Starting phenix.real_space_refine on Tue Jun 24 22:10:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euf_28613/06_2025/8euf_28613_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euf_28613/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8euf_28613/06_2025/8euf_28613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euf_28613/06_2025/8euf_28613.map" model { file = "/net/cci-nas-00/data/ceres_data/8euf_28613/06_2025/8euf_28613_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euf_28613/06_2025/8euf_28613_neut.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 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: 18.79, per 1000 atoms: 0.65 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: 6.46 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 3.67 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: 11.09 Time building geometry restraints manager: 7.91 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 463 or resid 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 463 or \ resid 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 463 or \ resid 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 459 or resid 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: 9.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.050 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 66.790 Find NCS groups from input model: 2.070 Set up NCS constraints: 0.140 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.060 ------------------------------------------------------------------------------- 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 : 5.84 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (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 TRP 0.103 0.005 TRP R 586 HIS 0.008 0.002 HIS Q1013 PHE 0.033 0.002 PHE R 28 TYR 0.051 0.003 TYR X 462 ARG 0.038 0.001 ARG U 350 Details of bonding type rmsd hydrogen bonds : bond 0.16490 ( 1098) hydrogen bonds : angle 6.75022 ( 3198) covalent geometry : bond 0.00604 (29139) covalent geometry : angle 1.02461 (39425) *********************** 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 : 3.221 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: 0.4651 time to fit residues: 909.7291 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 : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 305 optimal weight: 0.9990 chunk 274 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 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 155 GLN W 248 ASN W 401 ASN W 443 ASN W 446 GLN ** 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 = 0.3829 r_free = 0.3829 target = 0.129599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.110663 restraints weight = 57393.269| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.36 r_work: 0.3367 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 29139 Z= 0.170 Angle : 0.667 18.838 39425 Z= 0.335 Chirality : 0.046 0.287 4626 Planarity : 0.005 0.109 5049 Dihedral : 8.327 174.012 4012 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.04 % Allowed : 21.99 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 3626 helix: -0.04 (0.13), residues: 1533 sheet: -0.04 (0.21), residues: 603 loop : -0.86 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q1361 HIS 0.006 0.001 HIS Q1228 PHE 0.024 0.002 PHE X 102 TYR 0.026 0.002 TYR T 201 ARG 0.008 0.001 ARG X 55 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 1098) hydrogen bonds : angle 4.74093 ( 3198) covalent geometry : bond 0.00362 (29139) covalent geometry : angle 0.66689 (39425) *********************** 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 1315 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 1219 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.6701 (mmp) cc_final: 0.6067 (mmp) REVERT: Q 1023 ASP cc_start: 0.7559 (t0) cc_final: 0.7072 (t0) REVERT: Q 1027 SER cc_start: 0.8839 (m) cc_final: 0.8357 (p) REVERT: Q 1102 VAL cc_start: 0.8237 (p) cc_final: 0.7960 (m) REVERT: Q 1111 VAL cc_start: 0.8914 (t) cc_final: 0.8553 (p) REVERT: Q 1112 LYS cc_start: 0.8851 (mttp) cc_final: 0.8147 (ttmm) REVERT: Q 1127 PHE cc_start: 0.8769 (t80) cc_final: 0.8548 (t80) REVERT: Q 1134 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8138 (mm-30) REVERT: Q 1142 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7825 (mtm-85) REVERT: Q 1148 LEU cc_start: 0.8633 (tt) cc_final: 0.8021 (mp) REVERT: Q 1150 LYS cc_start: 0.8644 (tttm) cc_final: 0.7909 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: Q 1170 ILE cc_start: 0.8008 (mm) cc_final: 0.7734 (tp) REVERT: Q 1173 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7553 (mt-10) REVERT: Q 1195 LYS cc_start: 0.8310 (tppt) cc_final: 0.7536 (tppt) REVERT: Q 1208 ARG cc_start: 0.8594 (ttm170) cc_final: 0.8125 (mtp85) REVERT: Q 1219 VAL cc_start: 0.8913 (t) cc_final: 0.8464 (p) REVERT: Q 1230 THR cc_start: 0.8811 (m) cc_final: 0.8429 (p) REVERT: Q 1241 LEU cc_start: 0.9125 (tp) cc_final: 0.8903 (tp) REVERT: Q 1242 ILE cc_start: 0.9139 (mt) cc_final: 0.8716 (tp) REVERT: Q 1248 ASP cc_start: 0.7163 (t70) cc_final: 0.6604 (t0) REVERT: Q 1256 ASN cc_start: 0.8391 (m-40) cc_final: 0.8021 (m-40) REVERT: Q 1261 LYS cc_start: 0.8566 (mttt) cc_final: 0.8218 (mtmm) REVERT: Q 1267 ASP cc_start: 0.8534 (m-30) cc_final: 0.8210 (m-30) REVERT: Q 1280 LYS cc_start: 0.8646 (pttm) cc_final: 0.8331 (pttt) REVERT: Q 1291 MET cc_start: 0.7713 (tpp) cc_final: 0.7474 (tpt) REVERT: Q 1293 ARG cc_start: 0.7668 (mmm-85) cc_final: 0.6932 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8348 (mt) cc_final: 0.7961 (mm) REVERT: Q 1302 ARG cc_start: 0.7953 (ttt180) cc_final: 0.7339 (mtp85) REVERT: Q 1331 MET cc_start: 0.7881 (tpp) cc_final: 0.7442 (tpp) REVERT: Q 1337 TYR cc_start: 0.6826 (t80) cc_final: 0.6593 (t80) REVERT: R 17 ASP cc_start: 0.7223 (m-30) cc_final: 0.6937 (m-30) REVERT: R 55 ASN cc_start: 0.8461 (p0) cc_final: 0.8179 (p0) REVERT: R 182 LYS cc_start: 0.8569 (mmmm) cc_final: 0.8369 (mmmm) REVERT: R 192 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7081 (mt-10) REVERT: R 208 ASP cc_start: 0.7977 (t0) cc_final: 0.7633 (t0) REVERT: R 218 GLN cc_start: 0.8079 (mp10) cc_final: 0.7814 (mp10) REVERT: R 230 LYS cc_start: 0.8932 (tttt) cc_final: 0.8628 (tttt) REVERT: R 252 TYR cc_start: 0.8266 (p90) cc_final: 0.7877 (p90) REVERT: R 262 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7897 (mm-30) REVERT: R 592 HIS cc_start: 0.8215 (t-90) cc_final: 0.7527 (t-90) REVERT: R 627 GLN cc_start: 0.8371 (pt0) cc_final: 0.8105 (pt0) REVERT: R 640 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7844 (mt-10) REVERT: R 643 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7030 (mm-30) REVERT: R 647 LEU cc_start: 0.8272 (mp) cc_final: 0.7946 (mp) REVERT: R 659 GLN cc_start: 0.8509 (tp-100) cc_final: 0.8142 (tp-100) REVERT: R 661 SER cc_start: 0.8443 (m) cc_final: 0.8126 (p) REVERT: R 663 ASP cc_start: 0.8386 (m-30) cc_final: 0.7936 (m-30) REVERT: R 664 MET cc_start: 0.8719 (mtm) cc_final: 0.8465 (mtp) REVERT: R 681 LYS cc_start: 0.8900 (tptt) cc_final: 0.8575 (tptt) REVERT: R 724 TYR cc_start: 0.8259 (t80) cc_final: 0.7729 (t80) REVERT: R 728 VAL cc_start: 0.8865 (t) cc_final: 0.8664 (m) REVERT: S 32 PHE cc_start: 0.8225 (m-10) cc_final: 0.7994 (m-10) REVERT: S 65 GLN cc_start: 0.7508 (tp-100) cc_final: 0.7129 (tp-100) REVERT: S 110 ARG cc_start: 0.7838 (ptt180) cc_final: 0.7489 (mtm-85) REVERT: S 122 LYS cc_start: 0.8321 (mmmm) cc_final: 0.7716 (mtpp) REVERT: S 140 TYR cc_start: 0.8734 (t80) cc_final: 0.7899 (t80) REVERT: S 145 LYS cc_start: 0.8594 (tppp) cc_final: 0.8126 (tppp) REVERT: T 49 VAL cc_start: 0.8495 (p) cc_final: 0.8162 (m) REVERT: T 95 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8285 (mm-30) REVERT: T 108 SER cc_start: 0.8723 (m) cc_final: 0.8242 (m) REVERT: T 134 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7861 (mmmt) REVERT: T 165 HIS cc_start: 0.7954 (p-80) cc_final: 0.7616 (p-80) REVERT: T 177 LYS cc_start: 0.8515 (tttt) cc_final: 0.8028 (mtpp) REVERT: T 178 THR cc_start: 0.8993 (m) cc_final: 0.8722 (t) REVERT: T 193 LYS cc_start: 0.8420 (mmmt) cc_final: 0.8045 (mmmt) REVERT: T 229 TYR cc_start: 0.8661 (m-80) cc_final: 0.8235 (m-80) REVERT: T 240 LYS cc_start: 0.8358 (ttmt) cc_final: 0.8123 (ttmt) REVERT: T 251 ASP cc_start: 0.8110 (m-30) cc_final: 0.7802 (m-30) REVERT: T 279 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7405 (pt0) REVERT: T 294 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8789 (ttmm) REVERT: T 295 TYR cc_start: 0.8657 (m-80) cc_final: 0.8098 (m-80) REVERT: T 323 TYR cc_start: 0.8436 (t80) cc_final: 0.8161 (t80) REVERT: T 325 ASN cc_start: 0.8487 (t0) cc_final: 0.8236 (t0) REVERT: T 381 ARG cc_start: 0.8728 (ttt-90) cc_final: 0.8355 (ttm-80) REVERT: T 382 THR cc_start: 0.8590 (p) cc_final: 0.8316 (m) REVERT: T 385 GLU cc_start: 0.8488 (pt0) cc_final: 0.7843 (pp20) REVERT: T 395 VAL cc_start: 0.8201 (t) cc_final: 0.7903 (p) REVERT: T 401 ASP cc_start: 0.8548 (m-30) cc_final: 0.7951 (m-30) REVERT: T 417 GLN cc_start: 0.8286 (mt0) cc_final: 0.7935 (mt0) REVERT: T 419 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8259 (mp) REVERT: T 431 ARG cc_start: 0.7858 (mtm180) cc_final: 0.7333 (mtm180) REVERT: T 436 VAL cc_start: 0.8782 (m) cc_final: 0.8498 (p) REVERT: T 438 ASP cc_start: 0.8285 (m-30) cc_final: 0.7344 (m-30) REVERT: T 448 ASP cc_start: 0.7426 (p0) cc_final: 0.7032 (p0) REVERT: U 29 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7343 (mp) REVERT: U 42 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7675 (mt-10) REVERT: U 45 VAL cc_start: 0.7866 (OUTLIER) cc_final: 0.7659 (p) REVERT: U 73 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8471 (m) REVERT: U 81 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8317 (mtmm) REVERT: U 86 MET cc_start: 0.8181 (mmm) cc_final: 0.7580 (mmm) REVERT: U 90 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8129 (mm110) REVERT: U 110 GLU cc_start: 0.7938 (pp20) cc_final: 0.7577 (pp20) REVERT: U 123 LYS cc_start: 0.8284 (mttt) cc_final: 0.7902 (mttp) REVERT: U 128 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8102 (ttmm) REVERT: U 129 ILE cc_start: 0.8519 (mt) cc_final: 0.8295 (mm) REVERT: U 130 LYS cc_start: 0.8168 (mtmm) cc_final: 0.7963 (mtmm) REVERT: U 161 LYS cc_start: 0.8641 (ptmm) cc_final: 0.8062 (ptmm) REVERT: U 176 ILE cc_start: 0.8282 (mt) cc_final: 0.8069 (mt) REVERT: U 180 THR cc_start: 0.8530 (m) cc_final: 0.8256 (p) REVERT: U 193 ASP cc_start: 0.8007 (t0) cc_final: 0.7746 (t0) REVERT: U 198 LYS cc_start: 0.8602 (tttm) cc_final: 0.8205 (tttm) REVERT: U 221 PHE cc_start: 0.7350 (m-80) cc_final: 0.6990 (m-80) REVERT: U 223 GLN cc_start: 0.7123 (pp30) cc_final: 0.6470 (pp30) REVERT: U 238 THR cc_start: 0.8029 (m) cc_final: 0.7790 (t) REVERT: U 241 LEU cc_start: 0.8169 (mt) cc_final: 0.7851 (mt) REVERT: U 254 PHE cc_start: 0.8123 (p90) cc_final: 0.7912 (p90) REVERT: U 258 PHE cc_start: 0.8653 (m-80) cc_final: 0.8428 (m-10) REVERT: U 272 GLN cc_start: 0.7996 (tp40) cc_final: 0.7473 (tp40) REVERT: U 276 LYS cc_start: 0.8892 (tptt) cc_final: 0.8470 (tptm) REVERT: U 306 PHE cc_start: 0.8219 (m-10) cc_final: 0.7835 (m-10) REVERT: U 310 ASN cc_start: 0.8139 (m-40) cc_final: 0.7906 (m110) REVERT: U 313 LEU cc_start: 0.8857 (mt) cc_final: 0.8603 (mp) REVERT: U 321 VAL cc_start: 0.8820 (t) cc_final: 0.8606 (p) REVERT: U 338 LYS cc_start: 0.8905 (mttt) cc_final: 0.8600 (mtpp) REVERT: U 339 SER cc_start: 0.8881 (m) cc_final: 0.8591 (t) REVERT: U 349 ASP cc_start: 0.8658 (t0) cc_final: 0.8205 (m-30) REVERT: U 365 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8423 (ttmt) REVERT: U 373 GLN cc_start: 0.8804 (tm-30) cc_final: 0.7697 (tm-30) REVERT: U 374 GLU cc_start: 0.7873 (tt0) cc_final: 0.7485 (tp30) REVERT: U 376 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7985 (mm-30) REVERT: U 400 SER cc_start: 0.8135 (t) cc_final: 0.7827 (m) REVERT: U 407 GLN cc_start: 0.8336 (tt0) cc_final: 0.7783 (tt0) REVERT: U 411 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.7041 (mpt) REVERT: U 419 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6982 (mm-30) REVERT: U 421 GLU cc_start: 0.7211 (tp30) cc_final: 0.7003 (tp30) REVERT: U 428 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8116 (pp) REVERT: U 444 GLU cc_start: 0.8067 (tp30) cc_final: 0.7497 (tp30) REVERT: V 30 ILE cc_start: 0.8367 (mt) cc_final: 0.8142 (mt) REVERT: V 31 LYS cc_start: 0.7918 (mmpt) cc_final: 0.7604 (mmtt) REVERT: V 37 GLU cc_start: 0.8113 (pm20) cc_final: 0.7572 (mp0) REVERT: V 56 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7651 (mt-10) REVERT: V 95 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7782 (mt-10) REVERT: V 99 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8406 (mtpp) REVERT: V 100 VAL cc_start: 0.9011 (t) cc_final: 0.8591 (p) REVERT: V 109 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8130 (tt0) REVERT: V 114 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7553 (mt-10) REVERT: V 117 LYS cc_start: 0.8483 (ptpt) cc_final: 0.8195 (pttt) REVERT: V 132 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7739 (ttm-80) REVERT: V 144 VAL cc_start: 0.8360 (t) cc_final: 0.7997 (m) REVERT: V 148 THR cc_start: 0.8818 (t) cc_final: 0.8525 (p) REVERT: V 165 HIS cc_start: 0.7853 (m-70) cc_final: 0.7638 (m-70) REVERT: V 167 ILE cc_start: 0.8623 (mt) cc_final: 0.8387 (mp) REVERT: V 170 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7890 (mp) REVERT: V 180 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7411 (tpt-90) REVERT: V 187 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7683 (mt-10) REVERT: V 192 GLU cc_start: 0.7322 (tp30) cc_final: 0.7097 (tp30) REVERT: V 203 GLU cc_start: 0.7961 (tt0) cc_final: 0.7501 (tt0) REVERT: V 218 TYR cc_start: 0.8616 (m-80) cc_final: 0.8248 (m-80) REVERT: V 222 PHE cc_start: 0.8389 (m-80) cc_final: 0.7879 (m-10) REVERT: V 239 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7669 (mttt) REVERT: V 253 ASP cc_start: 0.7545 (m-30) cc_final: 0.7312 (m-30) REVERT: V 254 VAL cc_start: 0.8661 (t) cc_final: 0.8404 (m) REVERT: V 264 ASP cc_start: 0.7747 (p0) cc_final: 0.7505 (p0) REVERT: V 274 LYS cc_start: 0.8653 (tttp) cc_final: 0.8420 (tttp) REVERT: V 286 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8051 (mm-40) REVERT: V 287 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7465 (mm-30) REVERT: V 292 VAL cc_start: 0.8596 (t) cc_final: 0.8296 (m) REVERT: V 294 LYS cc_start: 0.8621 (tppt) cc_final: 0.8411 (tppt) REVERT: V 297 ASP cc_start: 0.8294 (m-30) cc_final: 0.8094 (m-30) REVERT: V 302 GLU cc_start: 0.8045 (pt0) cc_final: 0.7447 (pm20) REVERT: V 318 ILE cc_start: 0.8652 (tp) cc_final: 0.8405 (tt) REVERT: V 325 ASN cc_start: 0.8382 (t0) cc_final: 0.7658 (t0) REVERT: V 326 LYS cc_start: 0.8508 (tmmt) cc_final: 0.8289 (tttt) REVERT: V 329 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7251 (mt-10) REVERT: V 367 LEU cc_start: 0.8273 (mt) cc_final: 0.8063 (mm) REVERT: V 379 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8332 (mt-10) REVERT: V 403 LEU cc_start: 0.8701 (mt) cc_final: 0.8382 (mm) REVERT: V 418 LEU cc_start: 0.8892 (tp) cc_final: 0.8610 (tp) REVERT: V 432 LYS cc_start: 0.7271 (tptt) cc_final: 0.7023 (tptt) REVERT: V 440 ASN cc_start: 0.7830 (m-40) cc_final: 0.7337 (m-40) REVERT: V 443 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8270 (ptpt) REVERT: V 450 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7570 (mttt) REVERT: V 453 THR cc_start: 0.8673 (m) cc_final: 0.8355 (p) REVERT: V 454 LYS cc_start: 0.8722 (mptt) cc_final: 0.8277 (mmtt) REVERT: W 26 ILE cc_start: 0.8770 (mt) cc_final: 0.8540 (mm) REVERT: W 42 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7958 (mt-10) REVERT: W 79 THR cc_start: 0.8758 (m) cc_final: 0.8550 (p) REVERT: W 86 MET cc_start: 0.7617 (mmm) cc_final: 0.7235 (mmm) REVERT: W 146 ASP cc_start: 0.7933 (m-30) cc_final: 0.7713 (m-30) REVERT: W 154 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8292 (mtpt) REVERT: W 157 LYS cc_start: 0.8346 (mttm) cc_final: 0.8007 (mttp) REVERT: W 159 THR cc_start: 0.8062 (m) cc_final: 0.7662 (p) REVERT: W 160 ILE cc_start: 0.8819 (tt) cc_final: 0.8588 (tp) REVERT: W 164 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8202 (t0) REVERT: W 181 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7935 (mmtp) REVERT: W 185 LEU cc_start: 0.8124 (mt) cc_final: 0.7835 (mt) REVERT: W 188 ASP cc_start: 0.7434 (m-30) cc_final: 0.7070 (m-30) REVERT: W 191 SER cc_start: 0.8291 (t) cc_final: 0.7776 (p) REVERT: W 192 ILE cc_start: 0.8136 (mm) cc_final: 0.7894 (mt) REVERT: W 229 LEU cc_start: 0.8711 (tp) cc_final: 0.8504 (tp) REVERT: W 231 LYS cc_start: 0.8341 (mttm) cc_final: 0.8098 (mmmm) REVERT: W 233 LYS cc_start: 0.8646 (pttm) cc_final: 0.8388 (pttm) REVERT: W 246 VAL cc_start: 0.8568 (t) cc_final: 0.8312 (m) REVERT: W 264 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6612 (mt-10) REVERT: W 267 SER cc_start: 0.8425 (p) cc_final: 0.8099 (m) REVERT: W 271 ASP cc_start: 0.7977 (m-30) cc_final: 0.7610 (m-30) REVERT: W 275 THR cc_start: 0.8824 (t) cc_final: 0.8601 (p) REVERT: W 281 LYS cc_start: 0.8759 (tttm) cc_final: 0.8450 (tppt) REVERT: W 310 ASN cc_start: 0.8025 (m-40) cc_final: 0.7697 (m-40) REVERT: W 339 SER cc_start: 0.8263 (m) cc_final: 0.8021 (t) REVERT: W 362 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7862 (mm-40) REVERT: W 367 ILE cc_start: 0.8738 (mt) cc_final: 0.8524 (tt) REVERT: W 386 LEU cc_start: 0.8505 (tp) cc_final: 0.8216 (tt) REVERT: W 393 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7920 (mm-30) REVERT: W 413 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.7713 (ttp-170) REVERT: W 430 PHE cc_start: 0.7703 (m-80) cc_final: 0.7379 (m-10) REVERT: W 438 LYS cc_start: 0.8919 (pttt) cc_final: 0.8664 (pttt) REVERT: W 440 VAL cc_start: 0.8986 (t) cc_final: 0.8442 (t) REVERT: W 446 GLN cc_start: 0.8554 (mt0) cc_final: 0.8342 (mt0) REVERT: X 33 LEU cc_start: 0.8602 (mt) cc_final: 0.8302 (mm) REVERT: X 88 LEU cc_start: 0.8591 (mt) cc_final: 0.8306 (tt) REVERT: X 95 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8343 (mm-30) REVERT: X 99 LYS cc_start: 0.7689 (pttm) cc_final: 0.6972 (ptpp) REVERT: X 106 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7730 (p) REVERT: X 125 PHE cc_start: 0.8176 (m-80) cc_final: 0.7916 (t80) REVERT: X 188 SER cc_start: 0.8150 (m) cc_final: 0.7746 (p) REVERT: X 189 ILE cc_start: 0.9272 (mm) cc_final: 0.9039 (mm) REVERT: X 191 ARG cc_start: 0.7536 (ttp-110) cc_final: 0.7122 (ttp-110) REVERT: X 192 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6455 (mm-30) REVERT: X 198 ASP cc_start: 0.7514 (m-30) cc_final: 0.6412 (m-30) REVERT: X 201 TYR cc_start: 0.7139 (t80) cc_final: 0.6769 (t80) REVERT: X 211 ARG cc_start: 0.8248 (ttt-90) cc_final: 0.7597 (ttt-90) REVERT: X 245 GLN cc_start: 0.7977 (tp40) cc_final: 0.7724 (tp40) REVERT: X 263 GLN cc_start: 0.7263 (tm-30) cc_final: 0.6706 (tm-30) REVERT: X 274 LYS cc_start: 0.7881 (tmmt) cc_final: 0.7650 (ttmt) REVERT: X 277 LYS cc_start: 0.8675 (ttmm) cc_final: 0.8406 (mtmt) REVERT: X 282 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7089 (tp30) REVERT: X 289 ASN cc_start: 0.8609 (m-40) cc_final: 0.8355 (m-40) REVERT: X 290 LYS cc_start: 0.8442 (tppt) cc_final: 0.7963 (tppt) REVERT: X 292 VAL cc_start: 0.9106 (t) cc_final: 0.8875 (m) REVERT: X 310 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8337 (mt) REVERT: X 325 ASN cc_start: 0.8681 (m-40) cc_final: 0.8390 (m-40) REVERT: X 328 LEU cc_start: 0.8584 (mt) cc_final: 0.8252 (mm) REVERT: X 341 ASN cc_start: 0.8693 (p0) cc_final: 0.8447 (p0) REVERT: X 344 MET cc_start: 0.8133 (mmm) cc_final: 0.7818 (mpp) REVERT: X 345 THR cc_start: 0.7985 (t) cc_final: 0.7751 (p) REVERT: X 363 LEU cc_start: 0.8213 (tp) cc_final: 0.7975 (tp) REVERT: X 376 ASP cc_start: 0.7758 (m-30) cc_final: 0.7548 (m-30) REVERT: X 377 LYS cc_start: 0.8026 (ttpp) cc_final: 0.7678 (ttpp) REVERT: X 378 ASP cc_start: 0.7806 (p0) cc_final: 0.7307 (t0) REVERT: X 385 GLU cc_start: 0.8333 (pp20) cc_final: 0.8060 (pp20) REVERT: X 391 GLU cc_start: 0.8531 (tt0) cc_final: 0.7825 (tp30) REVERT: X 392 ARG cc_start: 0.8659 (mtm110) cc_final: 0.8430 (mpp80) REVERT: X 401 ASP cc_start: 0.8326 (m-30) cc_final: 0.7994 (m-30) REVERT: X 402 LEU cc_start: 0.8816 (tp) cc_final: 0.8538 (tt) REVERT: X 409 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7733 (mm-30) REVERT: X 443 LYS cc_start: 0.8454 (tmmt) cc_final: 0.8109 (ttmm) REVERT: X 448 ASP cc_start: 0.8147 (t0) cc_final: 0.7859 (t70) REVERT: X 450 LYS cc_start: 0.9056 (ttpt) cc_final: 0.8836 (mtpp) REVERT: X 454 LYS cc_start: 0.8616 (tmmt) cc_final: 0.7463 (tmmt) REVERT: X 458 THR cc_start: 0.8529 (m) cc_final: 0.7745 (p) REVERT: Y 59 LYS cc_start: 0.8419 (mmmt) cc_final: 0.8052 (tptp) REVERT: Y 78 SER cc_start: 0.8330 (t) cc_final: 0.7940 (m) REVERT: Y 136 ILE cc_start: 0.8598 (mt) cc_final: 0.8215 (tp) REVERT: Y 164 ASP cc_start: 0.8241 (m-30) cc_final: 0.8034 (m-30) REVERT: Y 166 GLU cc_start: 0.6542 (tm-30) cc_final: 0.6180 (tm-30) REVERT: Y 171 LEU cc_start: 0.8214 (mp) cc_final: 0.7982 (mm) REVERT: Y 173 ASN cc_start: 0.7904 (p0) cc_final: 0.6795 (m-40) REVERT: Y 175 MET cc_start: 0.8903 (tpp) cc_final: 0.8306 (tpp) REVERT: Y 182 GLU cc_start: 0.7581 (pt0) cc_final: 0.7354 (tm-30) REVERT: Y 188 ASP cc_start: 0.7820 (m-30) cc_final: 0.7606 (m-30) REVERT: Y 193 ASP cc_start: 0.8459 (t70) cc_final: 0.8194 (t70) REVERT: Y 213 ASP cc_start: 0.8115 (t0) cc_final: 0.7900 (t0) REVERT: Y 243 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7778 (mt-10) REVERT: Y 254 PHE cc_start: 0.7924 (p90) cc_final: 0.7669 (p90) REVERT: Y 271 ASP cc_start: 0.8452 (t0) cc_final: 0.8051 (t0) REVERT: Y 272 GLN cc_start: 0.8524 (mt0) cc_final: 0.8281 (tt0) REVERT: Y 273 ILE cc_start: 0.8692 (mt) cc_final: 0.8329 (mt) REVERT: Y 274 ASN cc_start: 0.8659 (m-40) cc_final: 0.8261 (m-40) REVERT: Y 277 VAL cc_start: 0.8630 (t) cc_final: 0.8381 (p) REVERT: Y 287 GLU cc_start: 0.7963 (pm20) cc_final: 0.7757 (pm20) REVERT: Y 310 ASN cc_start: 0.8097 (m-40) cc_final: 0.7654 (m-40) REVERT: Y 322 MET cc_start: 0.8507 (mtp) cc_final: 0.8170 (mtm) REVERT: Y 327 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.7588 (ttm-80) REVERT: Y 349 ASP cc_start: 0.8272 (t0) cc_final: 0.7987 (t0) REVERT: Y 370 ILE cc_start: 0.9073 (mt) cc_final: 0.8725 (mt) REVERT: Y 375 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7942 (tt0) REVERT: Y 378 GLU cc_start: 0.8194 (pt0) cc_final: 0.7989 (pm20) REVERT: Y 389 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8236 (mmmm) REVERT: Y 393 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7888 (mt-10) REVERT: Y 399 SER cc_start: 0.8947 (OUTLIER) cc_final: 0.8723 (p) REVERT: Y 405 VAL cc_start: 0.8891 (m) cc_final: 0.8667 (p) REVERT: Y 412 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8745 (tptm) REVERT: Y 420 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8274 (p) REVERT: Y 424 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8224 (mtmm) REVERT: Y 427 TYR cc_start: 0.8290 (t80) cc_final: 0.7558 (t80) REVERT: Y 441 GLN cc_start: 0.8472 (mm110) cc_final: 0.8155 (mt0) REVERT: Y 456 ILE cc_start: 0.8749 (mt) cc_final: 0.8254 (mt) REVERT: Z 310 ARG cc_start: 0.8099 (mtt-85) cc_final: 0.7447 (mmm-85) outliers start: 96 outliers final: 37 residues processed: 1266 average time/residue: 0.4471 time to fit residues: 853.7735 Evaluate side-chains 1194 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1141 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1270 LYS 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 640 GLU 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 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 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 170 LEU 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 V residue 406 MET 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 134 GLU Chi-restraints excluded: chain W residue 164 ASP Chi-restraints excluded: chain W residue 325 THR 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 68 LYS Chi-restraints excluded: chain X residue 106 VAL Chi-restraints excluded: chain X residue 166 VAL Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 310 ILE 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 200 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 347 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 277 optimal weight: 4.9990 chunk 79 optimal weight: 0.2980 chunk 139 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1110 ASN Q1228 HIS ** 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 242 GLN ** R 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 635 GLN T 27 HIS T 29 HIS T 124 ASN T 289 ASN U 119 GLN V 190 GLN V 263 GLN V 341 ASN V 417 GLN W 36 GLN W 63 ASN W 90 GLN W 119 GLN W 144 GLN W 248 ASN W 299 HIS ** W 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 373 GLN ** W 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 HIS X 440 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.128731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109660 restraints weight = 57505.762| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.36 r_work: 0.3352 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29139 Z= 0.157 Angle : 0.641 17.019 39425 Z= 0.318 Chirality : 0.045 0.232 4626 Planarity : 0.005 0.081 5049 Dihedral : 8.082 178.861 4012 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.58 % Allowed : 23.89 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3626 helix: 0.51 (0.13), residues: 1534 sheet: -0.09 (0.21), residues: 611 loop : -0.74 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q1361 HIS 0.007 0.001 HIS Q1228 PHE 0.023 0.001 PHE R 594 TYR 0.027 0.002 TYR R 737 ARG 0.008 0.001 ARG Y 266 Details of bonding type rmsd hydrogen bonds : bond 0.03860 ( 1098) hydrogen bonds : angle 4.57302 ( 3198) covalent geometry : bond 0.00334 (29139) covalent geometry : angle 0.64103 (39425) *********************** 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 1285 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1172 time to evaluate : 3.200 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: 0.6706 (mmp) cc_final: 0.6006 (mmp) REVERT: Q 1023 ASP cc_start: 0.7611 (t0) cc_final: 0.7113 (t0) REVERT: Q 1027 SER cc_start: 0.8806 (m) cc_final: 0.8335 (p) REVERT: Q 1087 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8319 (ttm-80) REVERT: Q 1112 LYS cc_start: 0.8829 (mttp) cc_final: 0.8298 (ttmm) REVERT: Q 1127 PHE cc_start: 0.8786 (t80) cc_final: 0.8534 (t80) REVERT: Q 1142 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7850 (mtm-85) REVERT: Q 1148 LEU cc_start: 0.8688 (tt) cc_final: 0.8093 (mp) REVERT: Q 1150 LYS cc_start: 0.8626 (tttm) cc_final: 0.7807 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: Q 1170 ILE cc_start: 0.8076 (mm) cc_final: 0.7839 (tp) REVERT: Q 1195 LYS cc_start: 0.8299 (tppt) cc_final: 0.7559 (tppt) REVERT: Q 1208 ARG cc_start: 0.8668 (ttm170) cc_final: 0.8054 (mtp85) REVERT: Q 1230 THR cc_start: 0.8690 (m) cc_final: 0.8300 (p) REVERT: Q 1234 ASN cc_start: 0.8430 (m-40) cc_final: 0.8214 (m-40) REVERT: Q 1241 LEU cc_start: 0.9135 (tp) cc_final: 0.8879 (tp) REVERT: Q 1248 ASP cc_start: 0.7282 (t70) cc_final: 0.6704 (t0) REVERT: Q 1267 ASP cc_start: 0.8538 (m-30) cc_final: 0.8174 (m-30) REVERT: Q 1293 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.6851 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8347 (mt) cc_final: 0.8048 (mm) REVERT: Q 1302 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7366 (mtp85) REVERT: Q 1305 ASP cc_start: 0.8580 (m-30) cc_final: 0.8301 (m-30) REVERT: Q 1331 MET cc_start: 0.7871 (tpp) cc_final: 0.7518 (tpp) REVERT: Q 1334 TYR cc_start: 0.7997 (p90) cc_final: 0.7584 (p90) REVERT: Q 1337 TYR cc_start: 0.6793 (t80) cc_final: 0.6583 (t80) REVERT: R 55 ASN cc_start: 0.8470 (p0) cc_final: 0.8069 (p0) REVERT: R 110 LEU cc_start: 0.8364 (mp) cc_final: 0.8149 (mt) REVERT: R 214 TRP cc_start: 0.7543 (t-100) cc_final: 0.6859 (t-100) REVERT: R 218 GLN cc_start: 0.8042 (mp10) cc_final: 0.7674 (mp10) REVERT: R 227 MET cc_start: 0.8337 (mmp) cc_final: 0.8131 (mmp) REVERT: R 230 LYS cc_start: 0.8920 (tttt) cc_final: 0.8094 (tttt) REVERT: R 231 TYR cc_start: 0.8495 (m-80) cc_final: 0.7792 (m-80) REVERT: R 238 MET cc_start: 0.7366 (tpp) cc_final: 0.7019 (tpt) REVERT: R 242 GLN cc_start: 0.8216 (mt0) cc_final: 0.7586 (mt0) REVERT: R 257 TYR cc_start: 0.7787 (t80) cc_final: 0.7301 (t80) REVERT: R 262 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7943 (mm-30) REVERT: R 592 HIS cc_start: 0.8215 (t-90) cc_final: 0.7510 (t-90) REVERT: R 612 MET cc_start: 0.6501 (tpp) cc_final: 0.5833 (tpp) REVERT: R 613 HIS cc_start: 0.5829 (OUTLIER) cc_final: 0.5537 (t-170) REVERT: R 647 LEU cc_start: 0.8307 (mp) cc_final: 0.7986 (mp) REVERT: R 659 GLN cc_start: 0.8523 (tp-100) cc_final: 0.8154 (tp-100) REVERT: R 663 ASP cc_start: 0.8357 (m-30) cc_final: 0.7951 (m-30) REVERT: R 664 MET cc_start: 0.8660 (mtm) cc_final: 0.8401 (mtp) REVERT: R 681 LYS cc_start: 0.8909 (tptt) cc_final: 0.8583 (tptt) REVERT: R 717 LEU cc_start: 0.8648 (tp) cc_final: 0.8416 (mm) REVERT: R 721 GLU cc_start: 0.8124 (tp30) cc_final: 0.7736 (tp30) REVERT: R 724 TYR cc_start: 0.8237 (t80) cc_final: 0.7699 (t80) REVERT: R 726 LYS cc_start: 0.8554 (tptp) cc_final: 0.8261 (tptt) REVERT: R 728 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8623 (m) REVERT: R 729 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6499 (tp) REVERT: S 32 PHE cc_start: 0.8268 (m-10) cc_final: 0.8068 (m-10) REVERT: S 44 PHE cc_start: 0.6530 (t80) cc_final: 0.6305 (t80) REVERT: S 65 GLN cc_start: 0.7541 (tp-100) cc_final: 0.7183 (tp-100) REVERT: S 110 ARG cc_start: 0.7900 (ptt180) cc_final: 0.7683 (mtm-85) REVERT: S 122 LYS cc_start: 0.8390 (mmmm) cc_final: 0.7827 (mtpp) REVERT: S 140 TYR cc_start: 0.8658 (t80) cc_final: 0.8160 (t80) REVERT: S 145 LYS cc_start: 0.8651 (tppp) cc_final: 0.8251 (tppp) REVERT: T 49 VAL cc_start: 0.8535 (p) cc_final: 0.8182 (m) REVERT: T 95 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8260 (mm-30) REVERT: T 134 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7870 (mmmt) REVERT: T 165 HIS cc_start: 0.7983 (p-80) cc_final: 0.7674 (p-80) REVERT: T 177 LYS cc_start: 0.8510 (tttt) cc_final: 0.8011 (mtpp) REVERT: T 178 THR cc_start: 0.8987 (m) cc_final: 0.8707 (t) REVERT: T 193 LYS cc_start: 0.8419 (mmmt) cc_final: 0.8089 (mmmt) REVERT: T 203 GLU cc_start: 0.7927 (tp30) cc_final: 0.7702 (tp30) REVERT: T 229 TYR cc_start: 0.8653 (m-80) cc_final: 0.8017 (m-80) REVERT: T 240 LYS cc_start: 0.8314 (ttmt) cc_final: 0.8091 (ttmt) REVERT: T 251 ASP cc_start: 0.8216 (m-30) cc_final: 0.7899 (m-30) REVERT: T 279 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7450 (pt0) REVERT: T 294 LYS cc_start: 0.9009 (mtpt) cc_final: 0.8783 (ttmm) REVERT: T 295 TYR cc_start: 0.8666 (m-80) cc_final: 0.8064 (m-80) REVERT: T 381 ARG cc_start: 0.8731 (ttt-90) cc_final: 0.8382 (ttm-80) REVERT: T 382 THR cc_start: 0.8605 (p) cc_final: 0.8177 (m) REVERT: T 385 GLU cc_start: 0.8496 (pt0) cc_final: 0.7842 (pp20) REVERT: T 391 GLU cc_start: 0.8390 (tp30) cc_final: 0.8150 (mm-30) REVERT: T 401 ASP cc_start: 0.8494 (m-30) cc_final: 0.7771 (m-30) REVERT: T 413 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7148 (mtp180) REVERT: T 417 GLN cc_start: 0.8300 (mt0) cc_final: 0.8006 (mt0) REVERT: T 431 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7412 (mtm180) REVERT: T 434 ILE cc_start: 0.7878 (mt) cc_final: 0.7384 (mt) REVERT: T 438 ASP cc_start: 0.8264 (m-30) cc_final: 0.7362 (m-30) REVERT: T 448 ASP cc_start: 0.7434 (p0) cc_final: 0.7049 (p0) REVERT: U 20 ILE cc_start: 0.8126 (mm) cc_final: 0.7879 (mm) REVERT: U 29 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7622 (mp) REVERT: U 45 VAL cc_start: 0.7901 (OUTLIER) cc_final: 0.7691 (p) REVERT: U 86 MET cc_start: 0.8132 (mmm) cc_final: 0.7556 (mmm) REVERT: U 94 LYS cc_start: 0.8731 (tppt) cc_final: 0.8306 (tptp) REVERT: U 110 GLU cc_start: 0.7933 (pp20) cc_final: 0.7595 (pp20) REVERT: U 123 LYS cc_start: 0.8278 (mttt) cc_final: 0.7980 (mttp) REVERT: U 128 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8462 (ttmm) REVERT: U 129 ILE cc_start: 0.8570 (mt) cc_final: 0.8346 (mm) REVERT: U 139 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6338 (tp30) REVERT: U 161 LYS cc_start: 0.8652 (ptmm) cc_final: 0.8063 (ptmm) REVERT: U 176 ILE cc_start: 0.8302 (mt) cc_final: 0.8059 (mt) REVERT: U 180 THR cc_start: 0.8489 (m) cc_final: 0.8216 (p) REVERT: U 193 ASP cc_start: 0.7968 (t0) cc_final: 0.7662 (t0) REVERT: U 198 LYS cc_start: 0.8573 (tttm) cc_final: 0.8233 (tttm) REVERT: U 221 PHE cc_start: 0.7545 (m-80) cc_final: 0.6998 (m-80) REVERT: U 223 GLN cc_start: 0.7149 (pp30) cc_final: 0.6538 (pp30) REVERT: U 238 THR cc_start: 0.8138 (m) cc_final: 0.7826 (t) REVERT: U 241 LEU cc_start: 0.8202 (mt) cc_final: 0.7956 (mt) REVERT: U 254 PHE cc_start: 0.8028 (p90) cc_final: 0.7794 (p90) REVERT: U 272 GLN cc_start: 0.7989 (tp40) cc_final: 0.7495 (tp40) REVERT: U 276 LYS cc_start: 0.8946 (tptt) cc_final: 0.8495 (tptm) REVERT: U 281 LYS cc_start: 0.8906 (tttm) cc_final: 0.8493 (ttmm) REVERT: U 310 ASN cc_start: 0.8082 (m-40) cc_final: 0.7858 (m-40) REVERT: U 313 LEU cc_start: 0.8854 (mt) cc_final: 0.8552 (mp) REVERT: U 321 VAL cc_start: 0.8869 (t) cc_final: 0.8586 (p) REVERT: U 338 LYS cc_start: 0.8878 (mttt) cc_final: 0.8627 (mtpp) REVERT: U 339 SER cc_start: 0.8852 (m) cc_final: 0.8563 (t) REVERT: U 349 ASP cc_start: 0.8661 (t0) cc_final: 0.8266 (m-30) REVERT: U 351 SER cc_start: 0.8382 (t) cc_final: 0.8124 (p) REVERT: U 365 LYS cc_start: 0.8810 (ttpt) cc_final: 0.8455 (ttmt) REVERT: U 373 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8282 (tm-30) REVERT: U 374 GLU cc_start: 0.7905 (tt0) cc_final: 0.7626 (tp30) REVERT: U 376 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7989 (mm-30) REVERT: U 399 SER cc_start: 0.8298 (m) cc_final: 0.7871 (p) REVERT: U 400 SER cc_start: 0.8170 (t) cc_final: 0.7715 (m) REVERT: U 407 GLN cc_start: 0.8273 (tt0) cc_final: 0.7177 (tp40) REVERT: U 411 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6288 (mpt) REVERT: U 444 GLU cc_start: 0.8082 (tp30) cc_final: 0.7500 (tp30) REVERT: V 30 ILE cc_start: 0.8419 (mt) cc_final: 0.8026 (mt) REVERT: V 31 LYS cc_start: 0.7966 (mmpt) cc_final: 0.7611 (mmtm) REVERT: V 35 LEU cc_start: 0.8209 (mt) cc_final: 0.7754 (mp) REVERT: V 37 GLU cc_start: 0.8109 (pm20) cc_final: 0.7559 (mp0) REVERT: V 56 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7285 (mm-30) REVERT: V 95 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7761 (mt-10) REVERT: V 99 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8252 (mtpp) REVERT: V 109 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8093 (tt0) REVERT: V 114 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7465 (mt-10) REVERT: V 132 ARG cc_start: 0.8241 (tpp80) cc_final: 0.7632 (ttm-80) REVERT: V 144 VAL cc_start: 0.8446 (t) cc_final: 0.8106 (m) REVERT: V 180 ARG cc_start: 0.8078 (ttm-80) cc_final: 0.7870 (ttm-80) REVERT: V 187 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7689 (mt-10) REVERT: V 192 GLU cc_start: 0.7270 (tp30) cc_final: 0.7017 (tp30) REVERT: V 203 GLU cc_start: 0.7987 (tt0) cc_final: 0.7491 (tt0) REVERT: V 218 TYR cc_start: 0.8641 (m-80) cc_final: 0.8285 (m-80) REVERT: V 222 PHE cc_start: 0.8298 (m-80) cc_final: 0.7974 (m-10) REVERT: V 239 LYS cc_start: 0.8044 (mtpt) cc_final: 0.7704 (mttt) REVERT: V 253 ASP cc_start: 0.7523 (m-30) cc_final: 0.7264 (m-30) REVERT: V 254 VAL cc_start: 0.8685 (t) cc_final: 0.8419 (m) REVERT: V 264 ASP cc_start: 0.7743 (p0) cc_final: 0.7527 (p0) REVERT: V 286 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7996 (mm-40) REVERT: V 294 LYS cc_start: 0.8631 (tppt) cc_final: 0.8420 (tppt) REVERT: V 297 ASP cc_start: 0.8329 (m-30) cc_final: 0.8095 (m-30) REVERT: V 302 GLU cc_start: 0.8046 (pt0) cc_final: 0.7441 (pm20) REVERT: V 318 ILE cc_start: 0.8673 (tp) cc_final: 0.8439 (tt) REVERT: V 325 ASN cc_start: 0.8411 (t0) cc_final: 0.7695 (t0) REVERT: V 326 LYS cc_start: 0.8481 (tmmt) cc_final: 0.8268 (tttt) REVERT: V 329 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7102 (mm-30) REVERT: V 344 MET cc_start: 0.8777 (mmt) cc_final: 0.8460 (mmm) REVERT: V 367 LEU cc_start: 0.8329 (mt) cc_final: 0.8122 (mm) REVERT: V 379 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8198 (mt-10) REVERT: V 403 LEU cc_start: 0.8696 (mt) cc_final: 0.8374 (mm) REVERT: V 418 LEU cc_start: 0.8902 (tp) cc_final: 0.8410 (tt) REVERT: V 440 ASN cc_start: 0.7805 (m-40) cc_final: 0.7505 (m-40) REVERT: V 443 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8294 (mtmm) REVERT: V 450 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7558 (mttt) REVERT: V 453 THR cc_start: 0.8666 (m) cc_final: 0.8381 (p) REVERT: V 454 LYS cc_start: 0.8733 (mptt) cc_final: 0.8294 (mmtt) REVERT: W 26 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8561 (mm) REVERT: W 86 MET cc_start: 0.7738 (mmm) cc_final: 0.7367 (mmm) REVERT: W 157 LYS cc_start: 0.8370 (mttm) cc_final: 0.8034 (mttp) REVERT: W 159 THR cc_start: 0.8037 (m) cc_final: 0.7524 (p) REVERT: W 167 THR cc_start: 0.8855 (t) cc_final: 0.8455 (p) REVERT: W 185 LEU cc_start: 0.8142 (mt) cc_final: 0.7809 (mt) REVERT: W 188 ASP cc_start: 0.7486 (m-30) cc_final: 0.7048 (m-30) REVERT: W 191 SER cc_start: 0.8473 (t) cc_final: 0.7989 (p) REVERT: W 192 ILE cc_start: 0.8283 (mm) cc_final: 0.8050 (mt) REVERT: W 198 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7974 (tppt) REVERT: W 229 LEU cc_start: 0.8676 (tp) cc_final: 0.8431 (tp) REVERT: W 231 LYS cc_start: 0.8381 (mttm) cc_final: 0.8119 (mmmm) REVERT: W 233 LYS cc_start: 0.8613 (pttm) cc_final: 0.8380 (pttt) REVERT: W 246 VAL cc_start: 0.8582 (t) cc_final: 0.8278 (m) REVERT: W 261 ASP cc_start: 0.8204 (t0) cc_final: 0.7741 (t0) REVERT: W 264 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6633 (mt-10) REVERT: W 267 SER cc_start: 0.8500 (p) cc_final: 0.8135 (m) REVERT: W 271 ASP cc_start: 0.7962 (m-30) cc_final: 0.7655 (m-30) REVERT: W 275 THR cc_start: 0.8820 (t) cc_final: 0.8616 (p) REVERT: W 281 LYS cc_start: 0.8761 (tttm) cc_final: 0.8455 (tppt) REVERT: W 306 PHE cc_start: 0.8448 (m-80) cc_final: 0.8045 (m-80) REVERT: W 310 ASN cc_start: 0.8047 (m-40) cc_final: 0.7753 (m-40) REVERT: W 367 ILE cc_start: 0.8652 (mt) cc_final: 0.8422 (tt) REVERT: W 375 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7748 (mt-10) REVERT: W 386 LEU cc_start: 0.8487 (tp) cc_final: 0.8262 (tt) REVERT: W 388 THR cc_start: 0.8595 (p) cc_final: 0.8392 (t) REVERT: W 393 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7917 (mm-30) REVERT: W 424 LYS cc_start: 0.8650 (ptpt) cc_final: 0.8421 (ptpt) REVERT: W 440 VAL cc_start: 0.8962 (t) cc_final: 0.8464 (p) REVERT: X 33 LEU cc_start: 0.8609 (mt) cc_final: 0.8372 (mm) REVERT: X 88 LEU cc_start: 0.8636 (mt) cc_final: 0.8282 (tt) REVERT: X 95 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8336 (mm-30) REVERT: X 99 LYS cc_start: 0.7543 (pttm) cc_final: 0.7065 (ptpp) REVERT: X 123 GLU cc_start: 0.8321 (pt0) cc_final: 0.7918 (tt0) REVERT: X 125 PHE cc_start: 0.8164 (m-80) cc_final: 0.7933 (t80) REVERT: X 186 TYR cc_start: 0.8416 (t80) cc_final: 0.8148 (t80) REVERT: X 188 SER cc_start: 0.8265 (m) cc_final: 0.7962 (p) REVERT: X 189 ILE cc_start: 0.9225 (mm) cc_final: 0.8977 (mt) REVERT: X 191 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.7127 (ttp-110) REVERT: X 198 ASP cc_start: 0.7488 (m-30) cc_final: 0.6280 (m-30) REVERT: X 201 TYR cc_start: 0.7158 (t80) cc_final: 0.6806 (t80) REVERT: X 211 ARG cc_start: 0.8147 (ttt-90) cc_final: 0.7515 (ttt-90) REVERT: X 239 LYS cc_start: 0.8386 (ptpt) cc_final: 0.7933 (ptpp) REVERT: X 245 GLN cc_start: 0.8023 (tp40) cc_final: 0.7722 (tp40) REVERT: X 251 ASP cc_start: 0.8001 (m-30) cc_final: 0.7579 (m-30) REVERT: X 263 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6668 (tm-30) REVERT: X 268 MET cc_start: 0.8492 (mtt) cc_final: 0.8264 (mtp) REVERT: X 272 LEU cc_start: 0.8814 (tt) cc_final: 0.8596 (tp) REVERT: X 274 LYS cc_start: 0.7947 (tmmt) cc_final: 0.7692 (ttmt) REVERT: X 277 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8455 (mtmt) REVERT: X 282 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7420 (tm-30) REVERT: X 285 ARG cc_start: 0.8285 (mtt90) cc_final: 0.7863 (mtm-85) REVERT: X 290 LYS cc_start: 0.8504 (tppt) cc_final: 0.7844 (tppt) REVERT: X 312 GLU cc_start: 0.7762 (mp0) cc_final: 0.7498 (mp0) REVERT: X 313 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7277 (t) REVERT: X 325 ASN cc_start: 0.8673 (m-40) cc_final: 0.8277 (m-40) REVERT: X 328 LEU cc_start: 0.8654 (mt) cc_final: 0.8343 (mm) REVERT: X 341 ASN cc_start: 0.8695 (p0) cc_final: 0.8470 (p0) REVERT: X 344 MET cc_start: 0.8163 (mmm) cc_final: 0.7610 (mpp) REVERT: X 345 THR cc_start: 0.8104 (t) cc_final: 0.7562 (p) REVERT: X 362 ASP cc_start: 0.7615 (p0) cc_final: 0.7318 (p0) REVERT: X 363 LEU cc_start: 0.8255 (tp) cc_final: 0.8040 (tp) REVERT: X 378 ASP cc_start: 0.7759 (p0) cc_final: 0.7362 (t0) REVERT: X 385 GLU cc_start: 0.8290 (pp20) cc_final: 0.7998 (pp20) REVERT: X 391 GLU cc_start: 0.8561 (tt0) cc_final: 0.8045 (tp30) REVERT: X 401 ASP cc_start: 0.8363 (m-30) cc_final: 0.8016 (m-30) REVERT: X 402 LEU cc_start: 0.8774 (tp) cc_final: 0.8562 (tt) REVERT: X 406 MET cc_start: 0.8324 (mtp) cc_final: 0.7563 (mtp) REVERT: X 409 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7688 (mm-30) REVERT: X 431 ARG cc_start: 0.7905 (ttp-110) cc_final: 0.7649 (ttp-110) REVERT: X 443 LYS cc_start: 0.8473 (tmmt) cc_final: 0.8059 (ttmm) REVERT: X 448 ASP cc_start: 0.8158 (t0) cc_final: 0.7920 (t70) REVERT: X 454 LYS cc_start: 0.8420 (tmmt) cc_final: 0.7945 (tmmt) REVERT: X 458 THR cc_start: 0.8463 (m) cc_final: 0.8222 (p) REVERT: Y 59 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8242 (tptp) REVERT: Y 105 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7645 (mp0) REVERT: Y 130 LYS cc_start: 0.7866 (ttmm) cc_final: 0.7645 (mtmm) REVERT: Y 136 ILE cc_start: 0.8600 (OUTLIER) cc_final: 0.8188 (tp) REVERT: Y 162 THR cc_start: 0.8594 (p) cc_final: 0.8215 (t) REVERT: Y 164 ASP cc_start: 0.8190 (m-30) cc_final: 0.7975 (m-30) REVERT: Y 166 GLU cc_start: 0.6740 (tm-30) cc_final: 0.6396 (tm-30) REVERT: Y 171 LEU cc_start: 0.8272 (mp) cc_final: 0.8022 (mm) REVERT: Y 173 ASN cc_start: 0.7938 (p0) cc_final: 0.6923 (m-40) REVERT: Y 174 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8259 (mmtm) REVERT: Y 175 MET cc_start: 0.8937 (tpp) cc_final: 0.8221 (tpp) REVERT: Y 188 ASP cc_start: 0.7820 (m-30) cc_final: 0.7506 (m-30) REVERT: Y 192 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8614 (mm) REVERT: Y 201 LYS cc_start: 0.8602 (tttm) cc_final: 0.8378 (ttpp) REVERT: Y 208 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7647 (mmm-85) REVERT: Y 254 PHE cc_start: 0.7884 (p90) cc_final: 0.7628 (p90) REVERT: Y 271 ASP cc_start: 0.8441 (t0) cc_final: 0.8067 (t0) REVERT: Y 272 GLN cc_start: 0.8513 (mt0) cc_final: 0.8254 (tt0) REVERT: Y 274 ASN cc_start: 0.8679 (m-40) cc_final: 0.8095 (m-40) REVERT: Y 277 VAL cc_start: 0.8615 (t) cc_final: 0.8382 (p) REVERT: Y 310 ASN cc_start: 0.8109 (m-40) cc_final: 0.7697 (m-40) REVERT: Y 320 ILE cc_start: 0.8721 (mm) cc_final: 0.8120 (tp) REVERT: Y 322 MET cc_start: 0.8488 (mtp) cc_final: 0.8173 (mtm) REVERT: Y 327 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7535 (ttm-80) REVERT: Y 349 ASP cc_start: 0.8311 (t0) cc_final: 0.8050 (t0) REVERT: Y 370 ILE cc_start: 0.9045 (mt) cc_final: 0.8786 (mt) REVERT: Y 375 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7928 (tt0) REVERT: Y 378 GLU cc_start: 0.8183 (pt0) cc_final: 0.7841 (pm20) REVERT: Y 384 LEU cc_start: 0.8978 (tp) cc_final: 0.8694 (tt) REVERT: Y 389 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8305 (mmmm) REVERT: Y 393 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8016 (mt-10) REVERT: Y 405 VAL cc_start: 0.8910 (m) cc_final: 0.8704 (p) REVERT: Y 412 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8766 (tptm) REVERT: Y 420 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8243 (p) REVERT: Y 424 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8212 (mtmm) REVERT: Y 432 ASP cc_start: 0.8496 (p0) cc_final: 0.7876 (p0) REVERT: Y 441 GLN cc_start: 0.8489 (mm110) cc_final: 0.8128 (mt0) REVERT: Y 444 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7360 (mm-30) REVERT: Y 456 ILE cc_start: 0.8792 (mt) cc_final: 0.8304 (mt) REVERT: Z 297 ARG cc_start: 0.8444 (tpp80) cc_final: 0.8206 (tpp80) REVERT: Z 310 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7462 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7611 (ttm110) cc_final: 0.7261 (ttm110) outliers start: 113 outliers final: 56 residues processed: 1222 average time/residue: 0.4495 time to fit residues: 829.3942 Evaluate side-chains 1180 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1109 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1071 THR Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1270 LYS Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 164 THR Chi-restraints excluded: chain R residue 200 VAL Chi-restraints excluded: chain R residue 613 HIS 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 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 304 ILE Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain U residue 29 LEU 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 389 LYS Chi-restraints excluded: chain U residue 411 MET 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 W residue 26 ILE Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 287 GLU Chi-restraints excluded: chain W residue 364 ILE 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 68 LYS 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 265 VAL Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 340 SER Chi-restraints excluded: chain Y residue 61 VAL Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 136 ILE 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 329 VAL Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 449 ASP Chi-restraints excluded: chain Z residue 302 SER 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 233 optimal weight: 0.6980 chunk 306 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 258 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 609 GLN R 613 HIS R 635 GLN T 27 HIS T 29 HIS ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 289 ASN T 394 GLN U 49 GLN U 119 GLN V 271 GLN V 341 ASN W 90 GLN W 373 GLN W 443 ASN W 446 GLN X 27 HIS ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 HIS X 190 GLN ** X 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.122858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104103 restraints weight = 57686.996| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.22 r_work: 0.3348 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29139 Z= 0.170 Angle : 0.637 16.783 39425 Z= 0.318 Chirality : 0.045 0.208 4626 Planarity : 0.004 0.071 5049 Dihedral : 7.882 175.467 4012 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.40 % Allowed : 24.40 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3626 helix: 0.75 (0.13), residues: 1537 sheet: -0.13 (0.21), residues: 600 loop : -0.74 (0.16), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q1361 HIS 0.005 0.001 HIS X 357 PHE 0.017 0.001 PHE X 102 TYR 0.025 0.002 TYR V 414 ARG 0.013 0.001 ARG X 258 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 1098) hydrogen bonds : angle 4.52233 ( 3198) covalent geometry : bond 0.00361 (29139) covalent geometry : angle 0.63690 (39425) *********************** 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 1269 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1130 time to evaluate : 3.394 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: 0.6633 (mmp) cc_final: 0.5894 (mmp) REVERT: Q 1023 ASP cc_start: 0.7630 (t0) cc_final: 0.7178 (t0) REVERT: Q 1027 SER cc_start: 0.8749 (m) cc_final: 0.8264 (p) REVERT: Q 1081 ILE cc_start: 0.8914 (mt) cc_final: 0.8595 (tt) REVERT: Q 1087 ARG cc_start: 0.8564 (ttm-80) cc_final: 0.8250 (ttm-80) REVERT: Q 1102 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8024 (m) REVERT: Q 1112 LYS cc_start: 0.8819 (mttp) cc_final: 0.8298 (ttmm) REVERT: Q 1148 LEU cc_start: 0.8573 (tt) cc_final: 0.7953 (mp) REVERT: Q 1150 LYS cc_start: 0.8616 (tttm) cc_final: 0.7717 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6797 (mp0) REVERT: Q 1173 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7253 (mp0) REVERT: Q 1186 VAL cc_start: 0.8941 (p) cc_final: 0.8630 (t) REVERT: Q 1195 LYS cc_start: 0.8255 (tppt) cc_final: 0.7514 (tppt) REVERT: Q 1208 ARG cc_start: 0.8692 (ttm170) cc_final: 0.8180 (mtp85) REVERT: Q 1230 THR cc_start: 0.8745 (m) cc_final: 0.8294 (p) REVERT: Q 1234 ASN cc_start: 0.8453 (m-40) cc_final: 0.8206 (m-40) REVERT: Q 1241 LEU cc_start: 0.9134 (tp) cc_final: 0.8888 (tp) REVERT: Q 1248 ASP cc_start: 0.7280 (t70) cc_final: 0.6801 (t0) REVERT: Q 1261 LYS cc_start: 0.8585 (mttt) cc_final: 0.8218 (mtpp) REVERT: Q 1267 ASP cc_start: 0.8503 (m-30) cc_final: 0.8149 (m-30) REVERT: Q 1291 MET cc_start: 0.7790 (tpp) cc_final: 0.7402 (tpt) REVERT: Q 1293 ARG cc_start: 0.7672 (mmm-85) cc_final: 0.6850 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8382 (mt) cc_final: 0.8010 (mm) REVERT: Q 1302 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7424 (mtp85) REVERT: Q 1305 ASP cc_start: 0.8588 (m-30) cc_final: 0.8300 (m-30) REVERT: Q 1331 MET cc_start: 0.7831 (tpp) cc_final: 0.7182 (tpp) REVERT: Q 1334 TYR cc_start: 0.7902 (p90) cc_final: 0.7239 (p90) REVERT: Q 1335 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7629 (mp) REVERT: Q 1337 TYR cc_start: 0.6698 (t80) cc_final: 0.6485 (t80) REVERT: R 55 ASN cc_start: 0.8451 (p0) cc_final: 0.8072 (p0) REVERT: R 110 LEU cc_start: 0.8417 (mp) cc_final: 0.8204 (mt) REVERT: R 155 PHE cc_start: 0.7302 (m-10) cc_final: 0.7010 (m-10) REVERT: R 211 ARG cc_start: 0.7514 (ttp-110) cc_final: 0.7311 (ttp-110) REVERT: R 214 TRP cc_start: 0.7514 (t-100) cc_final: 0.6800 (t-100) REVERT: R 218 GLN cc_start: 0.8002 (mp10) cc_final: 0.7641 (mp10) REVERT: R 227 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7917 (mmp) REVERT: R 230 LYS cc_start: 0.8857 (tttt) cc_final: 0.8168 (tttt) REVERT: R 231 TYR cc_start: 0.8532 (m-80) cc_final: 0.7817 (m-80) REVERT: R 238 MET cc_start: 0.6944 (tpp) cc_final: 0.5686 (tpt) REVERT: R 242 GLN cc_start: 0.8224 (mt0) cc_final: 0.7520 (mt0) REVERT: R 244 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: R 251 CYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6669 (m) REVERT: R 257 TYR cc_start: 0.7921 (t80) cc_final: 0.7392 (t80) REVERT: R 262 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7998 (mm-30) REVERT: R 592 HIS cc_start: 0.8167 (t-90) cc_final: 0.7443 (t-90) REVERT: R 609 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: R 612 MET cc_start: 0.6453 (tpp) cc_final: 0.5577 (tpp) REVERT: R 635 GLN cc_start: 0.8302 (mt0) cc_final: 0.8083 (mt0) REVERT: R 640 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.6766 (mm-30) REVERT: R 643 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7445 (mm-30) REVERT: R 647 LEU cc_start: 0.8349 (mp) cc_final: 0.7993 (mp) REVERT: R 659 GLN cc_start: 0.8474 (tp-100) cc_final: 0.8186 (tp-100) REVERT: R 663 ASP cc_start: 0.8226 (m-30) cc_final: 0.7866 (m-30) REVERT: R 664 MET cc_start: 0.8700 (mtm) cc_final: 0.8465 (mtp) REVERT: R 681 LYS cc_start: 0.8889 (tptt) cc_final: 0.8549 (tptt) REVERT: R 721 GLU cc_start: 0.7985 (tp30) cc_final: 0.7310 (tm-30) REVERT: R 722 GLU cc_start: 0.7948 (pp20) cc_final: 0.7489 (pp20) REVERT: R 723 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7341 (mm-40) REVERT: R 724 TYR cc_start: 0.8199 (t80) cc_final: 0.7749 (t80) REVERT: R 725 ARG cc_start: 0.8545 (mmt180) cc_final: 0.8251 (mmt180) REVERT: R 726 LYS cc_start: 0.8472 (tptp) cc_final: 0.8231 (tptp) REVERT: R 728 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8628 (m) REVERT: R 729 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6573 (tp) REVERT: R 751 LYS cc_start: 0.8424 (mmtm) cc_final: 0.8065 (mmtm) REVERT: S 100 TYR cc_start: 0.7793 (t80) cc_final: 0.7551 (t80) REVERT: S 110 ARG cc_start: 0.8000 (ptt180) cc_final: 0.7246 (mtm-85) REVERT: S 122 LYS cc_start: 0.8396 (mmmm) cc_final: 0.7904 (mtpp) REVERT: S 140 TYR cc_start: 0.8573 (t80) cc_final: 0.8091 (t80) REVERT: S 145 LYS cc_start: 0.8670 (tppp) cc_final: 0.8263 (tppp) REVERT: T 49 VAL cc_start: 0.8504 (p) cc_final: 0.8176 (m) REVERT: T 56 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7803 (mm-30) REVERT: T 95 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8233 (mm-30) REVERT: T 177 LYS cc_start: 0.8499 (tttt) cc_final: 0.8114 (mtpp) REVERT: T 178 THR cc_start: 0.8977 (m) cc_final: 0.8692 (t) REVERT: T 193 LYS cc_start: 0.8389 (mmmt) cc_final: 0.8087 (mmmt) REVERT: T 211 ARG cc_start: 0.8525 (ttt-90) cc_final: 0.8205 (ttt-90) REVERT: T 229 TYR cc_start: 0.8616 (m-80) cc_final: 0.7782 (m-80) REVERT: T 240 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8136 (ttmt) REVERT: T 251 ASP cc_start: 0.8168 (m-30) cc_final: 0.7856 (m-30) REVERT: T 279 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: T 295 TYR cc_start: 0.8666 (m-80) cc_final: 0.8108 (m-80) REVERT: T 381 ARG cc_start: 0.8748 (ttt-90) cc_final: 0.8357 (ttm-80) REVERT: T 382 THR cc_start: 0.8630 (p) cc_final: 0.8398 (m) REVERT: T 385 GLU cc_start: 0.8514 (pt0) cc_final: 0.7875 (pp20) REVERT: T 401 ASP cc_start: 0.8467 (m-30) cc_final: 0.7665 (m-30) REVERT: T 413 ARG cc_start: 0.7691 (mtp180) cc_final: 0.6577 (mtm-85) REVERT: T 417 GLN cc_start: 0.8285 (mt0) cc_final: 0.7893 (mt0) REVERT: T 418 LEU cc_start: 0.8493 (tp) cc_final: 0.8189 (tp) REVERT: T 424 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7981 (mt) REVERT: T 431 ARG cc_start: 0.7812 (mtm180) cc_final: 0.7422 (mtm180) REVERT: T 438 ASP cc_start: 0.8274 (m-30) cc_final: 0.7618 (m-30) REVERT: T 439 VAL cc_start: 0.8826 (t) cc_final: 0.8614 (t) REVERT: T 441 GLU cc_start: 0.8131 (tp30) cc_final: 0.7853 (tp30) REVERT: T 448 ASP cc_start: 0.7549 (p0) cc_final: 0.7170 (p0) REVERT: T 456 LEU cc_start: 0.8874 (tp) cc_final: 0.8306 (mt) REVERT: T 457 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7992 (mt-10) REVERT: U 29 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7775 (mp) REVERT: U 42 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7855 (mt-10) REVERT: U 45 VAL cc_start: 0.7951 (OUTLIER) cc_final: 0.7710 (p) REVERT: U 86 MET cc_start: 0.8106 (mmm) cc_final: 0.7594 (mmm) REVERT: U 94 LYS cc_start: 0.8727 (tppt) cc_final: 0.8310 (tptp) REVERT: U 110 GLU cc_start: 0.7908 (pp20) cc_final: 0.7303 (pp20) REVERT: U 111 LEU cc_start: 0.8534 (mt) cc_final: 0.8273 (mm) REVERT: U 123 LYS cc_start: 0.8336 (mttt) cc_final: 0.8038 (mttp) REVERT: U 128 LYS cc_start: 0.8657 (ttpt) cc_final: 0.8394 (ttmm) REVERT: U 139 GLU cc_start: 0.7332 (tp30) cc_final: 0.6381 (tp30) REVERT: U 161 LYS cc_start: 0.8636 (ptmm) cc_final: 0.8091 (ptmm) REVERT: U 193 ASP cc_start: 0.7985 (t0) cc_final: 0.7608 (t0) REVERT: U 198 LYS cc_start: 0.8518 (tttm) cc_final: 0.8203 (tttm) REVERT: U 221 PHE cc_start: 0.7470 (m-80) cc_final: 0.6951 (m-80) REVERT: U 223 GLN cc_start: 0.7041 (pp30) cc_final: 0.6449 (pp30) REVERT: U 241 LEU cc_start: 0.8160 (mt) cc_final: 0.7951 (mt) REVERT: U 272 GLN cc_start: 0.7979 (tp40) cc_final: 0.7475 (tp40) REVERT: U 276 LYS cc_start: 0.8946 (tptt) cc_final: 0.8508 (tptm) REVERT: U 281 LYS cc_start: 0.8919 (tttm) cc_final: 0.8514 (ttmm) REVERT: U 306 PHE cc_start: 0.8384 (m-10) cc_final: 0.7878 (m-10) REVERT: U 310 ASN cc_start: 0.8128 (m-40) cc_final: 0.7923 (m110) REVERT: U 313 LEU cc_start: 0.8829 (mt) cc_final: 0.8558 (mp) REVERT: U 321 VAL cc_start: 0.8848 (t) cc_final: 0.8597 (p) REVERT: U 338 LYS cc_start: 0.8880 (mttt) cc_final: 0.8662 (ttmm) REVERT: U 339 SER cc_start: 0.8847 (m) cc_final: 0.8568 (t) REVERT: U 349 ASP cc_start: 0.8680 (t0) cc_final: 0.8190 (m-30) REVERT: U 351 SER cc_start: 0.8471 (t) cc_final: 0.8199 (p) REVERT: U 365 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8496 (ttmt) REVERT: U 374 GLU cc_start: 0.7897 (tt0) cc_final: 0.7338 (tt0) REVERT: U 376 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7957 (mm-30) REVERT: U 393 GLU cc_start: 0.7487 (pp20) cc_final: 0.7278 (pp20) REVERT: U 399 SER cc_start: 0.8357 (m) cc_final: 0.8045 (p) REVERT: U 400 SER cc_start: 0.8306 (t) cc_final: 0.7866 (m) REVERT: U 409 ILE cc_start: 0.8928 (tp) cc_final: 0.8605 (tp) REVERT: U 411 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7108 (mpt) REVERT: U 419 GLU cc_start: 0.7518 (mm-30) cc_final: 0.7303 (mm-30) REVERT: U 424 LYS cc_start: 0.8303 (mmtt) cc_final: 0.8029 (mmtt) REVERT: U 444 GLU cc_start: 0.8123 (tp30) cc_final: 0.7561 (tp30) REVERT: V 30 ILE cc_start: 0.8475 (mt) cc_final: 0.8063 (mt) REVERT: V 31 LYS cc_start: 0.8056 (mmpt) cc_final: 0.7630 (mmtm) REVERT: V 35 LEU cc_start: 0.8290 (mt) cc_final: 0.7891 (mp) REVERT: V 37 GLU cc_start: 0.8164 (pm20) cc_final: 0.7616 (mp0) REVERT: V 52 ILE cc_start: 0.8583 (mp) cc_final: 0.8159 (mm) REVERT: V 56 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7318 (mm-30) REVERT: V 95 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7711 (mt-10) REVERT: V 99 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8355 (mtpp) REVERT: V 109 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8034 (tt0) REVERT: V 114 GLU cc_start: 0.7853 (mt-10) cc_final: 0.6771 (mt-10) REVERT: V 117 LYS cc_start: 0.8574 (ptpp) cc_final: 0.8359 (pttt) REVERT: V 132 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8075 (tpp80) REVERT: V 144 VAL cc_start: 0.8520 (t) cc_final: 0.8127 (m) REVERT: V 187 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7625 (mt-10) REVERT: V 192 GLU cc_start: 0.7196 (tp30) cc_final: 0.6943 (tp30) REVERT: V 203 GLU cc_start: 0.7933 (tt0) cc_final: 0.7468 (tt0) REVERT: V 218 TYR cc_start: 0.8655 (m-80) cc_final: 0.8274 (m-80) REVERT: V 222 PHE cc_start: 0.8325 (m-80) cc_final: 0.7936 (m-10) REVERT: V 239 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7824 (mttt) REVERT: V 253 ASP cc_start: 0.7500 (m-30) cc_final: 0.7207 (m-30) REVERT: V 268 MET cc_start: 0.8006 (mmm) cc_final: 0.7700 (mmm) REVERT: V 292 VAL cc_start: 0.8665 (t) cc_final: 0.8376 (m) REVERT: V 297 ASP cc_start: 0.8380 (m-30) cc_final: 0.8124 (m-30) REVERT: V 302 GLU cc_start: 0.8067 (pt0) cc_final: 0.7542 (pm20) REVERT: V 311 ASP cc_start: 0.8226 (t0) cc_final: 0.7846 (t0) REVERT: V 318 ILE cc_start: 0.8708 (tp) cc_final: 0.8475 (tt) REVERT: V 325 ASN cc_start: 0.8407 (t0) cc_final: 0.7580 (t0) REVERT: V 329 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7115 (mm-30) REVERT: V 365 ASP cc_start: 0.7811 (m-30) cc_final: 0.7365 (t70) REVERT: V 367 LEU cc_start: 0.8360 (mt) cc_final: 0.8133 (mm) REVERT: V 379 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8173 (mt-10) REVERT: V 403 LEU cc_start: 0.8727 (mt) cc_final: 0.8428 (mm) REVERT: V 440 ASN cc_start: 0.7768 (m-40) cc_final: 0.6999 (m-40) REVERT: V 443 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8249 (mtmt) REVERT: V 450 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7457 (mttm) REVERT: V 453 THR cc_start: 0.8672 (m) cc_final: 0.8402 (p) REVERT: V 454 LYS cc_start: 0.8774 (mptt) cc_final: 0.8334 (mmtt) REVERT: W 26 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8479 (mm) REVERT: W 45 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8274 (p) REVERT: W 86 MET cc_start: 0.7818 (mmm) cc_final: 0.7466 (mmm) REVERT: W 136 ILE cc_start: 0.8655 (mp) cc_final: 0.8342 (mp) REVERT: W 157 LYS cc_start: 0.8356 (mttm) cc_final: 0.8020 (mttp) REVERT: W 159 THR cc_start: 0.8238 (m) cc_final: 0.7709 (p) REVERT: W 185 LEU cc_start: 0.8159 (mt) cc_final: 0.7701 (mt) REVERT: W 188 ASP cc_start: 0.7523 (m-30) cc_final: 0.7006 (m-30) REVERT: W 191 SER cc_start: 0.8587 (t) cc_final: 0.8098 (p) REVERT: W 198 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7959 (tppt) REVERT: W 229 LEU cc_start: 0.8607 (tp) cc_final: 0.8388 (tp) REVERT: W 231 LYS cc_start: 0.8437 (mttm) cc_final: 0.8202 (mmmm) REVERT: W 233 LYS cc_start: 0.8626 (pttm) cc_final: 0.8401 (pttt) REVERT: W 246 VAL cc_start: 0.8614 (t) cc_final: 0.8293 (m) REVERT: W 261 ASP cc_start: 0.8146 (t0) cc_final: 0.7670 (t0) REVERT: W 264 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6483 (mt-10) REVERT: W 271 ASP cc_start: 0.7887 (m-30) cc_final: 0.7612 (m-30) REVERT: W 275 THR cc_start: 0.8839 (t) cc_final: 0.8634 (p) REVERT: W 281 LYS cc_start: 0.8761 (tttm) cc_final: 0.8469 (tppt) REVERT: W 287 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: W 306 PHE cc_start: 0.8437 (m-80) cc_final: 0.8108 (m-80) REVERT: W 310 ASN cc_start: 0.8181 (m-40) cc_final: 0.7882 (m-40) REVERT: W 311 ARG cc_start: 0.7980 (mmp80) cc_final: 0.7748 (mmp80) REVERT: W 365 LYS cc_start: 0.8950 (tmmt) cc_final: 0.8668 (tmmt) REVERT: W 367 ILE cc_start: 0.8632 (mt) cc_final: 0.8239 (tt) REVERT: W 386 LEU cc_start: 0.8473 (tp) cc_final: 0.8227 (tt) REVERT: W 388 THR cc_start: 0.8606 (p) cc_final: 0.8396 (t) REVERT: W 393 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7928 (mm-30) REVERT: W 438 LYS cc_start: 0.9029 (pttt) cc_final: 0.8713 (pttt) REVERT: W 440 VAL cc_start: 0.9087 (t) cc_final: 0.8833 (t) REVERT: X 33 LEU cc_start: 0.8678 (mt) cc_final: 0.8435 (mm) REVERT: X 95 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8295 (mm-30) REVERT: X 99 LYS cc_start: 0.7629 (pttm) cc_final: 0.7020 (mtmm) REVERT: X 106 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7967 (p) REVERT: X 123 GLU cc_start: 0.8302 (pt0) cc_final: 0.7931 (tt0) REVERT: X 125 PHE cc_start: 0.8142 (m-80) cc_final: 0.7939 (t80) REVERT: X 186 TYR cc_start: 0.8451 (t80) cc_final: 0.8187 (t80) REVERT: X 189 ILE cc_start: 0.9215 (mm) cc_final: 0.8965 (mt) REVERT: X 190 GLN cc_start: 0.8434 (mt0) cc_final: 0.8175 (mt0) REVERT: X 198 ASP cc_start: 0.7465 (m-30) cc_final: 0.6135 (m-30) REVERT: X 211 ARG cc_start: 0.8170 (ttt-90) cc_final: 0.7458 (ttt-90) REVERT: X 212 VAL cc_start: 0.8575 (m) cc_final: 0.8335 (p) REVERT: X 239 LYS cc_start: 0.8459 (ptpt) cc_final: 0.8013 (ptpp) REVERT: X 245 GLN cc_start: 0.8046 (tp40) cc_final: 0.7722 (tp40) REVERT: X 251 ASP cc_start: 0.7969 (m-30) cc_final: 0.7571 (m-30) REVERT: X 258 ARG cc_start: 0.7219 (mmm160) cc_final: 0.6946 (mmm160) REVERT: X 263 GLN cc_start: 0.7282 (tm-30) cc_final: 0.6622 (tm-30) REVERT: X 272 LEU cc_start: 0.8823 (tt) cc_final: 0.8544 (tp) REVERT: X 274 LYS cc_start: 0.7984 (tmmt) cc_final: 0.7714 (ttmt) REVERT: X 277 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8490 (mtmt) REVERT: X 282 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7459 (tm-30) REVERT: X 285 ARG cc_start: 0.8283 (mtt90) cc_final: 0.7980 (mtt-85) REVERT: X 290 LYS cc_start: 0.8530 (tppt) cc_final: 0.7900 (tppt) REVERT: X 298 GLN cc_start: 0.8165 (mt0) cc_final: 0.7944 (mp10) REVERT: X 311 ASP cc_start: 0.7735 (m-30) cc_final: 0.7530 (m-30) REVERT: X 313 VAL cc_start: 0.8085 (OUTLIER) cc_final: 0.7545 (t) REVERT: X 325 ASN cc_start: 0.8684 (m-40) cc_final: 0.8244 (m-40) REVERT: X 328 LEU cc_start: 0.8730 (mt) cc_final: 0.8456 (mm) REVERT: X 344 MET cc_start: 0.8069 (mmm) cc_final: 0.7732 (mpp) REVERT: X 345 THR cc_start: 0.8149 (t) cc_final: 0.7767 (p) REVERT: X 362 ASP cc_start: 0.7621 (p0) cc_final: 0.7354 (p0) REVERT: X 378 ASP cc_start: 0.7729 (p0) cc_final: 0.7359 (t0) REVERT: X 385 GLU cc_start: 0.8318 (pp20) cc_final: 0.7999 (pp20) REVERT: X 401 ASP cc_start: 0.8396 (m-30) cc_final: 0.8070 (m-30) REVERT: X 406 MET cc_start: 0.8233 (mtp) cc_final: 0.7893 (mtp) REVERT: X 409 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7770 (mm-30) REVERT: X 443 LYS cc_start: 0.8467 (tmmt) cc_final: 0.8150 (ttmm) REVERT: X 448 ASP cc_start: 0.8053 (t0) cc_final: 0.7841 (t70) REVERT: X 454 LYS cc_start: 0.8425 (tmmt) cc_final: 0.7712 (tmmt) REVERT: X 457 GLU cc_start: 0.7682 (pp20) cc_final: 0.7451 (pp20) REVERT: Y 59 LYS cc_start: 0.8467 (mmmt) cc_final: 0.8242 (tptp) REVERT: Y 130 LYS cc_start: 0.7793 (ttmm) cc_final: 0.7582 (mtmm) REVERT: Y 136 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8054 (tp) REVERT: Y 162 THR cc_start: 0.8602 (p) cc_final: 0.8222 (t) REVERT: Y 164 ASP cc_start: 0.8223 (m-30) cc_final: 0.7988 (m-30) REVERT: Y 171 LEU cc_start: 0.8401 (mp) cc_final: 0.8168 (mm) REVERT: Y 173 ASN cc_start: 0.7999 (p0) cc_final: 0.7042 (m-40) REVERT: Y 174 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8287 (mmtm) REVERT: Y 175 MET cc_start: 0.8867 (tpp) cc_final: 0.8199 (tpp) REVERT: Y 188 ASP cc_start: 0.7788 (m-30) cc_final: 0.7503 (m-30) REVERT: Y 192 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8728 (mm) REVERT: Y 266 ARG cc_start: 0.7712 (mtm110) cc_final: 0.7500 (mtm110) REVERT: Y 271 ASP cc_start: 0.8362 (t0) cc_final: 0.8001 (t0) REVERT: Y 272 GLN cc_start: 0.8452 (mt0) cc_final: 0.8235 (tt0) REVERT: Y 274 ASN cc_start: 0.8693 (m-40) cc_final: 0.8303 (m-40) REVERT: Y 277 VAL cc_start: 0.8643 (t) cc_final: 0.8403 (p) REVERT: Y 310 ASN cc_start: 0.8051 (m-40) cc_final: 0.7712 (m-40) REVERT: Y 315 ASP cc_start: 0.8187 (t0) cc_final: 0.7924 (t0) REVERT: Y 322 MET cc_start: 0.8469 (mtp) cc_final: 0.8232 (mtm) REVERT: Y 327 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7552 (ttm-80) REVERT: Y 370 ILE cc_start: 0.9028 (mt) cc_final: 0.8776 (mt) REVERT: Y 375 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7976 (tt0) REVERT: Y 384 LEU cc_start: 0.8986 (tp) cc_final: 0.8681 (tt) REVERT: Y 389 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8397 (mmmm) REVERT: Y 393 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8006 (mt-10) REVERT: Y 422 ASP cc_start: 0.7922 (m-30) cc_final: 0.7634 (t0) REVERT: Y 424 LYS cc_start: 0.8530 (mtmm) cc_final: 0.8314 (mtmm) REVERT: Y 441 GLN cc_start: 0.8481 (mm110) cc_final: 0.8122 (mt0) REVERT: Y 444 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7005 (tm-30) REVERT: Y 456 ILE cc_start: 0.8783 (mt) cc_final: 0.8306 (mt) REVERT: Z 297 ARG cc_start: 0.8434 (tpp80) cc_final: 0.8202 (tpp80) REVERT: Z 310 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7489 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7589 (ttm110) cc_final: 0.7237 (ttm110) outliers start: 139 outliers final: 82 residues processed: 1199 average time/residue: 0.4459 time to fit residues: 809.5280 Evaluate side-chains 1218 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1113 time to evaluate : 3.224 ------------------------------------------------------------------------------- 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 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 1335 LEU 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 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 227 MET Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 609 GLN 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 677 VAL 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 S residue 142 LEU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 246 ASP Chi-restraints excluded: chain T residue 265 VAL 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 390 VAL Chi-restraints excluded: chain T residue 406 MET Chi-restraints excluded: chain T residue 424 ILE Chi-restraints excluded: chain U residue 29 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 133 THR Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 331 LYS Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 404 SER Chi-restraints excluded: chain U residue 405 VAL 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 106 VAL 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 335 VAL Chi-restraints excluded: chain V residue 395 VAL Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 26 ILE 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 105 GLU Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 287 GLU Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 364 ILE Chi-restraints excluded: chain W residue 374 GLU Chi-restraints excluded: chain X residue 28 THR Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 106 VAL 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 178 THR Chi-restraints excluded: chain X residue 265 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 416 LEU Chi-restraints excluded: chain X residue 430 ASN Chi-restraints excluded: chain Y residue 61 VAL Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 113 LYS Chi-restraints excluded: chain Y residue 128 LYS Chi-restraints excluded: chain Y residue 136 ILE Chi-restraints excluded: chain Y residue 167 THR Chi-restraints excluded: chain Y residue 192 ILE Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 329 VAL Chi-restraints excluded: chain Y residue 368 LEU Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 445 SER Chi-restraints excluded: chain Y residue 449 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 72 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 207 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 GLN S 40 ASN T 27 HIS ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 289 ASN T 417 GLN U 237 HIS V 27 HIS V 263 GLN V 271 GLN V 341 ASN V 394 GLN W 90 GLN W 248 ASN W 373 GLN X 51 GLN X 165 HIS ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.121902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.103226 restraints weight = 57181.270| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.19 r_work: 0.3329 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29139 Z= 0.202 Angle : 0.657 16.742 39425 Z= 0.330 Chirality : 0.046 0.198 4626 Planarity : 0.005 0.065 5049 Dihedral : 7.782 168.045 4012 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.03 % Allowed : 24.94 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3626 helix: 0.77 (0.13), residues: 1534 sheet: -0.20 (0.20), residues: 604 loop : -0.71 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q1361 HIS 0.012 0.001 HIS R 613 PHE 0.023 0.002 PHE Q1127 TYR 0.025 0.002 TYR Q1198 ARG 0.013 0.001 ARG S 34 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 1098) hydrogen bonds : angle 4.58749 ( 3198) covalent geometry : bond 0.00421 (29139) covalent geometry : angle 0.65742 (39425) *********************** 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 1305 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 1146 time to evaluate : 3.382 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: 0.8307 (mm110) cc_final: 0.7988 (mm110) REVERT: Q 1005 MET cc_start: 0.6703 (mmp) cc_final: 0.5952 (mmp) REVERT: Q 1023 ASP cc_start: 0.7665 (t0) cc_final: 0.7221 (t0) REVERT: Q 1027 SER cc_start: 0.8760 (m) cc_final: 0.8217 (p) REVERT: Q 1102 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.8066 (m) REVERT: Q 1112 LYS cc_start: 0.8795 (mttp) cc_final: 0.8275 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8181 (t) REVERT: Q 1150 LYS cc_start: 0.8620 (tttm) cc_final: 0.7724 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: Q 1173 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7279 (mp0) REVERT: Q 1195 LYS cc_start: 0.8239 (tppt) cc_final: 0.7503 (tppt) REVERT: Q 1208 ARG cc_start: 0.8728 (ttm170) cc_final: 0.7769 (mtp180) REVERT: Q 1222 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7322 (tm-30) REVERT: Q 1230 THR cc_start: 0.8797 (m) cc_final: 0.8334 (p) REVERT: Q 1234 ASN cc_start: 0.8483 (m-40) cc_final: 0.8233 (m-40) REVERT: Q 1241 LEU cc_start: 0.9165 (tp) cc_final: 0.8889 (tp) REVERT: Q 1248 ASP cc_start: 0.7447 (t70) cc_final: 0.6978 (t0) REVERT: Q 1261 LYS cc_start: 0.8632 (mttt) cc_final: 0.8370 (mtpp) REVERT: Q 1267 ASP cc_start: 0.8523 (m-30) cc_final: 0.8181 (m-30) REVERT: Q 1293 ARG cc_start: 0.7702 (mmm-85) cc_final: 0.6833 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8395 (mt) cc_final: 0.8094 (mm) REVERT: Q 1302 ARG cc_start: 0.8042 (ttt180) cc_final: 0.7581 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8590 (m-30) cc_final: 0.8287 (m-30) REVERT: Q 1331 MET cc_start: 0.7859 (tpp) cc_final: 0.7200 (tpp) REVERT: Q 1334 TYR cc_start: 0.7892 (p90) cc_final: 0.7226 (p90) REVERT: Q 1335 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7677 (mp) REVERT: R 35 ASN cc_start: 0.8794 (t0) cc_final: 0.8280 (t0) REVERT: R 55 ASN cc_start: 0.8458 (p0) cc_final: 0.8087 (p0) REVERT: R 156 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: R 183 THR cc_start: 0.7365 (m) cc_final: 0.6812 (t) REVERT: R 211 ARG cc_start: 0.7580 (ttp-110) cc_final: 0.7025 (ttp-110) REVERT: R 214 TRP cc_start: 0.7563 (t-100) cc_final: 0.6846 (t-100) REVERT: R 218 GLN cc_start: 0.8052 (mp10) cc_final: 0.7840 (mp10) REVERT: R 227 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7876 (mmp) REVERT: R 238 MET cc_start: 0.7054 (tpp) cc_final: 0.6488 (tpp) REVERT: R 251 CYS cc_start: 0.7327 (OUTLIER) cc_final: 0.6859 (m) REVERT: R 262 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8079 (mm-30) REVERT: R 592 HIS cc_start: 0.8138 (t-90) cc_final: 0.7533 (t-90) REVERT: R 609 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7403 (mp10) REVERT: R 612 MET cc_start: 0.6718 (tpp) cc_final: 0.6262 (tpp) REVERT: R 640 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7163 (tp30) REVERT: R 643 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7492 (mm-30) REVERT: R 647 LEU cc_start: 0.8444 (mp) cc_final: 0.8072 (mp) REVERT: R 659 GLN cc_start: 0.8455 (tp-100) cc_final: 0.8117 (tp-100) REVERT: R 663 ASP cc_start: 0.8160 (m-30) cc_final: 0.7757 (m-30) REVERT: R 664 MET cc_start: 0.8737 (mtm) cc_final: 0.8472 (mtp) REVERT: R 721 GLU cc_start: 0.8061 (tp30) cc_final: 0.7531 (tp30) REVERT: R 722 GLU cc_start: 0.8084 (pp20) cc_final: 0.7376 (pp20) REVERT: R 723 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7275 (mm-40) REVERT: R 724 TYR cc_start: 0.8199 (t80) cc_final: 0.7587 (t80) REVERT: R 726 LYS cc_start: 0.8505 (tptp) cc_final: 0.8109 (tptp) REVERT: R 728 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8631 (m) REVERT: R 729 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6632 (tp) REVERT: R 743 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.7028 (mtmm) REVERT: S 100 TYR cc_start: 0.7891 (t80) cc_final: 0.7463 (t80) REVERT: S 110 ARG cc_start: 0.8101 (ptt180) cc_final: 0.7521 (mtm180) REVERT: S 122 LYS cc_start: 0.8425 (mmmm) cc_final: 0.7946 (mtpp) REVERT: S 140 TYR cc_start: 0.8591 (t80) cc_final: 0.8149 (t80) REVERT: S 145 LYS cc_start: 0.8698 (tppp) cc_final: 0.8298 (tppp) REVERT: T 49 VAL cc_start: 0.8493 (p) cc_final: 0.8137 (m) REVERT: T 56 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7757 (mm-30) REVERT: T 95 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8182 (mm-30) REVERT: T 177 LYS cc_start: 0.8475 (tttt) cc_final: 0.8075 (mtpp) REVERT: T 178 THR cc_start: 0.8979 (m) cc_final: 0.8652 (t) REVERT: T 193 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8054 (mmmt) REVERT: T 211 ARG cc_start: 0.8560 (ttt-90) cc_final: 0.8333 (ttt-90) REVERT: T 218 TYR cc_start: 0.7696 (m-80) cc_final: 0.7011 (m-80) REVERT: T 229 TYR cc_start: 0.8601 (m-80) cc_final: 0.7686 (m-80) REVERT: T 251 ASP cc_start: 0.8168 (m-30) cc_final: 0.7865 (m-30) REVERT: T 279 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: T 295 TYR cc_start: 0.8626 (m-80) cc_final: 0.8090 (m-80) REVERT: T 371 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7574 (ptm-80) REVERT: T 381 ARG cc_start: 0.8739 (ttt-90) cc_final: 0.8244 (ttm-80) REVERT: T 382 THR cc_start: 0.8641 (p) cc_final: 0.8409 (m) REVERT: T 385 GLU cc_start: 0.8521 (pt0) cc_final: 0.7851 (pp20) REVERT: T 401 ASP cc_start: 0.8477 (m-30) cc_final: 0.7617 (m-30) REVERT: T 413 ARG cc_start: 0.7766 (mtp180) cc_final: 0.6349 (mtm-85) REVERT: T 417 GLN cc_start: 0.8263 (mt0) cc_final: 0.7942 (mt0) REVERT: T 438 ASP cc_start: 0.8323 (m-30) cc_final: 0.7926 (m-30) REVERT: T 439 VAL cc_start: 0.8914 (t) cc_final: 0.8691 (t) REVERT: T 448 ASP cc_start: 0.7605 (p0) cc_final: 0.7232 (p0) REVERT: T 456 LEU cc_start: 0.8893 (tp) cc_final: 0.8304 (mt) REVERT: T 457 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8065 (mm-30) REVERT: U 38 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7934 (mpt-90) REVERT: U 45 VAL cc_start: 0.7999 (OUTLIER) cc_final: 0.7753 (p) REVERT: U 86 MET cc_start: 0.8101 (mmm) cc_final: 0.7641 (mmm) REVERT: U 90 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8065 (mm110) REVERT: U 94 LYS cc_start: 0.8783 (tppt) cc_final: 0.8378 (tptp) REVERT: U 104 SER cc_start: 0.8555 (m) cc_final: 0.8218 (t) REVERT: U 105 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7137 (mt-10) REVERT: U 110 GLU cc_start: 0.7955 (pp20) cc_final: 0.7623 (pp20) REVERT: U 123 LYS cc_start: 0.8318 (mttt) cc_final: 0.8005 (mttp) REVERT: U 128 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8485 (ttmm) REVERT: U 139 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6352 (tp30) REVERT: U 161 LYS cc_start: 0.8649 (ptmm) cc_final: 0.8082 (ptmm) REVERT: U 166 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7127 (tp30) REVERT: U 193 ASP cc_start: 0.7971 (t0) cc_final: 0.7555 (t0) REVERT: U 198 LYS cc_start: 0.8532 (tttm) cc_final: 0.8229 (tttm) REVERT: U 221 PHE cc_start: 0.7475 (m-80) cc_final: 0.7269 (m-80) REVERT: U 241 LEU cc_start: 0.8148 (mt) cc_final: 0.7932 (mt) REVERT: U 265 ILE cc_start: 0.8850 (mp) cc_final: 0.8612 (mm) REVERT: U 272 GLN cc_start: 0.7987 (tp40) cc_final: 0.7487 (tp40) REVERT: U 276 LYS cc_start: 0.8946 (tptt) cc_final: 0.8493 (tptm) REVERT: U 281 LYS cc_start: 0.8932 (tttm) cc_final: 0.8532 (ttmm) REVERT: U 306 PHE cc_start: 0.8356 (m-10) cc_final: 0.8094 (m-10) REVERT: U 310 ASN cc_start: 0.8168 (m-40) cc_final: 0.7967 (m-40) REVERT: U 313 LEU cc_start: 0.8817 (mt) cc_final: 0.8605 (mp) REVERT: U 321 VAL cc_start: 0.8836 (t) cc_final: 0.8578 (p) REVERT: U 338 LYS cc_start: 0.8903 (mttt) cc_final: 0.8673 (ttmm) REVERT: U 339 SER cc_start: 0.8873 (m) cc_final: 0.8576 (t) REVERT: U 349 ASP cc_start: 0.8672 (t0) cc_final: 0.8206 (m-30) REVERT: U 351 SER cc_start: 0.8504 (t) cc_final: 0.8231 (p) REVERT: U 365 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8516 (ttmt) REVERT: U 376 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7940 (mm-30) REVERT: U 378 GLU cc_start: 0.7357 (mp0) cc_final: 0.7091 (mp0) REVERT: U 393 GLU cc_start: 0.7537 (pp20) cc_final: 0.7284 (pp20) REVERT: U 399 SER cc_start: 0.8362 (m) cc_final: 0.8000 (p) REVERT: U 400 SER cc_start: 0.8291 (t) cc_final: 0.7810 (m) REVERT: U 407 GLN cc_start: 0.8342 (tt0) cc_final: 0.7324 (tp40) REVERT: U 411 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.6760 (mpt) REVERT: U 412 LYS cc_start: 0.8794 (tppt) cc_final: 0.8586 (tppt) REVERT: U 424 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8053 (mmtt) REVERT: U 428 LEU cc_start: 0.8722 (mt) cc_final: 0.8445 (pp) REVERT: U 444 GLU cc_start: 0.8164 (tp30) cc_final: 0.7592 (tp30) REVERT: V 30 ILE cc_start: 0.8542 (mt) cc_final: 0.8242 (mm) REVERT: V 31 LYS cc_start: 0.8115 (mmpt) cc_final: 0.7702 (mmtm) REVERT: V 35 LEU cc_start: 0.8323 (mt) cc_final: 0.7923 (mp) REVERT: V 52 ILE cc_start: 0.8644 (mp) cc_final: 0.8282 (mm) REVERT: V 56 GLU cc_start: 0.7897 (mt-10) cc_final: 0.7440 (mm-30) REVERT: V 95 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7770 (mt-10) REVERT: V 99 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8233 (mtpp) REVERT: V 109 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8055 (tt0) REVERT: V 114 GLU cc_start: 0.7907 (mt-10) cc_final: 0.6861 (mt-10) REVERT: V 132 ARG cc_start: 0.8339 (tpp80) cc_final: 0.7682 (ttm170) REVERT: V 144 VAL cc_start: 0.8460 (t) cc_final: 0.8086 (m) REVERT: V 187 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7616 (mt-10) REVERT: V 194 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.7960 (t) REVERT: V 203 GLU cc_start: 0.7991 (tt0) cc_final: 0.7724 (tt0) REVERT: V 218 TYR cc_start: 0.8676 (m-80) cc_final: 0.8249 (m-80) REVERT: V 222 PHE cc_start: 0.8360 (m-80) cc_final: 0.8063 (m-10) REVERT: V 253 ASP cc_start: 0.7539 (m-30) cc_final: 0.7244 (m-30) REVERT: V 263 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8462 (mm-40) REVERT: V 268 MET cc_start: 0.7925 (mmm) cc_final: 0.7638 (mmm) REVERT: V 286 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7856 (mp10) REVERT: V 297 ASP cc_start: 0.8303 (m-30) cc_final: 0.8062 (m-30) REVERT: V 302 GLU cc_start: 0.8082 (pt0) cc_final: 0.7639 (pm20) REVERT: V 318 ILE cc_start: 0.8709 (tp) cc_final: 0.8474 (tt) REVERT: V 325 ASN cc_start: 0.8406 (t0) cc_final: 0.7581 (t0) REVERT: V 329 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7112 (mm-30) REVERT: V 365 ASP cc_start: 0.7849 (m-30) cc_final: 0.7417 (t70) REVERT: V 367 LEU cc_start: 0.8405 (mt) cc_final: 0.8152 (mm) REVERT: V 379 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8157 (mt-10) REVERT: V 403 LEU cc_start: 0.8778 (mt) cc_final: 0.8459 (mm) REVERT: V 440 ASN cc_start: 0.7771 (m-40) cc_final: 0.6973 (m-40) REVERT: V 443 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8204 (mtmt) REVERT: V 450 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7410 (mttt) REVERT: V 453 THR cc_start: 0.8686 (m) cc_final: 0.8428 (p) REVERT: V 454 LYS cc_start: 0.8844 (mptt) cc_final: 0.8411 (mmtt) REVERT: W 26 ILE cc_start: 0.8801 (mt) cc_final: 0.8534 (mm) REVERT: W 45 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8310 (p) REVERT: W 86 MET cc_start: 0.7801 (mmm) cc_final: 0.7461 (mmm) REVERT: W 135 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7971 (mm) REVERT: W 136 ILE cc_start: 0.8684 (mp) cc_final: 0.8455 (mp) REVERT: W 142 GLU cc_start: 0.7669 (pp20) cc_final: 0.7226 (pp20) REVERT: W 157 LYS cc_start: 0.8398 (mttm) cc_final: 0.8085 (mttp) REVERT: W 159 THR cc_start: 0.8291 (m) cc_final: 0.7471 (p) REVERT: W 181 LYS cc_start: 0.8452 (tppt) cc_final: 0.8201 (mmtp) REVERT: W 185 LEU cc_start: 0.8228 (mt) cc_final: 0.7895 (mt) REVERT: W 188 ASP cc_start: 0.7631 (m-30) cc_final: 0.7131 (m-30) REVERT: W 191 SER cc_start: 0.8719 (t) cc_final: 0.8234 (p) REVERT: W 198 LYS cc_start: 0.8268 (mmmt) cc_final: 0.7976 (tppt) REVERT: W 229 LEU cc_start: 0.8552 (tp) cc_final: 0.8320 (tp) REVERT: W 231 LYS cc_start: 0.8462 (mttm) cc_final: 0.8216 (mmmm) REVERT: W 261 ASP cc_start: 0.8142 (t0) cc_final: 0.7315 (t0) REVERT: W 264 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6561 (mt-10) REVERT: W 271 ASP cc_start: 0.7934 (m-30) cc_final: 0.7697 (m-30) REVERT: W 275 THR cc_start: 0.8839 (t) cc_final: 0.8638 (p) REVERT: W 281 LYS cc_start: 0.8763 (tttm) cc_final: 0.8392 (tppt) REVERT: W 306 PHE cc_start: 0.8440 (m-80) cc_final: 0.8108 (m-80) REVERT: W 310 ASN cc_start: 0.8097 (m-40) cc_final: 0.7866 (m-40) REVERT: W 365 LYS cc_start: 0.8966 (tmmt) cc_final: 0.8685 (tmmt) REVERT: W 367 ILE cc_start: 0.8637 (mt) cc_final: 0.8247 (tt) REVERT: W 375 GLU cc_start: 0.8250 (tp30) cc_final: 0.7924 (tp30) REVERT: W 376 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: W 386 LEU cc_start: 0.8498 (tp) cc_final: 0.8254 (tt) REVERT: W 388 THR cc_start: 0.8640 (p) cc_final: 0.8435 (t) REVERT: W 393 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7963 (mm-30) REVERT: W 424 LYS cc_start: 0.8625 (ptpt) cc_final: 0.8362 (ptpt) REVERT: W 438 LYS cc_start: 0.9036 (pttt) cc_final: 0.8740 (pttt) REVERT: X 95 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8297 (mm-30) REVERT: X 99 LYS cc_start: 0.7642 (pttm) cc_final: 0.6989 (mtmm) REVERT: X 106 VAL cc_start: 0.8246 (OUTLIER) cc_final: 0.7952 (p) REVERT: X 123 GLU cc_start: 0.8310 (pt0) cc_final: 0.7923 (tt0) REVERT: X 186 TYR cc_start: 0.8502 (t80) cc_final: 0.8219 (t80) REVERT: X 189 ILE cc_start: 0.9237 (mm) cc_final: 0.8927 (mt) REVERT: X 198 ASP cc_start: 0.7407 (m-30) cc_final: 0.6228 (m-30) REVERT: X 211 ARG cc_start: 0.8164 (ttt-90) cc_final: 0.7494 (ttt-90) REVERT: X 239 LYS cc_start: 0.8491 (ptpt) cc_final: 0.8056 (ptpp) REVERT: X 245 GLN cc_start: 0.8132 (tp40) cc_final: 0.7815 (tp40) REVERT: X 251 ASP cc_start: 0.7968 (m-30) cc_final: 0.7590 (m-30) REVERT: X 258 ARG cc_start: 0.7265 (mmm160) cc_final: 0.6902 (mmm160) REVERT: X 263 GLN cc_start: 0.7252 (tm-30) cc_final: 0.6610 (tm-30) REVERT: X 272 LEU cc_start: 0.8831 (tt) cc_final: 0.8595 (tp) REVERT: X 274 LYS cc_start: 0.8005 (tmmt) cc_final: 0.7738 (ttmt) REVERT: X 277 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8514 (mtmt) REVERT: X 290 LYS cc_start: 0.8536 (tppt) cc_final: 0.7925 (tppt) REVERT: X 313 VAL cc_start: 0.8072 (OUTLIER) cc_final: 0.7536 (t) REVERT: X 325 ASN cc_start: 0.8690 (m-40) cc_final: 0.8254 (m-40) REVERT: X 328 LEU cc_start: 0.8768 (mt) cc_final: 0.8508 (mm) REVERT: X 362 ASP cc_start: 0.7593 (p0) cc_final: 0.7319 (p0) REVERT: X 378 ASP cc_start: 0.7757 (p0) cc_final: 0.7412 (t0) REVERT: X 385 GLU cc_start: 0.8363 (pp20) cc_final: 0.8034 (pp20) REVERT: X 391 GLU cc_start: 0.8485 (tt0) cc_final: 0.8015 (tp30) REVERT: X 401 ASP cc_start: 0.8399 (m-30) cc_final: 0.8089 (m-30) REVERT: X 406 MET cc_start: 0.8177 (mtp) cc_final: 0.7954 (mtp) REVERT: X 409 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7826 (mm-30) REVERT: X 410 THR cc_start: 0.8165 (p) cc_final: 0.7788 (t) REVERT: X 431 ARG cc_start: 0.7648 (ttp-110) cc_final: 0.7303 (ttp-110) REVERT: X 443 LYS cc_start: 0.8492 (tmmt) cc_final: 0.8203 (ttmm) REVERT: X 448 ASP cc_start: 0.8037 (t0) cc_final: 0.7241 (t0) REVERT: X 454 LYS cc_start: 0.8468 (tmmt) cc_final: 0.8057 (tmmt) REVERT: Y 59 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8305 (tptp) REVERT: Y 113 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7917 (mtmm) REVERT: Y 130 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7601 (mtmm) REVERT: Y 136 ILE cc_start: 0.8560 (mt) cc_final: 0.8005 (tp) REVERT: Y 161 LYS cc_start: 0.8577 (pttt) cc_final: 0.8092 (pttm) REVERT: Y 162 THR cc_start: 0.8583 (p) cc_final: 0.8165 (t) REVERT: Y 164 ASP cc_start: 0.8187 (m-30) cc_final: 0.7928 (m-30) REVERT: Y 166 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6440 (tm-30) REVERT: Y 171 LEU cc_start: 0.8416 (mp) cc_final: 0.8201 (mm) REVERT: Y 174 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8413 (mmtm) REVERT: Y 175 MET cc_start: 0.8849 (tpp) cc_final: 0.8281 (tpp) REVERT: Y 185 LEU cc_start: 0.8277 (mt) cc_final: 0.8057 (mt) REVERT: Y 188 ASP cc_start: 0.7824 (m-30) cc_final: 0.7534 (m-30) REVERT: Y 192 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8644 (mm) REVERT: Y 208 ARG cc_start: 0.8027 (mmm-85) cc_final: 0.7428 (mmm-85) REVERT: Y 229 LEU cc_start: 0.8526 (tp) cc_final: 0.8160 (tp) REVERT: Y 266 ARG cc_start: 0.7800 (mtm110) cc_final: 0.7506 (mtm110) REVERT: Y 271 ASP cc_start: 0.8340 (t0) cc_final: 0.8000 (t0) REVERT: Y 272 GLN cc_start: 0.8494 (mt0) cc_final: 0.8266 (tt0) REVERT: Y 274 ASN cc_start: 0.8719 (m-40) cc_final: 0.8305 (m-40) REVERT: Y 277 VAL cc_start: 0.8682 (t) cc_final: 0.8421 (p) REVERT: Y 310 ASN cc_start: 0.8075 (m-40) cc_final: 0.7651 (m-40) REVERT: Y 315 ASP cc_start: 0.8209 (t0) cc_final: 0.7884 (t70) REVERT: Y 322 MET cc_start: 0.8439 (mtp) cc_final: 0.8213 (mtm) REVERT: Y 339 SER cc_start: 0.8793 (t) cc_final: 0.8364 (p) REVERT: Y 370 ILE cc_start: 0.9039 (mt) cc_final: 0.8787 (mt) REVERT: Y 384 LEU cc_start: 0.9005 (tp) cc_final: 0.8701 (tt) REVERT: Y 389 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8361 (mmmm) REVERT: Y 393 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8056 (mt-10) REVERT: Y 412 LYS cc_start: 0.9156 (tptm) cc_final: 0.8792 (tptm) REVERT: Y 422 ASP cc_start: 0.7971 (m-30) cc_final: 0.7578 (t0) REVERT: Y 424 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8349 (mtmm) REVERT: Y 427 TYR cc_start: 0.8310 (t80) cc_final: 0.7583 (t80) REVERT: Y 441 GLN cc_start: 0.8502 (mm110) cc_final: 0.8137 (mt0) REVERT: Y 444 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7067 (tm-30) REVERT: Y 456 ILE cc_start: 0.8818 (mt) cc_final: 0.8381 (mt) REVERT: Z 310 ARG cc_start: 0.8236 (mtt-85) cc_final: 0.7584 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7702 (ttm110) cc_final: 0.7369 (ttm110) outliers start: 159 outliers final: 92 residues processed: 1224 average time/residue: 0.4563 time to fit residues: 846.9358 Evaluate side-chains 1217 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 1100 time to evaluate : 2.964 ------------------------------------------------------------------------------- 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 1125 CYS Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1265 VAL 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 R residue 22 ARG Chi-restraints excluded: chain R residue 58 THR Chi-restraints excluded: chain R residue 67 LEU 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 227 MET Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 263 LYS 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 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 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 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 436 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 109 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 405 VAL Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain U residue 442 GLU 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 265 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 335 VAL Chi-restraints excluded: chain V residue 441 GLU 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 141 VAL Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 235 VAL Chi-restraints excluded: chain W residue 336 ASN Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 364 ILE 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 51 GLN Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 68 LYS Chi-restraints excluded: chain X residue 106 VAL 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 178 THR Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 265 VAL Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 332 ILE 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 430 ASN Chi-restraints excluded: chain X residue 445 LEU Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 61 VAL 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 128 LYS Chi-restraints excluded: chain Y residue 167 THR Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 192 ILE Chi-restraints excluded: chain Y residue 323 MET Chi-restraints excluded: chain Y residue 368 LEU Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 402 LEU Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 445 SER Chi-restraints excluded: chain Z residue 305 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 241 optimal weight: 4.9990 chunk 273 optimal weight: 0.0070 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 325 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 298 optimal weight: 0.5980 chunk 213 optimal weight: 3.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN Q1228 HIS ** 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 175 ASN R 635 GLN T 27 HIS T 29 HIS U 49 GLN U 451 GLN V 341 ASN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 HIS X 417 GLN ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 401 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.127938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.109101 restraints weight = 56900.976| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.30 r_work: 0.3344 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29139 Z= 0.140 Angle : 0.645 16.280 39425 Z= 0.319 Chirality : 0.045 0.191 4626 Planarity : 0.005 0.058 5049 Dihedral : 7.540 153.454 4012 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.56 % Allowed : 26.14 % Favored : 69.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.14), residues: 3626 helix: 0.91 (0.13), residues: 1533 sheet: -0.08 (0.21), residues: 589 loop : -0.67 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q1361 HIS 0.007 0.001 HIS R 613 PHE 0.024 0.001 PHE Y 254 TYR 0.025 0.002 TYR Q1198 ARG 0.010 0.001 ARG U 69 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 1098) hydrogen bonds : angle 4.46735 ( 3198) covalent geometry : bond 0.00309 (29139) covalent geometry : angle 0.64531 (39425) *********************** 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 1269 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1125 time to evaluate : 3.275 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 960 GLN cc_start: 0.8283 (mm110) cc_final: 0.8044 (mm110) REVERT: Q 1005 MET cc_start: 0.6765 (mmp) cc_final: 0.6015 (mmp) REVERT: Q 1023 ASP cc_start: 0.7707 (t0) cc_final: 0.7241 (t0) REVERT: Q 1027 SER cc_start: 0.8732 (m) cc_final: 0.8185 (p) REVERT: Q 1102 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8056 (m) REVERT: Q 1112 LYS cc_start: 0.8809 (mttp) cc_final: 0.8299 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8193 (t) REVERT: Q 1150 LYS cc_start: 0.8572 (tttm) cc_final: 0.7654 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6721 (mp0) REVERT: Q 1173 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7291 (mp0) REVERT: Q 1186 VAL cc_start: 0.8995 (p) cc_final: 0.8693 (t) REVERT: Q 1195 LYS cc_start: 0.8213 (tppt) cc_final: 0.7444 (tppt) REVERT: Q 1204 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7191 (p0) REVERT: Q 1208 ARG cc_start: 0.8724 (ttm170) cc_final: 0.7716 (mtp180) REVERT: Q 1230 THR cc_start: 0.8762 (m) cc_final: 0.8342 (p) REVERT: Q 1234 ASN cc_start: 0.8498 (m-40) cc_final: 0.8228 (m-40) REVERT: Q 1241 LEU cc_start: 0.9206 (tp) cc_final: 0.8994 (tp) REVERT: Q 1248 ASP cc_start: 0.7464 (t70) cc_final: 0.6977 (t0) REVERT: Q 1267 ASP cc_start: 0.8539 (m-30) cc_final: 0.8221 (m-30) REVERT: Q 1293 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.6779 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8340 (mt) cc_final: 0.8014 (mm) REVERT: Q 1302 ARG cc_start: 0.8039 (ttt180) cc_final: 0.7578 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8609 (m-30) cc_final: 0.8305 (m-30) REVERT: Q 1331 MET cc_start: 0.7874 (tpp) cc_final: 0.7228 (tpp) REVERT: Q 1334 TYR cc_start: 0.7899 (p90) cc_final: 0.7174 (p90) REVERT: Q 1335 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7644 (mp) REVERT: R 35 ASN cc_start: 0.8805 (t0) cc_final: 0.8422 (t0) REVERT: R 55 ASN cc_start: 0.8460 (p0) cc_final: 0.8097 (p0) REVERT: R 70 PHE cc_start: 0.7605 (t80) cc_final: 0.7335 (t80) REVERT: R 156 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7709 (pm20) REVERT: R 183 THR cc_start: 0.7338 (m) cc_final: 0.6774 (t) REVERT: R 211 ARG cc_start: 0.7567 (ttp-110) cc_final: 0.7318 (ttp80) REVERT: R 214 TRP cc_start: 0.7520 (t-100) cc_final: 0.6722 (t-100) REVERT: R 227 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7916 (mmp) REVERT: R 230 LYS cc_start: 0.8836 (tttt) cc_final: 0.8330 (tttt) REVERT: R 238 MET cc_start: 0.7251 (tpp) cc_final: 0.6822 (tpp) REVERT: R 244 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: R 251 CYS cc_start: 0.7284 (OUTLIER) cc_final: 0.6830 (m) REVERT: R 257 TYR cc_start: 0.7933 (t80) cc_final: 0.7552 (t80) REVERT: R 262 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8020 (mm-30) REVERT: R 592 HIS cc_start: 0.8131 (t-90) cc_final: 0.7491 (t-90) REVERT: R 593 LEU cc_start: 0.8730 (mm) cc_final: 0.8437 (mm) REVERT: R 599 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.8050 (tpp-160) REVERT: R 609 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7340 (mp10) REVERT: R 612 MET cc_start: 0.6857 (tpp) cc_final: 0.6201 (tpp) REVERT: R 640 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: R 643 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7481 (mm-30) REVERT: R 647 LEU cc_start: 0.8389 (mp) cc_final: 0.8012 (mp) REVERT: R 659 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8109 (tp-100) REVERT: R 663 ASP cc_start: 0.8193 (m-30) cc_final: 0.7759 (m-30) REVERT: R 664 MET cc_start: 0.8764 (mtm) cc_final: 0.8480 (mtp) REVERT: R 681 LYS cc_start: 0.8961 (tttt) cc_final: 0.8732 (tptt) REVERT: R 721 GLU cc_start: 0.8035 (tp30) cc_final: 0.7468 (tp30) REVERT: R 722 GLU cc_start: 0.8130 (pp20) cc_final: 0.7478 (pp20) REVERT: R 723 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7301 (mm-40) REVERT: R 724 TYR cc_start: 0.8185 (t80) cc_final: 0.7558 (t80) REVERT: R 726 LYS cc_start: 0.8475 (tptp) cc_final: 0.8117 (tptp) REVERT: R 728 VAL cc_start: 0.8871 (OUTLIER) cc_final: 0.8592 (m) REVERT: R 729 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6493 (tp) REVERT: R 743 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.7002 (mtmm) REVERT: S 34 ARG cc_start: 0.8462 (ptt90) cc_final: 0.8243 (ptt90) REVERT: S 100 TYR cc_start: 0.7898 (t80) cc_final: 0.7576 (t80) REVERT: S 110 ARG cc_start: 0.8139 (ptt180) cc_final: 0.7893 (mtm-85) REVERT: S 122 LYS cc_start: 0.8409 (mmmm) cc_final: 0.7913 (mtpp) REVERT: S 140 TYR cc_start: 0.8568 (t80) cc_final: 0.8109 (t80) REVERT: S 145 LYS cc_start: 0.8676 (tppp) cc_final: 0.8269 (tppp) REVERT: T 49 VAL cc_start: 0.8455 (p) cc_final: 0.8082 (m) REVERT: T 56 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7735 (mm-30) REVERT: T 95 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8300 (mm-30) REVERT: T 177 LYS cc_start: 0.8492 (tttt) cc_final: 0.8109 (mtpp) REVERT: T 178 THR cc_start: 0.8961 (m) cc_final: 0.8655 (t) REVERT: T 193 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8025 (mmmt) REVERT: T 229 TYR cc_start: 0.8565 (m-80) cc_final: 0.7705 (m-80) REVERT: T 251 ASP cc_start: 0.8138 (m-30) cc_final: 0.7827 (m-30) REVERT: T 273 LEU cc_start: 0.7711 (tp) cc_final: 0.7449 (tt) REVERT: T 279 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: T 295 TYR cc_start: 0.8614 (m-80) cc_final: 0.8105 (m-80) REVERT: T 319 GLU cc_start: 0.8184 (mp0) cc_final: 0.7978 (mm-30) REVERT: T 371 ARG cc_start: 0.8023 (mtp-110) cc_final: 0.7698 (ptm160) REVERT: T 381 ARG cc_start: 0.8722 (ttt-90) cc_final: 0.8208 (ttm-80) REVERT: T 382 THR cc_start: 0.8605 (p) cc_final: 0.8376 (m) REVERT: T 385 GLU cc_start: 0.8530 (pt0) cc_final: 0.7826 (pp20) REVERT: T 401 ASP cc_start: 0.8514 (m-30) cc_final: 0.7672 (m-30) REVERT: T 417 GLN cc_start: 0.8250 (mt0) cc_final: 0.7839 (mt0) REVERT: T 424 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8043 (mt) REVERT: T 431 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7214 (mtm180) REVERT: T 439 VAL cc_start: 0.8820 (t) cc_final: 0.8597 (t) REVERT: T 448 ASP cc_start: 0.7618 (p0) cc_final: 0.7229 (p0) REVERT: T 456 LEU cc_start: 0.8902 (tp) cc_final: 0.8308 (mt) REVERT: T 457 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8129 (mm-30) REVERT: U 38 ARG cc_start: 0.8173 (mtt90) cc_final: 0.7518 (mtt90) REVERT: U 45 VAL cc_start: 0.7987 (OUTLIER) cc_final: 0.7749 (p) REVERT: U 86 MET cc_start: 0.8022 (mmm) cc_final: 0.7540 (mmm) REVERT: U 94 LYS cc_start: 0.8781 (tppt) cc_final: 0.8360 (tptp) REVERT: U 104 SER cc_start: 0.8550 (m) cc_final: 0.8235 (t) REVERT: U 105 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7115 (mt-10) REVERT: U 110 GLU cc_start: 0.7953 (pp20) cc_final: 0.7621 (pp20) REVERT: U 123 LYS cc_start: 0.8280 (mttt) cc_final: 0.7959 (mttp) REVERT: U 128 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8470 (ttmm) REVERT: U 139 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6338 (tp30) REVERT: U 161 LYS cc_start: 0.8587 (ptmm) cc_final: 0.8120 (ptmm) REVERT: U 166 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: U 193 ASP cc_start: 0.7994 (t0) cc_final: 0.7498 (t70) REVERT: U 194 LYS cc_start: 0.8616 (ttpp) cc_final: 0.8132 (ttpt) REVERT: U 198 LYS cc_start: 0.8550 (tttm) cc_final: 0.8223 (tttm) REVERT: U 221 PHE cc_start: 0.7454 (m-80) cc_final: 0.7238 (m-80) REVERT: U 245 ASP cc_start: 0.8070 (m-30) cc_final: 0.7805 (m-30) REVERT: U 270 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7587 (mtt180) REVERT: U 272 GLN cc_start: 0.7971 (tp40) cc_final: 0.7456 (tp40) REVERT: U 276 LYS cc_start: 0.8938 (tptt) cc_final: 0.8470 (tptm) REVERT: U 281 LYS cc_start: 0.8929 (tttm) cc_final: 0.8515 (ttmm) REVERT: U 306 PHE cc_start: 0.8364 (m-10) cc_final: 0.8138 (m-10) REVERT: U 311 ARG cc_start: 0.8095 (mpt180) cc_final: 0.7832 (mpt180) REVERT: U 313 LEU cc_start: 0.8823 (mt) cc_final: 0.8604 (mp) REVERT: U 321 VAL cc_start: 0.8817 (t) cc_final: 0.8570 (p) REVERT: U 338 LYS cc_start: 0.8902 (mttt) cc_final: 0.8668 (ttmm) REVERT: U 339 SER cc_start: 0.8869 (m) cc_final: 0.8562 (t) REVERT: U 349 ASP cc_start: 0.8674 (t0) cc_final: 0.8246 (m-30) REVERT: U 365 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8491 (ttmt) REVERT: U 376 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7990 (mm-30) REVERT: U 378 GLU cc_start: 0.7419 (mp0) cc_final: 0.7140 (mp0) REVERT: U 393 GLU cc_start: 0.7594 (pp20) cc_final: 0.7306 (pp20) REVERT: U 399 SER cc_start: 0.8389 (m) cc_final: 0.8113 (p) REVERT: U 400 SER cc_start: 0.8299 (t) cc_final: 0.7863 (m) REVERT: U 409 ILE cc_start: 0.8882 (tp) cc_final: 0.8542 (tp) REVERT: U 411 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7119 (mpt) REVERT: U 412 LYS cc_start: 0.8792 (tppt) cc_final: 0.8584 (tppt) REVERT: U 419 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6926 (mm-30) REVERT: U 428 LEU cc_start: 0.8701 (mt) cc_final: 0.8409 (pp) REVERT: U 432 ASP cc_start: 0.7920 (p0) cc_final: 0.7719 (p0) REVERT: U 444 GLU cc_start: 0.8178 (tp30) cc_final: 0.7587 (tp30) REVERT: V 30 ILE cc_start: 0.8496 (mt) cc_final: 0.8147 (mm) REVERT: V 31 LYS cc_start: 0.8096 (mmpt) cc_final: 0.7643 (mmtm) REVERT: V 35 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7908 (mp) REVERT: V 52 ILE cc_start: 0.8608 (mp) cc_final: 0.8326 (mm) REVERT: V 56 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7377 (mm-30) REVERT: V 95 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7708 (mt-10) REVERT: V 99 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8319 (mtpp) REVERT: V 114 GLU cc_start: 0.7952 (mt-10) cc_final: 0.6913 (mt-10) REVERT: V 132 ARG cc_start: 0.8347 (tpp80) cc_final: 0.8131 (ttp80) REVERT: V 144 VAL cc_start: 0.8415 (t) cc_final: 0.8030 (m) REVERT: V 180 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7600 (tpt-90) REVERT: V 187 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7653 (mt-10) REVERT: V 194 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.7904 (t) REVERT: V 203 GLU cc_start: 0.7983 (tt0) cc_final: 0.7719 (tt0) REVERT: V 218 TYR cc_start: 0.8684 (m-80) cc_final: 0.8249 (m-80) REVERT: V 222 PHE cc_start: 0.8338 (m-80) cc_final: 0.8097 (m-10) REVERT: V 239 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8024 (mttt) REVERT: V 254 VAL cc_start: 0.8688 (t) cc_final: 0.8402 (m) REVERT: V 263 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8387 (mm-40) REVERT: V 268 MET cc_start: 0.7822 (mmm) cc_final: 0.7518 (mmm) REVERT: V 302 GLU cc_start: 0.8114 (pt0) cc_final: 0.7503 (pm20) REVERT: V 312 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7881 (mm-30) REVERT: V 318 ILE cc_start: 0.8658 (tp) cc_final: 0.8415 (tt) REVERT: V 325 ASN cc_start: 0.8393 (t0) cc_final: 0.7616 (t0) REVERT: V 329 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7062 (mm-30) REVERT: V 344 MET cc_start: 0.8782 (mmt) cc_final: 0.8526 (mmm) REVERT: V 365 ASP cc_start: 0.7867 (m-30) cc_final: 0.7422 (t70) REVERT: V 367 LEU cc_start: 0.8384 (mt) cc_final: 0.8124 (mm) REVERT: V 379 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8136 (mt-10) REVERT: V 403 LEU cc_start: 0.8743 (mt) cc_final: 0.8407 (mm) REVERT: V 406 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7588 (tmm) REVERT: V 427 GLN cc_start: 0.8039 (pt0) cc_final: 0.7820 (pt0) REVERT: V 440 ASN cc_start: 0.7725 (m-40) cc_final: 0.7403 (m-40) REVERT: V 443 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8255 (mtmm) REVERT: V 450 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7500 (ptpt) REVERT: V 453 THR cc_start: 0.8680 (m) cc_final: 0.8407 (p) REVERT: V 454 LYS cc_start: 0.8849 (mptt) cc_final: 0.8437 (mmtt) REVERT: W 45 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8336 (p) REVERT: W 66 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8477 (mm) REVERT: W 86 MET cc_start: 0.7768 (mmm) cc_final: 0.7431 (mmm) REVERT: W 142 GLU cc_start: 0.7689 (pp20) cc_final: 0.7264 (pp20) REVERT: W 157 LYS cc_start: 0.8333 (mttm) cc_final: 0.8036 (mttp) REVERT: W 159 THR cc_start: 0.8301 (m) cc_final: 0.7441 (p) REVERT: W 185 LEU cc_start: 0.8123 (mt) cc_final: 0.7686 (mt) REVERT: W 188 ASP cc_start: 0.7628 (m-30) cc_final: 0.7089 (m-30) REVERT: W 191 SER cc_start: 0.8706 (t) cc_final: 0.7957 (m) REVERT: W 198 LYS cc_start: 0.8301 (mmmt) cc_final: 0.7994 (tppt) REVERT: W 200 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.7694 (p) REVERT: W 229 LEU cc_start: 0.8514 (tp) cc_final: 0.8241 (tp) REVERT: W 231 LYS cc_start: 0.8459 (mttm) cc_final: 0.8217 (mmmm) REVERT: W 243 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7587 (mt-10) REVERT: W 246 VAL cc_start: 0.8505 (p) cc_final: 0.8214 (m) REVERT: W 264 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6623 (mt-10) REVERT: W 271 ASP cc_start: 0.7913 (m-30) cc_final: 0.7658 (m-30) REVERT: W 273 ILE cc_start: 0.8814 (tp) cc_final: 0.8610 (tp) REVERT: W 281 LYS cc_start: 0.8721 (tttm) cc_final: 0.8340 (tppt) REVERT: W 306 PHE cc_start: 0.8449 (m-80) cc_final: 0.8099 (m-80) REVERT: W 310 ASN cc_start: 0.8119 (m-40) cc_final: 0.7862 (m-40) REVERT: W 365 LYS cc_start: 0.8952 (tmmt) cc_final: 0.8701 (tmmt) REVERT: W 367 ILE cc_start: 0.8605 (mt) cc_final: 0.8245 (tt) REVERT: W 375 GLU cc_start: 0.8304 (tp30) cc_final: 0.7919 (tp30) REVERT: W 376 GLU cc_start: 0.7936 (tp30) cc_final: 0.7624 (tp30) REVERT: W 386 LEU cc_start: 0.8501 (tp) cc_final: 0.8249 (tt) REVERT: W 389 LYS cc_start: 0.8786 (tppt) cc_final: 0.7719 (tppt) REVERT: W 393 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7925 (mm-30) REVERT: W 424 LYS cc_start: 0.8632 (ptpt) cc_final: 0.8356 (ptpt) REVERT: W 438 LYS cc_start: 0.9039 (pttt) cc_final: 0.8706 (pttt) REVERT: X 33 LEU cc_start: 0.8737 (mt) cc_final: 0.7829 (mm) REVERT: X 95 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8209 (mt-10) REVERT: X 99 LYS cc_start: 0.7615 (pttm) cc_final: 0.7342 (mtmm) REVERT: X 123 GLU cc_start: 0.8261 (pt0) cc_final: 0.7817 (tt0) REVERT: X 125 PHE cc_start: 0.8226 (OUTLIER) cc_final: 0.7888 (t80) REVERT: X 186 TYR cc_start: 0.8511 (t80) cc_final: 0.8226 (t80) REVERT: X 189 ILE cc_start: 0.9169 (mm) cc_final: 0.8897 (mt) REVERT: X 198 ASP cc_start: 0.7502 (m-30) cc_final: 0.5019 (m-30) REVERT: X 211 ARG cc_start: 0.8120 (ttt-90) cc_final: 0.7461 (ptm160) REVERT: X 239 LYS cc_start: 0.8463 (ptpt) cc_final: 0.8023 (ptpp) REVERT: X 245 GLN cc_start: 0.8098 (tp40) cc_final: 0.7776 (tp40) REVERT: X 251 ASP cc_start: 0.7995 (m-30) cc_final: 0.7618 (m-30) REVERT: X 263 GLN cc_start: 0.7280 (tm-30) cc_final: 0.6643 (tm-30) REVERT: X 272 LEU cc_start: 0.8826 (tt) cc_final: 0.8540 (tp) REVERT: X 274 LYS cc_start: 0.7971 (tmmt) cc_final: 0.7712 (ttmt) REVERT: X 277 LYS cc_start: 0.8728 (ttmm) cc_final: 0.8489 (mtmt) REVERT: X 282 GLU cc_start: 0.7859 (tp30) cc_final: 0.7189 (tp30) REVERT: X 290 LYS cc_start: 0.8544 (tppt) cc_final: 0.7890 (tppt) REVERT: X 312 GLU cc_start: 0.7749 (mp0) cc_final: 0.7344 (mp0) REVERT: X 313 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7605 (t) REVERT: X 325 ASN cc_start: 0.8642 (m-40) cc_final: 0.8361 (m-40) REVERT: X 328 LEU cc_start: 0.8775 (mt) cc_final: 0.8493 (mm) REVERT: X 378 ASP cc_start: 0.7755 (p0) cc_final: 0.7377 (t0) REVERT: X 385 GLU cc_start: 0.8323 (pp20) cc_final: 0.7988 (pp20) REVERT: X 391 GLU cc_start: 0.8520 (tt0) cc_final: 0.8074 (tp30) REVERT: X 401 ASP cc_start: 0.8324 (m-30) cc_final: 0.8021 (m-30) REVERT: X 406 MET cc_start: 0.8194 (mtp) cc_final: 0.7981 (mtp) REVERT: X 409 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7856 (mm-30) REVERT: X 410 THR cc_start: 0.8099 (p) cc_final: 0.7727 (t) REVERT: X 431 ARG cc_start: 0.7645 (ttp-110) cc_final: 0.7161 (ttp-110) REVERT: X 443 LYS cc_start: 0.8416 (tmmt) cc_final: 0.8093 (ttmm) REVERT: X 448 ASP cc_start: 0.8042 (t0) cc_final: 0.7209 (t0) REVERT: X 454 LYS cc_start: 0.8394 (tmmt) cc_final: 0.7997 (tmmt) REVERT: Y 59 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8258 (tptp) REVERT: Y 106 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8490 (tt) REVERT: Y 111 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7587 (tp) REVERT: Y 130 LYS cc_start: 0.7800 (ttmm) cc_final: 0.7581 (mtmm) REVERT: Y 136 ILE cc_start: 0.8542 (mt) cc_final: 0.7989 (tp) REVERT: Y 161 LYS cc_start: 0.8522 (pttt) cc_final: 0.8260 (pttm) REVERT: Y 162 THR cc_start: 0.8554 (p) cc_final: 0.8115 (t) REVERT: Y 164 ASP cc_start: 0.8197 (m-30) cc_final: 0.7948 (m-30) REVERT: Y 171 LEU cc_start: 0.8420 (mp) cc_final: 0.8203 (mm) REVERT: Y 173 ASN cc_start: 0.8077 (p0) cc_final: 0.6958 (m-40) REVERT: Y 174 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8308 (mmtm) REVERT: Y 175 MET cc_start: 0.8852 (tpp) cc_final: 0.8279 (tpp) REVERT: Y 192 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8702 (mm) REVERT: Y 229 LEU cc_start: 0.8522 (tp) cc_final: 0.8315 (tp) REVERT: Y 231 LYS cc_start: 0.8741 (mttp) cc_final: 0.8532 (mttp) REVERT: Y 266 ARG cc_start: 0.7852 (mtm110) cc_final: 0.7618 (mtm110) REVERT: Y 271 ASP cc_start: 0.8390 (t0) cc_final: 0.8009 (t0) REVERT: Y 272 GLN cc_start: 0.8460 (mt0) cc_final: 0.8246 (tt0) REVERT: Y 274 ASN cc_start: 0.8719 (m-40) cc_final: 0.8305 (m-40) REVERT: Y 277 VAL cc_start: 0.8672 (t) cc_final: 0.8404 (p) REVERT: Y 310 ASN cc_start: 0.8020 (m-40) cc_final: 0.7627 (m-40) REVERT: Y 315 ASP cc_start: 0.8181 (t0) cc_final: 0.7831 (t70) REVERT: Y 322 MET cc_start: 0.8423 (mtp) cc_final: 0.8205 (mtm) REVERT: Y 339 SER cc_start: 0.8808 (t) cc_final: 0.8380 (p) REVERT: Y 370 ILE cc_start: 0.9027 (mt) cc_final: 0.8776 (mt) REVERT: Y 374 GLU cc_start: 0.7929 (tp30) cc_final: 0.7645 (mm-30) REVERT: Y 375 GLU cc_start: 0.7855 (tt0) cc_final: 0.7255 (tm-30) REVERT: Y 384 LEU cc_start: 0.8995 (tp) cc_final: 0.8717 (tt) REVERT: Y 389 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8337 (mmmm) REVERT: Y 393 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8090 (mt-10) REVERT: Y 412 LYS cc_start: 0.9123 (tptm) cc_final: 0.8782 (tptm) REVERT: Y 424 LYS cc_start: 0.8560 (mtmm) cc_final: 0.8333 (mtmm) REVERT: Y 427 TYR cc_start: 0.8280 (t80) cc_final: 0.7587 (t80) REVERT: Y 441 GLN cc_start: 0.8488 (mm110) cc_final: 0.8091 (mt0) REVERT: Y 444 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7225 (tm-30) REVERT: Y 456 ILE cc_start: 0.8837 (mt) cc_final: 0.8458 (mt) REVERT: Z 310 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7502 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7705 (ttm110) cc_final: 0.7450 (ttm110) outliers start: 144 outliers final: 79 residues processed: 1190 average time/residue: 0.5286 time to fit residues: 959.7893 Evaluate side-chains 1216 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1103 time to evaluate : 3.607 ------------------------------------------------------------------------------- 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 1125 CYS Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1204 ASN Chi-restraints excluded: chain Q residue 1265 VAL 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 R residue 22 ARG Chi-restraints excluded: chain R residue 58 THR 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 186 VAL Chi-restraints excluded: chain R residue 212 ILE Chi-restraints excluded: chain R residue 227 MET Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 263 LYS 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 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 94 LEU Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 139 VAL 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 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 406 MET Chi-restraints excluded: chain T residue 424 ILE Chi-restraints excluded: chain T residue 436 VAL 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 166 GLU Chi-restraints excluded: chain U residue 233 LYS Chi-restraints excluded: chain U residue 331 LYS Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 117 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 329 GLU Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 335 VAL 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 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 105 GLU Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 364 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 68 LYS 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 171 LYS Chi-restraints excluded: chain X residue 265 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 345 THR Chi-restraints excluded: chain X residue 412 LEU Chi-restraints excluded: chain X residue 416 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 106 ILE Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 167 THR Chi-restraints excluded: chain Y residue 192 ILE Chi-restraints excluded: chain Y residue 368 LEU Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 401 ASN Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Z residue 302 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 225 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 285 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 195 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 257 optimal weight: 0.4980 chunk 179 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN Q1228 HIS ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 609 GLN T 27 HIS T 29 HIS V 341 ASN W 144 GLN W 248 ASN W 373 GLN W 446 GLN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 HIS X 394 GLN ** Y 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.126766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107929 restraints weight = 56761.585| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 3.27 r_work: 0.3328 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29139 Z= 0.182 Angle : 0.675 16.039 39425 Z= 0.335 Chirality : 0.046 0.183 4626 Planarity : 0.005 0.058 5049 Dihedral : 7.405 136.587 4012 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.87 % Allowed : 26.11 % Favored : 69.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3626 helix: 0.89 (0.13), residues: 1535 sheet: -0.11 (0.21), residues: 586 loop : -0.71 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q1361 HIS 0.007 0.001 HIS R 121 PHE 0.032 0.002 PHE U 254 TYR 0.025 0.002 TYR Q1198 ARG 0.021 0.001 ARG X 258 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 1098) hydrogen bonds : angle 4.54516 ( 3198) covalent geometry : bond 0.00389 (29139) covalent geometry : angle 0.67462 (39425) *********************** 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 1286 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1132 time to evaluate : 2.976 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 960 GLN cc_start: 0.8373 (mm110) cc_final: 0.8159 (mm110) REVERT: Q 1005 MET cc_start: 0.6801 (mmp) cc_final: 0.6075 (mmp) REVERT: Q 1023 ASP cc_start: 0.7761 (t0) cc_final: 0.7292 (t0) REVERT: Q 1027 SER cc_start: 0.8745 (m) cc_final: 0.8207 (p) REVERT: Q 1087 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8265 (ttm-80) REVERT: Q 1102 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.8091 (m) REVERT: Q 1112 LYS cc_start: 0.8802 (mttp) cc_final: 0.8291 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8194 (t) REVERT: Q 1150 LYS cc_start: 0.8576 (tttm) cc_final: 0.7688 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: Q 1173 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7374 (mp0) REVERT: Q 1195 LYS cc_start: 0.8243 (tppt) cc_final: 0.7480 (tppt) REVERT: Q 1208 ARG cc_start: 0.8723 (ttm170) cc_final: 0.7692 (mtp180) REVERT: Q 1222 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7293 (tm-30) REVERT: Q 1230 THR cc_start: 0.8801 (m) cc_final: 0.8366 (p) REVERT: Q 1234 ASN cc_start: 0.8534 (m-40) cc_final: 0.8288 (m-40) REVERT: Q 1241 LEU cc_start: 0.9240 (tp) cc_final: 0.8956 (tp) REVERT: Q 1248 ASP cc_start: 0.7485 (t70) cc_final: 0.7003 (t0) REVERT: Q 1267 ASP cc_start: 0.8580 (m-30) cc_final: 0.8224 (m-30) REVERT: Q 1295 ILE cc_start: 0.8304 (mt) cc_final: 0.7995 (mm) REVERT: Q 1302 ARG cc_start: 0.8074 (ttt180) cc_final: 0.7577 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8648 (m-30) cc_final: 0.8320 (m-30) REVERT: Q 1331 MET cc_start: 0.7889 (tpp) cc_final: 0.7283 (tpp) REVERT: Q 1334 TYR cc_start: 0.7908 (p90) cc_final: 0.7178 (p90) REVERT: Q 1335 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7693 (mp) REVERT: Q 1421 ARG cc_start: 0.7435 (mtt90) cc_final: 0.6832 (mtt90) REVERT: R 35 ASN cc_start: 0.8830 (t0) cc_final: 0.8571 (m-40) REVERT: R 55 ASN cc_start: 0.8467 (p0) cc_final: 0.8120 (p0) REVERT: R 70 PHE cc_start: 0.7666 (t80) cc_final: 0.7392 (t80) REVERT: R 156 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7740 (pm20) REVERT: R 183 THR cc_start: 0.7366 (m) cc_final: 0.6819 (t) REVERT: R 211 ARG cc_start: 0.7593 (ttp-110) cc_final: 0.7362 (ttp80) REVERT: R 214 TRP cc_start: 0.7502 (t-100) cc_final: 0.6948 (t-100) REVERT: R 230 LYS cc_start: 0.8888 (tttt) cc_final: 0.8653 (tttt) REVERT: R 238 MET cc_start: 0.7344 (tpp) cc_final: 0.6909 (tpp) REVERT: R 251 CYS cc_start: 0.7401 (OUTLIER) cc_final: 0.6990 (m) REVERT: R 592 HIS cc_start: 0.8214 (t-90) cc_final: 0.7488 (t-90) REVERT: R 593 LEU cc_start: 0.8718 (mm) cc_final: 0.8428 (mm) REVERT: R 609 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: R 612 MET cc_start: 0.7109 (tpp) cc_final: 0.6846 (tpp) REVERT: R 640 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7226 (tp30) REVERT: R 643 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7441 (mm-30) REVERT: R 647 LEU cc_start: 0.8457 (mp) cc_final: 0.8081 (mp) REVERT: R 659 GLN cc_start: 0.8482 (tp-100) cc_final: 0.8120 (tp-100) REVERT: R 663 ASP cc_start: 0.8169 (m-30) cc_final: 0.7732 (m-30) REVERT: R 664 MET cc_start: 0.8739 (mtm) cc_final: 0.8459 (mtp) REVERT: R 699 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7686 (p) REVERT: R 721 GLU cc_start: 0.8155 (tp30) cc_final: 0.7631 (tp30) REVERT: R 722 GLU cc_start: 0.8135 (pp20) cc_final: 0.7524 (pp20) REVERT: R 723 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7607 (mm-40) REVERT: R 724 TYR cc_start: 0.8214 (t80) cc_final: 0.7604 (t80) REVERT: R 726 LYS cc_start: 0.8456 (tptp) cc_final: 0.8063 (tptp) REVERT: R 728 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8598 (m) REVERT: R 729 ILE cc_start: 0.6832 (OUTLIER) cc_final: 0.6587 (tp) REVERT: S 32 PHE cc_start: 0.8211 (m-10) cc_final: 0.7983 (m-80) REVERT: S 100 TYR cc_start: 0.7980 (t80) cc_final: 0.7634 (t80) REVERT: S 110 ARG cc_start: 0.8222 (ptt180) cc_final: 0.7643 (mtm180) REVERT: S 122 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8095 (mtpp) REVERT: S 140 TYR cc_start: 0.8601 (t80) cc_final: 0.8142 (t80) REVERT: S 145 LYS cc_start: 0.8713 (tppp) cc_final: 0.8330 (tppp) REVERT: T 49 VAL cc_start: 0.8429 (p) cc_final: 0.8092 (m) REVERT: T 56 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7794 (mm-30) REVERT: T 70 MET cc_start: 0.7414 (mmm) cc_final: 0.6731 (mtm) REVERT: T 95 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8183 (mm-30) REVERT: T 177 LYS cc_start: 0.8514 (tttt) cc_final: 0.8121 (mtpp) REVERT: T 178 THR cc_start: 0.8949 (m) cc_final: 0.8643 (t) REVERT: T 193 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8045 (mmmt) REVERT: T 251 ASP cc_start: 0.8153 (m-30) cc_final: 0.7850 (m-30) REVERT: T 273 LEU cc_start: 0.7764 (tp) cc_final: 0.7514 (tt) REVERT: T 279 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7349 (pt0) REVERT: T 295 TYR cc_start: 0.8601 (m-80) cc_final: 0.8092 (m-80) REVERT: T 319 GLU cc_start: 0.8206 (mp0) cc_final: 0.7999 (mm-30) REVERT: T 371 ARG cc_start: 0.8069 (mtp-110) cc_final: 0.7731 (ptm160) REVERT: T 381 ARG cc_start: 0.8771 (ttt-90) cc_final: 0.8229 (ttm-80) REVERT: T 382 THR cc_start: 0.8641 (p) cc_final: 0.8156 (p) REVERT: T 385 GLU cc_start: 0.8515 (pt0) cc_final: 0.7822 (pp20) REVERT: T 401 ASP cc_start: 0.8488 (m-30) cc_final: 0.7613 (m-30) REVERT: T 409 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7675 (mt-10) REVERT: T 417 GLN cc_start: 0.8180 (mt0) cc_final: 0.7813 (mt0) REVERT: T 431 ARG cc_start: 0.7640 (mtm110) cc_final: 0.7164 (mtm180) REVERT: T 439 VAL cc_start: 0.8876 (t) cc_final: 0.8662 (t) REVERT: T 448 ASP cc_start: 0.7636 (p0) cc_final: 0.7182 (p0) REVERT: T 456 LEU cc_start: 0.8927 (tp) cc_final: 0.8337 (mt) REVERT: T 457 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8190 (mm-30) REVERT: U 45 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7771 (p) REVERT: U 86 MET cc_start: 0.8045 (mmm) cc_final: 0.7577 (mmm) REVERT: U 94 LYS cc_start: 0.8840 (tppt) cc_final: 0.8422 (tptp) REVERT: U 104 SER cc_start: 0.8582 (m) cc_final: 0.8182 (t) REVERT: U 105 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7153 (mt-10) REVERT: U 110 GLU cc_start: 0.7967 (pp20) cc_final: 0.7616 (pp20) REVERT: U 123 LYS cc_start: 0.8280 (mttt) cc_final: 0.7961 (mttp) REVERT: U 128 LYS cc_start: 0.8699 (ttpt) cc_final: 0.8453 (ttmm) REVERT: U 139 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6312 (tp30) REVERT: U 161 LYS cc_start: 0.8617 (ptmm) cc_final: 0.8153 (ptmm) REVERT: U 166 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7106 (tp30) REVERT: U 193 ASP cc_start: 0.7962 (t0) cc_final: 0.7421 (t70) REVERT: U 194 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8185 (ttpt) REVERT: U 198 LYS cc_start: 0.8568 (tttm) cc_final: 0.8245 (tttm) REVERT: U 221 PHE cc_start: 0.7476 (m-80) cc_final: 0.7217 (m-80) REVERT: U 245 ASP cc_start: 0.8093 (m-30) cc_final: 0.7808 (m-30) REVERT: U 265 ILE cc_start: 0.8865 (mp) cc_final: 0.8591 (mm) REVERT: U 270 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7597 (mtt180) REVERT: U 272 GLN cc_start: 0.8017 (tp40) cc_final: 0.7507 (tp40) REVERT: U 276 LYS cc_start: 0.8962 (tptt) cc_final: 0.8526 (tptm) REVERT: U 281 LYS cc_start: 0.8988 (tttm) cc_final: 0.8566 (ttmm) REVERT: U 311 ARG cc_start: 0.8101 (mpt180) cc_final: 0.7761 (mpt180) REVERT: U 321 VAL cc_start: 0.8830 (t) cc_final: 0.8576 (p) REVERT: U 338 LYS cc_start: 0.8916 (mttt) cc_final: 0.8661 (ttmm) REVERT: U 339 SER cc_start: 0.8859 (m) cc_final: 0.8518 (t) REVERT: U 349 ASP cc_start: 0.8692 (t0) cc_final: 0.8220 (m-30) REVERT: U 365 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8486 (ttmt) REVERT: U 376 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8097 (mm-30) REVERT: U 378 GLU cc_start: 0.7414 (mp0) cc_final: 0.7173 (mp0) REVERT: U 393 GLU cc_start: 0.7640 (pp20) cc_final: 0.7342 (pp20) REVERT: U 399 SER cc_start: 0.8399 (m) cc_final: 0.8130 (p) REVERT: U 400 SER cc_start: 0.8305 (t) cc_final: 0.7854 (m) REVERT: U 411 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7155 (mpt) REVERT: U 412 LYS cc_start: 0.8809 (tppt) cc_final: 0.8546 (tppt) REVERT: U 419 GLU cc_start: 0.7489 (mm-30) cc_final: 0.6907 (mm-30) REVERT: U 424 LYS cc_start: 0.8277 (mmtt) cc_final: 0.8014 (mmtt) REVERT: U 444 GLU cc_start: 0.8190 (tp30) cc_final: 0.7615 (tp30) REVERT: V 30 ILE cc_start: 0.8552 (mt) cc_final: 0.8239 (mm) REVERT: V 31 LYS cc_start: 0.8164 (mmpt) cc_final: 0.7723 (mmtm) REVERT: V 35 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7912 (mp) REVERT: V 52 ILE cc_start: 0.8665 (mp) cc_final: 0.8299 (mm) REVERT: V 56 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7380 (mm-30) REVERT: V 88 LEU cc_start: 0.8615 (mm) cc_final: 0.8372 (mt) REVERT: V 95 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7734 (mt-10) REVERT: V 99 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8337 (mtpp) REVERT: V 114 GLU cc_start: 0.7900 (mt-10) cc_final: 0.6859 (mt-10) REVERT: V 132 ARG cc_start: 0.8389 (tpp80) cc_final: 0.8132 (ttp80) REVERT: V 144 VAL cc_start: 0.8442 (t) cc_final: 0.8051 (m) REVERT: V 180 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7515 (tpt-90) REVERT: V 187 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7705 (mt-10) REVERT: V 194 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.7940 (t) REVERT: V 203 GLU cc_start: 0.8042 (tt0) cc_final: 0.7763 (tt0) REVERT: V 218 TYR cc_start: 0.8684 (m-80) cc_final: 0.8264 (m-80) REVERT: V 222 PHE cc_start: 0.8357 (m-80) cc_final: 0.8097 (m-10) REVERT: V 239 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8030 (mttt) REVERT: V 254 VAL cc_start: 0.8703 (t) cc_final: 0.8403 (m) REVERT: V 263 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8328 (mm-40) REVERT: V 268 MET cc_start: 0.7776 (mmm) cc_final: 0.7420 (mmm) REVERT: V 286 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7859 (mp10) REVERT: V 302 GLU cc_start: 0.8099 (pt0) cc_final: 0.7488 (pm20) REVERT: V 318 ILE cc_start: 0.8651 (tp) cc_final: 0.8403 (tt) REVERT: V 325 ASN cc_start: 0.8366 (t0) cc_final: 0.7516 (t0) REVERT: V 326 LYS cc_start: 0.8403 (tttt) cc_final: 0.8154 (ttpt) REVERT: V 344 MET cc_start: 0.8773 (mmt) cc_final: 0.8507 (mmm) REVERT: V 365 ASP cc_start: 0.7881 (m-30) cc_final: 0.7458 (t70) REVERT: V 367 LEU cc_start: 0.8373 (mt) cc_final: 0.8098 (mm) REVERT: V 379 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8215 (mt-10) REVERT: V 403 LEU cc_start: 0.8776 (mt) cc_final: 0.8463 (mm) REVERT: V 406 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7552 (tmm) REVERT: V 427 GLN cc_start: 0.8096 (pt0) cc_final: 0.7875 (pt0) REVERT: V 440 ASN cc_start: 0.7796 (m-40) cc_final: 0.7425 (m-40) REVERT: V 443 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8224 (mtmm) REVERT: V 450 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7378 (mttt) REVERT: V 453 THR cc_start: 0.8719 (m) cc_final: 0.8418 (p) REVERT: V 454 LYS cc_start: 0.8875 (mptt) cc_final: 0.8472 (mmtt) REVERT: W 45 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8332 (p) REVERT: W 66 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8506 (mm) REVERT: W 86 MET cc_start: 0.7856 (mmm) cc_final: 0.7531 (mmm) REVERT: W 135 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7907 (mm) REVERT: W 136 ILE cc_start: 0.8601 (mp) cc_final: 0.8387 (mp) REVERT: W 142 GLU cc_start: 0.7761 (pp20) cc_final: 0.7310 (pp20) REVERT: W 159 THR cc_start: 0.8321 (m) cc_final: 0.7487 (p) REVERT: W 185 LEU cc_start: 0.8182 (mt) cc_final: 0.7687 (mt) REVERT: W 188 ASP cc_start: 0.7668 (m-30) cc_final: 0.7073 (m-30) REVERT: W 191 SER cc_start: 0.8715 (t) cc_final: 0.7999 (m) REVERT: W 198 LYS cc_start: 0.8320 (mmmt) cc_final: 0.8012 (tppt) REVERT: W 200 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.7851 (p) REVERT: W 229 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8197 (tp) REVERT: W 231 LYS cc_start: 0.8428 (mttm) cc_final: 0.8164 (mmmm) REVERT: W 264 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6553 (mt-10) REVERT: W 271 ASP cc_start: 0.7899 (m-30) cc_final: 0.7686 (m-30) REVERT: W 273 ILE cc_start: 0.8844 (tp) cc_final: 0.8629 (tp) REVERT: W 281 LYS cc_start: 0.8785 (tttm) cc_final: 0.8404 (tppt) REVERT: W 296 ASP cc_start: 0.8423 (t0) cc_final: 0.8100 (t0) REVERT: W 306 PHE cc_start: 0.8460 (m-80) cc_final: 0.8122 (m-80) REVERT: W 310 ASN cc_start: 0.8146 (m-40) cc_final: 0.7874 (m-40) REVERT: W 365 LYS cc_start: 0.8960 (tmmt) cc_final: 0.8712 (tmmt) REVERT: W 367 ILE cc_start: 0.8617 (mt) cc_final: 0.8251 (tt) REVERT: W 375 GLU cc_start: 0.8357 (tp30) cc_final: 0.7943 (tp30) REVERT: W 386 LEU cc_start: 0.8543 (tp) cc_final: 0.8293 (tt) REVERT: W 389 LYS cc_start: 0.8797 (tppt) cc_final: 0.7510 (tppt) REVERT: W 393 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7961 (mm-30) REVERT: W 420 VAL cc_start: 0.8627 (t) cc_final: 0.8245 (m) REVERT: W 424 LYS cc_start: 0.8655 (ptpt) cc_final: 0.8403 (ptpt) REVERT: W 438 LYS cc_start: 0.9063 (pttt) cc_final: 0.8747 (pttt) REVERT: X 95 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8318 (mm-30) REVERT: X 106 VAL cc_start: 0.8227 (OUTLIER) cc_final: 0.7940 (p) REVERT: X 123 GLU cc_start: 0.8274 (pt0) cc_final: 0.7846 (tt0) REVERT: X 125 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7909 (t80) REVERT: X 186 TYR cc_start: 0.8538 (t80) cc_final: 0.8310 (t80) REVERT: X 189 ILE cc_start: 0.9179 (mm) cc_final: 0.8899 (mm) REVERT: X 198 ASP cc_start: 0.7484 (m-30) cc_final: 0.6910 (m-30) REVERT: X 211 ARG cc_start: 0.8233 (ttt-90) cc_final: 0.7617 (ttt-90) REVERT: X 228 GLU cc_start: 0.7592 (pm20) cc_final: 0.7200 (pm20) REVERT: X 239 LYS cc_start: 0.8498 (ptpt) cc_final: 0.8081 (ptpp) REVERT: X 245 GLN cc_start: 0.8130 (tp40) cc_final: 0.7797 (tp40) REVERT: X 251 ASP cc_start: 0.7994 (m-30) cc_final: 0.7579 (m-30) REVERT: X 258 ARG cc_start: 0.7305 (mmm160) cc_final: 0.7101 (mmm160) REVERT: X 263 GLN cc_start: 0.7295 (tm-30) cc_final: 0.6660 (tm-30) REVERT: X 269 MET cc_start: 0.8525 (tpp) cc_final: 0.8116 (mpp) REVERT: X 272 LEU cc_start: 0.8856 (tt) cc_final: 0.8583 (tp) REVERT: X 274 LYS cc_start: 0.7989 (tmmt) cc_final: 0.7731 (ttmt) REVERT: X 277 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8515 (mtmt) REVERT: X 282 GLU cc_start: 0.7876 (tp30) cc_final: 0.7193 (tp30) REVERT: X 290 LYS cc_start: 0.8591 (tppt) cc_final: 0.7957 (tppt) REVERT: X 325 ASN cc_start: 0.8632 (m-40) cc_final: 0.8207 (m-40) REVERT: X 328 LEU cc_start: 0.8801 (mt) cc_final: 0.8517 (mm) REVERT: X 362 ASP cc_start: 0.7641 (p0) cc_final: 0.7267 (p0) REVERT: X 378 ASP cc_start: 0.7797 (p0) cc_final: 0.7435 (t0) REVERT: X 385 GLU cc_start: 0.8381 (pp20) cc_final: 0.8040 (pp20) REVERT: X 391 GLU cc_start: 0.8546 (tt0) cc_final: 0.8164 (tp30) REVERT: X 401 ASP cc_start: 0.8363 (m-30) cc_final: 0.8042 (m-30) REVERT: X 406 MET cc_start: 0.8196 (mtp) cc_final: 0.7910 (mtp) REVERT: X 409 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7893 (mm-30) REVERT: X 410 THR cc_start: 0.8118 (p) cc_final: 0.7835 (t) REVERT: X 431 ARG cc_start: 0.7665 (ttp-110) cc_final: 0.7196 (ttp-110) REVERT: X 443 LYS cc_start: 0.8424 (tmmt) cc_final: 0.8100 (ttmm) REVERT: X 448 ASP cc_start: 0.8057 (t0) cc_final: 0.7496 (t70) REVERT: X 454 LYS cc_start: 0.8406 (tmmt) cc_final: 0.7736 (tmmt) REVERT: X 457 GLU cc_start: 0.7760 (pp20) cc_final: 0.7433 (pp20) REVERT: Y 59 LYS cc_start: 0.8547 (mmmt) cc_final: 0.8305 (tptp) REVERT: Y 78 SER cc_start: 0.8410 (t) cc_final: 0.8020 (p) REVERT: Y 111 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7622 (tp) REVERT: Y 113 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7878 (mtmm) REVERT: Y 128 LYS cc_start: 0.8484 (ttpp) cc_final: 0.7757 (ttpp) REVERT: Y 130 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7614 (mtmm) REVERT: Y 136 ILE cc_start: 0.8577 (mt) cc_final: 0.8199 (mm) REVERT: Y 161 LYS cc_start: 0.8545 (pttt) cc_final: 0.8058 (pttp) REVERT: Y 162 THR cc_start: 0.8550 (p) cc_final: 0.8098 (t) REVERT: Y 164 ASP cc_start: 0.8231 (m-30) cc_final: 0.7960 (m-30) REVERT: Y 166 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6432 (tm-30) REVERT: Y 171 LEU cc_start: 0.8429 (mp) cc_final: 0.8211 (mm) REVERT: Y 173 ASN cc_start: 0.8131 (p0) cc_final: 0.6982 (m-40) REVERT: Y 174 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8315 (mmtm) REVERT: Y 175 MET cc_start: 0.8838 (tpp) cc_final: 0.8288 (tpp) REVERT: Y 182 GLU cc_start: 0.7395 (tm-30) cc_final: 0.7135 (tm-30) REVERT: Y 192 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8781 (mm) REVERT: Y 208 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7470 (mmm-85) REVERT: Y 266 ARG cc_start: 0.7815 (mtm110) cc_final: 0.6557 (mtm110) REVERT: Y 271 ASP cc_start: 0.8429 (t0) cc_final: 0.8046 (t0) REVERT: Y 274 ASN cc_start: 0.8732 (m-40) cc_final: 0.8296 (m-40) REVERT: Y 277 VAL cc_start: 0.8665 (t) cc_final: 0.8390 (p) REVERT: Y 310 ASN cc_start: 0.8045 (m-40) cc_final: 0.7667 (m-40) REVERT: Y 315 ASP cc_start: 0.8204 (t0) cc_final: 0.7845 (t70) REVERT: Y 317 PHE cc_start: 0.8698 (m-80) cc_final: 0.8479 (m-80) REVERT: Y 322 MET cc_start: 0.8430 (mtp) cc_final: 0.8207 (mtm) REVERT: Y 327 ARG cc_start: 0.7972 (ttm-80) cc_final: 0.7623 (ttm-80) REVERT: Y 339 SER cc_start: 0.8746 (t) cc_final: 0.8329 (p) REVERT: Y 370 ILE cc_start: 0.9002 (mt) cc_final: 0.8765 (mt) REVERT: Y 384 LEU cc_start: 0.9021 (tp) cc_final: 0.8713 (tt) REVERT: Y 389 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8429 (mmmm) REVERT: Y 393 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8134 (mt-10) REVERT: Y 412 LYS cc_start: 0.9149 (tptm) cc_final: 0.8909 (tptm) REVERT: Y 417 THR cc_start: 0.7459 (t) cc_final: 0.7005 (t) REVERT: Y 419 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7771 (mp0) REVERT: Y 422 ASP cc_start: 0.7995 (m-30) cc_final: 0.7774 (t70) REVERT: Y 424 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8367 (mtmm) REVERT: Y 427 TYR cc_start: 0.8289 (t80) cc_final: 0.7629 (t80) REVERT: Y 444 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7263 (tm-30) REVERT: Y 456 ILE cc_start: 0.8815 (mt) cc_final: 0.8392 (mt) REVERT: Z 310 ARG cc_start: 0.8207 (mtt-85) cc_final: 0.7559 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7454 (ttm110) outliers start: 154 outliers final: 97 residues processed: 1199 average time/residue: 0.4893 time to fit residues: 904.4147 Evaluate side-chains 1232 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 1105 time to evaluate : 3.276 ------------------------------------------------------------------------------- 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 1125 CYS Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1265 VAL 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 34 TYR 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 227 MET Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 263 LYS 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 729 ILE Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 181 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 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain T residue 406 MET Chi-restraints excluded: chain T residue 436 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 109 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 335 THR Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 117 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 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 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 105 GLU Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 141 VAL 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 346 ASP 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 68 LYS 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 265 VAL Chi-restraints excluded: chain X residue 286 GLN 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 377 LYS Chi-restraints excluded: chain X residue 412 LEU Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 430 ASN Chi-restraints excluded: chain X residue 434 ILE 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 167 THR Chi-restraints excluded: chain Y residue 192 ILE Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 323 MET 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 401 ASN Chi-restraints excluded: chain Y residue 402 LEU Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Z residue 302 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 358 optimal weight: 0.9990 chunk 218 optimal weight: 0.3980 chunk 37 optimal weight: 20.0000 chunk 114 optimal weight: 0.7980 chunk 182 optimal weight: 0.8980 chunk 292 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 351 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN Q1228 HIS ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 635 GLN T 27 HIS T 29 HIS V 341 ASN W 144 GLN W 373 GLN ** W 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 446 GLN X 165 HIS X 394 GLN Y 272 GLN Y 373 GLN Y 401 ASN ** Y 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.127298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.108300 restraints weight = 57135.068| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.31 r_work: 0.3333 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29139 Z= 0.159 Angle : 0.680 15.344 39425 Z= 0.337 Chirality : 0.045 0.213 4626 Planarity : 0.005 0.083 5049 Dihedral : 7.212 129.027 4012 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 4.46 % Allowed : 27.28 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.14), residues: 3626 helix: 0.93 (0.13), residues: 1532 sheet: -0.12 (0.21), residues: 593 loop : -0.69 (0.16), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 108 HIS 0.005 0.001 HIS R 121 PHE 0.029 0.001 PHE U 254 TYR 0.025 0.002 TYR Q1198 ARG 0.012 0.001 ARG U 69 Details of bonding type rmsd hydrogen bonds : bond 0.03729 ( 1098) hydrogen bonds : angle 4.50917 ( 3198) covalent geometry : bond 0.00349 (29139) covalent geometry : angle 0.67984 (39425) *********************** 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 1254 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1113 time to evaluate : 3.054 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 960 GLN cc_start: 0.8374 (mm110) cc_final: 0.8172 (mm110) REVERT: Q 1005 MET cc_start: 0.6798 (mmp) cc_final: 0.6068 (mmp) REVERT: Q 1023 ASP cc_start: 0.7787 (t0) cc_final: 0.7325 (t0) REVERT: Q 1027 SER cc_start: 0.8730 (m) cc_final: 0.8207 (p) REVERT: Q 1087 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8263 (ttm-80) REVERT: Q 1102 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8095 (m) REVERT: Q 1112 LYS cc_start: 0.8809 (mttp) cc_final: 0.8265 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8661 (m) cc_final: 0.8208 (t) REVERT: Q 1150 LYS cc_start: 0.8554 (tttm) cc_final: 0.7665 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6709 (mp0) REVERT: Q 1173 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7328 (mp0) REVERT: Q 1179 ARG cc_start: 0.6944 (tpp80) cc_final: 0.6679 (tpp80) REVERT: Q 1195 LYS cc_start: 0.8233 (tppt) cc_final: 0.7478 (tppt) REVERT: Q 1208 ARG cc_start: 0.8702 (ttm170) cc_final: 0.7686 (mtp180) REVERT: Q 1222 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7268 (tm-30) REVERT: Q 1230 THR cc_start: 0.8779 (m) cc_final: 0.8360 (p) REVERT: Q 1234 ASN cc_start: 0.8522 (m-40) cc_final: 0.8267 (m-40) REVERT: Q 1241 LEU cc_start: 0.9217 (tp) cc_final: 0.8970 (tp) REVERT: Q 1248 ASP cc_start: 0.7490 (t70) cc_final: 0.6993 (t0) REVERT: Q 1261 LYS cc_start: 0.8643 (mttt) cc_final: 0.8410 (mtmm) REVERT: Q 1266 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7828 (tm-30) REVERT: Q 1267 ASP cc_start: 0.8595 (m-30) cc_final: 0.7974 (m-30) REVERT: Q 1293 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7462 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8318 (mt) cc_final: 0.8003 (mm) REVERT: Q 1302 ARG cc_start: 0.8064 (ttt180) cc_final: 0.7573 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8646 (m-30) cc_final: 0.8320 (m-30) REVERT: Q 1317 ARG cc_start: 0.8119 (ptm160) cc_final: 0.7875 (ptm160) REVERT: Q 1331 MET cc_start: 0.7874 (tpp) cc_final: 0.7348 (tpp) REVERT: Q 1334 TYR cc_start: 0.7872 (p90) cc_final: 0.7316 (p90) REVERT: Q 1335 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7662 (mp) REVERT: R 35 ASN cc_start: 0.8842 (t0) cc_final: 0.8600 (m-40) REVERT: R 55 ASN cc_start: 0.8470 (p0) cc_final: 0.8137 (p0) REVERT: R 70 PHE cc_start: 0.7645 (t80) cc_final: 0.7365 (t80) REVERT: R 155 PHE cc_start: 0.7322 (m-80) cc_final: 0.6974 (m-10) REVERT: R 156 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7746 (pm20) REVERT: R 183 THR cc_start: 0.7389 (m) cc_final: 0.6823 (t) REVERT: R 214 TRP cc_start: 0.7495 (t-100) cc_final: 0.6918 (t-100) REVERT: R 230 LYS cc_start: 0.8883 (tttt) cc_final: 0.8671 (tttt) REVERT: R 251 CYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7064 (m) REVERT: R 257 TYR cc_start: 0.8007 (t80) cc_final: 0.7642 (t80) REVERT: R 592 HIS cc_start: 0.8183 (t-90) cc_final: 0.7486 (t-90) REVERT: R 593 LEU cc_start: 0.8706 (mm) cc_final: 0.8416 (mm) REVERT: R 609 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: R 612 MET cc_start: 0.7024 (tpp) cc_final: 0.6800 (tpp) REVERT: R 640 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: R 643 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7421 (mm-30) REVERT: R 645 ILE cc_start: 0.9129 (mt) cc_final: 0.8751 (tt) REVERT: R 647 LEU cc_start: 0.8442 (mp) cc_final: 0.8062 (mp) REVERT: R 659 GLN cc_start: 0.8444 (tp-100) cc_final: 0.8088 (tp-100) REVERT: R 663 ASP cc_start: 0.8153 (m-30) cc_final: 0.7709 (m-30) REVERT: R 664 MET cc_start: 0.8739 (mtm) cc_final: 0.8466 (mtp) REVERT: R 681 LYS cc_start: 0.9021 (tptt) cc_final: 0.8815 (tptt) REVERT: R 699 THR cc_start: 0.8070 (OUTLIER) cc_final: 0.7697 (p) REVERT: R 721 GLU cc_start: 0.8175 (tp30) cc_final: 0.7064 (tp30) REVERT: R 722 GLU cc_start: 0.8163 (pp20) cc_final: 0.7574 (pp20) REVERT: R 723 GLN cc_start: 0.7959 (mm-40) cc_final: 0.7658 (mm-40) REVERT: R 724 TYR cc_start: 0.8183 (t80) cc_final: 0.7663 (t80) REVERT: R 725 ARG cc_start: 0.8603 (mmt180) cc_final: 0.8091 (mmt180) REVERT: R 726 LYS cc_start: 0.8428 (tptp) cc_final: 0.8205 (tptp) REVERT: R 728 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8589 (m) REVERT: R 729 ILE cc_start: 0.6731 (OUTLIER) cc_final: 0.6426 (tp) REVERT: S 32 PHE cc_start: 0.8148 (m-10) cc_final: 0.7928 (m-80) REVERT: S 122 LYS cc_start: 0.8424 (mmmm) cc_final: 0.8127 (mtpp) REVERT: S 140 TYR cc_start: 0.8605 (t80) cc_final: 0.8117 (t80) REVERT: S 145 LYS cc_start: 0.8700 (tppp) cc_final: 0.8313 (tppp) REVERT: T 49 VAL cc_start: 0.8403 (p) cc_final: 0.8054 (m) REVERT: T 56 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7859 (mm-30) REVERT: T 70 MET cc_start: 0.7556 (mmm) cc_final: 0.7237 (mmm) REVERT: T 95 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8297 (mm-30) REVERT: T 177 LYS cc_start: 0.8519 (tttt) cc_final: 0.8044 (mtpp) REVERT: T 178 THR cc_start: 0.8947 (m) cc_final: 0.8634 (t) REVERT: T 193 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8055 (mmmt) REVERT: T 251 ASP cc_start: 0.8121 (m-30) cc_final: 0.7816 (m-30) REVERT: T 269 MET cc_start: 0.7040 (mtp) cc_final: 0.6835 (mtm) REVERT: T 273 LEU cc_start: 0.7785 (tp) cc_final: 0.7522 (tt) REVERT: T 279 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7404 (pt0) REVERT: T 295 TYR cc_start: 0.8609 (m-80) cc_final: 0.8148 (m-80) REVERT: T 319 GLU cc_start: 0.8191 (mp0) cc_final: 0.7985 (mm-30) REVERT: T 371 ARG cc_start: 0.8040 (mtp-110) cc_final: 0.7722 (ptm160) REVERT: T 382 THR cc_start: 0.8624 (p) cc_final: 0.8110 (p) REVERT: T 385 GLU cc_start: 0.8509 (pt0) cc_final: 0.7861 (pp20) REVERT: T 409 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7641 (mt-10) REVERT: T 417 GLN cc_start: 0.8183 (mt0) cc_final: 0.7812 (mt0) REVERT: T 431 ARG cc_start: 0.7605 (mtm110) cc_final: 0.7160 (mtm180) REVERT: T 439 VAL cc_start: 0.8883 (t) cc_final: 0.8670 (t) REVERT: T 448 ASP cc_start: 0.7648 (p0) cc_final: 0.7183 (p0) REVERT: T 456 LEU cc_start: 0.8903 (tp) cc_final: 0.8314 (mt) REVERT: T 457 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8207 (mm-30) REVERT: U 45 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7769 (p) REVERT: U 86 MET cc_start: 0.8018 (mmm) cc_final: 0.7533 (mmm) REVERT: U 94 LYS cc_start: 0.8846 (tppt) cc_final: 0.8439 (tptp) REVERT: U 104 SER cc_start: 0.8576 (m) cc_final: 0.8186 (t) REVERT: U 105 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7207 (mt-10) REVERT: U 110 GLU cc_start: 0.7980 (pp20) cc_final: 0.7639 (pp20) REVERT: U 123 LYS cc_start: 0.8274 (mttt) cc_final: 0.7959 (mttp) REVERT: U 139 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6309 (tp30) REVERT: U 161 LYS cc_start: 0.8600 (ptmm) cc_final: 0.8144 (ptmm) REVERT: U 166 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7107 (tp30) REVERT: U 193 ASP cc_start: 0.7948 (t0) cc_final: 0.7422 (t70) REVERT: U 194 LYS cc_start: 0.8617 (ttpp) cc_final: 0.8346 (ttmt) REVERT: U 198 LYS cc_start: 0.8550 (tttm) cc_final: 0.8243 (tttm) REVERT: U 245 ASP cc_start: 0.8073 (m-30) cc_final: 0.7762 (m-30) REVERT: U 254 PHE cc_start: 0.8001 (p90) cc_final: 0.7624 (p90) REVERT: U 270 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7590 (mtt180) REVERT: U 272 GLN cc_start: 0.7987 (tp40) cc_final: 0.7480 (tp40) REVERT: U 276 LYS cc_start: 0.8970 (tptt) cc_final: 0.8516 (tptm) REVERT: U 281 LYS cc_start: 0.8979 (tttm) cc_final: 0.8555 (ttmm) REVERT: U 285 LYS cc_start: 0.8533 (mttp) cc_final: 0.7806 (mttp) REVERT: U 300 MET cc_start: 0.8432 (mmm) cc_final: 0.8198 (mmm) REVERT: U 302 ASP cc_start: 0.8279 (p0) cc_final: 0.8071 (p0) REVERT: U 306 PHE cc_start: 0.8268 (m-10) cc_final: 0.7944 (m-80) REVERT: U 311 ARG cc_start: 0.8055 (mpt180) cc_final: 0.7680 (mpt180) REVERT: U 321 VAL cc_start: 0.8828 (t) cc_final: 0.8587 (p) REVERT: U 338 LYS cc_start: 0.8909 (mttt) cc_final: 0.8664 (ttmm) REVERT: U 339 SER cc_start: 0.8867 (m) cc_final: 0.8482 (t) REVERT: U 365 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8474 (ttmt) REVERT: U 376 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8052 (mm-30) REVERT: U 393 GLU cc_start: 0.7670 (pp20) cc_final: 0.7374 (pp20) REVERT: U 399 SER cc_start: 0.8373 (m) cc_final: 0.8014 (p) REVERT: U 400 SER cc_start: 0.8263 (t) cc_final: 0.7771 (m) REVERT: U 411 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7145 (mpt) REVERT: U 412 LYS cc_start: 0.8805 (tppt) cc_final: 0.8539 (tppt) REVERT: U 419 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7084 (mm-30) REVERT: U 424 LYS cc_start: 0.8278 (mmtt) cc_final: 0.8032 (mmtt) REVERT: U 428 LEU cc_start: 0.8711 (mt) cc_final: 0.8432 (pp) REVERT: U 438 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8202 (ttpp) REVERT: U 444 GLU cc_start: 0.8218 (tp30) cc_final: 0.7630 (tp30) REVERT: V 30 ILE cc_start: 0.8540 (mt) cc_final: 0.8219 (mm) REVERT: V 31 LYS cc_start: 0.8162 (mmpt) cc_final: 0.7720 (mmtm) REVERT: V 35 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7882 (mp) REVERT: V 52 ILE cc_start: 0.8657 (mp) cc_final: 0.8391 (mm) REVERT: V 56 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7357 (mm-30) REVERT: V 88 LEU cc_start: 0.8597 (mm) cc_final: 0.8348 (mt) REVERT: V 95 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7734 (mt-10) REVERT: V 99 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8315 (mtpp) REVERT: V 114 GLU cc_start: 0.7900 (mt-10) cc_final: 0.6864 (mt-10) REVERT: V 127 ARG cc_start: 0.8272 (ttp-170) cc_final: 0.7932 (ttm110) REVERT: V 132 ARG cc_start: 0.8381 (tpp80) cc_final: 0.8098 (tpp80) REVERT: V 141 GLU cc_start: 0.7650 (pm20) cc_final: 0.7355 (pm20) REVERT: V 144 VAL cc_start: 0.8428 (t) cc_final: 0.8037 (m) REVERT: V 180 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7552 (tpt-90) REVERT: V 187 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7770 (mt-10) REVERT: V 192 GLU cc_start: 0.7372 (tp30) cc_final: 0.7123 (tp30) REVERT: V 194 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.7962 (t) REVERT: V 203 GLU cc_start: 0.8000 (tt0) cc_final: 0.7729 (tt0) REVERT: V 218 TYR cc_start: 0.8695 (m-80) cc_final: 0.8240 (m-80) REVERT: V 222 PHE cc_start: 0.8361 (m-80) cc_final: 0.8021 (m-10) REVERT: V 239 LYS cc_start: 0.8325 (mtpt) cc_final: 0.8067 (mttt) REVERT: V 254 VAL cc_start: 0.8704 (t) cc_final: 0.8417 (m) REVERT: V 268 MET cc_start: 0.7753 (mmm) cc_final: 0.7414 (mmm) REVERT: V 286 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7871 (mp10) REVERT: V 302 GLU cc_start: 0.8063 (pt0) cc_final: 0.7435 (pm20) REVERT: V 312 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7634 (mm-30) REVERT: V 318 ILE cc_start: 0.8636 (tp) cc_final: 0.8389 (tt) REVERT: V 325 ASN cc_start: 0.8287 (t0) cc_final: 0.7601 (t0) REVERT: V 344 MET cc_start: 0.8734 (mmt) cc_final: 0.8477 (mmm) REVERT: V 365 ASP cc_start: 0.7865 (m-30) cc_final: 0.7462 (t70) REVERT: V 367 LEU cc_start: 0.8371 (mt) cc_final: 0.8100 (mm) REVERT: V 379 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8170 (mt-10) REVERT: V 403 LEU cc_start: 0.8749 (mt) cc_final: 0.8415 (mm) REVERT: V 406 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7561 (tmm) REVERT: V 427 GLN cc_start: 0.8041 (pt0) cc_final: 0.7824 (pt0) REVERT: V 443 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8241 (mtmm) REVERT: V 450 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7366 (mttt) REVERT: V 453 THR cc_start: 0.8736 (m) cc_final: 0.8414 (p) REVERT: V 454 LYS cc_start: 0.8876 (mptt) cc_final: 0.8461 (mmtt) REVERT: W 26 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8514 (mm) REVERT: W 45 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8331 (p) REVERT: W 66 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8486 (mm) REVERT: W 86 MET cc_start: 0.7845 (mmm) cc_final: 0.7476 (mmm) REVERT: W 135 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7893 (mm) REVERT: W 142 GLU cc_start: 0.7662 (pp20) cc_final: 0.7312 (tm-30) REVERT: W 159 THR cc_start: 0.8238 (m) cc_final: 0.7726 (p) REVERT: W 185 LEU cc_start: 0.8152 (mt) cc_final: 0.7702 (mt) REVERT: W 188 ASP cc_start: 0.7669 (m-30) cc_final: 0.7076 (m-30) REVERT: W 191 SER cc_start: 0.8713 (t) cc_final: 0.8090 (m) REVERT: W 198 LYS cc_start: 0.8309 (mmmt) cc_final: 0.8004 (tppt) REVERT: W 200 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.7897 (p) REVERT: W 231 LYS cc_start: 0.8418 (mttm) cc_final: 0.8149 (mmmm) REVERT: W 232 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7726 (tpp80) REVERT: W 261 ASP cc_start: 0.8200 (t0) cc_final: 0.7812 (t0) REVERT: W 264 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6494 (mt-10) REVERT: W 271 ASP cc_start: 0.7900 (m-30) cc_final: 0.7695 (m-30) REVERT: W 273 ILE cc_start: 0.8831 (tp) cc_final: 0.8614 (tp) REVERT: W 281 LYS cc_start: 0.8744 (tttm) cc_final: 0.8332 (tppt) REVERT: W 306 PHE cc_start: 0.8447 (m-80) cc_final: 0.8124 (m-80) REVERT: W 310 ASN cc_start: 0.8142 (m-40) cc_final: 0.7862 (m-40) REVERT: W 365 LYS cc_start: 0.8930 (tmmt) cc_final: 0.8729 (tmmt) REVERT: W 367 ILE cc_start: 0.8601 (mt) cc_final: 0.8245 (tt) REVERT: W 373 GLN cc_start: 0.8504 (mp-120) cc_final: 0.8232 (mt0) REVERT: W 375 GLU cc_start: 0.8334 (tp30) cc_final: 0.7909 (tp30) REVERT: W 389 LYS cc_start: 0.8817 (tppt) cc_final: 0.7992 (tppt) REVERT: W 393 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7900 (mm-30) REVERT: W 420 VAL cc_start: 0.8607 (t) cc_final: 0.8193 (m) REVERT: W 424 LYS cc_start: 0.8626 (ptpt) cc_final: 0.8365 (ptpt) REVERT: W 438 LYS cc_start: 0.9058 (pttt) cc_final: 0.8703 (pttt) REVERT: X 33 LEU cc_start: 0.8730 (mt) cc_final: 0.8380 (mm) REVERT: X 48 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: X 95 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8183 (mm-30) REVERT: X 123 GLU cc_start: 0.8228 (pt0) cc_final: 0.7820 (tt0) REVERT: X 125 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7933 (t80) REVERT: X 186 TYR cc_start: 0.8549 (t80) cc_final: 0.8252 (t80) REVERT: X 189 ILE cc_start: 0.9161 (mm) cc_final: 0.8915 (mt) REVERT: X 198 ASP cc_start: 0.7501 (m-30) cc_final: 0.6935 (m-30) REVERT: X 211 ARG cc_start: 0.8248 (ttt-90) cc_final: 0.7624 (ttp80) REVERT: X 228 GLU cc_start: 0.7645 (pm20) cc_final: 0.6939 (pm20) REVERT: X 239 LYS cc_start: 0.8463 (ptpt) cc_final: 0.8060 (ptpp) REVERT: X 245 GLN cc_start: 0.8136 (tp40) cc_final: 0.7829 (tp40) REVERT: X 251 ASP cc_start: 0.7934 (m-30) cc_final: 0.7550 (m-30) REVERT: X 258 ARG cc_start: 0.7310 (mmm160) cc_final: 0.7043 (mmm160) REVERT: X 263 GLN cc_start: 0.7293 (tm-30) cc_final: 0.6652 (tm-30) REVERT: X 265 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8550 (t) REVERT: X 268 MET cc_start: 0.8446 (mtp) cc_final: 0.8203 (mtt) REVERT: X 269 MET cc_start: 0.8532 (tpp) cc_final: 0.8114 (mpp) REVERT: X 272 LEU cc_start: 0.8856 (tt) cc_final: 0.8587 (tp) REVERT: X 274 LYS cc_start: 0.7969 (tmmt) cc_final: 0.7705 (ttmt) REVERT: X 277 LYS cc_start: 0.8783 (ttmm) cc_final: 0.8528 (mtmt) REVERT: X 290 LYS cc_start: 0.8576 (tppt) cc_final: 0.7927 (tppt) REVERT: X 313 VAL cc_start: 0.8053 (OUTLIER) cc_final: 0.7590 (t) REVERT: X 325 ASN cc_start: 0.8611 (m-40) cc_final: 0.8346 (m-40) REVERT: X 328 LEU cc_start: 0.8794 (mt) cc_final: 0.8515 (mm) REVERT: X 378 ASP cc_start: 0.7756 (p0) cc_final: 0.7390 (t0) REVERT: X 385 GLU cc_start: 0.8395 (pp20) cc_final: 0.8052 (pp20) REVERT: X 391 GLU cc_start: 0.8536 (tt0) cc_final: 0.8179 (tp30) REVERT: X 401 ASP cc_start: 0.8351 (m-30) cc_final: 0.8023 (m-30) REVERT: X 409 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7888 (mm-30) REVERT: X 410 THR cc_start: 0.8118 (p) cc_final: 0.7814 (t) REVERT: X 441 GLU cc_start: 0.7945 (tp30) cc_final: 0.7614 (tp30) REVERT: X 443 LYS cc_start: 0.8470 (tmmt) cc_final: 0.8158 (ttmm) REVERT: X 448 ASP cc_start: 0.8024 (t0) cc_final: 0.7458 (t70) REVERT: X 454 LYS cc_start: 0.8383 (tmmt) cc_final: 0.7736 (tmmt) REVERT: X 457 GLU cc_start: 0.7759 (pp20) cc_final: 0.7453 (pp20) REVERT: Y 59 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8290 (tptp) REVERT: Y 78 SER cc_start: 0.8308 (t) cc_final: 0.7928 (p) REVERT: Y 111 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7642 (tp) REVERT: Y 113 LYS cc_start: 0.8356 (ptpp) cc_final: 0.7849 (mtmm) REVERT: Y 128 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8257 (ttpp) REVERT: Y 130 LYS cc_start: 0.7882 (ttmm) cc_final: 0.7675 (mtmm) REVERT: Y 136 ILE cc_start: 0.8560 (mt) cc_final: 0.8231 (mm) REVERT: Y 161 LYS cc_start: 0.8558 (pttt) cc_final: 0.8122 (pttp) REVERT: Y 162 THR cc_start: 0.8462 (p) cc_final: 0.8040 (t) REVERT: Y 164 ASP cc_start: 0.8251 (m-30) cc_final: 0.7991 (m-30) REVERT: Y 171 LEU cc_start: 0.8436 (mp) cc_final: 0.8215 (mm) REVERT: Y 173 ASN cc_start: 0.8129 (p0) cc_final: 0.6995 (m-40) REVERT: Y 174 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8302 (mmtm) REVERT: Y 175 MET cc_start: 0.8850 (tpp) cc_final: 0.8297 (tpp) REVERT: Y 182 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7137 (tm-30) REVERT: Y 192 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8784 (mm) REVERT: Y 208 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7494 (mmm-85) REVERT: Y 271 ASP cc_start: 0.8386 (t0) cc_final: 0.8024 (t0) REVERT: Y 274 ASN cc_start: 0.8729 (m-40) cc_final: 0.8281 (m-40) REVERT: Y 277 VAL cc_start: 0.8655 (t) cc_final: 0.8377 (p) REVERT: Y 304 GLU cc_start: 0.8022 (mp0) cc_final: 0.7800 (mp0) REVERT: Y 310 ASN cc_start: 0.8004 (m-40) cc_final: 0.7638 (m-40) REVERT: Y 315 ASP cc_start: 0.8193 (t0) cc_final: 0.7848 (t70) REVERT: Y 317 PHE cc_start: 0.8697 (m-80) cc_final: 0.8457 (m-80) REVERT: Y 322 MET cc_start: 0.8431 (mtp) cc_final: 0.8194 (mtm) REVERT: Y 327 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7647 (ttm-80) REVERT: Y 339 SER cc_start: 0.8747 (t) cc_final: 0.8332 (p) REVERT: Y 370 ILE cc_start: 0.8980 (mt) cc_final: 0.8752 (mt) REVERT: Y 373 GLN cc_start: 0.8629 (tt0) cc_final: 0.8335 (tp40) REVERT: Y 384 LEU cc_start: 0.9005 (tp) cc_final: 0.8694 (tt) REVERT: Y 389 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8344 (mmmm) REVERT: Y 390 THR cc_start: 0.8859 (p) cc_final: 0.8532 (p) REVERT: Y 393 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8144 (mt-10) REVERT: Y 412 LYS cc_start: 0.9138 (tptm) cc_final: 0.8898 (tptm) REVERT: Y 417 THR cc_start: 0.7527 (t) cc_final: 0.7162 (t) REVERT: Y 419 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7772 (mp0) REVERT: Y 422 ASP cc_start: 0.8018 (m-30) cc_final: 0.7813 (t70) REVERT: Y 427 TYR cc_start: 0.8257 (t80) cc_final: 0.7571 (t80) REVERT: Y 441 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8063 (mt0) REVERT: Y 456 ILE cc_start: 0.8823 (mt) cc_final: 0.8598 (mt) REVERT: Z 310 ARG cc_start: 0.8202 (mtt-85) cc_final: 0.7479 (mmm-85) REVERT: Z 311 ARG cc_start: 0.7733 (ttm110) cc_final: 0.7496 (ttm110) outliers start: 141 outliers final: 84 residues processed: 1178 average time/residue: 0.4541 time to fit residues: 811.0340 Evaluate side-chains 1208 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 1093 time to evaluate : 3.329 ------------------------------------------------------------------------------- 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 1265 VAL 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 R residue 22 ARG Chi-restraints excluded: chain R residue 34 TYR 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 227 MET Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 263 LYS 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 729 ILE Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 181 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 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain T residue 406 MET Chi-restraints excluded: chain T residue 436 VAL Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 109 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 331 LYS Chi-restraints excluded: chain U residue 335 THR Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 117 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 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 26 ILE 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 135 LEU Chi-restraints excluded: chain W residue 141 VAL Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 232 ARG Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 68 LYS 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 265 VAL Chi-restraints excluded: chain X residue 286 GLN 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 377 LYS Chi-restraints excluded: chain X residue 412 LEU Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 434 ILE 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 191 SER Chi-restraints excluded: chain Y residue 192 ILE Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 323 MET 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 401 ASN Chi-restraints excluded: chain Y residue 420 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 9 optimal weight: 0.8980 chunk 351 optimal weight: 0.9990 chunk 335 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 326 optimal weight: 0.8980 chunk 19 optimal weight: 0.0970 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 191 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1192 ASN Q1204 ASN Q1228 HIS ** Q1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN R 635 GLN T 27 HIS T 29 HIS V 341 ASN ** V 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 90 GLN ** W 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 HIS Y 237 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.127603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.108774 restraints weight = 56876.766| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.29 r_work: 0.3337 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 29139 Z= 0.147 Angle : 0.691 15.130 39425 Z= 0.342 Chirality : 0.046 0.274 4626 Planarity : 0.005 0.109 5049 Dihedral : 7.066 125.076 4012 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 4.30 % Allowed : 27.94 % Favored : 67.75 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3626 helix: 0.97 (0.13), residues: 1536 sheet: -0.07 (0.21), residues: 585 loop : -0.72 (0.16), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 586 HIS 0.004 0.001 HIS R 121 PHE 0.037 0.002 PHE R 119 TYR 0.025 0.002 TYR Q1198 ARG 0.012 0.001 ARG U 69 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 1098) hydrogen bonds : angle 4.47058 ( 3198) covalent geometry : bond 0.00329 (29139) covalent geometry : angle 0.69104 (39425) *********************** 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 1238 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1102 time to evaluate : 3.355 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: Q 1005 MET cc_start: 0.6748 (mmp) cc_final: 0.6016 (mmp) REVERT: Q 1023 ASP cc_start: 0.7794 (t0) cc_final: 0.7335 (t0) REVERT: Q 1027 SER cc_start: 0.8695 (m) cc_final: 0.8179 (p) REVERT: Q 1087 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8223 (ttm-80) REVERT: Q 1102 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8085 (m) REVERT: Q 1112 LYS cc_start: 0.8804 (mttp) cc_final: 0.8255 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8639 (m) cc_final: 0.8194 (t) REVERT: Q 1150 LYS cc_start: 0.8545 (tttm) cc_final: 0.7689 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6647 (mp0) REVERT: Q 1173 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7333 (mp0) REVERT: Q 1179 ARG cc_start: 0.6902 (tpp80) cc_final: 0.6690 (tpp80) REVERT: Q 1195 LYS cc_start: 0.8223 (tppt) cc_final: 0.7468 (tppt) REVERT: Q 1208 ARG cc_start: 0.8699 (ttm170) cc_final: 0.7682 (mtp180) REVERT: Q 1222 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7271 (tm-30) REVERT: Q 1230 THR cc_start: 0.8773 (m) cc_final: 0.8360 (p) REVERT: Q 1234 ASN cc_start: 0.8502 (m-40) cc_final: 0.8237 (m-40) REVERT: Q 1241 LEU cc_start: 0.9226 (tp) cc_final: 0.8961 (tp) REVERT: Q 1248 ASP cc_start: 0.7502 (t70) cc_final: 0.7002 (t0) REVERT: Q 1261 LYS cc_start: 0.8627 (mttt) cc_final: 0.8393 (mtmm) REVERT: Q 1266 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7842 (tm-30) REVERT: Q 1267 ASP cc_start: 0.8579 (m-30) cc_final: 0.7962 (m-30) REVERT: Q 1270 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8155 (tttt) REVERT: Q 1293 ARG cc_start: 0.7886 (mmm-85) cc_final: 0.7572 (mmm160) REVERT: Q 1295 ILE cc_start: 0.8365 (mt) cc_final: 0.8024 (tt) REVERT: Q 1302 ARG cc_start: 0.8128 (ttt180) cc_final: 0.7645 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8607 (m-30) cc_final: 0.8156 (m-30) REVERT: Q 1317 ARG cc_start: 0.8093 (ptm160) cc_final: 0.7783 (ptm160) REVERT: Q 1331 MET cc_start: 0.7833 (tpp) cc_final: 0.7301 (tpp) REVERT: Q 1334 TYR cc_start: 0.7784 (p90) cc_final: 0.7245 (p90) REVERT: Q 1335 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7541 (mp) REVERT: Q 1421 ARG cc_start: 0.7428 (mtt90) cc_final: 0.6809 (mtt90) REVERT: R 35 ASN cc_start: 0.8832 (t0) cc_final: 0.8597 (m-40) REVERT: R 55 ASN cc_start: 0.8448 (p0) cc_final: 0.8098 (p0) REVERT: R 70 PHE cc_start: 0.7631 (t80) cc_final: 0.7354 (t80) REVERT: R 155 PHE cc_start: 0.7299 (m-80) cc_final: 0.6963 (m-10) REVERT: R 156 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7729 (pm20) REVERT: R 183 THR cc_start: 0.7375 (m) cc_final: 0.6810 (t) REVERT: R 214 TRP cc_start: 0.7452 (t-100) cc_final: 0.6891 (t-100) REVERT: R 242 GLN cc_start: 0.8301 (pt0) cc_final: 0.7850 (pt0) REVERT: R 244 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6681 (mp0) REVERT: R 251 CYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7053 (m) REVERT: R 592 HIS cc_start: 0.8185 (t-90) cc_final: 0.7514 (t-90) REVERT: R 593 LEU cc_start: 0.8711 (mm) cc_final: 0.8424 (mm) REVERT: R 609 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: R 612 MET cc_start: 0.7126 (tpp) cc_final: 0.6873 (tpp) REVERT: R 640 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7558 (tp30) REVERT: R 642 SER cc_start: 0.8722 (m) cc_final: 0.8228 (p) REVERT: R 643 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7386 (mm-30) REVERT: R 645 ILE cc_start: 0.9119 (mt) cc_final: 0.8739 (tt) REVERT: R 647 LEU cc_start: 0.8434 (mp) cc_final: 0.8051 (mp) REVERT: R 659 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8081 (tp-100) REVERT: R 663 ASP cc_start: 0.8134 (m-30) cc_final: 0.7683 (m-30) REVERT: R 664 MET cc_start: 0.8733 (mtm) cc_final: 0.8454 (mtp) REVERT: R 699 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7711 (p) REVERT: R 721 GLU cc_start: 0.8227 (tp30) cc_final: 0.7041 (tp30) REVERT: R 723 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7513 (mm-40) REVERT: R 724 TYR cc_start: 0.8208 (t80) cc_final: 0.7668 (t80) REVERT: R 725 ARG cc_start: 0.8632 (mmt180) cc_final: 0.8190 (mmt180) REVERT: R 726 LYS cc_start: 0.8437 (tptp) cc_final: 0.8168 (tptp) REVERT: R 728 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8607 (m) REVERT: R 729 ILE cc_start: 0.6628 (OUTLIER) cc_final: 0.6333 (tp) REVERT: S 32 PHE cc_start: 0.8107 (m-10) cc_final: 0.7860 (m-80) REVERT: S 110 ARG cc_start: 0.8435 (mtm180) cc_final: 0.7914 (mtm180) REVERT: S 140 TYR cc_start: 0.8601 (t80) cc_final: 0.8361 (t80) REVERT: T 49 VAL cc_start: 0.8395 (p) cc_final: 0.8044 (m) REVERT: T 56 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7864 (mm-30) REVERT: T 95 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8311 (mm-30) REVERT: T 177 LYS cc_start: 0.8514 (tttt) cc_final: 0.8044 (mtpp) REVERT: T 178 THR cc_start: 0.8945 (m) cc_final: 0.8644 (t) REVERT: T 193 LYS cc_start: 0.8403 (mmmt) cc_final: 0.8060 (mmmt) REVERT: T 211 ARG cc_start: 0.8596 (ttt-90) cc_final: 0.8122 (ttt-90) REVERT: T 223 ASP cc_start: 0.6821 (m-30) cc_final: 0.6566 (m-30) REVERT: T 251 ASP cc_start: 0.8138 (m-30) cc_final: 0.7758 (m-30) REVERT: T 273 LEU cc_start: 0.7773 (tp) cc_final: 0.7500 (tt) REVERT: T 295 TYR cc_start: 0.8596 (m-80) cc_final: 0.8126 (m-80) REVERT: T 371 ARG cc_start: 0.8064 (mtp-110) cc_final: 0.7733 (ptm160) REVERT: T 381 ARG cc_start: 0.8707 (ttt-90) cc_final: 0.8358 (ttm-80) REVERT: T 382 THR cc_start: 0.8637 (p) cc_final: 0.8141 (p) REVERT: T 385 GLU cc_start: 0.8490 (pt0) cc_final: 0.7821 (pp20) REVERT: T 409 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7632 (mt-10) REVERT: T 417 GLN cc_start: 0.8179 (mt0) cc_final: 0.7804 (mt0) REVERT: T 431 ARG cc_start: 0.7599 (mtm110) cc_final: 0.7159 (mtm180) REVERT: T 439 VAL cc_start: 0.8894 (t) cc_final: 0.8678 (t) REVERT: T 456 LEU cc_start: 0.8907 (tp) cc_final: 0.8323 (mt) REVERT: U 45 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7775 (p) REVERT: U 86 MET cc_start: 0.7984 (mmm) cc_final: 0.7508 (mmm) REVERT: U 94 LYS cc_start: 0.8842 (tppt) cc_final: 0.8440 (tptp) REVERT: U 104 SER cc_start: 0.8607 (m) cc_final: 0.8212 (t) REVERT: U 105 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7218 (mt-10) REVERT: U 110 GLU cc_start: 0.7920 (pp20) cc_final: 0.7582 (pp20) REVERT: U 123 LYS cc_start: 0.8279 (mttt) cc_final: 0.7956 (mttp) REVERT: U 139 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6309 (tp30) REVERT: U 161 LYS cc_start: 0.8575 (ptmm) cc_final: 0.8116 (ptmm) REVERT: U 166 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: U 193 ASP cc_start: 0.7959 (t0) cc_final: 0.7429 (t70) REVERT: U 194 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8334 (ttmt) REVERT: U 198 LYS cc_start: 0.8572 (tttm) cc_final: 0.8252 (tttm) REVERT: U 245 ASP cc_start: 0.8088 (m-30) cc_final: 0.7751 (m-30) REVERT: U 270 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7538 (mtt180) REVERT: U 272 GLN cc_start: 0.7985 (tp40) cc_final: 0.7476 (tp40) REVERT: U 276 LYS cc_start: 0.8968 (tptt) cc_final: 0.8517 (tptm) REVERT: U 281 LYS cc_start: 0.8961 (tttm) cc_final: 0.8530 (ttmm) REVERT: U 300 MET cc_start: 0.8420 (mmm) cc_final: 0.8184 (mmm) REVERT: U 302 ASP cc_start: 0.8184 (p0) cc_final: 0.7978 (p0) REVERT: U 311 ARG cc_start: 0.8036 (mpt180) cc_final: 0.7665 (mpt180) REVERT: U 321 VAL cc_start: 0.8838 (t) cc_final: 0.8602 (p) REVERT: U 338 LYS cc_start: 0.8924 (mttt) cc_final: 0.8673 (ttmm) REVERT: U 339 SER cc_start: 0.8843 (m) cc_final: 0.8488 (t) REVERT: U 365 LYS cc_start: 0.8815 (ttpt) cc_final: 0.8473 (ttmt) REVERT: U 376 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7969 (mm-30) REVERT: U 393 GLU cc_start: 0.7684 (pp20) cc_final: 0.7376 (pp20) REVERT: U 399 SER cc_start: 0.8375 (m) cc_final: 0.8104 (p) REVERT: U 400 SER cc_start: 0.8279 (t) cc_final: 0.7832 (m) REVERT: U 411 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7124 (mpt) REVERT: U 412 LYS cc_start: 0.8800 (tppt) cc_final: 0.8536 (tppt) REVERT: U 419 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7033 (mm-30) REVERT: U 424 LYS cc_start: 0.8274 (mmtt) cc_final: 0.8022 (mmtt) REVERT: U 428 LEU cc_start: 0.8703 (mt) cc_final: 0.8429 (pp) REVERT: U 444 GLU cc_start: 0.8241 (tp30) cc_final: 0.7640 (tp30) REVERT: V 30 ILE cc_start: 0.8505 (mt) cc_final: 0.8181 (mm) REVERT: V 31 LYS cc_start: 0.8157 (mmpt) cc_final: 0.7691 (mmtm) REVERT: V 35 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7481 (mp) REVERT: V 52 ILE cc_start: 0.8655 (mp) cc_final: 0.8445 (mm) REVERT: V 56 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7379 (mm-30) REVERT: V 88 LEU cc_start: 0.8581 (mm) cc_final: 0.8327 (mt) REVERT: V 95 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7733 (mt-10) REVERT: V 99 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8348 (mtpp) REVERT: V 114 GLU cc_start: 0.7881 (mt-10) cc_final: 0.6499 (mt-10) REVERT: V 127 ARG cc_start: 0.8251 (ttp-170) cc_final: 0.7913 (ttm110) REVERT: V 132 ARG cc_start: 0.8383 (tpp80) cc_final: 0.8145 (tpp80) REVERT: V 141 GLU cc_start: 0.7651 (pm20) cc_final: 0.7382 (pm20) REVERT: V 144 VAL cc_start: 0.8416 (t) cc_final: 0.8015 (m) REVERT: V 180 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7576 (tpt-90) REVERT: V 187 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7733 (mt-10) REVERT: V 192 GLU cc_start: 0.7338 (tp30) cc_final: 0.7076 (tp30) REVERT: V 194 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.7916 (t) REVERT: V 203 GLU cc_start: 0.7956 (tt0) cc_final: 0.7679 (tt0) REVERT: V 218 TYR cc_start: 0.8693 (m-80) cc_final: 0.8233 (m-80) REVERT: V 222 PHE cc_start: 0.8349 (m-80) cc_final: 0.8103 (m-10) REVERT: V 239 LYS cc_start: 0.8311 (mtpt) cc_final: 0.8053 (mttt) REVERT: V 253 ASP cc_start: 0.7533 (m-30) cc_final: 0.7285 (m-30) REVERT: V 254 VAL cc_start: 0.8695 (t) cc_final: 0.8406 (m) REVERT: V 268 MET cc_start: 0.7668 (mmm) cc_final: 0.7189 (mmm) REVERT: V 286 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7878 (mp10) REVERT: V 297 ASP cc_start: 0.8299 (m-30) cc_final: 0.8057 (m-30) REVERT: V 312 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7623 (mm-30) REVERT: V 318 ILE cc_start: 0.8629 (tp) cc_final: 0.8368 (tt) REVERT: V 325 ASN cc_start: 0.8282 (t0) cc_final: 0.7589 (t0) REVERT: V 344 MET cc_start: 0.8693 (mmt) cc_final: 0.8434 (mmm) REVERT: V 365 ASP cc_start: 0.7901 (m-30) cc_final: 0.7368 (t0) REVERT: V 367 LEU cc_start: 0.8386 (mt) cc_final: 0.8108 (mm) REVERT: V 379 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8177 (mt-10) REVERT: V 403 LEU cc_start: 0.8729 (mt) cc_final: 0.8365 (mm) REVERT: V 406 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7520 (tmm) REVERT: V 427 GLN cc_start: 0.8013 (pt0) cc_final: 0.7786 (pt0) REVERT: V 443 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8212 (mtmm) REVERT: V 450 LYS cc_start: 0.7914 (mtmt) cc_final: 0.7328 (mttt) REVERT: V 453 THR cc_start: 0.8744 (m) cc_final: 0.8416 (p) REVERT: V 454 LYS cc_start: 0.8872 (mptt) cc_final: 0.8454 (mmtt) REVERT: W 26 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8479 (mm) REVERT: W 45 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8329 (p) REVERT: W 66 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8473 (mm) REVERT: W 86 MET cc_start: 0.7833 (mmm) cc_final: 0.7482 (mmm) REVERT: W 135 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7873 (mm) REVERT: W 142 GLU cc_start: 0.7651 (pp20) cc_final: 0.7330 (tm-30) REVERT: W 159 THR cc_start: 0.8288 (m) cc_final: 0.7776 (p) REVERT: W 185 LEU cc_start: 0.8161 (mt) cc_final: 0.7715 (mt) REVERT: W 188 ASP cc_start: 0.7665 (m-30) cc_final: 0.7081 (m-30) REVERT: W 191 SER cc_start: 0.8712 (t) cc_final: 0.8135 (m) REVERT: W 198 LYS cc_start: 0.8318 (mmmt) cc_final: 0.8009 (tppt) REVERT: W 200 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.7991 (p) REVERT: W 231 LYS cc_start: 0.8392 (mttm) cc_final: 0.8128 (mmmm) REVERT: W 232 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7772 (tpp80) REVERT: W 261 ASP cc_start: 0.8193 (t0) cc_final: 0.7756 (t0) REVERT: W 264 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6179 (mt-10) REVERT: W 271 ASP cc_start: 0.7917 (m-30) cc_final: 0.7694 (m-30) REVERT: W 273 ILE cc_start: 0.8829 (tp) cc_final: 0.8623 (tp) REVERT: W 281 LYS cc_start: 0.8761 (tttm) cc_final: 0.8326 (tppt) REVERT: W 306 PHE cc_start: 0.8438 (m-80) cc_final: 0.8119 (m-80) REVERT: W 310 ASN cc_start: 0.8154 (m-40) cc_final: 0.7847 (m-40) REVERT: W 365 LYS cc_start: 0.8942 (tmmt) cc_final: 0.8732 (tmmt) REVERT: W 367 ILE cc_start: 0.8604 (mt) cc_final: 0.8247 (tt) REVERT: W 375 GLU cc_start: 0.8341 (tp30) cc_final: 0.7928 (tp30) REVERT: W 389 LYS cc_start: 0.8824 (tppt) cc_final: 0.7987 (tppt) REVERT: W 393 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7878 (mm-30) REVERT: W 420 VAL cc_start: 0.8570 (t) cc_final: 0.8134 (m) REVERT: W 424 LYS cc_start: 0.8628 (ptpt) cc_final: 0.8348 (ptpt) REVERT: W 438 LYS cc_start: 0.9081 (pttt) cc_final: 0.8656 (pttt) REVERT: X 48 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: X 95 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8266 (mm-30) REVERT: X 117 LYS cc_start: 0.8129 (ptpp) cc_final: 0.7801 (ptpt) REVERT: X 123 GLU cc_start: 0.8212 (pt0) cc_final: 0.7816 (tt0) REVERT: X 125 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7943 (t80) REVERT: X 165 HIS cc_start: 0.8024 (p90) cc_final: 0.7271 (p-80) REVERT: X 186 TYR cc_start: 0.8543 (t80) cc_final: 0.8304 (t80) REVERT: X 189 ILE cc_start: 0.9162 (mm) cc_final: 0.8881 (mm) REVERT: X 198 ASP cc_start: 0.7478 (m-30) cc_final: 0.6853 (m-30) REVERT: X 211 ARG cc_start: 0.8223 (ttt-90) cc_final: 0.7632 (ttt-90) REVERT: X 228 GLU cc_start: 0.7613 (pm20) cc_final: 0.7230 (pm20) REVERT: X 239 LYS cc_start: 0.8457 (ptpt) cc_final: 0.8073 (ptpp) REVERT: X 245 GLN cc_start: 0.8130 (tp40) cc_final: 0.7819 (tp40) REVERT: X 251 ASP cc_start: 0.7948 (m-30) cc_final: 0.7560 (m-30) REVERT: X 258 ARG cc_start: 0.7305 (mmm160) cc_final: 0.7034 (mmm160) REVERT: X 263 GLN cc_start: 0.7296 (tm-30) cc_final: 0.6685 (tm-30) REVERT: X 265 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8579 (t) REVERT: X 268 MET cc_start: 0.8427 (mtp) cc_final: 0.8150 (mtt) REVERT: X 272 LEU cc_start: 0.8837 (tt) cc_final: 0.8565 (tp) REVERT: X 274 LYS cc_start: 0.7951 (tmmt) cc_final: 0.7690 (ttmt) REVERT: X 277 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8514 (mtmt) REVERT: X 290 LYS cc_start: 0.8583 (tppt) cc_final: 0.7942 (tppt) REVERT: X 313 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7548 (t) REVERT: X 325 ASN cc_start: 0.8605 (m-40) cc_final: 0.8244 (m-40) REVERT: X 328 LEU cc_start: 0.8777 (mt) cc_final: 0.8478 (mm) REVERT: X 362 ASP cc_start: 0.7629 (p0) cc_final: 0.7328 (p0) REVERT: X 378 ASP cc_start: 0.7723 (p0) cc_final: 0.7387 (t0) REVERT: X 385 GLU cc_start: 0.8369 (pp20) cc_final: 0.8027 (pp20) REVERT: X 391 GLU cc_start: 0.8537 (tt0) cc_final: 0.8039 (tp30) REVERT: X 401 ASP cc_start: 0.8340 (m-30) cc_final: 0.7999 (m-30) REVERT: X 409 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7887 (mm-30) REVERT: X 410 THR cc_start: 0.8101 (p) cc_final: 0.7795 (t) REVERT: X 441 GLU cc_start: 0.7931 (tp30) cc_final: 0.7603 (tp30) REVERT: X 443 LYS cc_start: 0.8452 (tmmt) cc_final: 0.8139 (ttmm) REVERT: X 448 ASP cc_start: 0.8005 (t0) cc_final: 0.7393 (t70) REVERT: X 454 LYS cc_start: 0.8365 (tmmt) cc_final: 0.7988 (tmmt) REVERT: Y 59 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8287 (tptp) REVERT: Y 62 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8651 (mt0) REVERT: Y 78 SER cc_start: 0.8192 (t) cc_final: 0.7797 (p) REVERT: Y 111 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7608 (tp) REVERT: Y 113 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7821 (mtmm) REVERT: Y 128 LYS cc_start: 0.8430 (ttpp) cc_final: 0.7823 (ttpp) REVERT: Y 130 LYS cc_start: 0.7892 (ttmm) cc_final: 0.7691 (mtmm) REVERT: Y 136 ILE cc_start: 0.8538 (mt) cc_final: 0.8199 (mm) REVERT: Y 161 LYS cc_start: 0.8585 (pttt) cc_final: 0.8152 (pttp) REVERT: Y 164 ASP cc_start: 0.8212 (m-30) cc_final: 0.7965 (m-30) REVERT: Y 171 LEU cc_start: 0.8434 (mp) cc_final: 0.8227 (mm) REVERT: Y 173 ASN cc_start: 0.8130 (p0) cc_final: 0.7003 (m-40) REVERT: Y 174 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8278 (mmtm) REVERT: Y 175 MET cc_start: 0.8829 (tpp) cc_final: 0.8116 (tpp) REVERT: Y 182 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7122 (tm-30) REVERT: Y 192 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8808 (mm) REVERT: Y 208 ARG cc_start: 0.7948 (mmm-85) cc_final: 0.7447 (mmm-85) REVERT: Y 271 ASP cc_start: 0.8388 (t0) cc_final: 0.8029 (t0) REVERT: Y 274 ASN cc_start: 0.8715 (m-40) cc_final: 0.8276 (m-40) REVERT: Y 277 VAL cc_start: 0.8664 (t) cc_final: 0.8376 (p) REVERT: Y 310 ASN cc_start: 0.8033 (m-40) cc_final: 0.7652 (m-40) REVERT: Y 315 ASP cc_start: 0.8158 (t0) cc_final: 0.7801 (t70) REVERT: Y 317 PHE cc_start: 0.8605 (m-80) cc_final: 0.8346 (m-80) REVERT: Y 327 ARG cc_start: 0.7937 (ttm-80) cc_final: 0.7590 (ttm-80) REVERT: Y 338 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8407 (mttm) REVERT: Y 339 SER cc_start: 0.8771 (t) cc_final: 0.8366 (p) REVERT: Y 357 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8620 (mtpp) REVERT: Y 370 ILE cc_start: 0.8985 (mt) cc_final: 0.8758 (mt) REVERT: Y 384 LEU cc_start: 0.9004 (tp) cc_final: 0.8694 (tt) REVERT: Y 389 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8332 (mmmm) REVERT: Y 390 THR cc_start: 0.8859 (p) cc_final: 0.8535 (p) REVERT: Y 393 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8116 (mt-10) REVERT: Y 412 LYS cc_start: 0.9132 (tptm) cc_final: 0.8903 (tptm) REVERT: Y 417 THR cc_start: 0.7531 (t) cc_final: 0.7161 (t) REVERT: Y 419 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7782 (mp0) REVERT: Y 432 ASP cc_start: 0.8426 (p0) cc_final: 0.7814 (p0) REVERT: Y 449 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8195 (m-30) REVERT: Y 456 ILE cc_start: 0.8852 (mt) cc_final: 0.8584 (mt) REVERT: Z 303 GLU cc_start: 0.8086 (tt0) cc_final: 0.7763 (tt0) REVERT: Z 310 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7504 (mmm-85) outliers start: 136 outliers final: 90 residues processed: 1164 average time/residue: 0.4636 time to fit residues: 818.0990 Evaluate side-chains 1223 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1099 time to evaluate : 3.129 ------------------------------------------------------------------------------- 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 1123 GLU Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1265 VAL 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 1405 MET Chi-restraints excluded: chain R residue 22 ARG Chi-restraints excluded: chain R residue 34 TYR Chi-restraints excluded: chain R residue 58 THR 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 227 MET Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 263 LYS 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 729 ILE Chi-restraints excluded: chain R residue 732 LYS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 181 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 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain T residue 406 MET Chi-restraints excluded: chain T residue 436 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 109 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 331 LYS Chi-restraints excluded: chain U residue 335 THR Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain V residue 35 LEU Chi-restraints excluded: chain V residue 99 LYS Chi-restraints excluded: chain V residue 117 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 W residue 20 ILE Chi-restraints excluded: chain W residue 26 ILE 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 135 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 232 ARG Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 387 LEU Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 64 LEU Chi-restraints excluded: chain X residue 68 LYS 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 265 VAL Chi-restraints excluded: chain X residue 286 GLN 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 377 LYS Chi-restraints excluded: chain X residue 412 LEU Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 434 ILE 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 191 SER 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 323 MET Chi-restraints excluded: chain Y residue 377 VAL Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 395 SER Chi-restraints excluded: chain Y residue 401 ASN Chi-restraints excluded: chain Y residue 402 LEU Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 449 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 316 optimal weight: 0.1980 chunk 298 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 209 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 310 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 609 GLN R 635 GLN T 27 HIS U 63 ASN V 341 ASN ** V 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 401 ASN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 272 GLN Y 373 GLN Y 401 ASN ** Y 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.126571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107747 restraints weight = 57128.596| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.29 r_work: 0.3328 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 29139 Z= 0.172 Angle : 0.712 15.596 39425 Z= 0.354 Chirality : 0.046 0.241 4626 Planarity : 0.005 0.061 5049 Dihedral : 7.016 120.665 4012 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.83 % Favored : 96.14 % Rotamer: Outliers : 3.96 % Allowed : 28.51 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.14), residues: 3626 helix: 0.93 (0.13), residues: 1530 sheet: -0.14 (0.21), residues: 605 loop : -0.71 (0.16), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 586 HIS 0.007 0.001 HIS X 165 PHE 0.035 0.002 PHE R 119 TYR 0.027 0.002 TYR Q1198 ARG 0.013 0.001 ARG R 719 Details of bonding type rmsd hydrogen bonds : bond 0.03798 ( 1098) hydrogen bonds : angle 4.53510 ( 3198) covalent geometry : bond 0.00374 (29139) covalent geometry : angle 0.71213 (39425) ********************** 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 1211 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1086 time to evaluate : 2.990 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: Q 1005 MET cc_start: 0.6815 (mmp) cc_final: 0.6114 (mmp) REVERT: Q 1023 ASP cc_start: 0.7829 (t0) cc_final: 0.7364 (t0) REVERT: Q 1027 SER cc_start: 0.8736 (m) cc_final: 0.8229 (p) REVERT: Q 1083 TYR cc_start: 0.8338 (t80) cc_final: 0.7960 (t80) REVERT: Q 1087 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8273 (ttm-80) REVERT: Q 1100 ASN cc_start: 0.8048 (t0) cc_final: 0.7720 (t0) REVERT: Q 1112 LYS cc_start: 0.8793 (mttp) cc_final: 0.8233 (ttmm) REVERT: Q 1125 CYS cc_start: 0.8653 (m) cc_final: 0.8206 (t) REVERT: Q 1150 LYS cc_start: 0.8541 (tttm) cc_final: 0.7700 (ttmm) REVERT: Q 1154 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: Q 1173 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7363 (mp0) REVERT: Q 1195 LYS cc_start: 0.8227 (tppt) cc_final: 0.7481 (tppt) REVERT: Q 1208 ARG cc_start: 0.8692 (ttm170) cc_final: 0.7693 (mtp180) REVERT: Q 1222 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7293 (tm-30) REVERT: Q 1230 THR cc_start: 0.8795 (m) cc_final: 0.8371 (p) REVERT: Q 1234 ASN cc_start: 0.8546 (m-40) cc_final: 0.8278 (m-40) REVERT: Q 1241 LEU cc_start: 0.9228 (tp) cc_final: 0.8972 (tp) REVERT: Q 1248 ASP cc_start: 0.7534 (t70) cc_final: 0.7043 (t0) REVERT: Q 1261 LYS cc_start: 0.8654 (mttt) cc_final: 0.8424 (mtmm) REVERT: Q 1267 ASP cc_start: 0.8557 (m-30) cc_final: 0.8239 (m-30) REVERT: Q 1270 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8188 (tttt) REVERT: Q 1293 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7298 (mmm-85) REVERT: Q 1295 ILE cc_start: 0.8320 (mt) cc_final: 0.8011 (mm) REVERT: Q 1302 ARG cc_start: 0.8143 (ttt180) cc_final: 0.7612 (mtp-110) REVERT: Q 1305 ASP cc_start: 0.8628 (m-30) cc_final: 0.8281 (m-30) REVERT: Q 1317 ARG cc_start: 0.8108 (ptm160) cc_final: 0.7845 (ptm160) REVERT: Q 1331 MET cc_start: 0.7835 (tpp) cc_final: 0.7304 (tpp) REVERT: Q 1334 TYR cc_start: 0.7785 (p90) cc_final: 0.7245 (p90) REVERT: Q 1335 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7432 (mp) REVERT: R 21 LEU cc_start: 0.6944 (tp) cc_final: 0.6640 (tp) REVERT: R 35 ASN cc_start: 0.8835 (t0) cc_final: 0.8610 (m-40) REVERT: R 55 ASN cc_start: 0.8457 (p0) cc_final: 0.8116 (p0) REVERT: R 70 PHE cc_start: 0.7651 (t80) cc_final: 0.7360 (t80) REVERT: R 156 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: R 182 LYS cc_start: 0.8473 (mmmm) cc_final: 0.8106 (mmmm) REVERT: R 214 TRP cc_start: 0.7473 (t-100) cc_final: 0.6730 (t-100) REVERT: R 242 GLN cc_start: 0.8433 (pt0) cc_final: 0.7877 (pt0) REVERT: R 244 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: R 251 CYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7093 (m) REVERT: R 257 TYR cc_start: 0.8036 (t80) cc_final: 0.7654 (t80) REVERT: R 592 HIS cc_start: 0.8192 (t-90) cc_final: 0.7532 (t-90) REVERT: R 593 LEU cc_start: 0.8726 (mm) cc_final: 0.8455 (mm) REVERT: R 609 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7156 (mp10) REVERT: R 610 HIS cc_start: 0.8169 (m90) cc_final: 0.7750 (m90) REVERT: R 612 MET cc_start: 0.7087 (tpp) cc_final: 0.6857 (tpp) REVERT: R 627 GLN cc_start: 0.8486 (pt0) cc_final: 0.8204 (pt0) REVERT: R 633 GLN cc_start: 0.8271 (mp10) cc_final: 0.8058 (mp10) REVERT: R 640 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7484 (mm-30) REVERT: R 642 SER cc_start: 0.8712 (m) cc_final: 0.8216 (p) REVERT: R 643 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7422 (mm-30) REVERT: R 645 ILE cc_start: 0.9111 (mt) cc_final: 0.8684 (tt) REVERT: R 646 LEU cc_start: 0.9129 (mt) cc_final: 0.8872 (mp) REVERT: R 647 LEU cc_start: 0.8459 (mp) cc_final: 0.8085 (mp) REVERT: R 659 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8008 (tp-100) REVERT: R 663 ASP cc_start: 0.8091 (m-30) cc_final: 0.7589 (m-30) REVERT: R 664 MET cc_start: 0.8713 (mtm) cc_final: 0.8505 (mtp) REVERT: R 686 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8677 (ttmm) REVERT: R 699 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7693 (p) REVERT: R 721 GLU cc_start: 0.8231 (tp30) cc_final: 0.7107 (tp30) REVERT: R 722 GLU cc_start: 0.8159 (pp20) cc_final: 0.7481 (pp20) REVERT: R 723 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7512 (mm-40) REVERT: R 724 TYR cc_start: 0.8228 (t80) cc_final: 0.7697 (t80) REVERT: R 725 ARG cc_start: 0.8639 (mmt180) cc_final: 0.8117 (mmt180) REVERT: R 728 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8644 (m) REVERT: R 729 ILE cc_start: 0.6743 (OUTLIER) cc_final: 0.6430 (tp) REVERT: R 749 ASN cc_start: 0.8023 (m-40) cc_final: 0.7480 (m110) REVERT: S 32 PHE cc_start: 0.8167 (m-10) cc_final: 0.7941 (m-80) REVERT: S 34 ARG cc_start: 0.8498 (ptt90) cc_final: 0.8243 (ptt90) REVERT: S 110 ARG cc_start: 0.8530 (mtm180) cc_final: 0.7707 (mtm180) REVERT: S 140 TYR cc_start: 0.8620 (t80) cc_final: 0.8329 (t80) REVERT: T 56 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7878 (mm-30) REVERT: T 95 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8132 (mm-30) REVERT: T 177 LYS cc_start: 0.8518 (tttt) cc_final: 0.8034 (mtpp) REVERT: T 178 THR cc_start: 0.8945 (m) cc_final: 0.8640 (t) REVERT: T 193 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8060 (mmmt) REVERT: T 211 ARG cc_start: 0.8622 (ttt-90) cc_final: 0.8285 (ttt-90) REVERT: T 223 ASP cc_start: 0.6867 (m-30) cc_final: 0.6603 (m-30) REVERT: T 230 VAL cc_start: 0.9022 (OUTLIER) cc_final: 0.8752 (m) REVERT: T 251 ASP cc_start: 0.8145 (m-30) cc_final: 0.7773 (m-30) REVERT: T 273 LEU cc_start: 0.7776 (tp) cc_final: 0.7499 (tt) REVERT: T 295 TYR cc_start: 0.8599 (m-80) cc_final: 0.8127 (m-80) REVERT: T 371 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7761 (ptm160) REVERT: T 381 ARG cc_start: 0.8690 (ttt-90) cc_final: 0.8342 (ttm-80) REVERT: T 382 THR cc_start: 0.8655 (p) cc_final: 0.8169 (p) REVERT: T 385 GLU cc_start: 0.8474 (pt0) cc_final: 0.7802 (pp20) REVERT: T 409 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7655 (mt-10) REVERT: T 413 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7172 (mtm-85) REVERT: T 417 GLN cc_start: 0.8169 (mt0) cc_final: 0.7792 (mt0) REVERT: T 431 ARG cc_start: 0.7625 (mtm110) cc_final: 0.7253 (mtm180) REVERT: T 438 ASP cc_start: 0.8421 (m-30) cc_final: 0.8028 (m-30) REVERT: T 439 VAL cc_start: 0.8912 (t) cc_final: 0.8689 (t) REVERT: T 456 LEU cc_start: 0.8957 (tp) cc_final: 0.8370 (mt) REVERT: U 38 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7293 (mtt90) REVERT: U 45 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7782 (p) REVERT: U 86 MET cc_start: 0.8000 (mmm) cc_final: 0.7518 (mmm) REVERT: U 94 LYS cc_start: 0.8836 (tppt) cc_final: 0.8441 (tptp) REVERT: U 104 SER cc_start: 0.8605 (m) cc_final: 0.8225 (t) REVERT: U 105 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7218 (mt-10) REVERT: U 110 GLU cc_start: 0.7934 (pp20) cc_final: 0.7615 (pp20) REVERT: U 123 LYS cc_start: 0.8268 (mttt) cc_final: 0.7805 (mttm) REVERT: U 139 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6285 (tp30) REVERT: U 161 LYS cc_start: 0.8568 (ptmm) cc_final: 0.8110 (ptmm) REVERT: U 166 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7083 (tp30) REVERT: U 188 ASP cc_start: 0.7750 (m-30) cc_final: 0.6766 (m-30) REVERT: U 193 ASP cc_start: 0.7946 (t0) cc_final: 0.7489 (t0) REVERT: U 194 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8389 (ttpt) REVERT: U 198 LYS cc_start: 0.8519 (tttm) cc_final: 0.8219 (tttm) REVERT: U 235 VAL cc_start: 0.8594 (t) cc_final: 0.8132 (p) REVERT: U 245 ASP cc_start: 0.8103 (m-30) cc_final: 0.7810 (m-30) REVERT: U 270 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7553 (mtt180) REVERT: U 272 GLN cc_start: 0.8025 (tp40) cc_final: 0.7436 (tp40) REVERT: U 276 LYS cc_start: 0.8976 (tptt) cc_final: 0.8457 (tppp) REVERT: U 281 LYS cc_start: 0.8983 (tttm) cc_final: 0.8587 (ttmm) REVERT: U 285 LYS cc_start: 0.8611 (mttp) cc_final: 0.8050 (mttp) REVERT: U 300 MET cc_start: 0.8421 (mmm) cc_final: 0.8177 (mmm) REVERT: U 311 ARG cc_start: 0.8040 (mpt180) cc_final: 0.7681 (mpt180) REVERT: U 315 ASP cc_start: 0.8119 (t0) cc_final: 0.7801 (t0) REVERT: U 321 VAL cc_start: 0.8836 (t) cc_final: 0.8609 (p) REVERT: U 338 LYS cc_start: 0.8919 (mttt) cc_final: 0.8667 (ttmm) REVERT: U 339 SER cc_start: 0.8876 (m) cc_final: 0.8496 (t) REVERT: U 349 ASP cc_start: 0.8714 (t0) cc_final: 0.8224 (m-30) REVERT: U 365 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8463 (ttmt) REVERT: U 376 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7865 (mm-30) REVERT: U 378 GLU cc_start: 0.7476 (mp0) cc_final: 0.7239 (mp0) REVERT: U 393 GLU cc_start: 0.7701 (pp20) cc_final: 0.7386 (pp20) REVERT: U 399 SER cc_start: 0.8391 (m) cc_final: 0.8119 (p) REVERT: U 400 SER cc_start: 0.8280 (t) cc_final: 0.7832 (m) REVERT: U 411 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7128 (mpt) REVERT: U 412 LYS cc_start: 0.8796 (tppt) cc_final: 0.8518 (tppt) REVERT: U 419 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7061 (mm-30) REVERT: U 424 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7997 (mmtt) REVERT: U 428 LEU cc_start: 0.8677 (mt) cc_final: 0.8401 (pp) REVERT: U 444 GLU cc_start: 0.8192 (tp30) cc_final: 0.7568 (tp30) REVERT: V 30 ILE cc_start: 0.8517 (mt) cc_final: 0.8203 (mm) REVERT: V 31 LYS cc_start: 0.8175 (mmpt) cc_final: 0.7738 (mmtm) REVERT: V 35 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7503 (mp) REVERT: V 56 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7429 (mm-30) REVERT: V 88 LEU cc_start: 0.8613 (mm) cc_final: 0.8373 (mt) REVERT: V 95 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7737 (mt-10) REVERT: V 99 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8289 (mtpp) REVERT: V 114 GLU cc_start: 0.7871 (mt-10) cc_final: 0.6515 (mt-10) REVERT: V 127 ARG cc_start: 0.8263 (ttp-170) cc_final: 0.7924 (ttm110) REVERT: V 141 GLU cc_start: 0.7657 (pm20) cc_final: 0.7368 (pm20) REVERT: V 144 VAL cc_start: 0.8421 (t) cc_final: 0.8021 (m) REVERT: V 180 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7617 (tpt-90) REVERT: V 187 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7751 (mt-10) REVERT: V 192 GLU cc_start: 0.7355 (tp30) cc_final: 0.7135 (tp30) REVERT: V 194 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8508 (m) REVERT: V 203 GLU cc_start: 0.7987 (tt0) cc_final: 0.7688 (tt0) REVERT: V 218 TYR cc_start: 0.8687 (m-80) cc_final: 0.8232 (m-80) REVERT: V 222 PHE cc_start: 0.8370 (m-80) cc_final: 0.8125 (m-10) REVERT: V 236 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7702 (mm-30) REVERT: V 239 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8063 (mttt) REVERT: V 253 ASP cc_start: 0.7538 (m-30) cc_final: 0.7291 (m-30) REVERT: V 254 VAL cc_start: 0.8693 (t) cc_final: 0.8404 (m) REVERT: V 268 MET cc_start: 0.7683 (mmm) cc_final: 0.7297 (mmm) REVERT: V 286 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7877 (mp10) REVERT: V 292 VAL cc_start: 0.8620 (t) cc_final: 0.8326 (m) REVERT: V 297 ASP cc_start: 0.8281 (m-30) cc_final: 0.8044 (m-30) REVERT: V 311 ASP cc_start: 0.8190 (t0) cc_final: 0.7947 (t0) REVERT: V 312 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7746 (mm-30) REVERT: V 318 ILE cc_start: 0.8646 (tp) cc_final: 0.8377 (tt) REVERT: V 325 ASN cc_start: 0.8264 (t0) cc_final: 0.7595 (t0) REVERT: V 344 MET cc_start: 0.8686 (mmt) cc_final: 0.8432 (mmm) REVERT: V 365 ASP cc_start: 0.7903 (m-30) cc_final: 0.7439 (t70) REVERT: V 367 LEU cc_start: 0.8373 (mt) cc_final: 0.8094 (mm) REVERT: V 379 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8205 (mt-10) REVERT: V 403 LEU cc_start: 0.8731 (mt) cc_final: 0.8388 (mm) REVERT: V 406 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7545 (tmm) REVERT: V 427 GLN cc_start: 0.8046 (pt0) cc_final: 0.7824 (pt0) REVERT: V 443 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8263 (mtmm) REVERT: V 450 LYS cc_start: 0.7936 (mtmt) cc_final: 0.7508 (ptpt) REVERT: V 453 THR cc_start: 0.8733 (m) cc_final: 0.8410 (p) REVERT: V 454 LYS cc_start: 0.8879 (mptt) cc_final: 0.8462 (mmtt) REVERT: W 26 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8503 (mm) REVERT: W 45 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8314 (p) REVERT: W 66 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8477 (mm) REVERT: W 86 MET cc_start: 0.7876 (mmm) cc_final: 0.7523 (mmm) REVERT: W 135 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7863 (mm) REVERT: W 183 LYS cc_start: 0.8483 (mptt) cc_final: 0.8256 (mptt) REVERT: W 185 LEU cc_start: 0.8179 (mt) cc_final: 0.7707 (mt) REVERT: W 188 ASP cc_start: 0.7706 (m-30) cc_final: 0.7106 (m-30) REVERT: W 191 SER cc_start: 0.8718 (t) cc_final: 0.8187 (m) REVERT: W 198 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8014 (tppt) REVERT: W 200 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8050 (p) REVERT: W 231 LYS cc_start: 0.8358 (mttm) cc_final: 0.8102 (mmmm) REVERT: W 232 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7714 (tpp80) REVERT: W 261 ASP cc_start: 0.8236 (t0) cc_final: 0.7779 (t0) REVERT: W 264 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6253 (mt-10) REVERT: W 271 ASP cc_start: 0.7855 (m-30) cc_final: 0.7654 (m-30) REVERT: W 273 ILE cc_start: 0.8828 (tp) cc_final: 0.8622 (tp) REVERT: W 281 LYS cc_start: 0.8751 (tttm) cc_final: 0.8340 (tppt) REVERT: W 306 PHE cc_start: 0.8458 (m-80) cc_final: 0.8133 (m-80) REVERT: W 310 ASN cc_start: 0.8110 (m-40) cc_final: 0.7806 (m-40) REVERT: W 338 LYS cc_start: 0.8668 (mttt) cc_final: 0.8378 (mttm) REVERT: W 365 LYS cc_start: 0.8945 (tmmt) cc_final: 0.8720 (tmmt) REVERT: W 367 ILE cc_start: 0.8609 (mt) cc_final: 0.8270 (tt) REVERT: W 373 GLN cc_start: 0.8516 (mp-120) cc_final: 0.8208 (mt0) REVERT: W 375 GLU cc_start: 0.8336 (tp30) cc_final: 0.7931 (tp30) REVERT: W 389 LYS cc_start: 0.8808 (tppt) cc_final: 0.7962 (tppt) REVERT: W 393 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7903 (mm-30) REVERT: W 420 VAL cc_start: 0.8593 (t) cc_final: 0.8126 (m) REVERT: W 424 LYS cc_start: 0.8670 (ptpt) cc_final: 0.8377 (ptpt) REVERT: W 438 LYS cc_start: 0.9050 (pttt) cc_final: 0.8638 (pttt) REVERT: X 95 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8272 (mm-30) REVERT: X 106 VAL cc_start: 0.8319 (OUTLIER) cc_final: 0.8018 (p) REVERT: X 123 GLU cc_start: 0.8221 (pt0) cc_final: 0.7842 (tt0) REVERT: X 125 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7976 (t80) REVERT: X 165 HIS cc_start: 0.7901 (p90) cc_final: 0.7568 (p-80) REVERT: X 177 LYS cc_start: 0.8051 (tptm) cc_final: 0.7849 (tptm) REVERT: X 186 TYR cc_start: 0.8565 (t80) cc_final: 0.8323 (t80) REVERT: X 189 ILE cc_start: 0.9152 (mm) cc_final: 0.8867 (mm) REVERT: X 198 ASP cc_start: 0.7481 (m-30) cc_final: 0.6864 (m-30) REVERT: X 211 ARG cc_start: 0.8241 (ttt-90) cc_final: 0.7612 (ttp80) REVERT: X 228 GLU cc_start: 0.7645 (pm20) cc_final: 0.6926 (pm20) REVERT: X 239 LYS cc_start: 0.8476 (ptpt) cc_final: 0.8095 (ptpp) REVERT: X 245 GLN cc_start: 0.8180 (tp40) cc_final: 0.7877 (tp40) REVERT: X 253 ASP cc_start: 0.8064 (m-30) cc_final: 0.7749 (t0) REVERT: X 258 ARG cc_start: 0.7325 (mmm160) cc_final: 0.7059 (mmm160) REVERT: X 263 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6721 (tm-30) REVERT: X 268 MET cc_start: 0.8452 (mtp) cc_final: 0.8189 (mtt) REVERT: X 272 LEU cc_start: 0.8857 (tt) cc_final: 0.8593 (tp) REVERT: X 274 LYS cc_start: 0.7974 (tmmt) cc_final: 0.7707 (ttmt) REVERT: X 277 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8546 (mtmt) REVERT: X 290 LYS cc_start: 0.8591 (tppt) cc_final: 0.7968 (tppt) REVERT: X 313 VAL cc_start: 0.8043 (OUTLIER) cc_final: 0.7575 (t) REVERT: X 325 ASN cc_start: 0.8607 (m-40) cc_final: 0.8234 (m-40) REVERT: X 328 LEU cc_start: 0.8793 (mt) cc_final: 0.8478 (mm) REVERT: X 329 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7267 (tp30) REVERT: X 362 ASP cc_start: 0.7601 (p0) cc_final: 0.7312 (p0) REVERT: X 378 ASP cc_start: 0.7710 (p0) cc_final: 0.7395 (t0) REVERT: X 385 GLU cc_start: 0.8401 (pp20) cc_final: 0.8059 (pp20) REVERT: X 391 GLU cc_start: 0.8544 (tt0) cc_final: 0.8038 (tp30) REVERT: X 401 ASP cc_start: 0.8361 (m-30) cc_final: 0.8009 (m-30) REVERT: X 409 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7917 (mm-30) REVERT: X 410 THR cc_start: 0.8107 (p) cc_final: 0.7813 (t) REVERT: X 441 GLU cc_start: 0.7955 (tp30) cc_final: 0.7631 (tp30) REVERT: X 443 LYS cc_start: 0.8451 (tmmt) cc_final: 0.8101 (ttmm) REVERT: X 448 ASP cc_start: 0.7990 (t0) cc_final: 0.7404 (t70) REVERT: X 454 LYS cc_start: 0.8388 (tmmt) cc_final: 0.7730 (tmmt) REVERT: X 457 GLU cc_start: 0.7787 (pp20) cc_final: 0.7453 (pp20) REVERT: Y 59 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8226 (tppt) REVERT: Y 78 SER cc_start: 0.8122 (t) cc_final: 0.7737 (p) REVERT: Y 113 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7858 (mtmm) REVERT: Y 122 ARG cc_start: 0.8251 (mtt90) cc_final: 0.8021 (mtp85) REVERT: Y 130 LYS cc_start: 0.7908 (ttmm) cc_final: 0.7665 (mtmm) REVERT: Y 136 ILE cc_start: 0.8545 (mt) cc_final: 0.8204 (mm) REVERT: Y 171 LEU cc_start: 0.8436 (mp) cc_final: 0.8232 (mm) REVERT: Y 173 ASN cc_start: 0.8154 (p0) cc_final: 0.7840 (p0) REVERT: Y 174 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8361 (mmmt) REVERT: Y 175 MET cc_start: 0.8833 (tpp) cc_final: 0.8103 (tpp) REVERT: Y 182 GLU cc_start: 0.7466 (tm-30) cc_final: 0.7158 (tm-30) REVERT: Y 192 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8815 (mm) REVERT: Y 271 ASP cc_start: 0.8400 (t0) cc_final: 0.8039 (t0) REVERT: Y 274 ASN cc_start: 0.8729 (m-40) cc_final: 0.8281 (m-40) REVERT: Y 277 VAL cc_start: 0.8682 (t) cc_final: 0.8405 (p) REVERT: Y 281 LYS cc_start: 0.8467 (tptm) cc_final: 0.7946 (tppt) REVERT: Y 304 GLU cc_start: 0.7989 (mp0) cc_final: 0.7765 (mp0) REVERT: Y 310 ASN cc_start: 0.8007 (m-40) cc_final: 0.7632 (m-40) REVERT: Y 315 ASP cc_start: 0.8140 (t0) cc_final: 0.7756 (t70) REVERT: Y 327 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7522 (ttm-80) REVERT: Y 338 LYS cc_start: 0.8666 (mtpp) cc_final: 0.8427 (mttt) REVERT: Y 339 SER cc_start: 0.8744 (t) cc_final: 0.8329 (p) REVERT: Y 370 ILE cc_start: 0.8991 (mt) cc_final: 0.8755 (mt) REVERT: Y 373 GLN cc_start: 0.8667 (tt0) cc_final: 0.8366 (tp40) REVERT: Y 375 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7340 (tp30) REVERT: Y 382 ASP cc_start: 0.8365 (p0) cc_final: 0.8013 (p0) REVERT: Y 384 LEU cc_start: 0.9012 (tp) cc_final: 0.8689 (tt) REVERT: Y 389 LYS cc_start: 0.8923 (ttpt) cc_final: 0.8617 (tppt) REVERT: Y 390 THR cc_start: 0.8869 (p) cc_final: 0.8523 (p) REVERT: Y 393 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8103 (mt-10) REVERT: Y 419 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8083 (mm-30) REVERT: Y 427 TYR cc_start: 0.8249 (t80) cc_final: 0.7630 (t80) REVERT: Y 441 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8243 (mm-40) REVERT: Y 449 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8222 (m-30) REVERT: Y 456 ILE cc_start: 0.8854 (mt) cc_final: 0.8375 (mt) REVERT: Z 303 GLU cc_start: 0.8098 (tt0) cc_final: 0.7763 (tt0) REVERT: Z 310 ARG cc_start: 0.8321 (mtt-85) cc_final: 0.7562 (mmm-85) outliers start: 125 outliers final: 84 residues processed: 1146 average time/residue: 0.4451 time to fit residues: 776.7478 Evaluate side-chains 1202 residues out of total 3175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1086 time to evaluate : 3.052 ------------------------------------------------------------------------------- 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 1123 GLU Chi-restraints excluded: chain Q residue 1154 GLU Chi-restraints excluded: chain Q residue 1265 VAL 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 1405 MET Chi-restraints excluded: chain R residue 22 ARG Chi-restraints excluded: chain R residue 34 TYR 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 227 MET Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 251 CYS Chi-restraints excluded: chain R residue 263 LYS 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 729 ILE Chi-restraints excluded: chain R residue 732 LYS Chi-restraints excluded: chain S residue 52 HIS Chi-restraints excluded: chain S residue 94 LEU Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 181 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 380 ILE Chi-restraints excluded: chain T residue 390 VAL Chi-restraints excluded: chain T residue 398 SER Chi-restraints excluded: chain T residue 406 MET Chi-restraints excluded: chain T residue 436 VAL Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 109 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 331 LYS Chi-restraints excluded: chain U residue 335 THR Chi-restraints excluded: chain U residue 389 LYS Chi-restraints excluded: chain U residue 405 VAL Chi-restraints excluded: chain U residue 411 MET Chi-restraints excluded: chain V residue 35 LEU 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 406 MET Chi-restraints excluded: chain V residue 455 ILE Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 26 ILE 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 135 LEU Chi-restraints excluded: chain W residue 154 LYS Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 220 ARG Chi-restraints excluded: chain W residue 232 ARG Chi-restraints excluded: chain W residue 346 ASP Chi-restraints excluded: chain W residue 401 ASN 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 68 LYS 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 286 GLN 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 377 LYS Chi-restraints excluded: chain X residue 412 LEU Chi-restraints excluded: chain X residue 416 LEU Chi-restraints excluded: chain X residue 418 LEU Chi-restraints excluded: chain X residue 434 ILE 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 191 SER 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 323 MET Chi-restraints excluded: chain Y residue 377 VAL Chi-restraints excluded: chain Y residue 392 VAL Chi-restraints excluded: chain Y residue 449 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 265 optimal weight: 0.0980 chunk 268 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 chunk 239 optimal weight: 0.6980 chunk 339 optimal weight: 1.9990 chunk 286 optimal weight: 0.9990 chunk 345 optimal weight: 0.4980 chunk 190 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 635 GLN T 27 HIS U 63 ASN V 341 ASN W 401 ASN W 446 GLN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 408 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 = 0.3808 r_free = 0.3808 target = 0.127979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.109080 restraints weight = 56997.400| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.31 r_work: 0.3352 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 29139 Z= 0.140 Angle : 0.719 15.107 39425 Z= 0.356 Chirality : 0.046 0.243 4626 Planarity : 0.005 0.148 5049 Dihedral : 6.931 116.867 4012 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 3.77 % Allowed : 29.05 % Favored : 67.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3626 helix: 0.99 (0.13), residues: 1535 sheet: -0.04 (0.21), residues: 597 loop : -0.73 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 586 HIS 0.004 0.001 HIS U 242 PHE 0.035 0.002 PHE R 119 TYR 0.028 0.002 TYR V 186 ARG 0.013 0.001 ARG U 69 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 1098) hydrogen bonds : angle 4.47460 ( 3198) covalent geometry : bond 0.00317 (29139) covalent geometry : angle 0.71877 (39425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19301.45 seconds wall clock time: 332 minutes 19.62 seconds (19939.62 seconds total)