 ARG cc_start: 0.8428 (tmm-80) cc_final: 0.7813 (tmm-80) REVERT: S 100 TYR cc_start: 0.8005 (t80) cc_final: 0.7597 (t80) REVERT: S 114 LYS cc_start: 0.8496 (mttt) cc_final: 0.8249 (mttt) REVERT: S 122 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8056 (mtpp) REVERT: S 140 TYR cc_start: 0.8592 (t80) cc_final: 0.8122 (t80) REVERT: S 145 LYS cc_start: 0.8702 (tppp) cc_final: 0.8320 (tppp) REVERT: T 49 VAL cc_start: 0.8270 (p) cc_final: 0.7955 (m) REVERT: T 56 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7816 (mt-10) REVERT: T 95 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8272 (mm-30) REVERT: T 177 LYS cc_start: 0.8484 (tttt) cc_final: 0.8103 (mtpp) REVERT: T 178 THR cc_start: 0.8938 (m) cc_final: 0.8653 (t) REVERT: T 193 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8110 (mmmt) REVERT: T 224 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8434 (tp) REVERT: T 230 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8768 (m) REVERT: T 245 GLN cc_start: 0.8262 (mm110) cc_final: 0.8024 (mm110) REVERT: T 251 ASP cc_start: 0.8131 (m-30) cc_final: 0.7810 (m-30) REVERT: T 273 LEU cc_start: 0.7829 (tp) cc_final: 0.7590 (tt) REVERT: T 279 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7425 (pt0) REVERT: T 295 TYR cc_start: 0.8599 (m-80) cc_final: 0.8068 (m-80) REVERT: T 371 ARG cc_start: 0.7980 (mtp-110) cc_final: 0.7625 (ptm-80) REVERT: T 381 ARG cc_start: 0.8739 (ttt-90) cc_final: 0.8250 (ttm-80) REVERT: T 382 THR cc_start: 0.8607 (p) cc_final: 0.8110 (p) REVERT: T 385 GLU cc_start: 0.8487 (pt0) cc_final: 0.7776 (pp20) REVERT: T 395 VAL cc_start: 0.8553 (t) cc_final: 0.8350 (t) REVERT: T 396 GLU cc_start: 0.7361 (pt0) cc_final: 0.7137 (pt0) REVERT: T 401 ASP cc_start: 0.8502 (m-30) cc_final: 0.7683 (m-30) REVERT: T 409 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: T 414 TYR cc_start: 0.8055 (t80) cc_final: 0.7728 (t80) REVERT: T 417 GLN cc_start: 0.8262 (mt0) cc_final: 0.7893 (mt0) REVERT: T 431 ARG cc_start: 0.7820 (mtm180) cc_final: 0.7482 (mtm180) REVERT: T 434 ILE cc_start: 0.7719 (mt) cc_final: 0.7092 (mt) REVERT: T 438 ASP cc_start: 0.8407 (m-30) cc_final: 0.7516 (m-30) REVERT: T 439 VAL cc_start: 0.8899 (t) cc_final: 0.8695 (t) REVERT: T 448 ASP cc_start: 0.7681 (p0) cc_final: 0.7259 (p0) REVERT: T 456 LEU cc_start: 0.8909 (tp) cc_final: 0.8319 (mt) REVERT: T 457 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8145 (mm-30) REVERT: U 38 ARG cc_start: 0.8147 (mtt90) cc_final: 0.7672 (mtt180) REVERT: U 86 MET cc_start: 0.8057 (mmm) cc_final: 0.7576 (mmm) REVERT: U 94 LYS cc_start: 0.8851 (tppt) cc_final: 0.8449 (tptp) REVERT: U 104 SER cc_start: 0.8539 (m) cc_final: 0.8233 (t) REVERT: U 105 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7129 (mt-10) REVERT: U 110 GLU cc_start: 0.7943 (pp20) cc_final: 0.7598 (pp20) REVERT: U 123 LYS cc_start: 0.8230 (mttt) cc_final: 0.7913 (mttp) REVERT: U 128 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8462 (ttmm) REVERT: U 139 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: U 161 LYS cc_start: 0.8631 (ptmm) cc_final: 0.7469 (ptmm) REVERT: U 164 ASP cc_start: 0.7914 (t70) cc_final: 0.7601 (t70) REVERT: U 166 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7108 (tp30) REVERT: U 182 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7744 (tm-30) REVERT: U 193 ASP cc_start: 0.7972 (t0) cc_final: 0.7463 (t70) REVERT: U 198 LYS cc_start: 0.8542 (tttm) cc_final: 0.8236 (tttm) REVERT: U 272 GLN cc_start: 0.8027 (tp40) cc_final: 0.7539 (tp40) REVERT: U 276 LYS cc_start: 0.8936 (tptt) cc_final: 0.8513 (tptm) REVERT: U 281 LYS cc_start: 0.8935 (tttm) cc_final: 0.8504 (ttmm) REVERT: U 313 LEU cc_start: 0.8801 (mt) cc_final: 0.8535 (mp) REVERT: U 314 GLU cc_start: 0.8056 (mp0) cc_final: 0.7834 (mp0) REVERT: U 338 LYS cc_start: 0.8883 (mttt) cc_final: 0.8645 (ttmm) REVERT: U 339 SER cc_start: 0.8846 (m) cc_final: 0.8546 (t) REVERT: U 349 ASP cc_start: 0.8642 (t0) cc_final: 0.8188 (m-30) REVERT: U 365 LYS cc_start: 0.8869 (ttpt) cc_final: 0.8529 (ttmt) REVERT: U 376 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7983 (mm-30) REVERT: U 378 GLU cc_start: 0.7358 (mp0) cc_final: 0.7126 (mp0) REVERT: U 393 GLU cc_start: 0.7660 (pp20) cc_final: 0.7380 (pp20) REVERT: U 399 SER cc_start: 0.8339 (m) cc_final: 0.8090 (p) REVERT: U 400 SER cc_start: 0.8185 (t) cc_final: 0.7737 (m) REVERT: U 411 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7091 (mpt) REVERT: U 412 LYS cc_start: 0.8817 (tppt) cc_final: 0.8560 (tppt) REVERT: U 419 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6986 (mm-30) REVERT: U 424 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7947 (mmtt) REVERT: U 428 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8350 (pp) REVERT: U 444 GLU cc_start: 0.8220 (tp30) cc_final: 0.7659 (tp30) REVERT: V 30 ILE cc_start: 0.8502 (mt) cc_final: 0.8276 (mp) REVERT: V 31 LYS cc_start: 0.8104 (mmpt) cc_final: 0.7673 (mmtm) REVERT: V 35 LEU cc_start: 0.8453 (mm) cc_final: 0.7599 (mm) REVERT: V 52 ILE cc_start: 0.8633 (mp) cc_final: 0.8285 (mm) REVERT: V 56 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7382 (mm-30) REVERT: V 69 LYS cc_start: 0.7865 (mtmm) cc_final: 0.7656 (mtmm) REVERT: V 95 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7741 (mt-10) REVERT: V 99 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8368 (mtpp) REVERT: V 127 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7809 (ttm110) REVERT: V 132 ARG cc_start: 0.8346 (tpp80) cc_final: 0.8045 (tpp80) REVERT: V 141 GLU cc_start: 0.7630 (pm20) cc_final: 0.7379 (pm20) REVERT: V 144 VAL cc_start: 0.8515 (t) cc_final: 0.8069 (m) REVERT: V 180 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7397 (ttt90) REVERT: V 187 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7685 (mt-10) REVERT: V 194 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.7694 (t) REVERT: V 201 TYR cc_start: 0.8380 (t80) cc_final: 0.8135 (t80) REVERT: V 203 GLU cc_start: 0.7980 (tt0) cc_final: 0.7719 (tt0) REVERT: V 218 TYR cc_start: 0.8674 (m-80) cc_final: 0.8221 (m-80) REVERT: V 222 PHE cc_start: 0.8351 (m-80) cc_final: 0.8100 (m-10) REVERT: V 239 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8086 (mttt) REVERT: V 253 ASP cc_start: 0.7463 (m-30) cc_final: 0.7221 (m-30) REVERT: V 254 VAL cc_start: 0.8688 (t) cc_final: 0.8402 (m) REVERT: V 263 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8370 (mm-40) REVERT: V 268 MET cc_start: 0.7908 (mmm) cc_final: 0.7203 (mmm) REVERT: V 302 GLU cc_start: 0.8143 (pt0) cc_final: 0.7532 (pm20) REVERT: V 325 ASN cc_start: 0.8408 (t0) cc_final: 0.7550 (t0) REVERT: V 326 LYS cc_start: 0.8552 (tmmt) cc_final: 0.8322 (tttt) REVERT: V 329 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: V 344 MET cc_start: 0.8787 (mmt) cc_final: 0.8550 (mmm) REVERT: V 365 ASP cc_start: 0.7831 (m-30) cc_final: 0.7430 (t70) REVERT: V 367 LEU cc_start: 0.8406 (mt) cc_final: 0.8131 (mm) REVERT: V 379 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8187 (mt-10) REVERT: V 403 LEU cc_start: 0.8837 (mt) cc_final: 0.8595 (mm) REVERT: V 427 GLN cc_start: 0.8035 (pt0) cc_final: 0.7821 (pt0) REVERT: V 433 GLU cc_start: 0.7488 (pm20) cc_final: 0.7283 (pm20) REVERT: V 440 ASN cc_start: 0.7848 (m-40) cc_final: 0.7527 (m-40) REVERT: V 443 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8144 (mtmm) REVERT: V 450 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7495 (mttt) REVERT: V 453 THR cc_start: 0.8747 (m) cc_final: 0.8391 (p) REVERT: V 454 LYS cc_start: 0.8822 (mptt) cc_final: 0.8373 (mmtt) REVERT: W 45 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8287 (p) REVERT: W 66 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8537 (mm) REVERT: W 69 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7458 (mmt90) REVERT: W 86 MET cc_start: 0.7771 (mmm) cc_final: 0.7452 (mmm) REVERT: W 105 GLU cc_start: 0.7929 (mp0) cc_final: 0.7625 (mp0) REVERT: W 113 LYS cc_start: 0.8607 (mttp) cc_final: 0.8235 (mtpt) REVERT: W 135 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7842 (mm) REVERT: W 136 ILE cc_start: 0.8659 (mp) cc_final: 0.8436 (mp) REVERT: W 142 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: W 157 LYS cc_start: 0.8217 (mttm) cc_final: 0.7894 (mttp) REVERT: W 159 THR cc_start: 0.8397 (m) cc_final: 0.7820 (p) REVERT: W 185 LEU cc_start: 0.8140 (mt) cc_final: 0.7693 (mt) REVERT: W 188 ASP cc_start: 0.7612 (m-30) cc_final: 0.7066 (m-30) REVERT: W 191 SER cc_start: 0.8732 (t) cc_final: 0.7983 (m) REVERT: W 200 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.7753 (p) REVERT: W 229 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8225 (tp) REVERT: W 231 LYS cc_start: 0.8488 (mttm) cc_final: 0.8203 (mmmm) REVERT: W 264 GLU cc_start: 0.7324 (mt-10) cc_final: 0.6678 (mt-10) REVERT: W 269 VAL cc_start: 0.8615 (t) cc_final: 0.8349 (m) REVERT: W 271 ASP cc_start: 0.7891 (m-30) cc_final: 0.7680 (m-30) REVERT: W 273 ILE cc_start: 0.8843 (tp) cc_final: 0.8626 (tp) REVERT: W 281 LYS cc_start: 0.8745 (tttm) cc_final: 0.8382 (tppt) REVERT: W 306 PHE cc_start: 0.8307 (m-80) cc_final: 0.7918 (m-80) REVERT: W 310 ASN cc_start: 0.7955 (m-40) cc_final: 0.7605 (m-40) REVERT: W 365 LYS cc_start: 0.8951 (tmmt) cc_final: 0.8707 (tmmt) REVERT: W 367 ILE cc_start: 0.8609 (mt) cc_final: 0.8255 (tt) REVERT: W 373 GLN cc_start: 0.8531 (mp10) cc_final: 0.8207 (mt0) REVERT: W 375 GLU cc_start: 0.8324 (tp30) cc_final: 0.7903 (tp30) REVERT: W 376 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7671 (tp30) REVERT: W 386 LEU cc_start: 0.8532 (tp) cc_final: 0.8308 (tt) REVERT: W 389 LYS cc_start: 0.8820 (tppt) cc_final: 0.7696 (tppt) REVERT: W 393 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7907 (mm-30) REVERT: W 420 VAL cc_start: 0.8614 (t) cc_final: 0.8227 (m) REVERT: W 424 LYS cc_start: 0.8628 (ptpt) cc_final: 0.8357 (ptpt) REVERT: W 438 LYS cc_start: 0.9032 (pttt) cc_final: 0.8713 (pttt) REVERT: X 95 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8172 (mt-10) REVERT: X 117 LYS cc_start: 0.8110 (ptpp) cc_final: 0.7842 (ptpt) REVERT: X 123 GLU cc_start: 0.8232 (pt0) cc_final: 0.7853 (tt0) REVERT: X 125 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7912 (t80) REVERT: X 141 GLU cc_start: 0.7334 (pm20) cc_final: 0.6891 (pm20) REVERT: X 177 LYS cc_start: 0.8385 (pttm) cc_final: 0.8140 (pttm) REVERT: X 186 TYR cc_start: 0.8517 (t80) cc_final: 0.8258 (t80) REVERT: X 189 ILE cc_start: 0.9173 (mm) cc_final: 0.8897 (mm) REVERT: X 198 ASP cc_start: 0.7760 (m-30) cc_final: 0.7474 (m-30) REVERT: X 205 ASN cc_start: 0.8134 (m-40) cc_final: 0.7906 (t0) REVERT: X 211 ARG cc_start: 0.8123 (ttt-90) cc_final: 0.7800 (ttt-90) REVERT: X 239 LYS cc_start: 0.8542 (ptpt) cc_final: 0.8068 (ptpp) REVERT: X 245 GLN cc_start: 0.8130 (tp40) cc_final: 0.7820 (tp40) REVERT: X 251 ASP cc_start: 0.7913 (m-30) cc_final: 0.7527 (m-30) REVERT: X 253 ASP cc_start: 0.8070 (m-30) cc_final: 0.7720 (t0) REVERT: X 258 ARG cc_start: 0.7178 (mmm-85) cc_final: 0.6945 (mmm-85) REVERT: X 263 GLN cc_start: 0.7202 (tm-30) cc_final: 0.6593 (tm-30) REVERT: X 268 MET cc_start: 0.8440 (mtp) cc_final: 0.8208 (mtt) REVERT: X 271 GLN cc_start: 0.8305 (tp40) cc_final: 0.8064 (tp40) REVERT: X 272 LEU cc_start: 0.8932 (tt) cc_final: 0.8692 (tp) REVERT: X 277 LYS cc_start: 0.8739 (ttmm) cc_final: 0.8476 (mtmt) REVERT: X 285 ARG cc_start: 0.8280 (mtt90) cc_final: 0.8065 (mtt-85) REVERT: X 313 VAL cc_start: 0.8092 (OUTLIER) cc_final: 0.7561 (t) REVERT: X 325 ASN cc_start: 0.8660 (m-40) cc_final: 0.8304 (m-40) REVERT: X 328 LEU cc_start: 0.8785 (mt) cc_final: 0.8489 (mm) REVERT: X 362 ASP cc_start: 0.7638 (p0) cc_final: 0.7387 (p0) REVERT: X 377 LYS cc_start: 0.8542 (mmmm) cc_final: 0.8222 (mmmm) REVERT: X 378 ASP cc_start: 0.7678 (p0) cc_final: 0.7415 (t0) REVERT: X 385 GLU cc_start: 0.8388 (pp20) cc_final: 0.8050 (pp20) REVERT: X 401 ASP cc_start: 0.8384 (m-30) cc_final: 0.8085 (m-30) REVERT: X 406 MET cc_start: 0.8485 (mtp) cc_final: 0.8252 (ttm) REVERT: X 409 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7931 (mm-30) REVERT: X 417 GLN cc_start: 0.8057 (mt0) cc_final: 0.7788 (mt0) REVERT: X 431 ARG cc_start: 0.7723 (ttp-110) cc_final: 0.7269 (ttp-110) REVERT: X 441 GLU cc_start: 0.7889 (tp30) cc_final: 0.7581 (tp30) REVERT: X 443 LYS cc_start: 0.8382 (tmmt) cc_final: 0.8058 (ttmm) REVERT: X 454 LYS cc_start: 0.8375 (tmmt) cc_final: 0.7809 (tmmt) REVERT: X 457 GLU cc_start: 0.7751 (pp20) cc_final: 0.7497 (pp20) REVERT: Y 59 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8314 (tptp) REVERT: Y 62 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8626 (mt0) REVERT: Y 66 ILE cc_start: 0.8775 (mp) cc_final: 0.8501 (mp) REVERT: Y 106 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8493 (tt) REVERT: Y 111 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7619 (tp) REVERT: Y 113 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7821 (mtmm) REVERT: Y 122 ARG cc_start: 0.8212 (mtt90) cc_final: 0.7836 (mmm-85) REVERT: Y 128 LYS cc_start: 0.8559 (ttpp) cc_final: 0.8177 (ttpp) REVERT: Y 130 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7422 (mtmm) REVERT: Y 131 GLU cc_start: 0.6417 (mm-30) cc_final: 0.5967 (mm-30) REVERT: Y 164 ASP cc_start: 0.8211 (m-30) cc_final: 0.7921 (m-30) REVERT: Y 171 LEU cc_start: 0.8453 (mp) cc_final: 0.8236 (mm) REVERT: Y 173 ASN cc_start: 0.7972 (p0) cc_final: 0.7209 (m-40) REVERT: Y 174 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8375 (mmtm) REVERT: Y 175 MET cc_start: 0.8863 (tpp) cc_final: 0.8270 (tpp) REVERT: Y 194 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8359 (mmmt) REVERT: Y 208 ARG cc_start: 0.7944 (mmm-85) cc_final: 0.7441 (mmm-85) REVERT: Y 271 ASP cc_start: 0.8405 (t0) cc_final: 0.8031 (t0) REVERT: Y 272 GLN cc_start: 0.8511 (mt0) cc_final: 0.8280 (tt0) REVERT: Y 274 ASN cc_start: 0.8686 (m-40) cc_final: 0.8399 (m-40) REVERT: Y 277 VAL cc_start: 0.8633 (t) cc_final: 0.8366 (p) REVERT: Y 287 GLU cc_start: 0.7521 (pm20) cc_final: 0.7168 (pm20) REVERT: Y 310 ASN cc_start: 0.8100 (m-40) cc_final: 0.7684 (m-40) REVERT: Y 339 SER cc_start: 0.8798 (t) cc_final: 0.8384 (p) REVERT: Y 370 ILE cc_start: 0.8983 (mt) cc_final: 0.8746 (mt) REVERT: Y 373 GLN cc_start: 0.8721 (tt0) cc_final: 0.8472 (mm-40) REVERT: Y 374 GLU cc_start: 0.7967 (tp30) cc_final: 0.7696 (mm-30) REVERT: Y 384 LEU cc_start: 0.8971 (tp) cc_final: 0.8688 (tt) REVERT: Y 389 LYS cc_start: 0.8925 (ttpt) cc_final: 0.8428 (mmmm) REVERT: Y 393 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8130 (mt-10) REVERT: Y 407 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8257 (tp-100) REVERT: Y 412 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8762 (tptm) REVERT: Y 424 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8319 (mtmm) REVERT: Y 444 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7340 (tp30) REVERT: Y 456 ILE cc_start: 0.8801 (mt) cc_final: 0.8370 (mt) REVERT: Z 310 ARG cc_start: 0.8222 (mtt-85) cc_final: 0.7580 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7742 (ttm110) cc_final: 0.7502 (ttm110) outliers start: 147 outliers final: 74 residues processed: 1220 average time/residue: 0.2187 time to fit residues: 405.9555 Evaluate side-chains 1241 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1129 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 957 THR Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1204 ASN Chi-restraints excluded: chain Q residue 1270 LYS Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1335 LEU Chi-restraints excluded: chain Q residue 1389 VAL Chi-restraints excluded: chain Q residue 1405 MET Chi-restraints excluded: chain Q residue 1430 GLU Chi-restraints excluded: chain R residue 22 ARG Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 165 PHE Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 599 ARG Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 699 THR Chi-restraints excluded: chain R residue 728 VAL Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 265 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 315 MET Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 331 LYS Chi-restraints excluded: chain U residue 375 GLU Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain U residue 428 LEU Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 300 VAL Chi-restraints excluded: chain V residue 329 GLU Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 393 LEU Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain V residue 455 ILE Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 69 ARG Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 142 GLU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 229 LEU Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 340 SER Chi-restraints excluded: chain X residue 412 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 430 ASN Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain X residue 448 ASP Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 113 LYS Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 377 VAL Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 412 LYS Chi-restraints excluded: chain Z residue 312 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 258 optimal weight: 2.9990 chunk 42 optimal weight: 0.0370 chunk 361 optimal weight: 0.9990 chunk 285 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 209 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1204 ASN Q1228 HIS ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 HIS T 29 HIS ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 394 GLN U 63 ASN V 289 ASN V 341 ASN W 248 ASN ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.127675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.108937 restraints weight = 56815.060| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.30 r_work: 0.3351 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 29139 Z= 0.131 Angle : 0.645 16.627 39425 Z= 0.315 Chirality : 0.044 0.188 4626 Planarity : 0.005 0.060 5049 Dihedral : 7.292 129.865 4012 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.30 % Allowed : 27.25 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.14), residues: 3626 helix: 0.98 (0.13), residues: 1537 sheet: -0.12 (0.20), residues: 611 loop : -0.58 (0.16), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG S 34 TYR 0.023 0.002 TYR Q1198 PHE 0.033 0.001 PHE U 254 TRP 0.013 0.001 TRP Q1361 HIS 0.003 0.001 HIS U 242 Details of bonding type rmsd covalent geometry : bond 0.00293 (29139) covalent geometry : angle 0.64478 (39425) hydrogen bonds : bond 0.03468 ( 1098) hydrogen bonds : angle 4.33981 ( 3198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1135 time to evaluate : 1.191 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: Q 1005 MET cc_start: 0.6789 (mmp) cc_final: 0.6071 (mmp) REVERT: Q 1023 ASP cc_start: 0.7796 (t0) cc_final: 0.7311 (t0) REVERT: Q 1027 SER cc_start: 0.8698 (m) cc_final: 0.8169 (p) REVERT: Q 1081 ILE cc_start: 0.8951 (mt) cc_final: 0.8622 (tt) REVERT: Q 1083 TYR cc_start: 0.8269 (t80) cc_final: 0.7888 (t80) REVERT: Q 1087 ARG cc_start: 0.8534 (ttm-80) cc_final: 0.8285 (ttm-80) REVERT: Q 1102 VAL cc_start: 0.8235 (OUTLIER) cc_final: 0.8022 (m) REVERT: Q 1112 LYS cc_start: 0.8803 (mttp) cc_final: 0.8291 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8166 (t) REVERT: Q 1150 LYS cc_start: 0.8527 (tttm) cc_final: 0.7686 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: Q 1173 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7187 (mp0) REVERT: Q 1186 VAL cc_start: 0.8967 (p) cc_final: 0.8678 (t) REVERT: Q 1195 LYS cc_start: 0.8204 (tppt) cc_final: 0.7438 (tppt) REVERT: Q 1222 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7408 (tm-30) REVERT: Q 1230 THR cc_start: 0.8760 (m) cc_final: 0.8387 (p) REVERT: Q 1231 ASN cc_start: 0.8638 (t0) cc_final: 0.8373 (t0) REVERT: Q 1234 ASN cc_start: 0.8501 (m-40) cc_final: 0.8286 (m-40) REVERT: Q 1242 ILE cc_start: 0.9166 (tp) cc_final: 0.8833 (tt) REVERT: Q 1248 ASP cc_start: 0.7396 (t70) cc_final: 0.6891 (t0) REVERT: Q 1256 ASN cc_start: 0.8501 (m-40) cc_final: 0.8298 (m-40) REVERT: Q 1266 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7843 (tm-30) REVERT: Q 1267 ASP cc_start: 0.8569 (m-30) cc_final: 0.7873 (m-30) REVERT: Q 1276 GLU cc_start: 0.8300 (tp30) cc_final: 0.8072 (tp30) REVERT: Q 1291 MET cc_start: 0.8008 (tpt) cc_final: 0.7770 (tpp) REVERT: Q 1293 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.6776 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8338 (mt) cc_final: 0.8009 (mm) REVERT: Q 1302 ARG cc_start: 0.8047 (ttt180) cc_final: 0.7545 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8551 (m-30) cc_final: 0.8234 (m-30) REVERT: Q 1317 ARG cc_start: 0.8112 (ptm160) cc_final: 0.7860 (ptm160) REVERT: Q 1331 MET cc_start: 0.7803 (tpp) cc_final: 0.7304 (tpp) REVERT: Q 1334 TYR cc_start: 0.7831 (p90) cc_final: 0.7244 (p90) REVERT: Q 1335 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7782 (mp) REVERT: Q 1421 ARG cc_start: 0.7437 (mtt90) cc_final: 0.6817 (mtt90) REVERT: R 21 LEU cc_start: 0.6888 (tp) cc_final: 0.6548 (tp) REVERT: R 35 ASN cc_start: 0.8843 (t0) cc_final: 0.8303 (t0) REVERT: R 55 ASN cc_start: 0.8395 (p0) cc_final: 0.8033 (p0) REVERT: R 70 PHE cc_start: 0.7519 (t80) cc_final: 0.7244 (t80) REVERT: R 119 PHE cc_start: 0.8215 (m-10) cc_final: 0.7977 (m-10) REVERT: R 154 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7623 (mm) REVERT: R 155 PHE cc_start: 0.7358 (m-80) cc_final: 0.6989 (m-10) REVERT: R 156 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7695 (pm20) REVERT: R 182 LYS cc_start: 0.8418 (mmmm) cc_final: 0.8097 (mmmm) REVERT: R 214 TRP cc_start: 0.7502 (t-100) cc_final: 0.6481 (t-100) REVERT: R 218 GLN cc_start: 0.7928 (mp10) cc_final: 0.7513 (mp10) REVERT: R 230 LYS cc_start: 0.8882 (tttt) cc_final: 0.8583 (tttt) REVERT: R 242 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7885 (pt0) REVERT: R 251 CYS cc_start: 0.7277 (OUTLIER) cc_final: 0.7017 (m) REVERT: R 252 TYR cc_start: 0.8286 (p90) cc_final: 0.8059 (p90) REVERT: R 260 ASP cc_start: 0.7875 (m-30) cc_final: 0.7581 (p0) REVERT: R 262 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8193 (mm-30) REVERT: R 592 HIS cc_start: 0.8141 (t-90) cc_final: 0.7442 (t-90) REVERT: R 609 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7199 (mp10) REVERT: R 612 MET cc_start: 0.6751 (tpp) cc_final: 0.6452 (tpp) REVERT: R 627 GLN cc_start: 0.8495 (pt0) cc_final: 0.8093 (pt0) REVERT: R 642 SER cc_start: 0.8725 (m) cc_final: 0.8233 (p) REVERT: R 643 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7376 (mm-30) REVERT: R 645 ILE cc_start: 0.9121 (mt) cc_final: 0.8777 (tt) REVERT: R 647 LEU cc_start: 0.8483 (mp) cc_final: 0.8116 (mp) REVERT: R 659 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8150 (tp-100) REVERT: R 663 ASP cc_start: 0.8121 (m-30) cc_final: 0.7778 (m-30) REVERT: R 664 MET cc_start: 0.8769 (mtm) cc_final: 0.8489 (mtp) REVERT: R 681 LYS cc_start: 0.8952 (tptt) cc_final: 0.8698 (tptt) REVERT: R 699 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7714 (p) REVERT: R 721 GLU cc_start: 0.8064 (tp30) cc_final: 0.7860 (tp30) REVERT: R 722 GLU cc_start: 0.8345 (pp20) cc_final: 0.7499 (pp20) REVERT: R 723 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7683 (mm-40) REVERT: R 724 TYR cc_start: 0.8191 (t80) cc_final: 0.7682 (t80) REVERT: R 728 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8620 (m) REVERT: S 70 GLU cc_start: 0.7358 (tp30) cc_final: 0.6660 (tp30) REVERT: S 73 ARG cc_start: 0.8440 (tmm-80) cc_final: 0.8031 (tmm-80) REVERT: S 100 TYR cc_start: 0.8010 (t80) cc_final: 0.7548 (t80) REVERT: S 110 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.8056 (mtm-85) REVERT: S 114 LYS cc_start: 0.8500 (mttt) cc_final: 0.8240 (mttt) REVERT: S 122 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8184 (mtpp) REVERT: S 140 TYR cc_start: 0.8608 (t80) cc_final: 0.8317 (t80) REVERT: T 49 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.7928 (m) REVERT: T 56 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7789 (mt-10) REVERT: T 95 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8224 (mm-30) REVERT: T 177 LYS cc_start: 0.8486 (tttt) cc_final: 0.8110 (mtpp) REVERT: T 178 THR cc_start: 0.8924 (m) cc_final: 0.8636 (t) REVERT: T 193 LYS cc_start: 0.8395 (mmmt) cc_final: 0.8088 (mmmt) REVERT: T 224 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8418 (tp) REVERT: T 230 VAL cc_start: 0.9017 (OUTLIER) cc_final: 0.8757 (m) REVERT: T 251 ASP cc_start: 0.8109 (m-30) cc_final: 0.7776 (m-30) REVERT: T 273 LEU cc_start: 0.7855 (tp) cc_final: 0.7599 (tt) REVERT: T 280 ILE cc_start: 0.8768 (mm) cc_final: 0.8541 (mp) REVERT: T 295 TYR cc_start: 0.8577 (m-80) cc_final: 0.8044 (m-80) REVERT: T 371 ARG cc_start: 0.7975 (mtp-110) cc_final: 0.7634 (ptm-80) REVERT: T 381 ARG cc_start: 0.8726 (ttt-90) cc_final: 0.8235 (ttm-80) REVERT: T 382 THR cc_start: 0.8576 (p) cc_final: 0.8097 (p) REVERT: T 385 GLU cc_start: 0.8515 (pt0) cc_final: 0.7767 (pp20) REVERT: T 396 GLU cc_start: 0.7373 (pt0) cc_final: 0.7144 (pt0) REVERT: T 401 ASP cc_start: 0.8510 (m-30) cc_final: 0.7689 (m-30) REVERT: T 409 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7600 (mt-10) REVERT: T 414 TYR cc_start: 0.8076 (t80) cc_final: 0.7561 (t80) REVERT: T 417 GLN cc_start: 0.8260 (mt0) cc_final: 0.7866 (mt0) REVERT: T 424 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7857 (mt) REVERT: T 434 ILE cc_start: 0.7722 (mt) cc_final: 0.7108 (mt) REVERT: T 438 ASP cc_start: 0.8440 (m-30) cc_final: 0.7943 (m-30) REVERT: T 439 VAL cc_start: 0.8910 (t) cc_final: 0.8703 (t) REVERT: T 448 ASP cc_start: 0.7619 (p0) cc_final: 0.7084 (p0) REVERT: T 456 LEU cc_start: 0.8923 (tp) cc_final: 0.8334 (mt) REVERT: T 457 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8165 (mm-30) REVERT: U 34 ASN cc_start: 0.8467 (m-40) cc_final: 0.8258 (m110) REVERT: U 38 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7557 (mpt180) REVERT: U 86 MET cc_start: 0.8008 (mmm) cc_final: 0.7523 (mmm) REVERT: U 94 LYS cc_start: 0.8843 (tppt) cc_final: 0.8437 (tptp) REVERT: U 104 SER cc_start: 0.8550 (m) cc_final: 0.8246 (t) REVERT: U 105 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7094 (mt-10) REVERT: U 110 GLU cc_start: 0.7908 (pp20) cc_final: 0.7581 (pp20) REVERT: U 123 LYS cc_start: 0.8234 (mttt) cc_final: 0.7904 (mttp) REVERT: U 128 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8442 (ttmm) REVERT: U 139 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6282 (tp30) REVERT: U 161 LYS cc_start: 0.8615 (ptmm) cc_final: 0.7534 (ptmm) REVERT: U 164 ASP cc_start: 0.7888 (t70) cc_final: 0.7574 (t70) REVERT: U 166 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7140 (tp30) REVERT: U 182 GLU cc_start: 0.8135 (tm-30) cc_final: 0.7734 (tm-30) REVERT: U 193 ASP cc_start: 0.7972 (t0) cc_final: 0.7540 (t0) REVERT: U 194 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8100 (ttpt) REVERT: U 198 LYS cc_start: 0.8558 (tttm) cc_final: 0.8245 (tttm) REVERT: U 272 GLN cc_start: 0.8008 (tp40) cc_final: 0.7510 (tp40) REVERT: U 276 LYS cc_start: 0.8958 (tptt) cc_final: 0.8518 (tptm) REVERT: U 281 LYS cc_start: 0.8944 (tttm) cc_final: 0.8505 (ttmm) REVERT: U 313 LEU cc_start: 0.8813 (mt) cc_final: 0.8527 (mp) REVERT: U 338 LYS cc_start: 0.8900 (mttt) cc_final: 0.8649 (ttmm) REVERT: U 339 SER cc_start: 0.8852 (m) cc_final: 0.8550 (t) REVERT: U 349 ASP cc_start: 0.8632 (t0) cc_final: 0.8179 (m-30) REVERT: U 365 LYS cc_start: 0.8833 (ttpt) cc_final: 0.8492 (ttmt) REVERT: U 376 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7943 (mm-30) REVERT: U 378 GLU cc_start: 0.7354 (mp0) cc_final: 0.7132 (mp0) REVERT: U 393 GLU cc_start: 0.7675 (pp20) cc_final: 0.7377 (pp20) REVERT: U 399 SER cc_start: 0.8315 (m) cc_final: 0.8054 (p) REVERT: U 400 SER cc_start: 0.8171 (t) cc_final: 0.7716 (m) REVERT: U 411 MET cc_start: 0.7430 (OUTLIER) cc_final: 0.7091 (mpt) REVERT: U 412 LYS cc_start: 0.8816 (tppt) cc_final: 0.8546 (tppt) REVERT: U 419 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6608 (mp0) REVERT: U 424 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7921 (mmtt) REVERT: U 428 LEU cc_start: 0.8672 (tp) cc_final: 0.8344 (pp) REVERT: U 444 GLU cc_start: 0.8175 (tp30) cc_final: 0.7607 (tp30) REVERT: V 30 ILE cc_start: 0.8478 (mt) cc_final: 0.8233 (mp) REVERT: V 31 LYS cc_start: 0.8105 (mmpt) cc_final: 0.7665 (mmtm) REVERT: V 35 LEU cc_start: 0.8451 (mm) cc_final: 0.7634 (mm) REVERT: V 52 ILE cc_start: 0.8616 (mp) cc_final: 0.8254 (mm) REVERT: V 56 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7307 (mm-30) REVERT: V 69 LYS cc_start: 0.7865 (mtmm) cc_final: 0.7657 (mtmm) REVERT: V 95 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7737 (mt-10) REVERT: V 99 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8289 (mtpp) REVERT: V 127 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7744 (ttm110) REVERT: V 132 ARG cc_start: 0.8325 (tpp80) cc_final: 0.7883 (tpp80) REVERT: V 141 GLU cc_start: 0.7648 (pm20) cc_final: 0.7368 (pm20) REVERT: V 144 VAL cc_start: 0.8484 (t) cc_final: 0.8027 (m) REVERT: V 180 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7673 (tpt-90) REVERT: V 187 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7696 (mt-10) REVERT: V 194 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.7401 (t) REVERT: V 201 TYR cc_start: 0.8373 (t80) cc_final: 0.8119 (t80) REVERT: V 203 GLU cc_start: 0.7985 (tt0) cc_final: 0.7723 (tt0) REVERT: V 214 ARG cc_start: 0.7940 (tpp-160) cc_final: 0.7703 (ttm170) REVERT: V 218 TYR cc_start: 0.8663 (m-80) cc_final: 0.8166 (m-80) REVERT: V 222 PHE cc_start: 0.8315 (m-80) cc_final: 0.8049 (m-10) REVERT: V 223 ASP cc_start: 0.7771 (m-30) cc_final: 0.7263 (t0) REVERT: V 239 LYS cc_start: 0.8274 (mtpt) cc_final: 0.8045 (mttt) REVERT: V 253 ASP cc_start: 0.7502 (m-30) cc_final: 0.7249 (m-30) REVERT: V 254 VAL cc_start: 0.8688 (t) cc_final: 0.8401 (m) REVERT: V 263 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8417 (mm-40) REVERT: V 268 MET cc_start: 0.7804 (mmm) cc_final: 0.7099 (mmm) REVERT: V 302 GLU cc_start: 0.8115 (pt0) cc_final: 0.7496 (pm20) REVERT: V 325 ASN cc_start: 0.8400 (t0) cc_final: 0.7500 (t0) REVERT: V 326 LYS cc_start: 0.8535 (tmmt) cc_final: 0.8303 (tttt) REVERT: V 329 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7054 (mm-30) REVERT: V 344 MET cc_start: 0.8778 (mmt) cc_final: 0.8543 (mmm) REVERT: V 365 ASP cc_start: 0.7821 (m-30) cc_final: 0.7445 (t70) REVERT: V 367 LEU cc_start: 0.8376 (mt) cc_final: 0.8107 (mm) REVERT: V 379 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8174 (mt-10) REVERT: V 403 LEU cc_start: 0.8852 (mt) cc_final: 0.8609 (mm) REVERT: V 427 GLN cc_start: 0.7996 (pt0) cc_final: 0.7788 (pt0) REVERT: V 443 LYS cc_start: 0.8334 (mtpt) cc_final: 0.8108 (mtmm) REVERT: V 450 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7472 (mttt) REVERT: V 453 THR cc_start: 0.8749 (m) cc_final: 0.8375 (p) REVERT: V 454 LYS cc_start: 0.8838 (mptt) cc_final: 0.8399 (mmtt) REVERT: W 45 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8297 (p) REVERT: W 66 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8538 (mm) REVERT: W 69 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7449 (mmt90) REVERT: W 86 MET cc_start: 0.7750 (mmm) cc_final: 0.7424 (mmm) REVERT: W 105 GLU cc_start: 0.7895 (mp0) cc_final: 0.7595 (mp0) REVERT: W 113 LYS cc_start: 0.8586 (mttp) cc_final: 0.8205 (mtpt) REVERT: W 135 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7829 (mm) REVERT: W 136 ILE cc_start: 0.8656 (mp) cc_final: 0.8434 (mp) REVERT: W 142 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: W 159 THR cc_start: 0.8420 (m) cc_final: 0.7882 (p) REVERT: W 191 SER cc_start: 0.8731 (t) cc_final: 0.8017 (m) REVERT: W 200 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.7773 (p) REVERT: W 229 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8162 (tp) REVERT: W 231 LYS cc_start: 0.8486 (mttm) cc_final: 0.8202 (mmmm) REVERT: W 261 ASP cc_start: 0.8220 (t0) cc_final: 0.7669 (t0) REVERT: W 264 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6687 (mt-10) REVERT: W 269 VAL cc_start: 0.8604 (t) cc_final: 0.8336 (m) REVERT: W 271 ASP cc_start: 0.7896 (m-30) cc_final: 0.7693 (m-30) REVERT: W 273 ILE cc_start: 0.8833 (tp) cc_final: 0.8593 (tp) REVERT: W 281 LYS cc_start: 0.8738 (tttm) cc_final: 0.8344 (tppt) REVERT: W 306 PHE cc_start: 0.8296 (m-80) cc_final: 0.7895 (m-80) REVERT: W 310 ASN cc_start: 0.7906 (m-40) cc_final: 0.7608 (m-40) REVERT: W 365 LYS cc_start: 0.8958 (tmmt) cc_final: 0.8730 (tmmt) REVERT: W 367 ILE cc_start: 0.8621 (mt) cc_final: 0.8271 (tt) REVERT: W 373 GLN cc_start: 0.8530 (mp10) cc_final: 0.8186 (mt0) REVERT: W 386 LEU cc_start: 0.8540 (tp) cc_final: 0.8308 (tt) REVERT: W 389 LYS cc_start: 0.8812 (tppt) cc_final: 0.7641 (tppt) REVERT: W 393 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7881 (mm-30) REVERT: W 420 VAL cc_start: 0.8607 (t) cc_final: 0.8195 (m) REVERT: W 424 LYS cc_start: 0.8616 (ptpt) cc_final: 0.8344 (ptpt) REVERT: W 438 LYS cc_start: 0.9094 (pttt) cc_final: 0.8733 (pttt) REVERT: X 95 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8183 (mt-10) REVERT: X 106 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7932 (p) REVERT: X 117 LYS cc_start: 0.8016 (ptpp) cc_final: 0.7742 (ptpt) REVERT: X 125 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7921 (t80) REVERT: X 141 GLU cc_start: 0.7319 (pm20) cc_final: 0.6878 (pm20) REVERT: X 177 LYS cc_start: 0.8365 (pttm) cc_final: 0.8165 (pttm) REVERT: X 186 TYR cc_start: 0.8513 (t80) cc_final: 0.8204 (t80) REVERT: X 189 ILE cc_start: 0.9160 (mm) cc_final: 0.8919 (mt) REVERT: X 198 ASP cc_start: 0.7707 (m-30) cc_final: 0.7403 (m-30) REVERT: X 211 ARG cc_start: 0.8060 (ttt-90) cc_final: 0.7738 (ttt-90) REVERT: X 239 LYS cc_start: 0.8514 (ptpt) cc_final: 0.8056 (ptpp) REVERT: X 245 GLN cc_start: 0.8112 (tp40) cc_final: 0.7786 (tp40) REVERT: X 251 ASP cc_start: 0.7881 (m-30) cc_final: 0.7521 (m-30) REVERT: X 253 ASP cc_start: 0.8090 (m-30) cc_final: 0.7766 (t0) REVERT: X 258 ARG cc_start: 0.7135 (mmm-85) cc_final: 0.6907 (mmm-85) REVERT: X 263 GLN cc_start: 0.7203 (tm-30) cc_final: 0.6595 (tm-30) REVERT: X 268 MET cc_start: 0.8407 (mtp) cc_final: 0.8131 (mtt) REVERT: X 272 LEU cc_start: 0.8901 (tt) cc_final: 0.8664 (tp) REVERT: X 274 LYS cc_start: 0.7891 (tmmt) cc_final: 0.7631 (ttmt) REVERT: X 277 LYS cc_start: 0.8741 (ttmm) cc_final: 0.8498 (mtmt) REVERT: X 313 VAL cc_start: 0.8020 (OUTLIER) cc_final: 0.7496 (t) REVERT: X 325 ASN cc_start: 0.8626 (m-40) cc_final: 0.8356 (m-40) REVERT: X 328 LEU cc_start: 0.8769 (mt) cc_final: 0.8489 (mm) REVERT: X 377 LYS cc_start: 0.8495 (mmmm) cc_final: 0.8181 (mmmm) REVERT: X 378 ASP cc_start: 0.7667 (p0) cc_final: 0.7378 (t70) REVERT: X 385 GLU cc_start: 0.8376 (pp20) cc_final: 0.8044 (pp20) REVERT: X 401 ASP cc_start: 0.8337 (m-30) cc_final: 0.8094 (m-30) REVERT: X 406 MET cc_start: 0.8487 (mtp) cc_final: 0.8277 (ttm) REVERT: X 409 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7857 (mm-30) REVERT: X 417 GLN cc_start: 0.8039 (mt0) cc_final: 0.7732 (mt0) REVERT: X 431 ARG cc_start: 0.7715 (ttp-110) cc_final: 0.7229 (ttp-110) REVERT: X 441 GLU cc_start: 0.7904 (tp30) cc_final: 0.7548 (tp30) REVERT: X 443 LYS cc_start: 0.8429 (tmmt) cc_final: 0.8100 (ttmm) REVERT: X 448 ASP cc_start: 0.7917 (t70) cc_final: 0.7235 (t0) REVERT: X 454 LYS cc_start: 0.8372 (tmmt) cc_final: 0.8006 (tmmt) REVERT: Y 59 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8288 (tptp) REVERT: Y 62 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8650 (mt0) REVERT: Y 66 ILE cc_start: 0.8747 (mp) cc_final: 0.8452 (mp) REVERT: Y 111 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7588 (tp) REVERT: Y 113 LYS cc_start: 0.8245 (ptpp) cc_final: 0.7845 (mtmm) REVERT: Y 122 ARG cc_start: 0.8204 (mtt90) cc_final: 0.7946 (mtp85) REVERT: Y 128 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8088 (ttpp) REVERT: Y 130 LYS cc_start: 0.7949 (ttmm) cc_final: 0.7459 (mtmm) REVERT: Y 131 GLU cc_start: 0.6390 (mm-30) cc_final: 0.6028 (mm-30) REVERT: Y 161 LYS cc_start: 0.8573 (pttt) cc_final: 0.8180 (pttm) REVERT: Y 164 ASP cc_start: 0.8207 (m-30) cc_final: 0.7882 (m-30) REVERT: Y 171 LEU cc_start: 0.8447 (mp) cc_final: 0.8242 (mm) REVERT: Y 174 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8591 (mmtm) REVERT: Y 175 MET cc_start: 0.8874 (tpp) cc_final: 0.8278 (tpp) REVERT: Y 194 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8358 (mmmt) REVERT: Y 271 ASP cc_start: 0.8415 (t0) cc_final: 0.8035 (t0) REVERT: Y 272 GLN cc_start: 0.8517 (mt0) cc_final: 0.8258 (tt0) REVERT: Y 274 ASN cc_start: 0.8692 (m-40) cc_final: 0.8248 (m-40) REVERT: Y 277 VAL cc_start: 0.8642 (t) cc_final: 0.8377 (p) REVERT: Y 287 GLU cc_start: 0.7481 (pm20) cc_final: 0.7116 (pm20) REVERT: Y 310 ASN cc_start: 0.8069 (m-40) cc_final: 0.7644 (m-40) REVERT: Y 339 SER cc_start: 0.8799 (t) cc_final: 0.8362 (p) REVERT: Y 370 ILE cc_start: 0.8973 (mt) cc_final: 0.8726 (mt) REVERT: Y 373 GLN cc_start: 0.8712 (tt0) cc_final: 0.8481 (mm-40) REVERT: Y 374 GLU cc_start: 0.7947 (tp30) cc_final: 0.7680 (mm-30) REVERT: Y 384 LEU cc_start: 0.8973 (tp) cc_final: 0.8686 (tt) REVERT: Y 389 LYS cc_start: 0.8916 (ttpt) cc_final: 0.8347 (mmmm) REVERT: Y 393 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8146 (mt-10) REVERT: Y 407 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8273 (tp-100) REVERT: Y 412 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8750 (tptm) REVERT: Y 422 ASP cc_start: 0.7962 (m-30) cc_final: 0.7576 (t0) REVERT: Y 444 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7374 (tp30) REVERT: Y 456 ILE cc_start: 0.8813 (mt) cc_final: 0.8383 (mt) REVERT: Z 310 ARG cc_start: 0.8225 (mtt-85) cc_final: 0.7568 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7520 (ttm110) outliers start: 136 outliers final: 76 residues processed: 1195 average time/residue: 0.2218 time to fit residues: 401.7666 Evaluate side-chains 1219 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 1109 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1030 THR Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1125 CYS Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1270 LYS Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1335 LEU Chi-restraints excluded: chain Q residue 1389 VAL Chi-restraints excluded: chain Q residue 1405 MET Chi-restraints excluded: chain Q residue 1430 GLU Chi-restraints excluded: chain R residue 22 ARG Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 165 PHE Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 242 GLN Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 699 THR Chi-restraints excluded: chain R residue 728 VAL Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 265 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 315 MET Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 409 GLU Chi-restraints excluded: chain T residue 424 ILE Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 331 LYS Chi-restraints excluded: chain U residue 375 GLU Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 300 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 393 LEU Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain V residue 455 ILE Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 63 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 69 ARG Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 142 GLU Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 229 LEU Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 412 LEU Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 401 ASN Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 412 LYS Chi-restraints excluded: chain Y residue 420 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 8 optimal weight: 2.9990 chunk 302 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 78 optimal weight: 0.0980 chunk 221 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 247 optimal weight: 6.9990 chunk 327 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 285 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN Q1228 HIS ** Q1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 609 GLN ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 HIS ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 401 ASN U 446 GLN V 289 ASN V 341 ASN W 90 GLN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.125688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.107076 restraints weight = 57302.657| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.26 r_work: 0.3316 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29139 Z= 0.212 Angle : 0.691 17.219 39425 Z= 0.342 Chirality : 0.046 0.219 4626 Planarity : 0.005 0.070 5049 Dihedral : 7.401 127.557 4012 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.68 % Allowed : 27.59 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.14), residues: 3626 helix: 0.85 (0.13), residues: 1539 sheet: -0.17 (0.21), residues: 608 loop : -0.65 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG S 34 TYR 0.026 0.002 TYR Q1198 PHE 0.034 0.002 PHE U 254 TRP 0.013 0.002 TRP Q1361 HIS 0.006 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00445 (29139) covalent geometry : angle 0.69095 (39425) hydrogen bonds : bond 0.03956 ( 1098) hydrogen bonds : angle 4.50431 ( 3198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 1142 time to evaluate : 1.225 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: Q 1005 MET cc_start: 0.6763 (mmp) cc_final: 0.6041 (mmp) REVERT: Q 1023 ASP cc_start: 0.7897 (t0) cc_final: 0.7435 (t0) REVERT: Q 1027 SER cc_start: 0.8737 (m) cc_final: 0.8196 (p) REVERT: Q 1081 ILE cc_start: 0.8961 (mt) cc_final: 0.8620 (tt) REVERT: Q 1102 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.8065 (m) REVERT: Q 1112 LYS cc_start: 0.8817 (mttp) cc_final: 0.8311 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8192 (t) REVERT: Q 1150 LYS cc_start: 0.8581 (tttm) cc_final: 0.7777 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: Q 1186 VAL cc_start: 0.8990 (p) cc_final: 0.8755 (t) REVERT: Q 1195 LYS cc_start: 0.8232 (tppt) cc_final: 0.7473 (tppt) REVERT: Q 1208 ARG cc_start: 0.8729 (ttm170) cc_final: 0.7693 (mtp180) REVERT: Q 1222 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7405 (tm-30) REVERT: Q 1230 THR cc_start: 0.8835 (m) cc_final: 0.8431 (p) REVERT: Q 1231 ASN cc_start: 0.8656 (t0) cc_final: 0.8369 (t0) REVERT: Q 1242 ILE cc_start: 0.9150 (tp) cc_final: 0.8916 (tp) REVERT: Q 1248 ASP cc_start: 0.7449 (t70) cc_final: 0.6989 (t0) REVERT: Q 1256 ASN cc_start: 0.8482 (m-40) cc_final: 0.8267 (m-40) REVERT: Q 1266 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7904 (tm-30) REVERT: Q 1267 ASP cc_start: 0.8602 (m-30) cc_final: 0.7933 (m-30) REVERT: Q 1276 GLU cc_start: 0.8310 (tp30) cc_final: 0.8069 (tp30) REVERT: Q 1291 MET cc_start: 0.8085 (tpt) cc_final: 0.7826 (tpp) REVERT: Q 1295 ILE cc_start: 0.8349 (mt) cc_final: 0.8014 (mm) REVERT: Q 1302 ARG cc_start: 0.8096 (ttt180) cc_final: 0.7599 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8588 (m-30) cc_final: 0.8279 (m-30) REVERT: Q 1317 ARG cc_start: 0.8100 (ptm160) cc_final: 0.7809 (ptm160) REVERT: Q 1331 MET cc_start: 0.7839 (tpp) cc_final: 0.7047 (tpp) REVERT: Q 1335 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7730 (mp) REVERT: R 21 LEU cc_start: 0.6970 (tp) cc_final: 0.6642 (tp) REVERT: R 35 ASN cc_start: 0.8859 (t0) cc_final: 0.8365 (t0) REVERT: R 55 ASN cc_start: 0.8435 (p0) cc_final: 0.8090 (p0) REVERT: R 70 PHE cc_start: 0.7572 (t80) cc_final: 0.7304 (t80) REVERT: R 119 PHE cc_start: 0.8259 (m-10) cc_final: 0.8008 (m-10) REVERT: R 144 GLN cc_start: 0.7623 (pm20) cc_final: 0.6439 (pm20) REVERT: R 154 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7685 (mm) REVERT: R 155 PHE cc_start: 0.7352 (m-80) cc_final: 0.6936 (m-10) REVERT: R 156 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: R 182 LYS cc_start: 0.8471 (mmmm) cc_final: 0.8133 (mmmm) REVERT: R 183 THR cc_start: 0.7518 (m) cc_final: 0.7024 (t) REVERT: R 214 TRP cc_start: 0.7495 (t-100) cc_final: 0.6343 (t-100) REVERT: R 218 GLN cc_start: 0.8000 (mp10) cc_final: 0.7589 (mp10) REVERT: R 230 LYS cc_start: 0.8874 (tttt) cc_final: 0.8478 (ttpt) REVERT: R 242 GLN cc_start: 0.8214 (pt0) cc_final: 0.7883 (pt0) REVERT: R 244 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: R 251 CYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6984 (m) REVERT: R 260 ASP cc_start: 0.7904 (m-30) cc_final: 0.7505 (p0) REVERT: R 262 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8189 (mm-30) REVERT: R 592 HIS cc_start: 0.8216 (t-90) cc_final: 0.7507 (t-90) REVERT: R 599 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8039 (tpp-160) REVERT: R 609 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: R 612 MET cc_start: 0.6814 (tpp) cc_final: 0.6426 (tpp) REVERT: R 627 GLN cc_start: 0.8520 (pt0) cc_final: 0.8271 (pt0) REVERT: R 633 GLN cc_start: 0.8301 (mp10) cc_final: 0.7953 (mp10) REVERT: R 642 SER cc_start: 0.8757 (m) cc_final: 0.8267 (p) REVERT: R 643 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7486 (mm-30) REVERT: R 645 ILE cc_start: 0.9113 (mt) cc_final: 0.8761 (tt) REVERT: R 647 LEU cc_start: 0.8555 (mp) cc_final: 0.8193 (mp) REVERT: R 659 GLN cc_start: 0.8484 (tp-100) cc_final: 0.8242 (tp-100) REVERT: R 663 ASP cc_start: 0.8116 (m-30) cc_final: 0.7829 (m-30) REVERT: R 664 MET cc_start: 0.8776 (mtm) cc_final: 0.8471 (mtp) REVERT: R 681 LYS cc_start: 0.8979 (tptt) cc_final: 0.8772 (tptt) REVERT: R 699 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7765 (p) REVERT: R 721 GLU cc_start: 0.8134 (tp30) cc_final: 0.7931 (tp30) REVERT: R 722 GLU cc_start: 0.8396 (pp20) cc_final: 0.7538 (pp20) REVERT: R 723 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7766 (mm-40) REVERT: R 724 TYR cc_start: 0.8253 (t80) cc_final: 0.7752 (t80) REVERT: R 728 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8651 (m) REVERT: S 70 GLU cc_start: 0.7308 (tp30) cc_final: 0.5558 (tp30) REVERT: S 114 LYS cc_start: 0.8555 (mttt) cc_final: 0.8319 (mttt) REVERT: S 122 LYS cc_start: 0.8475 (mmmm) cc_final: 0.8063 (mtpp) REVERT: S 140 TYR cc_start: 0.8660 (t80) cc_final: 0.8324 (t80) REVERT: T 56 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7879 (mm-30) REVERT: T 95 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8097 (mm-30) REVERT: T 177 LYS cc_start: 0.8505 (tttt) cc_final: 0.8114 (mtpp) REVERT: T 178 THR cc_start: 0.8927 (m) cc_final: 0.8627 (t) REVERT: T 193 LYS cc_start: 0.8439 (mmmt) cc_final: 0.8111 (mmmt) REVERT: T 224 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8501 (tp) REVERT: T 230 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8759 (m) REVERT: T 251 ASP cc_start: 0.8109 (m-30) cc_final: 0.7806 (m-30) REVERT: T 273 LEU cc_start: 0.7896 (tp) cc_final: 0.7623 (tt) REVERT: T 274 LYS cc_start: 0.8487 (mmtm) cc_final: 0.8041 (tppt) REVERT: T 279 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7359 (pt0) REVERT: T 295 TYR cc_start: 0.8611 (m-80) cc_final: 0.8080 (m-80) REVERT: T 371 ARG cc_start: 0.8003 (mtp-110) cc_final: 0.7702 (ptm-80) REVERT: T 381 ARG cc_start: 0.8728 (ttt-90) cc_final: 0.8236 (ttm-80) REVERT: T 382 THR cc_start: 0.8621 (p) cc_final: 0.8165 (p) REVERT: T 385 GLU cc_start: 0.8501 (pt0) cc_final: 0.7786 (pp20) REVERT: T 401 ASP cc_start: 0.8490 (m-30) cc_final: 0.7649 (m-30) REVERT: T 409 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7623 (mt-10) REVERT: T 413 ARG cc_start: 0.7769 (tpp80) cc_final: 0.7229 (tpp80) REVERT: T 414 TYR cc_start: 0.8101 (t80) cc_final: 0.7616 (t80) REVERT: T 417 GLN cc_start: 0.8244 (mt0) cc_final: 0.7936 (mt0) REVERT: T 434 ILE cc_start: 0.7733 (mt) cc_final: 0.7131 (mt) REVERT: T 439 VAL cc_start: 0.8841 (t) cc_final: 0.8612 (t) REVERT: T 448 ASP cc_start: 0.7682 (p0) cc_final: 0.7129 (p0) REVERT: T 456 LEU cc_start: 0.8931 (tp) cc_final: 0.8345 (mt) REVERT: U 38 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7476 (mpt180) REVERT: U 60 MET cc_start: 0.8395 (tpp) cc_final: 0.8191 (mmm) REVERT: U 86 MET cc_start: 0.8051 (mmm) cc_final: 0.7556 (mmm) REVERT: U 94 LYS cc_start: 0.8859 (tppt) cc_final: 0.8455 (tptp) REVERT: U 104 SER cc_start: 0.8545 (m) cc_final: 0.8187 (t) REVERT: U 105 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7278 (mt-10) REVERT: U 110 GLU cc_start: 0.7916 (pp20) cc_final: 0.7581 (pp20) REVERT: U 123 LYS cc_start: 0.8277 (mttt) cc_final: 0.7997 (mttp) REVERT: U 128 LYS cc_start: 0.8706 (ttpt) cc_final: 0.8469 (ttmm) REVERT: U 139 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6275 (tp30) REVERT: U 161 LYS cc_start: 0.8661 (ptmm) cc_final: 0.8105 (ptmm) REVERT: U 164 ASP cc_start: 0.7875 (t70) cc_final: 0.7594 (t70) REVERT: U 166 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7099 (tp30) REVERT: U 193 ASP cc_start: 0.7965 (t0) cc_final: 0.7523 (t0) REVERT: U 194 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8245 (ttpt) REVERT: U 198 LYS cc_start: 0.8526 (tttm) cc_final: 0.8215 (tttm) REVERT: U 272 GLN cc_start: 0.8063 (tp40) cc_final: 0.7574 (tp40) REVERT: U 276 LYS cc_start: 0.8988 (tptt) cc_final: 0.8531 (tptm) REVERT: U 281 LYS cc_start: 0.9008 (tttm) cc_final: 0.8588 (ttmm) REVERT: U 313 LEU cc_start: 0.8795 (mt) cc_final: 0.8557 (mp) REVERT: U 338 LYS cc_start: 0.8921 (mttt) cc_final: 0.8661 (mtpp) REVERT: U 339 SER cc_start: 0.8852 (m) cc_final: 0.8503 (t) REVERT: U 349 ASP cc_start: 0.8673 (t0) cc_final: 0.8208 (m-30) REVERT: U 365 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8497 (ttmt) REVERT: U 374 GLU cc_start: 0.8339 (tp30) cc_final: 0.7856 (tm-30) REVERT: U 376 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7907 (mm-30) REVERT: U 393 GLU cc_start: 0.7715 (pp20) cc_final: 0.7412 (pp20) REVERT: U 399 SER cc_start: 0.8368 (m) cc_final: 0.8118 (p) REVERT: U 400 SER cc_start: 0.8212 (t) cc_final: 0.7740 (m) REVERT: U 411 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.7013 (mpt) REVERT: U 419 GLU cc_start: 0.7270 (mm-30) cc_final: 0.6630 (mp0) REVERT: U 424 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7911 (mmtt) REVERT: U 428 LEU cc_start: 0.8689 (tp) cc_final: 0.8378 (pp) REVERT: U 444 GLU cc_start: 0.8116 (tp30) cc_final: 0.7538 (tp30) REVERT: V 30 ILE cc_start: 0.8580 (mt) cc_final: 0.8278 (mm) REVERT: V 31 LYS cc_start: 0.8175 (mmpt) cc_final: 0.7753 (mmtm) REVERT: V 52 ILE cc_start: 0.8668 (mp) cc_final: 0.8332 (mm) REVERT: V 56 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7321 (mm-30) REVERT: V 88 LEU cc_start: 0.8637 (mm) cc_final: 0.8390 (mt) REVERT: V 95 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7791 (mt-10) REVERT: V 99 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8397 (mtpp) REVERT: V 109 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8078 (tt0) REVERT: V 132 ARG cc_start: 0.8409 (tpp80) cc_final: 0.8068 (tpp80) REVERT: V 144 VAL cc_start: 0.8523 (t) cc_final: 0.8088 (m) REVERT: V 180 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7719 (tpt-90) REVERT: V 187 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7773 (mt-10) REVERT: V 203 GLU cc_start: 0.8007 (tt0) cc_final: 0.7696 (tt0) REVERT: V 218 TYR cc_start: 0.8720 (m-80) cc_final: 0.8175 (m-80) REVERT: V 222 PHE cc_start: 0.8277 (m-80) cc_final: 0.7925 (m-10) REVERT: V 223 ASP cc_start: 0.7824 (m-30) cc_final: 0.7416 (t0) REVERT: V 239 LYS cc_start: 0.8328 (mtpt) cc_final: 0.8021 (mttt) REVERT: V 253 ASP cc_start: 0.7525 (m-30) cc_final: 0.7239 (m-30) REVERT: V 263 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8370 (mm-40) REVERT: V 268 MET cc_start: 0.7809 (mmm) cc_final: 0.7495 (mmm) REVERT: V 286 GLN cc_start: 0.8310 (mm-40) cc_final: 0.7942 (mp10) REVERT: V 292 VAL cc_start: 0.8591 (t) cc_final: 0.8286 (m) REVERT: V 302 GLU cc_start: 0.8093 (pt0) cc_final: 0.7529 (pm20) REVERT: V 325 ASN cc_start: 0.8399 (t0) cc_final: 0.7406 (t0) REVERT: V 326 LYS cc_start: 0.8557 (tmmt) cc_final: 0.8253 (tttt) REVERT: V 329 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: V 344 MET cc_start: 0.8758 (mmt) cc_final: 0.8522 (mmm) REVERT: V 365 ASP cc_start: 0.7864 (m-30) cc_final: 0.7467 (t70) REVERT: V 367 LEU cc_start: 0.8433 (mt) cc_final: 0.8167 (mm) REVERT: V 379 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8263 (mt-10) REVERT: V 403 LEU cc_start: 0.8876 (mt) cc_final: 0.8499 (mm) REVERT: V 427 GLN cc_start: 0.8051 (pt0) cc_final: 0.7832 (pt0) REVERT: V 443 LYS cc_start: 0.8345 (mtpt) cc_final: 0.8114 (mtmm) REVERT: V 450 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7522 (mttt) REVERT: V 453 THR cc_start: 0.8828 (m) cc_final: 0.8418 (p) REVERT: V 454 LYS cc_start: 0.8858 (mptt) cc_final: 0.8422 (mmtt) REVERT: W 45 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8293 (p) REVERT: W 66 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8525 (mm) REVERT: W 69 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7568 (mmm-85) REVERT: W 86 MET cc_start: 0.7869 (mmm) cc_final: 0.7530 (mmm) REVERT: W 105 GLU cc_start: 0.7926 (mp0) cc_final: 0.7629 (mp0) REVERT: W 113 LYS cc_start: 0.8659 (mttp) cc_final: 0.8280 (mtpt) REVERT: W 142 GLU cc_start: 0.7712 (pp20) cc_final: 0.7455 (tm-30) REVERT: W 159 THR cc_start: 0.8414 (m) cc_final: 0.7760 (p) REVERT: W 164 ASP cc_start: 0.8538 (m-30) cc_final: 0.8334 (m-30) REVERT: W 185 LEU cc_start: 0.8194 (mt) cc_final: 0.7667 (mt) REVERT: W 188 ASP cc_start: 0.7665 (m-30) cc_final: 0.7023 (m-30) REVERT: W 191 SER cc_start: 0.8765 (t) cc_final: 0.8128 (m) REVERT: W 200 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.7887 (p) REVERT: W 231 LYS cc_start: 0.8482 (mttm) cc_final: 0.8191 (mmmm) REVERT: W 261 ASP cc_start: 0.8293 (t0) cc_final: 0.7655 (t0) REVERT: W 264 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6614 (mt-10) REVERT: W 273 ILE cc_start: 0.8819 (tp) cc_final: 0.8589 (tp) REVERT: W 281 LYS cc_start: 0.8762 (tttm) cc_final: 0.8411 (tppt) REVERT: W 296 ASP cc_start: 0.8364 (t0) cc_final: 0.8043 (t0) REVERT: W 306 PHE cc_start: 0.8314 (m-80) cc_final: 0.7914 (m-80) REVERT: W 310 ASN cc_start: 0.7921 (m-40) cc_final: 0.7622 (m-40) REVERT: W 365 LYS cc_start: 0.8969 (tmmt) cc_final: 0.8712 (tmmt) REVERT: W 367 ILE cc_start: 0.8642 (mt) cc_final: 0.8299 (tt) REVERT: W 373 GLN cc_start: 0.8608 (mp10) cc_final: 0.8207 (mt0) REVERT: W 386 LEU cc_start: 0.8551 (tp) cc_final: 0.8325 (tt) REVERT: W 389 LYS cc_start: 0.8808 (tppt) cc_final: 0.7639 (tppt) REVERT: W 393 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7917 (mm-30) REVERT: W 420 VAL cc_start: 0.8637 (t) cc_final: 0.8200 (m) REVERT: W 424 LYS cc_start: 0.8598 (ptpt) cc_final: 0.8335 (ptpt) REVERT: W 438 LYS cc_start: 0.9092 (pttt) cc_final: 0.8772 (pttt) REVERT: X 95 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8181 (mt-10) REVERT: X 117 LYS cc_start: 0.8053 (ptpp) cc_final: 0.7755 (ptpt) REVERT: X 123 GLU cc_start: 0.8256 (pt0) cc_final: 0.7898 (tt0) REVERT: X 125 PHE cc_start: 0.8251 (OUTLIER) cc_final: 0.7957 (t80) REVERT: X 177 LYS cc_start: 0.8394 (pttm) cc_final: 0.8137 (pttm) REVERT: X 186 TYR cc_start: 0.8559 (t80) cc_final: 0.8328 (t80) REVERT: X 189 ILE cc_start: 0.9172 (mm) cc_final: 0.8906 (mm) REVERT: X 198 ASP cc_start: 0.7696 (m-30) cc_final: 0.7437 (m-30) REVERT: X 201 TYR cc_start: 0.7255 (t80) cc_final: 0.6875 (t80) REVERT: X 211 ARG cc_start: 0.8136 (ttt-90) cc_final: 0.7856 (ttt-90) REVERT: X 228 GLU cc_start: 0.7384 (pm20) cc_final: 0.6910 (pm20) REVERT: X 239 LYS cc_start: 0.8487 (ptpt) cc_final: 0.8245 (ptpp) REVERT: X 245 GLN cc_start: 0.8132 (tp40) cc_final: 0.7845 (tp40) REVERT: X 253 ASP cc_start: 0.8096 (m-30) cc_final: 0.7775 (t0) REVERT: X 263 GLN cc_start: 0.7160 (tm-30) cc_final: 0.6571 (tm-30) REVERT: X 271 GLN cc_start: 0.8353 (tp40) cc_final: 0.8040 (tp40) REVERT: X 272 LEU cc_start: 0.8908 (tt) cc_final: 0.8664 (tp) REVERT: X 274 LYS cc_start: 0.7952 (tmmt) cc_final: 0.7691 (ttmt) REVERT: X 277 LYS cc_start: 0.8792 (ttmm) cc_final: 0.8538 (mtmt) REVERT: X 313 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7515 (t) REVERT: X 325 ASN cc_start: 0.8677 (m-40) cc_final: 0.8406 (m-40) REVERT: X 328 LEU cc_start: 0.8801 (mt) cc_final: 0.8491 (mm) REVERT: X 329 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7302 (tp30) REVERT: X 377 LYS cc_start: 0.8503 (mmmm) cc_final: 0.8208 (mmmm) REVERT: X 378 ASP cc_start: 0.7643 (p0) cc_final: 0.7345 (t0) REVERT: X 385 GLU cc_start: 0.8435 (pp20) cc_final: 0.8094 (pp20) REVERT: X 401 ASP cc_start: 0.8366 (m-30) cc_final: 0.8055 (m-30) REVERT: X 406 MET cc_start: 0.8506 (mtp) cc_final: 0.8246 (ttm) REVERT: X 409 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7886 (mm-30) REVERT: X 431 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7245 (ttp-110) REVERT: X 441 GLU cc_start: 0.7943 (tp30) cc_final: 0.7600 (tp30) REVERT: X 443 LYS cc_start: 0.8478 (tmmt) cc_final: 0.8155 (ttmm) REVERT: X 448 ASP cc_start: 0.7908 (t70) cc_final: 0.7246 (t0) REVERT: X 454 LYS cc_start: 0.8396 (tmmt) cc_final: 0.8023 (tmmt) REVERT: Y 59 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8258 (tppt) REVERT: Y 62 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8520 (mt0) REVERT: Y 66 ILE cc_start: 0.8772 (mp) cc_final: 0.8427 (mp) REVERT: Y 113 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7864 (mtmm) REVERT: Y 122 ARG cc_start: 0.8230 (mtt90) cc_final: 0.7982 (mtp85) REVERT: Y 130 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7482 (mtmm) REVERT: Y 131 GLU cc_start: 0.6396 (mm-30) cc_final: 0.6105 (mm-30) REVERT: Y 164 ASP cc_start: 0.8222 (m-30) cc_final: 0.7878 (m-30) REVERT: Y 171 LEU cc_start: 0.8443 (mp) cc_final: 0.8242 (mm) REVERT: Y 175 MET cc_start: 0.8878 (tpp) cc_final: 0.8222 (tpp) REVERT: Y 192 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8642 (mm) REVERT: Y 208 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7610 (mmm-85) REVERT: Y 233 LYS cc_start: 0.8463 (ttmt) cc_final: 0.8060 (ttpp) REVERT: Y 271 ASP cc_start: 0.8395 (t0) cc_final: 0.8030 (t0) REVERT: Y 272 GLN cc_start: 0.8536 (mt0) cc_final: 0.8323 (tt0) REVERT: Y 274 ASN cc_start: 0.8725 (m-40) cc_final: 0.8298 (m-40) REVERT: Y 277 VAL cc_start: 0.8687 (t) cc_final: 0.8421 (p) REVERT: Y 281 LYS cc_start: 0.8478 (tptm) cc_final: 0.7941 (tppt) REVERT: Y 302 ASP cc_start: 0.7674 (m-30) cc_final: 0.7452 (m-30) REVERT: Y 304 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: Y 310 ASN cc_start: 0.8099 (m-40) cc_final: 0.7677 (m-40) REVERT: Y 338 LYS cc_start: 0.8657 (mtpp) cc_final: 0.8398 (mttt) REVERT: Y 339 SER cc_start: 0.8769 (t) cc_final: 0.8351 (p) REVERT: Y 370 ILE cc_start: 0.8975 (mt) cc_final: 0.8749 (mt) REVERT: Y 373 GLN cc_start: 0.8748 (tt0) cc_final: 0.8483 (mm-40) REVERT: Y 374 GLU cc_start: 0.8033 (tp30) cc_final: 0.7784 (mm-30) REVERT: Y 389 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8696 (tppt) REVERT: Y 390 THR cc_start: 0.8874 (p) cc_final: 0.8536 (p) REVERT: Y 393 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8132 (mt-10) REVERT: Y 407 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8240 (tp-100) REVERT: Y 412 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8768 (tptm) REVERT: Y 422 ASP cc_start: 0.8025 (m-30) cc_final: 0.7816 (t70) REVERT: Y 427 TYR cc_start: 0.8283 (t80) cc_final: 0.7660 (t80) REVERT: Y 444 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7487 (tp30) REVERT: Y 456 ILE cc_start: 0.8864 (mt) cc_final: 0.8420 (mt) REVERT: Z 297 ARG cc_start: 0.8460 (tpp80) cc_final: 0.8254 (tpp80) REVERT: Z 310 ARG cc_start: 0.8272 (mtt-85) cc_final: 0.7644 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7798 (ttm110) cc_final: 0.7593 (ttm110) outliers start: 148 outliers final: 94 residues processed: 1207 average time/residue: 0.2239 time to fit residues: 409.0604 Evaluate side-chains 1243 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1118 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 957 THR Chi-restraints excluded: chain Q residue 1030 THR Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1102 VAL Chi-restraints excluded: chain Q residue 1125 CYS Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1204 ASN Chi-restraints excluded: chain Q residue 1270 LYS Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1328 MET Chi-restraints excluded: chain Q residue 1335 LEU Chi-restraints excluded: chain Q residue 1430 GLU Chi-restraints excluded: chain R residue 22 ARG Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 165 PHE Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 593 LEU Chi-restraints excluded: chain R residue 599 ARG Chi-restraints excluded: chain R residue 607 HIS Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 699 THR Chi-restraints excluded: chain R residue 728 VAL Chi-restraints excluded: chain R residue 735 GLU Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 240 LYS Chi-restraints excluded: chain T residue 265 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 315 MET Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 331 LYS Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 171 LYS Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 300 VAL Chi-restraints excluded: chain V residue 329 GLU Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 393 LEU Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain V residue 441 GLU Chi-restraints excluded: chain V residue 455 ILE Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 63 ASN Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 69 ARG Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 412 LEU Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain X residue 425 LEU Chi-restraints excluded: chain X residue 430 ASN Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 113 LYS Chi-restraints excluded: chain Y residue 192 ILE Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 356 THR Chi-restraints excluded: chain Y residue 376 GLU Chi-restraints excluded: chain Y residue 377 VAL Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 399 SER Chi-restraints excluded: chain Y residue 401 ASN Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 412 LYS Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 449 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 266 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 351 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 22 optimal weight: 0.0070 chunk 9 optimal weight: 0.8980 chunk 114 optimal weight: 0.0060 chunk 208 optimal weight: 0.5980 chunk 125 optimal weight: 0.9990 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN Q1228 HIS ** Q1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 HIS T 29 HIS ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN U 248 ASN V 289 ASN ** V 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 341 ASN W 90 GLN X 165 HIS ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.127849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.109111 restraints weight = 57030.905| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.30 r_work: 0.3350 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29139 Z= 0.127 Angle : 0.682 15.717 39425 Z= 0.333 Chirality : 0.045 0.178 4626 Planarity : 0.005 0.070 5049 Dihedral : 7.218 122.137 4012 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.47 % Rotamer: Outliers : 4.18 % Allowed : 28.45 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.14), residues: 3626 helix: 0.96 (0.13), residues: 1543 sheet: -0.13 (0.21), residues: 610 loop : -0.64 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG S 34 TYR 0.023 0.002 TYR Q1198 PHE 0.033 0.001 PHE Y 254 TRP 0.020 0.002 TRP R 108 HIS 0.003 0.001 HIS W 341 Details of bonding type rmsd covalent geometry : bond 0.00292 (29139) covalent geometry : angle 0.68217 (39425) hydrogen bonds : bond 0.03375 ( 1098) hydrogen bonds : angle 4.34663 ( 3198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1263 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1131 time to evaluate : 1.226 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: Q 1005 MET cc_start: 0.6825 (mmp) cc_final: 0.6116 (mmp) REVERT: Q 1027 SER cc_start: 0.8673 (m) cc_final: 0.8163 (p) REVERT: Q 1112 LYS cc_start: 0.8803 (mttp) cc_final: 0.8310 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8199 (t) REVERT: Q 1154 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6636 (mp0) REVERT: Q 1195 LYS cc_start: 0.8211 (tppt) cc_final: 0.7436 (tppt) REVERT: Q 1222 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7419 (tm-30) REVERT: Q 1230 THR cc_start: 0.8732 (m) cc_final: 0.8476 (p) REVERT: Q 1231 ASN cc_start: 0.8672 (t0) cc_final: 0.8383 (t0) REVERT: Q 1242 ILE cc_start: 0.9144 (tp) cc_final: 0.8920 (tp) REVERT: Q 1248 ASP cc_start: 0.7409 (t70) cc_final: 0.6943 (t0) REVERT: Q 1256 ASN cc_start: 0.8447 (m-40) cc_final: 0.8238 (m-40) REVERT: Q 1266 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7848 (tm-30) REVERT: Q 1267 ASP cc_start: 0.8547 (m-30) cc_final: 0.7931 (m-30) REVERT: Q 1276 GLU cc_start: 0.8334 (tp30) cc_final: 0.8084 (tp30) REVERT: Q 1291 MET cc_start: 0.8087 (tpt) cc_final: 0.7822 (tpp) REVERT: Q 1295 ILE cc_start: 0.8288 (mt) cc_final: 0.7942 (mm) REVERT: Q 1302 ARG cc_start: 0.8085 (ttt180) cc_final: 0.7585 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8599 (m-30) cc_final: 0.8272 (m-30) REVERT: Q 1317 ARG cc_start: 0.8089 (ptm160) cc_final: 0.7812 (ptm160) REVERT: Q 1331 MET cc_start: 0.7816 (tpp) cc_final: 0.7286 (tpp) REVERT: Q 1334 TYR cc_start: 0.7783 (p90) cc_final: 0.7179 (p90) REVERT: Q 1335 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7808 (mp) REVERT: Q 1421 ARG cc_start: 0.7390 (mtt90) cc_final: 0.6825 (mtt90) REVERT: R 21 LEU cc_start: 0.6876 (tp) cc_final: 0.6526 (tp) REVERT: R 35 ASN cc_start: 0.8836 (t0) cc_final: 0.8333 (t0) REVERT: R 55 ASN cc_start: 0.8435 (p0) cc_final: 0.8082 (p0) REVERT: R 70 PHE cc_start: 0.7578 (t80) cc_final: 0.7328 (t80) REVERT: R 119 PHE cc_start: 0.8193 (m-10) cc_final: 0.7928 (m-10) REVERT: R 154 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7629 (mm) REVERT: R 155 PHE cc_start: 0.7295 (m-80) cc_final: 0.6938 (m-10) REVERT: R 156 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: R 182 LYS cc_start: 0.8388 (mmmm) cc_final: 0.8050 (mmmm) REVERT: R 214 TRP cc_start: 0.7501 (t-100) cc_final: 0.6477 (t-100) REVERT: R 218 GLN cc_start: 0.7925 (mp10) cc_final: 0.7534 (mp10) REVERT: R 230 LYS cc_start: 0.8870 (tttt) cc_final: 0.8559 (tttt) REVERT: R 239 SER cc_start: 0.5723 (OUTLIER) cc_final: 0.5494 (p) REVERT: R 242 GLN cc_start: 0.8167 (pt0) cc_final: 0.7873 (pt0) REVERT: R 244 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6846 (mp0) REVERT: R 251 CYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6909 (m) REVERT: R 260 ASP cc_start: 0.7887 (m-30) cc_final: 0.7587 (p0) REVERT: R 262 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8234 (mm-30) REVERT: R 592 HIS cc_start: 0.8186 (t-90) cc_final: 0.7474 (t-90) REVERT: R 599 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.8045 (tpp-160) REVERT: R 609 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7226 (mp10) REVERT: R 612 MET cc_start: 0.6793 (tpp) cc_final: 0.6544 (tpp) REVERT: R 627 GLN cc_start: 0.8498 (pt0) cc_final: 0.8099 (pt0) REVERT: R 642 SER cc_start: 0.8683 (m) cc_final: 0.8181 (p) REVERT: R 643 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7415 (mm-30) REVERT: R 645 ILE cc_start: 0.9108 (mt) cc_final: 0.8759 (tt) REVERT: R 647 LEU cc_start: 0.8517 (mp) cc_final: 0.8149 (mp) REVERT: R 659 GLN cc_start: 0.8446 (tp-100) cc_final: 0.8203 (tp-100) REVERT: R 663 ASP cc_start: 0.8088 (m-30) cc_final: 0.7789 (m-30) REVERT: R 664 MET cc_start: 0.8705 (mtm) cc_final: 0.8424 (mtp) REVERT: R 681 LYS cc_start: 0.8938 (tptt) cc_final: 0.8735 (tptt) REVERT: R 699 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7754 (p) REVERT: R 721 GLU cc_start: 0.8055 (tp30) cc_final: 0.7502 (tp30) REVERT: R 722 GLU cc_start: 0.8386 (pp20) cc_final: 0.7511 (pp20) REVERT: R 723 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7675 (mm-40) REVERT: R 724 TYR cc_start: 0.8179 (t80) cc_final: 0.7624 (t80) REVERT: R 725 ARG cc_start: 0.8649 (mmt180) cc_final: 0.7976 (tpp80) REVERT: R 728 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8592 (m) REVERT: S 70 GLU cc_start: 0.7290 (tp30) cc_final: 0.6890 (tp30) REVERT: S 122 LYS cc_start: 0.8460 (mmmm) cc_final: 0.8244 (mtpp) REVERT: S 140 TYR cc_start: 0.8624 (t80) cc_final: 0.8368 (t80) REVERT: T 49 VAL cc_start: 0.8209 (OUTLIER) cc_final: 0.7885 (m) REVERT: T 56 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7782 (mm-30) REVERT: T 70 MET cc_start: 0.7377 (mtm) cc_final: 0.6104 (mtp) REVERT: T 95 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8236 (mm-30) REVERT: T 177 LYS cc_start: 0.8492 (tttt) cc_final: 0.8023 (mtpp) REVERT: T 178 THR cc_start: 0.8908 (m) cc_final: 0.8622 (t) REVERT: T 193 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8113 (mmmt) REVERT: T 211 ARG cc_start: 0.8550 (ttt-90) cc_final: 0.8278 (ttt-90) REVERT: T 224 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8433 (tp) REVERT: T 230 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8767 (m) REVERT: T 251 ASP cc_start: 0.8057 (m-30) cc_final: 0.7727 (m-30) REVERT: T 273 LEU cc_start: 0.7882 (tp) cc_final: 0.7622 (tt) REVERT: T 274 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8036 (tppt) REVERT: T 279 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7332 (pt0) REVERT: T 295 TYR cc_start: 0.8570 (m-80) cc_final: 0.8093 (m-80) REVERT: T 371 ARG cc_start: 0.8089 (mtp-110) cc_final: 0.7781 (ptm-80) REVERT: T 381 ARG cc_start: 0.8724 (ttt-90) cc_final: 0.8206 (ttm-80) REVERT: T 382 THR cc_start: 0.8603 (p) cc_final: 0.8131 (p) REVERT: T 385 GLU cc_start: 0.8474 (pt0) cc_final: 0.7753 (pp20) REVERT: T 401 ASP cc_start: 0.8473 (m-30) cc_final: 0.7676 (m-30) REVERT: T 409 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7566 (mt-10) REVERT: T 413 ARG cc_start: 0.7733 (tpp80) cc_final: 0.6974 (tpp80) REVERT: T 414 TYR cc_start: 0.8075 (t80) cc_final: 0.7527 (t80) REVERT: T 417 GLN cc_start: 0.8222 (mt0) cc_final: 0.7835 (mt0) REVERT: T 431 ARG cc_start: 0.7600 (mtm180) cc_final: 0.7144 (ptt90) REVERT: T 434 ILE cc_start: 0.7710 (mt) cc_final: 0.6764 (mt) REVERT: T 439 VAL cc_start: 0.8803 (t) cc_final: 0.8590 (t) REVERT: T 448 ASP cc_start: 0.7642 (p0) cc_final: 0.7119 (p0) REVERT: T 456 LEU cc_start: 0.8957 (tp) cc_final: 0.8375 (mt) REVERT: U 38 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7569 (mpt180) REVERT: U 44 MET cc_start: 0.7329 (ttp) cc_final: 0.7054 (ttm) REVERT: U 60 MET cc_start: 0.8420 (tpp) cc_final: 0.8202 (mmm) REVERT: U 81 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8094 (mtmm) REVERT: U 86 MET cc_start: 0.7971 (mmm) cc_final: 0.7357 (mmm) REVERT: U 94 LYS cc_start: 0.8842 (tppt) cc_final: 0.8454 (tptp) REVERT: U 104 SER cc_start: 0.8532 (m) cc_final: 0.8159 (t) REVERT: U 105 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7114 (mt-10) REVERT: U 110 GLU cc_start: 0.7894 (pp20) cc_final: 0.7557 (pp20) REVERT: U 123 LYS cc_start: 0.8245 (mttt) cc_final: 0.7979 (mttp) REVERT: U 128 LYS cc_start: 0.8693 (ttpt) cc_final: 0.8450 (ttmm) REVERT: U 139 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6311 (tp30) REVERT: U 161 LYS cc_start: 0.8616 (ptmm) cc_final: 0.7522 (ptmm) REVERT: U 164 ASP cc_start: 0.7916 (t70) cc_final: 0.7597 (t0) REVERT: U 166 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7078 (tp30) REVERT: U 182 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7627 (tm-30) REVERT: U 193 ASP cc_start: 0.7972 (t0) cc_final: 0.7525 (t0) REVERT: U 194 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8207 (ttpt) REVERT: U 198 LYS cc_start: 0.8550 (tttm) cc_final: 0.8235 (tttm) REVERT: U 272 GLN cc_start: 0.8011 (tp40) cc_final: 0.7518 (tp40) REVERT: U 276 LYS cc_start: 0.8942 (tptt) cc_final: 0.8511 (tptm) REVERT: U 281 LYS cc_start: 0.8921 (tttm) cc_final: 0.8497 (ttmm) REVERT: U 313 LEU cc_start: 0.8776 (mt) cc_final: 0.8536 (mp) REVERT: U 338 LYS cc_start: 0.8912 (mttt) cc_final: 0.8660 (ttmm) REVERT: U 339 SER cc_start: 0.8857 (m) cc_final: 0.8487 (t) REVERT: U 349 ASP cc_start: 0.8668 (t0) cc_final: 0.8141 (m-30) REVERT: U 365 LYS cc_start: 0.8824 (ttpt) cc_final: 0.8479 (ttmt) REVERT: U 376 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7905 (mm-30) REVERT: U 393 GLU cc_start: 0.7701 (pp20) cc_final: 0.7390 (pp20) REVERT: U 399 SER cc_start: 0.8312 (m) cc_final: 0.8056 (p) REVERT: U 400 SER cc_start: 0.8181 (t) cc_final: 0.7735 (m) REVERT: U 411 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7021 (mpt) REVERT: U 412 LYS cc_start: 0.8801 (tppt) cc_final: 0.8580 (tppt) REVERT: U 419 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6632 (mp0) REVERT: U 424 LYS cc_start: 0.8220 (mmtt) cc_final: 0.7883 (mmtt) REVERT: U 428 LEU cc_start: 0.8684 (tp) cc_final: 0.8356 (pp) REVERT: U 444 GLU cc_start: 0.8112 (tp30) cc_final: 0.7529 (tp30) REVERT: U 456 ILE cc_start: 0.8667 (mt) cc_final: 0.8464 (mt) REVERT: V 30 ILE cc_start: 0.8447 (mt) cc_final: 0.8138 (mm) REVERT: V 31 LYS cc_start: 0.8117 (mmpt) cc_final: 0.7693 (mmtm) REVERT: V 35 LEU cc_start: 0.8464 (mm) cc_final: 0.7658 (mm) REVERT: V 52 ILE cc_start: 0.8622 (mp) cc_final: 0.8266 (mm) REVERT: V 56 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7280 (mm-30) REVERT: V 88 LEU cc_start: 0.8602 (mm) cc_final: 0.8324 (mt) REVERT: V 95 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7730 (mt-10) REVERT: V 99 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8380 (mtpp) REVERT: V 127 ARG cc_start: 0.8172 (ttp-170) cc_final: 0.7817 (ttm110) REVERT: V 141 GLU cc_start: 0.7630 (pm20) cc_final: 0.7336 (pm20) REVERT: V 144 VAL cc_start: 0.8441 (t) cc_final: 0.8000 (m) REVERT: V 180 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7712 (tpt-90) REVERT: V 187 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7691 (mt-10) REVERT: V 203 GLU cc_start: 0.7967 (tt0) cc_final: 0.7692 (tt0) REVERT: V 218 TYR cc_start: 0.8662 (m-80) cc_final: 0.8185 (m-80) REVERT: V 222 PHE cc_start: 0.8301 (m-80) cc_final: 0.7918 (m-10) REVERT: V 223 ASP cc_start: 0.7792 (m-30) cc_final: 0.7363 (t0) REVERT: V 239 LYS cc_start: 0.8291 (mtpt) cc_final: 0.8025 (mttt) REVERT: V 253 ASP cc_start: 0.7499 (m-30) cc_final: 0.7202 (m-30) REVERT: V 263 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8375 (mm-40) REVERT: V 286 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7934 (mp10) REVERT: V 292 VAL cc_start: 0.8564 (t) cc_final: 0.8252 (m) REVERT: V 311 ASP cc_start: 0.8212 (t0) cc_final: 0.7946 (t0) REVERT: V 319 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7172 (pt0) REVERT: V 320 ILE cc_start: 0.8254 (mt) cc_final: 0.8020 (tp) REVERT: V 325 ASN cc_start: 0.8414 (t0) cc_final: 0.7422 (t0) REVERT: V 326 LYS cc_start: 0.8532 (tmmt) cc_final: 0.8241 (tttt) REVERT: V 332 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8331 (mm) REVERT: V 344 MET cc_start: 0.8707 (mmt) cc_final: 0.8480 (mmm) REVERT: V 365 ASP cc_start: 0.7827 (m-30) cc_final: 0.7314 (t0) REVERT: V 367 LEU cc_start: 0.8383 (mt) cc_final: 0.8110 (mm) REVERT: V 379 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8210 (mt-10) REVERT: V 427 GLN cc_start: 0.7985 (pt0) cc_final: 0.7769 (pt0) REVERT: V 443 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8063 (mtmm) REVERT: V 450 LYS cc_start: 0.8042 (mtmt) cc_final: 0.7476 (mttt) REVERT: V 453 THR cc_start: 0.8792 (m) cc_final: 0.8387 (p) REVERT: V 454 LYS cc_start: 0.8825 (mptt) cc_final: 0.8363 (mmtt) REVERT: W 45 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8314 (p) REVERT: W 69 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7458 (mmm-85) REVERT: W 86 MET cc_start: 0.7754 (mmm) cc_final: 0.7431 (mmm) REVERT: W 105 GLU cc_start: 0.7866 (mp0) cc_final: 0.7568 (mp0) REVERT: W 113 LYS cc_start: 0.8608 (mttp) cc_final: 0.8244 (mtpt) REVERT: W 131 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7356 (pt0) REVERT: W 142 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: W 159 THR cc_start: 0.8359 (m) cc_final: 0.7388 (p) REVERT: W 164 ASP cc_start: 0.8493 (m-30) cc_final: 0.8283 (m-30) REVERT: W 185 LEU cc_start: 0.8201 (mt) cc_final: 0.7673 (mt) REVERT: W 188 ASP cc_start: 0.7623 (m-30) cc_final: 0.7000 (m-30) REVERT: W 191 SER cc_start: 0.8702 (t) cc_final: 0.8140 (m) REVERT: W 200 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.7939 (p) REVERT: W 201 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8225 (mtpp) REVERT: W 231 LYS cc_start: 0.8456 (mttm) cc_final: 0.8188 (mmmm) REVERT: W 261 ASP cc_start: 0.8295 (t0) cc_final: 0.7662 (t0) REVERT: W 264 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6457 (mt-10) REVERT: W 273 ILE cc_start: 0.8785 (tp) cc_final: 0.8559 (tp) REVERT: W 275 THR cc_start: 0.8849 (t) cc_final: 0.8647 (p) REVERT: W 281 LYS cc_start: 0.8730 (tttm) cc_final: 0.8305 (tppt) REVERT: W 296 ASP cc_start: 0.8354 (t0) cc_final: 0.7894 (t0) REVERT: W 306 PHE cc_start: 0.8281 (m-80) cc_final: 0.7871 (m-80) REVERT: W 310 ASN cc_start: 0.7885 (m-40) cc_final: 0.7584 (m-40) REVERT: W 365 LYS cc_start: 0.8961 (tmmt) cc_final: 0.8704 (tmmt) REVERT: W 367 ILE cc_start: 0.8628 (mt) cc_final: 0.8287 (tt) REVERT: W 373 GLN cc_start: 0.8551 (mp10) cc_final: 0.8168 (mt0) REVERT: W 386 LEU cc_start: 0.8533 (tp) cc_final: 0.8310 (tt) REVERT: W 389 LYS cc_start: 0.8816 (tppt) cc_final: 0.7946 (tppt) REVERT: W 393 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7836 (mm-30) REVERT: W 420 VAL cc_start: 0.8561 (t) cc_final: 0.8115 (m) REVERT: W 424 LYS cc_start: 0.8586 (ptpt) cc_final: 0.8311 (ptpt) REVERT: W 438 LYS cc_start: 0.9101 (pttt) cc_final: 0.8722 (pttt) REVERT: X 95 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8252 (mm-30) REVERT: X 117 LYS cc_start: 0.7986 (ptpp) cc_final: 0.7636 (ptpt) REVERT: X 125 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7941 (t80) REVERT: X 186 TYR cc_start: 0.8540 (t80) cc_final: 0.8295 (t80) REVERT: X 189 ILE cc_start: 0.9157 (mm) cc_final: 0.8872 (mm) REVERT: X 198 ASP cc_start: 0.7676 (m-30) cc_final: 0.7395 (m-30) REVERT: X 211 ARG cc_start: 0.8071 (ttt-90) cc_final: 0.7739 (ttt-90) REVERT: X 245 GLN cc_start: 0.8108 (tp40) cc_final: 0.7831 (tp40) REVERT: X 251 ASP cc_start: 0.7921 (m-30) cc_final: 0.7554 (m-30) REVERT: X 253 ASP cc_start: 0.8103 (m-30) cc_final: 0.7790 (t0) REVERT: X 263 GLN cc_start: 0.7181 (tm-30) cc_final: 0.6580 (tm-30) REVERT: X 268 MET cc_start: 0.8393 (mtp) cc_final: 0.8136 (mtt) REVERT: X 271 GLN cc_start: 0.8278 (tp40) cc_final: 0.8061 (tp40) REVERT: X 272 LEU cc_start: 0.8899 (tt) cc_final: 0.8649 (tp) REVERT: X 274 LYS cc_start: 0.7849 (tmmt) cc_final: 0.7588 (ttmt) REVERT: X 277 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8514 (mtmt) REVERT: X 313 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7483 (t) REVERT: X 325 ASN cc_start: 0.8653 (m-40) cc_final: 0.8365 (m-40) REVERT: X 328 LEU cc_start: 0.8768 (mt) cc_final: 0.8444 (mm) REVERT: X 329 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7202 (tp30) REVERT: X 377 LYS cc_start: 0.8468 (mmmm) cc_final: 0.8174 (mmmm) REVERT: X 378 ASP cc_start: 0.7633 (p0) cc_final: 0.7353 (t70) REVERT: X 385 GLU cc_start: 0.8409 (pp20) cc_final: 0.8071 (pp20) REVERT: X 391 GLU cc_start: 0.8541 (tt0) cc_final: 0.7852 (tm-30) REVERT: X 401 ASP cc_start: 0.8376 (m-30) cc_final: 0.8123 (m-30) REVERT: X 406 MET cc_start: 0.8438 (mtp) cc_final: 0.8144 (ttp) REVERT: X 409 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7813 (mm-30) REVERT: X 441 GLU cc_start: 0.7957 (tp30) cc_final: 0.7608 (tp30) REVERT: X 443 LYS cc_start: 0.8412 (tmmt) cc_final: 0.8099 (ttmm) REVERT: X 448 ASP cc_start: 0.7909 (t70) cc_final: 0.7284 (t0) REVERT: X 454 LYS cc_start: 0.8346 (tmmt) cc_final: 0.8001 (tmmt) REVERT: Y 59 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8244 (tppt) REVERT: Y 62 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8555 (mt0) REVERT: Y 105 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7565 (mp0) REVERT: Y 111 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7670 (tp) REVERT: Y 113 LYS cc_start: 0.8239 (ptpp) cc_final: 0.7860 (mtmm) REVERT: Y 122 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7959 (mtp85) REVERT: Y 130 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7455 (mtmm) REVERT: Y 131 GLU cc_start: 0.6365 (mm-30) cc_final: 0.6047 (mm-30) REVERT: Y 164 ASP cc_start: 0.8191 (m-30) cc_final: 0.7875 (m-30) REVERT: Y 171 LEU cc_start: 0.8457 (mp) cc_final: 0.8223 (mm) REVERT: Y 173 ASN cc_start: 0.8080 (p0) cc_final: 0.6846 (m-40) REVERT: Y 174 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8154 (mmmt) REVERT: Y 175 MET cc_start: 0.8846 (tpp) cc_final: 0.8271 (tpp) REVERT: Y 271 ASP cc_start: 0.8419 (t0) cc_final: 0.8043 (t0) REVERT: Y 272 GLN cc_start: 0.8485 (mt0) cc_final: 0.8271 (tt0) REVERT: Y 274 ASN cc_start: 0.8679 (m-40) cc_final: 0.8256 (m-40) REVERT: Y 277 VAL cc_start: 0.8677 (t) cc_final: 0.8409 (p) REVERT: Y 304 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7468 (mt-10) REVERT: Y 310 ASN cc_start: 0.8080 (m-40) cc_final: 0.7655 (m-40) REVERT: Y 327 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7617 (ttm-80) REVERT: Y 338 LYS cc_start: 0.8639 (mtpp) cc_final: 0.8397 (mttt) REVERT: Y 339 SER cc_start: 0.8798 (t) cc_final: 0.8359 (p) REVERT: Y 370 ILE cc_start: 0.8942 (mt) cc_final: 0.8692 (mt) REVERT: Y 373 GLN cc_start: 0.8741 (tt0) cc_final: 0.8487 (mm-40) REVERT: Y 374 GLU cc_start: 0.7923 (tp30) cc_final: 0.7690 (mm-30) REVERT: Y 389 LYS cc_start: 0.8947 (ttpt) cc_final: 0.8619 (tppt) REVERT: Y 390 THR cc_start: 0.8849 (p) cc_final: 0.8485 (p) REVERT: Y 393 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8056 (mt-10) REVERT: Y 407 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8019 (tp-100) REVERT: Y 422 ASP cc_start: 0.7990 (m-30) cc_final: 0.7593 (t0) REVERT: Y 427 TYR cc_start: 0.8261 (t80) cc_final: 0.7624 (t80) REVERT: Y 444 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7419 (tp30) REVERT: Y 456 ILE cc_start: 0.8857 (mt) cc_final: 0.8392 (mt) REVERT: Z 303 GLU cc_start: 0.8117 (tt0) cc_final: 0.7771 (tt0) REVERT: Z 310 ARG cc_start: 0.8296 (mtt-85) cc_final: 0.7448 (mmm-85) outliers start: 132 outliers final: 77 residues processed: 1190 average time/residue: 0.2236 time to fit residues: 403.2027 Evaluate side-chains 1217 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1109 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 957 THR Chi-restraints excluded: chain Q residue 1030 THR Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1125 CYS Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1270 LYS Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1335 LEU Chi-restraints excluded: chain Q residue 1405 MET Chi-restraints excluded: chain Q residue 1430 GLU Chi-restraints excluded: chain R residue 22 ARG Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 165 PHE Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 239 SER Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 258 ASP Chi-restraints excluded: chain R residue 593 LEU Chi-restraints excluded: chain R residue 599 ARG Chi-restraints excluded: chain R residue 607 HIS Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 699 THR Chi-restraints excluded: chain R residue 728 VAL Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 265 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 279 GLU Chi-restraints excluded: chain T residue 315 MET Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 375 GLU Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 393 LEU Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain V residue 441 GLU Chi-restraints excluded: chain V residue 455 ILE Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 69 ARG Chi-restraints excluded: chain W residue 142 GLU Chi-restraints excluded: chain W residue 154 LYS Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 165 HIS Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Y residue 235 VAL Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 356 THR Chi-restraints excluded: chain Y residue 376 GLU Chi-restraints excluded: chain Y residue 377 VAL Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 401 ASN Chi-restraints excluded: chain Y residue 407 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 134 optimal weight: 1.9990 chunk 313 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 140 optimal weight: 0.5980 chunk 210 optimal weight: 0.7980 chunk 246 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN Q1228 HIS ** Q1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN T 27 HIS T 29 HIS U 63 ASN U 248 ASN U 362 GLN V 289 ASN V 341 ASN W 90 GLN W 230 GLN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 47 GLN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.126336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107742 restraints weight = 56857.348| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.28 r_work: 0.3326 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29139 Z= 0.165 Angle : 0.717 15.945 39425 Z= 0.351 Chirality : 0.046 0.171 4626 Planarity : 0.005 0.088 5049 Dihedral : 7.241 118.264 4012 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.64 % Favored : 96.33 % Rotamer: Outliers : 3.54 % Allowed : 29.87 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.14), residues: 3626 helix: 0.94 (0.13), residues: 1539 sheet: -0.13 (0.21), residues: 608 loop : -0.68 (0.16), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG X 258 TYR 0.025 0.002 TYR V 186 PHE 0.032 0.002 PHE Y 254 TRP 0.015 0.002 TRP R 108 HIS 0.017 0.001 HIS X 165 Details of bonding type rmsd covalent geometry : bond 0.00365 (29139) covalent geometry : angle 0.71705 (39425) hydrogen bonds : bond 0.03642 ( 1098) hydrogen bonds : angle 4.43002 ( 3198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7252 Ramachandran restraints generated. 3626 Oldfield, 0 Emsley, 3626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1123 time to evaluate : 1.073 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: Q 1005 MET cc_start: 0.6794 (mmp) cc_final: 0.6089 (mmp) REVERT: Q 1027 SER cc_start: 0.8720 (m) cc_final: 0.8183 (p) REVERT: Q 1112 LYS cc_start: 0.8784 (mttp) cc_final: 0.8301 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8188 (t) REVERT: Q 1150 LYS cc_start: 0.8571 (tttm) cc_final: 0.7749 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6703 (mp0) REVERT: Q 1195 LYS cc_start: 0.8228 (tppt) cc_final: 0.7466 (tppt) REVERT: Q 1222 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7347 (tm-30) REVERT: Q 1230 THR cc_start: 0.8709 (m) cc_final: 0.8487 (p) REVERT: Q 1231 ASN cc_start: 0.8681 (t0) cc_final: 0.8385 (t0) REVERT: Q 1242 ILE cc_start: 0.9133 (tp) cc_final: 0.8911 (tp) REVERT: Q 1248 ASP cc_start: 0.7466 (t70) cc_final: 0.7037 (t0) REVERT: Q 1256 ASN cc_start: 0.8502 (m-40) cc_final: 0.8294 (m-40) REVERT: Q 1266 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7843 (tm-30) REVERT: Q 1267 ASP cc_start: 0.8574 (m-30) cc_final: 0.7948 (m-30) REVERT: Q 1276 GLU cc_start: 0.8342 (tp30) cc_final: 0.8078 (tp30) REVERT: Q 1291 MET cc_start: 0.8036 (tpt) cc_final: 0.7768 (tpp) REVERT: Q 1295 ILE cc_start: 0.8344 (mt) cc_final: 0.7999 (mm) REVERT: Q 1302 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7614 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8569 (m-30) cc_final: 0.8250 (m-30) REVERT: Q 1317 ARG cc_start: 0.8061 (ptm160) cc_final: 0.7790 (ptm160) REVERT: Q 1331 MET cc_start: 0.7809 (tpp) cc_final: 0.7259 (tpp) REVERT: Q 1334 TYR cc_start: 0.7766 (p90) cc_final: 0.7172 (p90) REVERT: Q 1335 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7834 (mp) REVERT: R 21 LEU cc_start: 0.6942 (tp) cc_final: 0.6404 (tp) REVERT: R 35 ASN cc_start: 0.8837 (t0) cc_final: 0.8593 (m-40) REVERT: R 55 ASN cc_start: 0.8440 (p0) cc_final: 0.8104 (p0) REVERT: R 70 PHE cc_start: 0.7546 (t80) cc_final: 0.7300 (t80) REVERT: R 119 PHE cc_start: 0.8178 (m-10) cc_final: 0.7921 (m-10) REVERT: R 144 GLN cc_start: 0.7636 (pm20) cc_final: 0.6621 (pm20) REVERT: R 152 GLN cc_start: 0.8414 (tt0) cc_final: 0.8006 (tt0) REVERT: R 154 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7736 (mm) REVERT: R 156 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7691 (pm20) REVERT: R 182 LYS cc_start: 0.8421 (mmmm) cc_final: 0.8083 (mmmm) REVERT: R 214 TRP cc_start: 0.7510 (t-100) cc_final: 0.6374 (t-100) REVERT: R 218 GLN cc_start: 0.7962 (mp10) cc_final: 0.7556 (mp10) REVERT: R 239 SER cc_start: 0.5845 (OUTLIER) cc_final: 0.5644 (p) REVERT: R 242 GLN cc_start: 0.8179 (pt0) cc_final: 0.7837 (pt0) REVERT: R 244 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: R 251 CYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7025 (m) REVERT: R 260 ASP cc_start: 0.7907 (m-30) cc_final: 0.7530 (p0) REVERT: R 262 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8171 (mm-30) REVERT: R 592 HIS cc_start: 0.8280 (t-90) cc_final: 0.7564 (t-90) REVERT: R 609 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: R 612 MET cc_start: 0.6995 (tpp) cc_final: 0.6583 (tpp) REVERT: R 627 GLN cc_start: 0.8519 (pt0) cc_final: 0.8124 (pt0) REVERT: R 633 GLN cc_start: 0.8271 (mp10) cc_final: 0.7900 (mp10) REVERT: R 640 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7628 (tp30) REVERT: R 642 SER cc_start: 0.8695 (m) cc_final: 0.8185 (p) REVERT: R 643 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7456 (mm-30) REVERT: R 645 ILE cc_start: 0.9116 (mt) cc_final: 0.8754 (tt) REVERT: R 647 LEU cc_start: 0.8555 (mp) cc_final: 0.8195 (mp) REVERT: R 659 GLN cc_start: 0.8481 (tp-100) cc_final: 0.8238 (tp-100) REVERT: R 663 ASP cc_start: 0.8101 (m-30) cc_final: 0.7807 (m-30) REVERT: R 664 MET cc_start: 0.8738 (mtm) cc_final: 0.8436 (mtp) REVERT: R 681 LYS cc_start: 0.8954 (tptt) cc_final: 0.8742 (tptt) REVERT: R 699 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7775 (p) REVERT: R 721 GLU cc_start: 0.8101 (tp30) cc_final: 0.7703 (tp30) REVERT: R 722 GLU cc_start: 0.8413 (pp20) cc_final: 0.7556 (pp20) REVERT: R 723 GLN cc_start: 0.8132 (mm-40) cc_final: 0.7734 (mm-40) REVERT: R 724 TYR cc_start: 0.8233 (t80) cc_final: 0.7742 (t80) REVERT: R 728 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8635 (m) REVERT: S 70 GLU cc_start: 0.7316 (tp30) cc_final: 0.5636 (tp30) REVERT: S 110 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8116 (mtm180) REVERT: S 122 LYS cc_start: 0.8478 (mmmm) cc_final: 0.8106 (mtpp) REVERT: S 140 TYR cc_start: 0.8656 (t80) cc_final: 0.8347 (t80) REVERT: T 49 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.7927 (m) REVERT: T 56 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7810 (mm-30) REVERT: T 66 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8455 (mtmm) REVERT: T 95 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8233 (mm-30) REVERT: T 177 LYS cc_start: 0.8497 (tttt) cc_final: 0.8120 (mtpp) REVERT: T 178 THR cc_start: 0.8900 (m) cc_final: 0.8617 (t) REVERT: T 193 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8088 (mmmt) REVERT: T 211 ARG cc_start: 0.8581 (ttt-90) cc_final: 0.8287 (ttt-90) REVERT: T 230 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8745 (m) REVERT: T 251 ASP cc_start: 0.8047 (m-30) cc_final: 0.7738 (m-30) REVERT: T 273 LEU cc_start: 0.7909 (tp) cc_final: 0.7637 (tt) REVERT: T 274 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8096 (tppt) REVERT: T 277 LYS cc_start: 0.8264 (mmmm) cc_final: 0.8059 (mtmt) REVERT: T 295 TYR cc_start: 0.8603 (m-80) cc_final: 0.8119 (m-80) REVERT: T 371 ARG cc_start: 0.8096 (mtp-110) cc_final: 0.7799 (ptm-80) REVERT: T 381 ARG cc_start: 0.8724 (ttt-90) cc_final: 0.8206 (ttm-80) REVERT: T 382 THR cc_start: 0.8605 (p) cc_final: 0.8135 (p) REVERT: T 385 GLU cc_start: 0.8479 (pt0) cc_final: 0.7758 (pp20) REVERT: T 401 ASP cc_start: 0.8445 (m-30) cc_final: 0.7633 (m-30) REVERT: T 409 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7603 (mt-10) REVERT: T 414 TYR cc_start: 0.8086 (t80) cc_final: 0.7520 (t80) REVERT: T 417 GLN cc_start: 0.8240 (mt0) cc_final: 0.7888 (mt0) REVERT: T 431 ARG cc_start: 0.7591 (mtm180) cc_final: 0.7105 (ptt90) REVERT: T 439 VAL cc_start: 0.8841 (t) cc_final: 0.8616 (t) REVERT: T 448 ASP cc_start: 0.7662 (p0) cc_final: 0.7132 (p0) REVERT: T 456 LEU cc_start: 0.8971 (tp) cc_final: 0.8385 (mt) REVERT: U 38 ARG cc_start: 0.8090 (mtt90) cc_final: 0.7771 (mpt180) REVERT: U 44 MET cc_start: 0.7402 (ttp) cc_final: 0.7108 (ttm) REVERT: U 60 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8265 (mtp) REVERT: U 81 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8091 (mtmm) REVERT: U 86 MET cc_start: 0.8004 (mmm) cc_final: 0.7445 (mmm) REVERT: U 94 LYS cc_start: 0.8854 (tppt) cc_final: 0.8457 (tptp) REVERT: U 104 SER cc_start: 0.8544 (m) cc_final: 0.8171 (t) REVERT: U 105 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7242 (mt-10) REVERT: U 110 GLU cc_start: 0.7884 (pp20) cc_final: 0.7552 (pp20) REVERT: U 123 LYS cc_start: 0.8242 (mttt) cc_final: 0.7923 (mttp) REVERT: U 128 LYS cc_start: 0.8674 (ttpt) cc_final: 0.8413 (ttmm) REVERT: U 139 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6304 (tp30) REVERT: U 161 LYS cc_start: 0.8620 (ptmm) cc_final: 0.8083 (ptmm) REVERT: U 166 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: U 182 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7606 (tm-30) REVERT: U 193 ASP cc_start: 0.7974 (t0) cc_final: 0.7518 (t0) REVERT: U 194 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8192 (ttpt) REVERT: U 198 LYS cc_start: 0.8538 (tttm) cc_final: 0.8230 (tttm) REVERT: U 272 GLN cc_start: 0.8037 (tp40) cc_final: 0.7546 (tp40) REVERT: U 276 LYS cc_start: 0.8960 (tptt) cc_final: 0.8561 (tptm) REVERT: U 281 LYS cc_start: 0.8955 (tttm) cc_final: 0.8534 (ttmm) REVERT: U 313 LEU cc_start: 0.8780 (mt) cc_final: 0.8555 (mp) REVERT: U 338 LYS cc_start: 0.8917 (mttt) cc_final: 0.8658 (ttmm) REVERT: U 339 SER cc_start: 0.8863 (m) cc_final: 0.8545 (t) REVERT: U 349 ASP cc_start: 0.8614 (t0) cc_final: 0.8079 (m-30) REVERT: U 365 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8499 (ttmt) REVERT: U 376 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7878 (mm-30) REVERT: U 393 GLU cc_start: 0.7709 (pp20) cc_final: 0.7292 (pp20) REVERT: U 399 SER cc_start: 0.8335 (m) cc_final: 0.8083 (p) REVERT: U 400 SER cc_start: 0.8173 (t) cc_final: 0.7747 (m) REVERT: U 411 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.7028 (mpt) REVERT: U 412 LYS cc_start: 0.8798 (tppt) cc_final: 0.8563 (tppt) REVERT: U 419 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6542 (mp0) REVERT: U 424 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7893 (mmtt) REVERT: U 428 LEU cc_start: 0.8686 (tp) cc_final: 0.8337 (pp) REVERT: U 444 GLU cc_start: 0.8117 (tp30) cc_final: 0.7534 (tp30) REVERT: V 30 ILE cc_start: 0.8488 (mt) cc_final: 0.8162 (mm) REVERT: V 31 LYS cc_start: 0.8144 (mmpt) cc_final: 0.7710 (mmtm) REVERT: V 35 LEU cc_start: 0.8462 (mm) cc_final: 0.7686 (mm) REVERT: V 52 ILE cc_start: 0.8657 (mp) cc_final: 0.8306 (mm) REVERT: V 56 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7304 (mm-30) REVERT: V 88 LEU cc_start: 0.8597 (mm) cc_final: 0.8335 (mt) REVERT: V 95 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7735 (mt-10) REVERT: V 99 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8368 (mtpp) REVERT: V 127 ARG cc_start: 0.8155 (ttp-170) cc_final: 0.7804 (ttm110) REVERT: V 132 ARG cc_start: 0.8408 (tpp80) cc_final: 0.8032 (tpp80) REVERT: V 133 ILE cc_start: 0.8840 (mt) cc_final: 0.8532 (tt) REVERT: V 141 GLU cc_start: 0.7593 (pm20) cc_final: 0.7323 (pm20) REVERT: V 144 VAL cc_start: 0.8452 (t) cc_final: 0.8009 (m) REVERT: V 180 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7721 (tpt-90) REVERT: V 187 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7750 (mt-10) REVERT: V 203 GLU cc_start: 0.7989 (tt0) cc_final: 0.7696 (tt0) REVERT: V 218 TYR cc_start: 0.8677 (m-80) cc_final: 0.8214 (m-80) REVERT: V 239 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8085 (mttt) REVERT: V 253 ASP cc_start: 0.7519 (m-30) cc_final: 0.7231 (m-30) REVERT: V 263 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8367 (mm-40) REVERT: V 286 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7937 (mp10) REVERT: V 292 VAL cc_start: 0.8572 (t) cc_final: 0.8277 (m) REVERT: V 302 GLU cc_start: 0.8078 (pt0) cc_final: 0.7742 (pm20) REVERT: V 311 ASP cc_start: 0.8208 (t0) cc_final: 0.7902 (t0) REVERT: V 312 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7808 (mm-30) REVERT: V 319 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7182 (pt0) REVERT: V 325 ASN cc_start: 0.8374 (t0) cc_final: 0.7752 (t0) REVERT: V 326 LYS cc_start: 0.8562 (tmmt) cc_final: 0.8298 (tttt) REVERT: V 344 MET cc_start: 0.8721 (mmt) cc_final: 0.8486 (mmm) REVERT: V 365 ASP cc_start: 0.7858 (m-30) cc_final: 0.7413 (t70) REVERT: V 367 LEU cc_start: 0.8379 (mt) cc_final: 0.8091 (mm) REVERT: V 371 ARG cc_start: 0.8340 (ttp80) cc_final: 0.8078 (ttp80) REVERT: V 379 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8249 (mt-10) REVERT: V 403 LEU cc_start: 0.8905 (mt) cc_final: 0.8577 (mm) REVERT: V 427 GLN cc_start: 0.7996 (pt0) cc_final: 0.7764 (pt0) REVERT: V 443 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8123 (mtmm) REVERT: V 450 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7455 (mttt) REVERT: V 453 THR cc_start: 0.8821 (m) cc_final: 0.8410 (p) REVERT: V 454 LYS cc_start: 0.8850 (mptt) cc_final: 0.8419 (mmtt) REVERT: W 45 VAL cc_start: 0.8534 (OUTLIER) cc_final: 0.8317 (p) REVERT: W 69 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7412 (mmm-85) REVERT: W 86 MET cc_start: 0.7828 (mmm) cc_final: 0.7612 (mmm) REVERT: W 105 GLU cc_start: 0.7911 (mp0) cc_final: 0.7606 (mp0) REVERT: W 113 LYS cc_start: 0.8635 (mttp) cc_final: 0.8260 (mtpt) REVERT: W 142 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: W 159 THR cc_start: 0.8350 (m) cc_final: 0.7787 (p) REVERT: W 185 LEU cc_start: 0.8213 (mt) cc_final: 0.7691 (mt) REVERT: W 188 ASP cc_start: 0.7632 (m-30) cc_final: 0.7023 (m-30) REVERT: W 191 SER cc_start: 0.8704 (t) cc_final: 0.8189 (m) REVERT: W 200 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8008 (p) REVERT: W 231 LYS cc_start: 0.8410 (mttm) cc_final: 0.8163 (mmmm) REVERT: W 261 ASP cc_start: 0.8294 (t0) cc_final: 0.7646 (t0) REVERT: W 264 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6778 (mt-10) REVERT: W 273 ILE cc_start: 0.8783 (tp) cc_final: 0.8563 (tp) REVERT: W 281 LYS cc_start: 0.8700 (tttm) cc_final: 0.8314 (tppt) REVERT: W 296 ASP cc_start: 0.8387 (t0) cc_final: 0.7929 (t0) REVERT: W 306 PHE cc_start: 0.8279 (m-80) cc_final: 0.7881 (m-80) REVERT: W 310 ASN cc_start: 0.7913 (m-40) cc_final: 0.7611 (m-40) REVERT: W 365 LYS cc_start: 0.8955 (tmmt) cc_final: 0.8683 (tmmt) REVERT: W 367 ILE cc_start: 0.8642 (mt) cc_final: 0.8300 (tt) REVERT: W 373 GLN cc_start: 0.8577 (mp10) cc_final: 0.8168 (mt0) REVERT: W 386 LEU cc_start: 0.8549 (tp) cc_final: 0.8307 (tt) REVERT: W 389 LYS cc_start: 0.8816 (tppt) cc_final: 0.7673 (tppt) REVERT: W 393 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7911 (mm-30) REVERT: W 420 VAL cc_start: 0.8584 (t) cc_final: 0.8119 (m) REVERT: W 424 LYS cc_start: 0.8610 (ptpt) cc_final: 0.8331 (ptpt) REVERT: W 438 LYS cc_start: 0.9094 (pttt) cc_final: 0.8724 (pttt) REVERT: X 95 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8231 (mm-30) REVERT: X 117 LYS cc_start: 0.8039 (ptpp) cc_final: 0.7644 (ptpt) REVERT: X 125 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7961 (t80) REVERT: X 186 TYR cc_start: 0.8556 (t80) cc_final: 0.8309 (t80) REVERT: X 189 ILE cc_start: 0.9164 (mm) cc_final: 0.8886 (mm) REVERT: X 198 ASP cc_start: 0.7683 (m-30) cc_final: 0.6964 (m-30) REVERT: X 211 ARG cc_start: 0.8219 (ttt-90) cc_final: 0.7695 (ttp80) REVERT: X 228 GLU cc_start: 0.7534 (pm20) cc_final: 0.7264 (pm20) REVERT: X 245 GLN cc_start: 0.8130 (tp40) cc_final: 0.7840 (tp40) REVERT: X 251 ASP cc_start: 0.7911 (m-30) cc_final: 0.7548 (m-30) REVERT: X 253 ASP cc_start: 0.8114 (m-30) cc_final: 0.7806 (t0) REVERT: X 263 GLN cc_start: 0.7124 (tm-30) cc_final: 0.6528 (tm-30) REVERT: X 268 MET cc_start: 0.8422 (mtp) cc_final: 0.8198 (mtt) REVERT: X 271 GLN cc_start: 0.8297 (tp40) cc_final: 0.8040 (tp40) REVERT: X 272 LEU cc_start: 0.8912 (tt) cc_final: 0.8672 (tp) REVERT: X 274 LYS cc_start: 0.7882 (tmmt) cc_final: 0.7629 (ttmt) REVERT: X 277 LYS cc_start: 0.8781 (ttmm) cc_final: 0.8551 (mtmt) REVERT: X 313 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7496 (t) REVERT: X 325 ASN cc_start: 0.8621 (m-40) cc_final: 0.8338 (m-40) REVERT: X 328 LEU cc_start: 0.8798 (mt) cc_final: 0.8479 (mm) REVERT: X 329 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7245 (tp30) REVERT: X 377 LYS cc_start: 0.8468 (mmmm) cc_final: 0.8184 (mmmm) REVERT: X 378 ASP cc_start: 0.7637 (p0) cc_final: 0.7369 (t70) REVERT: X 385 GLU cc_start: 0.8406 (pp20) cc_final: 0.8078 (pp20) REVERT: X 391 GLU cc_start: 0.8561 (tt0) cc_final: 0.8078 (tp30) REVERT: X 401 ASP cc_start: 0.8380 (m-30) cc_final: 0.8140 (m-30) REVERT: X 406 MET cc_start: 0.8454 (mtp) cc_final: 0.8194 (ttp) REVERT: X 409 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7847 (mm-30) REVERT: X 441 GLU cc_start: 0.7973 (tp30) cc_final: 0.7607 (tp30) REVERT: X 443 LYS cc_start: 0.8426 (tmmt) cc_final: 0.8127 (ttmm) REVERT: X 448 ASP cc_start: 0.7875 (t70) cc_final: 0.7266 (t0) REVERT: X 454 LYS cc_start: 0.8362 (tmmt) cc_final: 0.8009 (tmmt) REVERT: Y 59 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8301 (tptp) REVERT: Y 62 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8687 (mt0) REVERT: Y 105 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7591 (mp0) REVERT: Y 113 LYS cc_start: 0.8300 (ptpp) cc_final: 0.7776 (mtmm) REVERT: Y 122 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7986 (mtp85) REVERT: Y 128 LYS cc_start: 0.8640 (ttpt) cc_final: 0.8026 (ptpt) REVERT: Y 130 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7499 (mtmm) REVERT: Y 131 GLU cc_start: 0.6380 (mm-30) cc_final: 0.6080 (mm-30) REVERT: Y 161 LYS cc_start: 0.8596 (pttt) cc_final: 0.8216 (pttm) REVERT: Y 164 ASP cc_start: 0.8211 (m-30) cc_final: 0.7871 (m-30) REVERT: Y 174 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8467 (mmtm) REVERT: Y 175 MET cc_start: 0.8848 (tpp) cc_final: 0.8295 (tpp) REVERT: Y 271 ASP cc_start: 0.8399 (t0) cc_final: 0.8024 (t0) REVERT: Y 272 GLN cc_start: 0.8511 (mt0) cc_final: 0.8293 (tt0) REVERT: Y 274 ASN cc_start: 0.8704 (m-40) cc_final: 0.8289 (m-40) REVERT: Y 277 VAL cc_start: 0.8678 (t) cc_final: 0.8405 (p) REVERT: Y 287 GLU cc_start: 0.8264 (pm20) cc_final: 0.7949 (pm20) REVERT: Y 304 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7511 (mt-10) REVERT: Y 310 ASN cc_start: 0.8054 (m-40) cc_final: 0.7614 (m-40) REVERT: Y 327 ARG cc_start: 0.7934 (ttm-80) cc_final: 0.7625 (ttm-80) REVERT: Y 338 LYS cc_start: 0.8643 (mtpp) cc_final: 0.8356 (mttm) REVERT: Y 339 SER cc_start: 0.8776 (t) cc_final: 0.8362 (p) REVERT: Y 370 ILE cc_start: 0.8938 (mt) cc_final: 0.8702 (mt) REVERT: Y 373 GLN cc_start: 0.8699 (tt0) cc_final: 0.8461 (mm-40) REVERT: Y 374 GLU cc_start: 0.7705 (tp30) cc_final: 0.7500 (mm-30) REVERT: Y 389 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8332 (mmmm) REVERT: Y 390 THR cc_start: 0.8834 (p) cc_final: 0.8524 (p) REVERT: Y 393 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8114 (mt-10) REVERT: Y 407 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8010 (tp-100) REVERT: Y 412 LYS cc_start: 0.9198 (tptt) cc_final: 0.8905 (tptm) REVERT: Y 422 ASP cc_start: 0.7950 (m-30) cc_final: 0.7601 (t0) REVERT: Y 427 TYR cc_start: 0.8318 (t80) cc_final: 0.7664 (t80) REVERT: Y 444 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7493 (tp30) REVERT: Y 456 ILE cc_start: 0.8874 (mt) cc_final: 0.8373 (mt) REVERT: Z 303 GLU cc_start: 0.8107 (tt0) cc_final: 0.7783 (tt0) REVERT: Z 309 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8256 (tt) REVERT: Z 310 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.7721 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7753 (ttm110) cc_final: 0.7024 (mtm110) outliers start: 112 outliers final: 73 residues processed: 1172 average time/residue: 0.2239 time to fit residues: 396.0752 Evaluate side-chains 1204 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 1102 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 957 THR Chi-restraints excluded: chain Q residue 1030 THR Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1125 CYS Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1270 LYS Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1296 THR Chi-restraints excluded: chain Q residue 1335 LEU Chi-restraints excluded: chain Q residue 1405 MET Chi-restraints excluded: chain R residue 22 ARG Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 156 GLU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 165 PHE Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 239 SER Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 593 LEU Chi-restraints excluded: chain R residue 607 HIS Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 621 VAL Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 694 THR Chi-restraints excluded: chain R residue 699 THR Chi-restraints excluded: chain R residue 728 VAL Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 265 VAL Chi-restraints excluded: chain T residue 271 GLN Chi-restraints excluded: chain T residue 303 LEU Chi-restraints excluded: chain T residue 315 MET Chi-restraints excluded: chain T residue 380 ILE Chi-restraints excluded: chain T residue 436 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 60 MET Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 166 GLU Chi-restraints excluded: chain U residue 269 VAL Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain U residue 442 GLU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 393 LEU Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain V residue 455 ILE Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 20 ILE Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 69 ARG Chi-restraints excluded: chain W residue 142 GLU Chi-restraints excluded: chain W residue 154 LYS Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 210 ARG Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 156 LEU Chi-restraints excluded: chain X residue 178 THR Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 94 LYS Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 304 GLU Chi-restraints excluded: chain Y residue 376 GLU Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 401 ASN Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Z residue 309 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 357 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 303 optimal weight: 0.6980 chunk 251 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 200 optimal weight: 0.5980 chunk 355 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 243 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 37 optimal weight: 20.0000 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1228 HIS ** Q1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 609 GLN T 27 HIS ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** U 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 289 ASN V 341 ASN ** W 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 GLN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108684 restraints weight = 57214.348| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.30 r_work: 0.3346 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29139 Z= 0.141 Angle : 0.708 15.874 39425 Z= 0.346 Chirality : 0.045 0.172 4626 Planarity : 0.005 0.079 5049 Dihedral : 7.150 113.326 4012 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.53 % Rotamer: Outliers : 3.48 % Allowed : 29.84 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.14), residues: 3626 helix: 0.94 (0.13), residues: 1549 sheet: -0.16 (0.21), residues: 604 loop : -0.67 (0.16), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG X 258 TYR 0.027 0.002 TYR V 186 PHE 0.031 0.001 PHE Y 254 TRP 0.019 0.002 TRP R 108 HIS 0.004 0.001 HIS U 242 Details of bonding type rmsd covalent geometry : bond 0.00323 (29139) covalent geometry : angle 0.70768 (39425) hydrogen bonds : bond 0.03449 ( 1098) hydrogen bonds : angle 4.37747 ( 3198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8743.44 seconds wall clock time: 150 minutes 19.20 seconds (9019.20 seconds total)