Starting phenix.real_space_refine on Mon Aug 25 14:38:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eu9_28609/08_2025/8eu9_28609_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eu9_28609/08_2025/8eu9_28609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eu9_28609/08_2025/8eu9_28609.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eu9_28609/08_2025/8eu9_28609.map" model { file = "/net/cci-nas-00/data/ceres_data/8eu9_28609/08_2025/8eu9_28609_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eu9_28609/08_2025/8eu9_28609_neut.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 95 5.16 5 C 17928 2.51 5 N 4917 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28517 Number of models: 1 Model: "" Number of chains: 16 Chain: "Q" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3413 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 22, 'TRANS': 403} Chain breaks: 6 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "R" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3489 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 28, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "S" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 969 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 112} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 3338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3338 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3333 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "V" Number of atoms: 3388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3388 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "W" Number of atoms: 3389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3389 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "X" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3376 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 423} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "Y" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3412 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 248 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 25} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.08, per 1000 atoms: 0.21 Number of scatterers: 28517 At special positions: 0 Unit cell: (134.435, 194.555, 147.795, 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 5565 8.00 N 4917 7.00 C 17928 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 867.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6830 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 35 sheets defined 44.4% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'Q' and resid 957 through 970 removed outlier: 4.506A pdb=" N GLN Q 970 " --> pdb=" O VAL Q 966 " (cutoff:3.500A) Processing helix chain 'Q' and resid 980 through 985 Processing helix chain 'Q' and resid 1000 through 1013 removed outlier: 3.597A pdb=" N HIS Q1013 " --> pdb=" O LYS Q1009 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 3.945A 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 removed outlier: 3.927A pdb=" N CYS Q1125 " --> pdb=" O ASN Q1121 " (cutoff:3.500A) 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 removed outlier: 3.592A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1185 through 1191 removed outlier: 3.587A pdb=" N LEU Q1190 " --> pdb=" O VAL Q1186 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU Q1191 " --> pdb=" O MET Q1187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1193 through 1201 Processing helix chain 'Q' and resid 1202 through 1206 removed outlier: 3.892A pdb=" N ILE Q1206 " --> pdb=" O LEU Q1203 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1227 through 1238 Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1264 through 1268 Processing helix chain 'Q' and resid 1279 through 1283 removed outlier: 3.660A pdb=" N SER Q1283 " --> pdb=" O LYS Q1280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1290 through 1297 Processing helix chain 'Q' and resid 1300 through 1311 Processing helix chain 'Q' and resid 1321 through 1323 No H-bonds generated for 'chain 'Q' and resid 1321 through 1323' Processing helix chain 'Q' and resid 1327 through 1337 Processing helix chain 'Q' and resid 1357 through 1364 removed outlier: 4.524A pdb=" N TRP Q1361 " --> pdb=" O LEU Q1357 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN Q1362 " --> pdb=" O VAL Q1358 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR Q1363 " --> pdb=" O HIS Q1359 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN Q1364 " --> pdb=" O ASP Q1360 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1357 through 1364' Processing helix chain 'Q' and resid 1397 through 1408 removed outlier: 4.125A pdb=" N ASP Q1401 " --> pdb=" O ASN Q1397 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG Q1407 " --> pdb=" O GLN Q1403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1427 through 1433 removed outlier: 4.112A pdb=" N ARG Q1431 " --> pdb=" O THR Q1427 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1435 through 1440 removed outlier: 3.602A pdb=" N LYS Q1439 " --> pdb=" O ARG Q1435 " (cutoff:3.500A) Processing helix chain 'R' and resid 83 through 88 Processing helix chain 'R' and resid 89 through 96 Processing helix chain 'R' and resid 107 through 123 Processing helix chain 'R' and resid 143 through 155 Processing helix chain 'R' and resid 168 through 177 Processing helix chain 'R' and resid 215 through 231 removed outlier: 3.764A 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 261 removed outlier: 3.617A pdb=" N ASP R 260 " --> pdb=" O ASN R 256 " (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 621 through 625 removed outlier: 4.074A pdb=" N VAL R 624 " --> pdb=" O VAL R 621 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE R 625 " --> pdb=" O PRO R 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 621 through 625' Processing helix chain 'R' and resid 627 through 632 Processing helix chain 'R' and resid 637 through 647 Processing helix chain 'R' and resid 658 through 667 Processing helix chain 'R' and resid 679 through 692 removed outlier: 3.509A pdb=" N PHE R 691 " --> pdb=" O GLU R 687 " (cutoff:3.500A) Processing helix chain 'R' and resid 708 through 720 removed outlier: 3.618A pdb=" N LYS R 712 " --> pdb=" O LEU R 708 " (cutoff:3.500A) Processing helix chain 'R' and resid 720 through 728 Processing helix chain 'R' and resid 730 through 737 Processing helix chain 'R' and resid 738 through 741 removed outlier: 3.815A pdb=" N TYR R 741 " --> pdb=" O GLY R 738 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 738 through 741' Processing helix chain 'S' and resid 30 through 41 Processing helix chain 'S' and resid 62 through 83 Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 150 through 160 removed outlier: 4.134A pdb=" N GLU S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU S 158 " --> pdb=" O GLU S 154 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG S 159 " --> pdb=" O TYR S 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.667A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 removed outlier: 3.611A pdb=" N GLY T 97 " --> pdb=" O SER T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.716A 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 129 removed outlier: 3.502A pdb=" N ILE T 129 " --> pdb=" O PHE T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 182 through 191 Processing helix chain 'T' and resid 218 through 222 removed outlier: 4.038A pdb=" N GLU T 221 " --> pdb=" O TYR T 218 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE T 222 " --> pdb=" O ALA T 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 218 through 222' Processing helix chain 'T' and resid 249 through 255 Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.767A 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 356 through 359 Processing helix chain 'T' and resid 360 through 367 removed outlier: 3.995A pdb=" N ARG T 366 " --> pdb=" O ASP T 362 " (cutoff:3.500A) 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 429 removed outlier: 3.615A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 459 removed outlier: 3.619A pdb=" N SER T 452 " --> pdb=" O ASP T 448 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 80 through 93 removed outlier: 3.731A pdb=" N GLY U 93 " --> pdb=" O SER U 89 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 181 removed outlier: 3.640A pdb=" N LYS U 181 " --> pdb=" O ASP U 177 " (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 283 removed outlier: 3.733A 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 311 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 376 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 4.352A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 removed outlier: 3.679A pdb=" N VAL U 423 " --> pdb=" O GLU U 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 432 through 443 removed outlier: 3.502A pdb=" N SER U 436 " --> pdb=" O ASP U 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.758A 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 removed outlier: 3.567A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 129 removed outlier: 3.574A pdb=" N ILE V 129 " --> pdb=" O PHE V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 154 through 158 removed outlier: 3.622A pdb=" N GLY V 157 " --> pdb=" O ASN V 154 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY V 158 " --> pdb=" O PRO V 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 154 through 158' Processing helix chain 'V' and resid 182 through 192 removed outlier: 3.890A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 249 through 258 Processing helix chain 'V' and resid 264 through 273 removed outlier: 3.853A pdb=" N LEU V 272 " --> pdb=" O MET V 268 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU V 273 " --> pdb=" O MET V 269 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 299 removed outlier: 3.620A 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: 3.544A pdb=" N PHE V 321 " --> pdb=" O ASP V 317 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 360 through 365 removed outlier: 3.828A pdb=" N ASP V 365 " --> pdb=" O PRO V 361 " (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 418 removed outlier: 3.560A pdb=" N ALA V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 429 removed outlier: 3.516A pdb=" N CYS V 422 " --> pdb=" O LEU V 418 " (cutoff:3.500A) Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 459 removed outlier: 3.514A pdb=" N SER V 452 " --> pdb=" O ASP V 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'W' and resid 80 through 92 Processing helix chain 'W' and resid 103 through 107 removed outlier: 3.768A pdb=" N ILE W 106 " --> pdb=" O GLY W 103 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE W 107 " --> pdb=" O SER W 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 103 through 107' Processing helix chain 'W' and resid 112 through 125 removed outlier: 3.665A pdb=" N ILE W 125 " --> pdb=" O PHE W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 172 through 181 Processing helix chain 'W' and resid 241 through 250 removed outlier: 3.960A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 255 through 260 Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.854A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 297 through 301 Processing helix chain 'W' and resid 302 through 313 Processing helix chain 'W' and resid 344 through 351 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: 3.702A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 4.051A 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: 3.837A pdb=" N ASN W 443 " --> pdb=" O TYR W 439 " (cutoff:3.500A) Processing helix chain 'W' and resid 444 through 447 Processing helix chain 'X' and resid 51 through 68 Processing helix chain 'X' and resid 84 through 97 Processing helix chain 'X' and resid 108 through 110 No H-bonds generated for 'chain 'X' and resid 108 through 110' Processing helix chain 'X' and resid 116 through 129 removed outlier: 3.727A pdb=" N ALA X 128 " --> pdb=" O ASN X 124 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE X 129 " --> pdb=" O PHE X 125 " (cutoff:3.500A) Processing helix chain 'X' and resid 184 through 192 removed outlier: 4.326A pdb=" N SER X 188 " --> pdb=" O THR X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 265 through 273 Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.673A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 316 removed outlier: 3.643A pdb=" N LEU X 316 " --> pdb=" O VAL X 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 313 through 316' Processing helix chain 'X' and resid 317 through 328 removed outlier: 3.948A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 360 through 365 removed outlier: 3.722A pdb=" N ASP X 365 " --> pdb=" O PRO X 361 " (cutoff:3.500A) 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 417 removed outlier: 3.671A pdb=" N ALA X 415 " --> pdb=" O SER X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 418 through 429 removed outlier: 3.527A pdb=" N SER X 429 " --> pdb=" O LEU X 425 " (cutoff:3.500A) Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 removed outlier: 3.713A pdb=" N THR X 458 " --> pdb=" O LYS X 454 " (cutoff:3.500A) Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 80 through 93 removed outlier: 3.588A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 182 Processing helix chain 'Y' and resid 241 through 250 removed outlier: 3.901A pdb=" N ASP Y 245 " --> pdb=" O LEU Y 241 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG Y 250 " --> pdb=" O VAL Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 252 through 254 No H-bonds generated for 'chain 'Y' and resid 252 through 254' Processing helix chain 'Y' and resid 255 through 260 removed outlier: 3.554A pdb=" N GLY Y 260 " --> pdb=" O ALA Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 266 through 283 removed outlier: 3.670A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 297 through 301 removed outlier: 3.524A pdb=" N MET Y 300 " --> pdb=" O GLU Y 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 312 removed outlier: 3.773A pdb=" N ARG Y 311 " --> pdb=" O SER Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 351 removed outlier: 3.745A pdb=" N ARG Y 350 " --> pdb=" O ASP Y 346 " (cutoff:3.500A) 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: 3.792A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE Y 403 " --> pdb=" O SER Y 399 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL Y 405 " --> pdb=" O ASN Y 401 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.677A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 443 removed outlier: 3.805A pdb=" N ASN Y 443 " --> pdb=" O TYR Y 439 " (cutoff:3.500A) Processing helix chain 'Y' and resid 444 through 447 Processing sheet with id=AA1, first strand: chain 'Q' and resid 949 through 954 Processing sheet with id=AA2, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 5.816A 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 1072 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 1071 through 1072 current: chain 'V' and resid 163 through 171 removed outlier: 3.502A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 176 through 181 current: chain 'V' and resid 209 through 215 removed outlier: 6.495A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 6.384A 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 1085 removed outlier: 6.080A 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 'Q' and resid 1317 through 1319 removed outlier: 4.175A pdb=" N LEU Q1372 " --> pdb=" O VAL Q1318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 16 through 17 removed outlier: 5.342A pdb=" N ASP R 17 " --> pdb=" O GLU R 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 61 through 62 removed outlier: 3.504A pdb=" N ARG R 50 " --> pdb=" O ASP R 43 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR R 137 " --> pdb=" O ILE R 42 " (cutoff:3.500A) Processing sheet with id=AA8, 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 702 Processing sheet with id=AA9, first strand: chain 'S' and resid 125 through 126 removed outlier: 3.586A pdb=" N TYR S 125 " --> pdb=" O TYR S 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB2, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.404A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU T 308 " --> pdb=" O VAL T 337 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ALA T 339 " --> pdb=" O LEU T 308 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ILE T 310 " --> pdb=" O ALA T 339 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE T 75 " --> pdb=" O LEU T 338 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 130 through 150 removed outlier: 6.449A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS T 165 " --> pdb=" O PRO T 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 175 through 181 current: chain 'T' and resid 209 through 215 removed outlier: 6.149A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 345 through 346 Processing sheet with id=AB5, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AB6, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.271A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU U 293 " --> pdb=" O MET U 322 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ALA U 324 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ILE U 295 " --> pdb=" O ALA U 324 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 233 through 240 removed outlier: 3.611A pdb=" N LYS U 233 " --> pdb=" O THR U 133 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU U 131 " --> pdb=" O VAL U 235 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 166 through 171 removed outlier: 4.226A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN U 155 " --> pdb=" O ILE U 145 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILE U 145 " --> pdb=" O GLN U 155 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY U 203 " --> pdb=" O VAL U 189 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) 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: 4.022A 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: 6.784A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU V 308 " --> pdb=" O VAL V 337 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N ALA V 339 " --> pdb=" O LEU V 308 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE V 310 " --> pdb=" O ALA V 339 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER V 340 " --> pdb=" O LEU V 77 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.907A 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 'W' and resid 40 through 41 Processing sheet with id=AC5, first strand: chain 'W' and resid 98 through 99 removed outlier: 6.230A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 126 through 143 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 126 through 143 current: chain 'W' and resid 154 through 161 removed outlier: 4.042A 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 'Z' and resid 315 through 319 Processing sheet with id=AC7, first strand: chain 'W' and resid 329 through 331 Processing sheet with id=AC8, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.393A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU X 308 " --> pdb=" O VAL X 337 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA X 339 " --> pdb=" O LEU X 308 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE X 310 " --> pdb=" O ALA X 339 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE X 75 " --> pdb=" O LEU X 338 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N SER X 340 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU X 77 " --> pdb=" O SER X 340 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'X' and resid 245 through 248 Processing sheet with id=AD1, first strand: chain 'X' and resid 137 through 150 removed outlier: 6.580A pdb=" N GLY X 169 " --> pdb=" O THR X 145 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU X 147 " --> pdb=" O ILE X 167 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE X 167 " --> pdb=" O LEU X 147 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N HIS X 165 " --> pdb=" O PRO X 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 210 through 215 removed outlier: 6.254A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) 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: 7.702A 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: 3.714A pdb=" N SER Y 41 " --> pdb=" O MET Y 44 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET Y 44 " --> pdb=" O SER Y 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'Y' and resid 98 through 101 removed outlier: 6.175A pdb=" N THR Y 99 " --> pdb=" O PHE Y 294 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Y' and resid 125 through 139 removed outlier: 3.515A pdb=" N GLY Y 203 " --> pdb=" O VAL Y 189 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL Y 222 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG Y 204 " --> pdb=" O VAL Y 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 157 through 158 Processing sheet with id=AD8, first strand: chain 'Y' and resid 330 through 331 1093 hydrogen bonds defined for protein. 3156 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: 5.82 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8448 1.33 - 1.46: 5920 1.46 - 1.58: 14389 1.58 - 1.71: 18 1.71 - 1.83: 166 Bond restraints: 28941 Sorted by residual: bond pdb=" N SER S 50 " pdb=" CA SER S 50 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.21e-02 6.83e+03 7.01e+00 bond pdb=" N ASP R 29 " pdb=" CA ASP R 29 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.86e+00 bond pdb=" N PHE R 28 " pdb=" CA PHE R 28 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.34e-02 5.57e+03 6.57e+00 bond pdb=" N LYS S 49 " pdb=" CA LYS S 49 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.28e-02 6.10e+03 6.32e+00 bond pdb=" N LEU R 614 " pdb=" CA LEU R 614 " ideal model delta sigma weight residual 1.452 1.484 -0.033 1.30e-02 5.92e+03 6.31e+00 ... (remaining 28936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 38788 4.26 - 8.52: 332 8.52 - 12.78: 44 12.78 - 17.05: 4 17.05 - 21.31: 7 Bond angle restraints: 39175 Sorted by residual: angle pdb=" CB MET Q1288 " pdb=" CG MET Q1288 " pdb=" SD MET Q1288 " ideal model delta sigma weight residual 112.70 134.01 -21.31 3.00e+00 1.11e-01 5.04e+01 angle pdb=" CB MET S 147 " pdb=" CG MET S 147 " pdb=" SD MET S 147 " ideal model delta sigma weight residual 112.70 131.29 -18.59 3.00e+00 1.11e-01 3.84e+01 angle pdb=" CB MET X 122 " pdb=" CG MET X 122 " pdb=" SD MET X 122 " ideal model delta sigma weight residual 112.70 131.00 -18.30 3.00e+00 1.11e-01 3.72e+01 angle pdb=" CB MET W 215 " pdb=" CG MET W 215 " pdb=" SD MET W 215 " ideal model delta sigma weight residual 112.70 130.37 -17.67 3.00e+00 1.11e-01 3.47e+01 angle pdb=" CA LEU Q1319 " pdb=" CB LEU Q1319 " pdb=" CG LEU Q1319 " ideal model delta sigma weight residual 116.30 136.81 -20.51 3.50e+00 8.16e-02 3.44e+01 ... (remaining 39170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 17163 35.38 - 70.76: 535 70.76 - 106.14: 60 106.14 - 141.52: 5 141.52 - 176.91: 3 Dihedral angle restraints: 17766 sinusoidal: 7193 harmonic: 10573 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 -60.00 116.91 -176.91 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP V 501 " pdb=" O5' ADP V 501 " pdb=" PA ADP V 501 " pdb=" O2A ADP V 501 " ideal model delta sinusoidal sigma weight residual -60.00 88.87 -148.87 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C5' ADP W 501 " pdb=" O5' ADP W 501 " pdb=" PA ADP W 501 " pdb=" O2A ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 82.88 -142.88 1 2.00e+01 2.50e-03 4.31e+01 ... (remaining 17763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 4506 0.138 - 0.277: 100 0.277 - 0.415: 3 0.415 - 0.553: 0 0.553 - 0.691: 1 Chirality restraints: 4610 Sorted by residual: chirality pdb=" CB ILE U 125 " pdb=" CA ILE U 125 " pdb=" CG1 ILE U 125 " pdb=" CG2 ILE U 125 " both_signs ideal model delta sigma weight residual False 2.64 1.95 0.69 2.00e-01 2.50e+01 1.19e+01 chirality pdb=" CB ILE Y 149 " pdb=" CA ILE Y 149 " pdb=" CG1 ILE Y 149 " pdb=" CG2 ILE Y 149 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CG LEU Q1335 " pdb=" CB LEU Q1335 " pdb=" CD1 LEU Q1335 " pdb=" CD2 LEU Q1335 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 4607 not shown) Planarity restraints: 5022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP V 63 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" CG ASP V 63 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASP V 63 " 0.025 2.00e-02 2.50e+03 pdb=" OD2 ASP V 63 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP X 182 " 0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO X 183 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO X 183 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO X 183 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS V 174 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C LYS V 174 " -0.053 2.00e-02 2.50e+03 pdb=" O LYS V 174 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY V 175 " 0.018 2.00e-02 2.50e+03 ... (remaining 5019 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 3 2.20 - 2.88: 10556 2.88 - 3.55: 41046 3.55 - 4.23: 66466 4.23 - 4.90: 113588 Nonbonded interactions: 231659 Sorted by model distance: nonbonded pdb=" OD1 ASN T 325 " pdb=" NE ARG T 366 " model vdw 1.528 3.120 nonbonded pdb=" OD1 ASN T 325 " pdb=" CZ ARG T 366 " model vdw 2.125 3.270 nonbonded pdb=" O LEU R 647 " pdb=" OG SER R 652 " model vdw 2.173 3.040 nonbonded pdb=" OG SER T 355 " pdb=" O VAL T 359 " model vdw 2.229 3.040 nonbonded pdb=" O GLU Q1332 " pdb=" OG1 THR Q1336 " model vdw 2.274 3.040 ... (remaining 231654 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 or (resid 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 98 or (resid 99 through 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 187 or (resid 188 a \ nd (name N or name CA or name C or name O or name CB )) or resid 189 through 233 \ or (resid 234 and (name N or name CA or name C or name O or name CB )) or resid \ 235 through 259 or (resid 260 and (name N or name CA or name C or name O or nam \ e CB )) or resid 261 through 313 or (resid 314 and (name N or name CA or name C \ or name O or name CB )) or resid 315 through 337 or (resid 338 through 339 and ( \ name N or name CA or name C or name O or name CB )) or resid 340 through 380 or \ (resid 381 and (name N or name CA or name C or name O or name CB )) or resid 382 \ through 440 or (resid 441 through 442 and (name N or name CA or name C or name \ O or name CB )) or resid 443 through 501)) selection = (chain 'V' and (resid 22 through 116 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 through 154 or (resid 161 through 163 a \ nd (name N or name CA or name C or name O or name CB )) or resid 164 through 233 \ or (resid 234 and (name N or name CA or name C or name O or name CB )) or resid \ 235 through 259 or (resid 260 and (name N or name CA or name C or name O or nam \ e CB )) or resid 261 through 262 or (resid 263 and (name N or name CA or name C \ or name O or name CB )) or resid 264 through 273 or (resid 274 and (name N or na \ me CA or name C or name O or name CB )) or resid 275 through 337 or (resid 338 t \ hrough 339 and (name N or name CA or name C or name O or name CB )) or resid 340 \ through 380 or (resid 381 and (name N or name CA or name C or name O or name CB \ )) or resid 382 through 440 or (resid 441 through 442 and (name N or name CA or \ name C or name O or name CB )) or resid 443 through 455 or (resid 456 and (name \ N or name CA or name C or name O or name CB )) or resid 457 through 462 or (res \ id 463 and (name N or name CA or name C or name O or name CB )) or resid 501)) selection = (chain 'X' and (resid 22 or (resid 23 and (name N or name CA or name C or name O \ or name CB )) or resid 24 through 98 or (resid 99 through 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 116 or (resid 117 a \ nd (name N or name CA or name C or name O or name CB )) or resid 118 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 187 or (resid 188 and (name N or name CA or name C or n \ ame O or name CB )) or resid 189 through 262 or (resid 263 and (name N or name C \ A or name C or name O or name CB )) or resid 264 through 273 or (resid 274 and ( \ name N or name CA or name C or name O or name CB )) or resid 275 through 313 or \ (resid 314 and (name N or name CA or name C or name O or name CB )) or resid 315 \ through 455 or (resid 456 and (name N or name CA or name C or name O or name CB \ )) or resid 457 through 462 or (resid 463 and (name N or name CA or name C or n \ ame O or name CB )) or resid 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 162 or (resid 163 through 164 and (name N or na \ me CA or name C or name O or name CB )) or resid 165 through 170 or (resid 171 a \ nd (name N or name CA or name C or name O or name CB )) or resid 172 through 181 \ or (resid 182 and (name N or name CA or name C or name O or name CB )) or resid \ 183 through 232 or (resid 233 and (name N or name CA or name C or name O or nam \ e CB )) or resid 234 through 297 or (resid 298 and (name N or name CA or name C \ or name O or name CB )) or resid 299 through 459 or resid 501)) selection = (chain 'W' and (resid 18 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 44 or (resid 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 170 o \ r (resid 171 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 72 through 200 or (resid 201 and (name N or name CA or name C or name O or name \ CB )) or resid 202 through 210 or resid 221 through 232 or (resid 233 and (name \ N or name CA or name C or name O or name CB )) or resid 234 through 297 or (resi \ d 298 and (name N or name CA or name C or name O or name CB )) or resid 299 thro \ ugh 412 or (resid 413 and (name N or name CA or name C or name O or name CB )) o \ r resid 414 through 501)) selection = (chain 'Y' and (resid 18 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 44 or (resid 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 through 133 or (resid 134 and \ (name N or name CA or name C or name O or name CB )) or resid 135 through 162 o \ r (resid 163 through 164 and (name N or name CA or name C or name O or name CB ) \ ) or resid 165 through 181 or (resid 182 and (name N or name CA or name C or nam \ e O or name CB )) or resid 183 through 200 or (resid 201 and (name N or name CA \ or name C or name O or name CB )) or resid 202 through 210 or resid 221 through \ 412 or (resid 413 and (name N or name CA or name C or name O or name CB )) or re \ sid 414 through 459 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.770 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 0.074 28942 Z= 0.268 Angle : 1.056 21.307 39175 Z= 0.549 Chirality : 0.056 0.691 4610 Planarity : 0.007 0.108 5022 Dihedral : 17.255 176.906 10936 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 20.55 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.12), residues: 3618 helix: -1.39 (0.11), residues: 1469 sheet: -0.25 (0.22), residues: 559 loop : -1.22 (0.14), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG X 392 TYR 0.036 0.003 TYR R 151 PHE 0.042 0.002 PHE R 281 TRP 0.043 0.003 TRP Y 280 HIS 0.011 0.002 HIS V 27 Details of bonding type rmsd covalent geometry : bond 0.00583 (28941) covalent geometry : angle 1.05600 (39175) hydrogen bonds : bond 0.16414 ( 1093) hydrogen bonds : angle 6.57894 ( 3156) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1225 time to evaluate : 0.722 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 1027 SER cc_start: 0.9081 (m) cc_final: 0.8533 (p) REVERT: Q 1028 PHE cc_start: 0.8500 (t80) cc_final: 0.8139 (t80) REVERT: Q 1033 LYS cc_start: 0.8381 (ptmt) cc_final: 0.7799 (ptpp) REVERT: Q 1075 TYR cc_start: 0.7784 (t80) cc_final: 0.7304 (t80) REVERT: Q 1077 SER cc_start: 0.8051 (m) cc_final: 0.7671 (p) REVERT: Q 1092 ASP cc_start: 0.7587 (t0) cc_final: 0.7264 (t0) REVERT: Q 1097 ASN cc_start: 0.7634 (t0) cc_final: 0.7140 (t0) REVERT: Q 1109 LYS cc_start: 0.8114 (mtpp) cc_final: 0.7790 (mtpp) REVERT: Q 1112 LYS cc_start: 0.8090 (mttt) cc_final: 0.7828 (ttmm) REVERT: Q 1128 LEU cc_start: 0.8645 (mm) cc_final: 0.8422 (mp) REVERT: Q 1130 LYS cc_start: 0.8532 (tptp) cc_final: 0.8275 (tptp) REVERT: Q 1134 GLU cc_start: 0.8048 (tp30) cc_final: 0.7791 (tp30) REVERT: Q 1138 ASN cc_start: 0.7918 (m110) cc_final: 0.7216 (p0) REVERT: Q 1142 ARG cc_start: 0.7826 (ttm110) cc_final: 0.7405 (ttm110) REVERT: Q 1150 LYS cc_start: 0.8313 (tttp) cc_final: 0.7936 (tttp) REVERT: Q 1163 ASP cc_start: 0.7476 (p0) cc_final: 0.7204 (p0) REVERT: Q 1169 THR cc_start: 0.8556 (m) cc_final: 0.8012 (p) REVERT: Q 1172 GLN cc_start: 0.7498 (mp10) cc_final: 0.7019 (mp10) REVERT: Q 1173 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7735 (mt-10) REVERT: Q 1186 VAL cc_start: 0.8780 (m) cc_final: 0.8418 (m) REVERT: Q 1187 MET cc_start: 0.8154 (pmm) cc_final: 0.7878 (pmm) REVERT: Q 1193 VAL cc_start: 0.8506 (m) cc_final: 0.8107 (t) REVERT: Q 1194 GLU cc_start: 0.7966 (pm20) cc_final: 0.7546 (pm20) REVERT: Q 1200 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7287 (ttp-110) REVERT: Q 1239 ASP cc_start: 0.7246 (t70) cc_final: 0.6919 (t70) REVERT: Q 1241 LEU cc_start: 0.8887 (mm) cc_final: 0.8569 (mp) REVERT: Q 1242 ILE cc_start: 0.8593 (mt) cc_final: 0.8340 (mt) REVERT: Q 1266 GLU cc_start: 0.7972 (pm20) cc_final: 0.7477 (pm20) REVERT: Q 1267 ASP cc_start: 0.8860 (m-30) cc_final: 0.8620 (m-30) REVERT: Q 1286 ILE cc_start: 0.8346 (mt) cc_final: 0.8136 (mt) REVERT: Q 1331 MET cc_start: 0.7321 (tpp) cc_final: 0.7114 (tpp) REVERT: Q 1405 MET cc_start: 0.6290 (ptm) cc_final: 0.6069 (ptm) REVERT: R 110 LEU cc_start: 0.8644 (mp) cc_final: 0.8334 (mp) REVERT: R 113 GLU cc_start: 0.8704 (tp30) cc_final: 0.8141 (tp30) REVERT: R 195 ASN cc_start: 0.6967 (m-40) cc_final: 0.6477 (m-40) REVERT: R 211 ARG cc_start: 0.6765 (ptt90) cc_final: 0.5595 (ptm160) REVERT: R 218 GLN cc_start: 0.7433 (mp10) cc_final: 0.7138 (mp10) REVERT: R 252 TYR cc_start: 0.6992 (p90) cc_final: 0.6292 (p90) REVERT: R 257 TYR cc_start: 0.8193 (t80) cc_final: 0.7808 (t80) REVERT: R 261 ILE cc_start: 0.8514 (tp) cc_final: 0.8215 (tp) REVERT: R 585 ASP cc_start: 0.7670 (m-30) cc_final: 0.7321 (m-30) REVERT: R 593 LEU cc_start: 0.8558 (mt) cc_final: 0.8311 (mm) REVERT: R 609 GLN cc_start: 0.8638 (tp-100) cc_final: 0.8345 (tp-100) REVERT: R 640 GLU cc_start: 0.7458 (tp30) cc_final: 0.7130 (mt-10) REVERT: R 656 LYS cc_start: 0.8054 (pptt) cc_final: 0.7516 (pptt) REVERT: R 724 TYR cc_start: 0.8651 (t80) cc_final: 0.8300 (t80) REVERT: R 725 ARG cc_start: 0.8261 (tpp-160) cc_final: 0.7741 (tpp-160) REVERT: R 736 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7406 (tm-30) REVERT: R 744 GLU cc_start: 0.8055 (mp0) cc_final: 0.7225 (mp0) REVERT: R 751 LYS cc_start: 0.7200 (mmmt) cc_final: 0.6689 (mmmt) REVERT: S 65 GLN cc_start: 0.8592 (mm110) cc_final: 0.8373 (mm110) REVERT: S 70 GLU cc_start: 0.8753 (tp30) cc_final: 0.8513 (tp30) REVERT: S 99 THR cc_start: 0.7920 (p) cc_final: 0.7675 (p) REVERT: S 117 ASP cc_start: 0.6908 (m-30) cc_final: 0.6699 (m-30) REVERT: S 157 LYS cc_start: 0.8044 (ttpt) cc_final: 0.7655 (ttpt) REVERT: T 35 LEU cc_start: 0.7981 (pt) cc_final: 0.7746 (mp) REVERT: T 36 ASP cc_start: 0.7618 (t0) cc_final: 0.7280 (t70) REVERT: T 37 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7826 (tm-30) REVERT: T 42 LYS cc_start: 0.7784 (tptp) cc_final: 0.7400 (tppp) REVERT: T 66 LYS cc_start: 0.7609 (mttt) cc_final: 0.7228 (mttm) REVERT: T 95 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8014 (mm-30) REVERT: T 134 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7387 (mmmm) REVERT: T 137 LYS cc_start: 0.8430 (tttp) cc_final: 0.7744 (ttmm) REVERT: T 139 VAL cc_start: 0.8492 (t) cc_final: 0.8137 (m) REVERT: T 150 GLU cc_start: 0.7980 (tp30) cc_final: 0.7622 (tp30) REVERT: T 190 GLN cc_start: 0.8085 (mt0) cc_final: 0.7643 (mt0) REVERT: T 225 GLU cc_start: 0.7471 (tp30) cc_final: 0.6897 (tp30) REVERT: T 238 HIS cc_start: 0.8193 (t70) cc_final: 0.7579 (t70) REVERT: T 244 VAL cc_start: 0.8406 (t) cc_final: 0.8177 (m) REVERT: T 269 MET cc_start: 0.7746 (mmm) cc_final: 0.6599 (mmm) REVERT: T 282 GLU cc_start: 0.7916 (tp30) cc_final: 0.7305 (tp30) REVERT: T 287 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7858 (mm-30) REVERT: T 289 ASN cc_start: 0.8696 (m-40) cc_final: 0.8343 (m-40) REVERT: T 302 GLU cc_start: 0.7674 (tt0) cc_final: 0.7194 (tt0) REVERT: T 304 ILE cc_start: 0.8443 (pt) cc_final: 0.8110 (mm) REVERT: T 323 TYR cc_start: 0.8406 (t80) cc_final: 0.8152 (t80) REVERT: T 329 GLU cc_start: 0.7776 (pp20) cc_final: 0.7441 (pp20) REVERT: T 341 ASN cc_start: 0.8359 (p0) cc_final: 0.7881 (p0) REVERT: T 346 THR cc_start: 0.8681 (p) cc_final: 0.8430 (p) REVERT: T 396 GLU cc_start: 0.7436 (tm-30) cc_final: 0.6834 (tm-30) REVERT: T 401 ASP cc_start: 0.8049 (m-30) cc_final: 0.7751 (m-30) REVERT: T 413 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7371 (mtp85) REVERT: T 417 GLN cc_start: 0.8522 (mt0) cc_final: 0.8152 (mt0) REVERT: T 440 ASN cc_start: 0.8170 (m110) cc_final: 0.7828 (m110) REVERT: T 441 GLU cc_start: 0.8006 (tt0) cc_final: 0.7425 (tt0) REVERT: T 454 LYS cc_start: 0.8315 (mtpt) cc_final: 0.8030 (mtpt) REVERT: U 34 ASN cc_start: 0.8412 (m-40) cc_final: 0.7364 (m-40) REVERT: U 86 MET cc_start: 0.7973 (tpt) cc_final: 0.7689 (tpp) REVERT: U 99 THR cc_start: 0.7850 (m) cc_final: 0.7563 (p) REVERT: U 107 PHE cc_start: 0.8622 (m-80) cc_final: 0.8247 (m-80) REVERT: U 110 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7878 (mp0) REVERT: U 130 LYS cc_start: 0.8499 (mppt) cc_final: 0.8189 (mppt) REVERT: U 140 VAL cc_start: 0.7799 (t) cc_final: 0.7394 (p) REVERT: U 161 LYS cc_start: 0.8435 (tmmt) cc_final: 0.7772 (tmtt) REVERT: U 166 GLU cc_start: 0.7540 (tp30) cc_final: 0.6612 (tp30) REVERT: U 170 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7382 (mt-10) REVERT: U 175 MET cc_start: 0.8007 (tpp) cc_final: 0.7798 (tpp) REVERT: U 180 THR cc_start: 0.8647 (m) cc_final: 0.8193 (t) REVERT: U 189 VAL cc_start: 0.8284 (t) cc_final: 0.7891 (p) REVERT: U 223 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7147 (tm-30) REVERT: U 226 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6996 (mm-30) REVERT: U 235 VAL cc_start: 0.8607 (t) cc_final: 0.8399 (m) REVERT: U 249 SER cc_start: 0.7704 (t) cc_final: 0.7085 (p) REVERT: U 274 ASN cc_start: 0.8213 (m-40) cc_final: 0.7897 (m110) REVERT: U 279 GLU cc_start: 0.7884 (tt0) cc_final: 0.7482 (tt0) REVERT: U 281 LYS cc_start: 0.8843 (tttt) cc_final: 0.8356 (tptp) REVERT: U 287 GLU cc_start: 0.7401 (tp30) cc_final: 0.7116 (tp30) REVERT: U 289 VAL cc_start: 0.8081 (t) cc_final: 0.7828 (p) REVERT: U 300 MET cc_start: 0.7815 (mmm) cc_final: 0.7167 (mtp) REVERT: U 302 ASP cc_start: 0.7808 (m-30) cc_final: 0.7595 (m-30) REVERT: U 305 CYS cc_start: 0.8556 (m) cc_final: 0.8311 (m) REVERT: U 307 SER cc_start: 0.8828 (m) cc_final: 0.8535 (p) REVERT: U 323 MET cc_start: 0.7819 (mtm) cc_final: 0.7498 (mtp) REVERT: U 339 SER cc_start: 0.8801 (m) cc_final: 0.8519 (m) REVERT: U 346 ASP cc_start: 0.8234 (p0) cc_final: 0.7807 (p0) REVERT: U 353 ILE cc_start: 0.8538 (mt) cc_final: 0.8239 (tp) REVERT: U 357 LYS cc_start: 0.7422 (mppt) cc_final: 0.7053 (mppt) REVERT: U 373 GLN cc_start: 0.8212 (tt0) cc_final: 0.7806 (tm-30) REVERT: U 403 ILE cc_start: 0.8262 (mt) cc_final: 0.7796 (tt) REVERT: U 407 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7455 (tm-30) REVERT: U 414 LYS cc_start: 0.8261 (tppt) cc_final: 0.8040 (tppt) REVERT: U 415 ASN cc_start: 0.7796 (t0) cc_final: 0.7501 (p0) REVERT: U 416 ASN cc_start: 0.7904 (t0) cc_final: 0.7671 (t0) REVERT: U 417 THR cc_start: 0.8607 (p) cc_final: 0.8185 (t) REVERT: U 419 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7448 (mm-30) REVERT: U 437 VAL cc_start: 0.8060 (t) cc_final: 0.7800 (p) REVERT: U 439 TYR cc_start: 0.7739 (m-80) cc_final: 0.7394 (m-80) REVERT: U 455 GLN cc_start: 0.7523 (tp-100) cc_final: 0.7082 (tp40) REVERT: U 456 ILE cc_start: 0.8301 (mp) cc_final: 0.8017 (mm) REVERT: V 36 ASP cc_start: 0.7260 (m-30) cc_final: 0.6940 (m-30) REVERT: V 69 LYS cc_start: 0.8340 (mtmm) cc_final: 0.8031 (mtmm) REVERT: V 95 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7464 (mm-30) REVERT: V 103 CYS cc_start: 0.8456 (t) cc_final: 0.8004 (t) REVERT: V 114 GLU cc_start: 0.7688 (pm20) cc_final: 0.7414 (pm20) REVERT: V 119 GLU cc_start: 0.7721 (tp30) cc_final: 0.6862 (tm-30) REVERT: V 143 GLU cc_start: 0.7545 (tt0) cc_final: 0.7185 (tt0) REVERT: V 167 ILE cc_start: 0.7552 (mp) cc_final: 0.7018 (mp) REVERT: V 180 ARG cc_start: 0.8162 (ttp80) cc_final: 0.7704 (ttm-80) REVERT: V 193 LYS cc_start: 0.8373 (mmmt) cc_final: 0.7860 (mmmt) REVERT: V 203 GLU cc_start: 0.7710 (tt0) cc_final: 0.7082 (tm-30) REVERT: V 205 ASN cc_start: 0.8336 (m-40) cc_final: 0.7631 (m-40) REVERT: V 206 THR cc_start: 0.8564 (p) cc_final: 0.8135 (p) REVERT: V 220 THR cc_start: 0.8164 (p) cc_final: 0.7733 (p) REVERT: V 227 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6841 (mt-10) REVERT: V 237 VAL cc_start: 0.7740 (m) cc_final: 0.7187 (t) REVERT: V 268 MET cc_start: 0.7910 (mtm) cc_final: 0.7580 (mtt) REVERT: V 274 LYS cc_start: 0.8002 (tttp) cc_final: 0.7738 (tttp) REVERT: V 276 LYS cc_start: 0.8085 (mptt) cc_final: 0.7481 (mptt) REVERT: V 278 THR cc_start: 0.8677 (p) cc_final: 0.8362 (p) REVERT: V 286 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7446 (mm-40) REVERT: V 287 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7154 (mm-30) REVERT: V 355 SER cc_start: 0.8048 (t) cc_final: 0.7759 (t) REVERT: V 385 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7459 (tm-30) REVERT: V 391 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7714 (mt-10) REVERT: V 396 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6485 (tp30) REVERT: V 409 GLU cc_start: 0.7499 (tp30) cc_final: 0.7172 (tp30) REVERT: V 414 TYR cc_start: 0.8403 (t80) cc_final: 0.8014 (t80) REVERT: V 425 LEU cc_start: 0.9110 (mt) cc_final: 0.8861 (mt) REVERT: V 429 SER cc_start: 0.8543 (t) cc_final: 0.8087 (t) REVERT: V 437 ASN cc_start: 0.8355 (m110) cc_final: 0.8140 (m110) REVERT: V 454 LYS cc_start: 0.8259 (tttt) cc_final: 0.7905 (tttt) REVERT: W 23 HIS cc_start: 0.8285 (m90) cc_final: 0.7905 (m-70) REVERT: W 82 THR cc_start: 0.7717 (m) cc_final: 0.7434 (p) REVERT: W 86 MET cc_start: 0.6752 (tmm) cc_final: 0.6551 (tpp) REVERT: W 90 GLN cc_start: 0.8610 (mm110) cc_final: 0.8249 (mm-40) REVERT: W 105 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7310 (mp0) REVERT: W 123 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7529 (mtmm) REVERT: W 165 MET cc_start: 0.7460 (ppp) cc_final: 0.7250 (ppp) REVERT: W 170 GLU cc_start: 0.8466 (mm-30) cc_final: 0.7831 (mm-30) REVERT: W 189 VAL cc_start: 0.7119 (t) cc_final: 0.6468 (m) REVERT: W 193 ASP cc_start: 0.7648 (t70) cc_final: 0.7316 (t0) REVERT: W 201 LYS cc_start: 0.8521 (tttt) cc_final: 0.7969 (tttp) REVERT: W 220 ARG cc_start: 0.7445 (mmm160) cc_final: 0.7202 (mmm160) REVERT: W 231 LYS cc_start: 0.7759 (mmtp) cc_final: 0.7459 (mmmm) REVERT: W 233 LYS cc_start: 0.7821 (tppt) cc_final: 0.7265 (tppt) REVERT: W 243 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7715 (mt-10) REVERT: W 257 LEU cc_start: 0.8678 (mt) cc_final: 0.8393 (mm) REVERT: W 258 PHE cc_start: 0.8469 (m-80) cc_final: 0.8263 (m-10) REVERT: W 261 ASP cc_start: 0.7810 (t0) cc_final: 0.7299 (t0) REVERT: W 273 ILE cc_start: 0.8751 (mt) cc_final: 0.8462 (mt) REVERT: W 276 LYS cc_start: 0.8042 (tptt) cc_final: 0.7667 (tptm) REVERT: W 281 LYS cc_start: 0.8493 (ttpp) cc_final: 0.8282 (ttpp) REVERT: W 294 PHE cc_start: 0.8321 (t80) cc_final: 0.7920 (t80) REVERT: W 296 ASP cc_start: 0.7981 (t0) cc_final: 0.7681 (t0) REVERT: W 304 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8095 (mt-10) REVERT: W 316 GLU cc_start: 0.7612 (tt0) cc_final: 0.7336 (tp30) REVERT: W 326 ASN cc_start: 0.7513 (p0) cc_final: 0.7072 (p0) REVERT: W 338 LYS cc_start: 0.8103 (ttpp) cc_final: 0.7826 (ttmm) REVERT: W 349 ASP cc_start: 0.8294 (t0) cc_final: 0.7984 (t0) REVERT: W 365 LYS cc_start: 0.8587 (tmmt) cc_final: 0.8126 (tmmt) REVERT: W 374 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7874 (tp30) REVERT: W 378 GLU cc_start: 0.7697 (mp0) cc_final: 0.7410 (mp0) REVERT: W 384 LEU cc_start: 0.8563 (tp) cc_final: 0.8275 (tp) REVERT: W 385 ASP cc_start: 0.8657 (m-30) cc_final: 0.8432 (m-30) REVERT: W 393 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7493 (mt-10) REVERT: W 398 TYR cc_start: 0.7598 (t80) cc_final: 0.7290 (t80) REVERT: W 407 GLN cc_start: 0.8224 (tp40) cc_final: 0.7788 (tp40) REVERT: W 412 LYS cc_start: 0.8378 (mtpp) cc_final: 0.8092 (mmmt) REVERT: W 413 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7190 (ptm160) REVERT: W 419 GLU cc_start: 0.8201 (tp30) cc_final: 0.7893 (tp30) REVERT: W 424 LYS cc_start: 0.9061 (mmtt) cc_final: 0.8630 (mmmm) REVERT: W 439 TYR cc_start: 0.8349 (m-80) cc_final: 0.7703 (m-80) REVERT: W 440 VAL cc_start: 0.8863 (t) cc_final: 0.8655 (p) REVERT: X 35 LEU cc_start: 0.9092 (tp) cc_final: 0.8686 (tp) REVERT: X 56 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7363 (mm-30) REVERT: X 95 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7640 (mm-30) REVERT: X 96 LEU cc_start: 0.8637 (mt) cc_final: 0.8415 (mt) REVERT: X 103 CYS cc_start: 0.8525 (t) cc_final: 0.8173 (t) REVERT: X 114 GLU cc_start: 0.7799 (tt0) cc_final: 0.7474 (tt0) REVERT: X 117 LYS cc_start: 0.7731 (ptmt) cc_final: 0.7418 (mtpt) REVERT: X 119 GLU cc_start: 0.7720 (tp30) cc_final: 0.7475 (tp30) REVERT: X 132 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.7536 (tpp80) REVERT: X 140 TYR cc_start: 0.7922 (m-80) cc_final: 0.7675 (m-80) REVERT: X 150 GLU cc_start: 0.6567 (tm-30) cc_final: 0.5686 (tm-30) REVERT: X 151 ASP cc_start: 0.7370 (t0) cc_final: 0.7124 (t0) REVERT: X 153 GLU cc_start: 0.7743 (pp20) cc_final: 0.7351 (pp20) REVERT: X 162 THR cc_start: 0.7833 (m) cc_final: 0.7631 (t) REVERT: X 165 HIS cc_start: 0.8164 (p90) cc_final: 0.7202 (p-80) REVERT: X 171 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7937 (tptt) REVERT: X 177 LYS cc_start: 0.8653 (tptp) cc_final: 0.8416 (tptp) REVERT: X 201 TYR cc_start: 0.7031 (t80) cc_final: 0.6647 (t80) REVERT: X 221 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7878 (mp0) REVERT: X 240 LYS cc_start: 0.8168 (mptt) cc_final: 0.7330 (mptt) REVERT: X 241 LYS cc_start: 0.7889 (ptpt) cc_final: 0.7685 (ptpt) REVERT: X 243 ILE cc_start: 0.8226 (mm) cc_final: 0.7645 (mm) REVERT: X 251 ASP cc_start: 0.8170 (m-30) cc_final: 0.7770 (m-30) REVERT: X 258 ARG cc_start: 0.7106 (ptm-80) cc_final: 0.6755 (ptm-80) REVERT: X 268 MET cc_start: 0.7464 (mtp) cc_final: 0.7227 (mtp) REVERT: X 269 MET cc_start: 0.8067 (mmm) cc_final: 0.7599 (mmm) REVERT: X 274 LYS cc_start: 0.8220 (ptmt) cc_final: 0.7972 (ttpp) REVERT: X 283 LYS cc_start: 0.8572 (tttm) cc_final: 0.8320 (tptm) REVERT: X 290 LYS cc_start: 0.8284 (ttmm) cc_final: 0.8017 (ttmm) REVERT: X 311 ASP cc_start: 0.8027 (t0) cc_final: 0.7504 (t0) REVERT: X 312 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7729 (mm-30) REVERT: X 335 VAL cc_start: 0.7159 (p) cc_final: 0.6666 (t) REVERT: X 348 ARG cc_start: 0.7623 (mtp-110) cc_final: 0.6896 (ttm-80) REVERT: X 386 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7645 (mmm-85) REVERT: X 387 ARG cc_start: 0.8591 (mmm160) cc_final: 0.8168 (tpt90) REVERT: X 391 GLU cc_start: 0.8870 (tt0) cc_final: 0.8269 (tm-30) REVERT: X 394 GLN cc_start: 0.7696 (tp-100) cc_final: 0.7186 (tp-100) REVERT: X 397 SER cc_start: 0.8741 (p) cc_final: 0.8539 (t) REVERT: X 405 THR cc_start: 0.7707 (p) cc_final: 0.7446 (p) REVERT: X 406 MET cc_start: 0.7526 (mmp) cc_final: 0.6990 (mmp) REVERT: X 409 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7828 (tm-30) REVERT: X 436 VAL cc_start: 0.7663 (t) cc_final: 0.7376 (p) REVERT: X 447 LEU cc_start: 0.8398 (mt) cc_final: 0.8176 (mp) REVERT: X 454 LYS cc_start: 0.8449 (mttt) cc_final: 0.8047 (mptt) REVERT: X 457 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7339 (mp0) REVERT: Y 20 ILE cc_start: 0.7890 (mt) cc_final: 0.7504 (mp) REVERT: Y 26 ILE cc_start: 0.8554 (mt) cc_final: 0.8252 (pt) REVERT: Y 32 ASP cc_start: 0.7033 (m-30) cc_final: 0.6829 (m-30) REVERT: Y 36 GLN cc_start: 0.7997 (tt0) cc_final: 0.7504 (tt0) REVERT: Y 38 ARG cc_start: 0.7596 (mpt180) cc_final: 0.7299 (mpt-90) REVERT: Y 58 LEU cc_start: 0.8366 (tp) cc_final: 0.8039 (tp) REVERT: Y 59 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7537 (mmmt) REVERT: Y 62 GLN cc_start: 0.8381 (mt0) cc_final: 0.8082 (mt0) REVERT: Y 63 ASN cc_start: 0.8616 (m-40) cc_final: 0.8164 (m-40) REVERT: Y 86 MET cc_start: 0.7031 (tpp) cc_final: 0.6007 (tpp) REVERT: Y 96 VAL cc_start: 0.8313 (t) cc_final: 0.8044 (p) REVERT: Y 113 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7669 (mtmm) REVERT: Y 123 LYS cc_start: 0.8189 (mtpt) cc_final: 0.7844 (mttt) REVERT: Y 128 LYS cc_start: 0.7564 (ttmm) cc_final: 0.7090 (ttmm) REVERT: Y 129 ILE cc_start: 0.8355 (mt) cc_final: 0.8043 (tp) REVERT: Y 130 LYS cc_start: 0.8602 (pttm) cc_final: 0.8197 (pttm) REVERT: Y 131 GLU cc_start: 0.7452 (mm-30) cc_final: 0.6855 (mm-30) REVERT: Y 142 GLU cc_start: 0.7365 (tm-30) cc_final: 0.6880 (tm-30) REVERT: Y 165 MET cc_start: 0.7072 (tmm) cc_final: 0.6841 (tmm) REVERT: Y 173 ASN cc_start: 0.8274 (p0) cc_final: 0.7753 (p0) REVERT: Y 174 LYS cc_start: 0.8487 (mmtm) cc_final: 0.8110 (mmtm) REVERT: Y 179 LEU cc_start: 0.8903 (mm) cc_final: 0.8503 (mt) REVERT: Y 182 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7134 (mm-30) REVERT: Y 193 ASP cc_start: 0.8483 (t0) cc_final: 0.8066 (t70) REVERT: Y 208 ARG cc_start: 0.7874 (mtt180) cc_final: 0.7223 (mtm-85) REVERT: Y 211 ASP cc_start: 0.8477 (m-30) cc_final: 0.8003 (m-30) REVERT: Y 223 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7300 (mm110) REVERT: Y 226 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7449 (mp0) REVERT: Y 245 ASP cc_start: 0.7816 (m-30) cc_final: 0.7467 (m-30) REVERT: Y 276 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8015 (mmmm) REVERT: Y 277 VAL cc_start: 0.8272 (t) cc_final: 0.8034 (p) REVERT: Y 281 LYS cc_start: 0.8486 (tmmt) cc_final: 0.8261 (tmmt) REVERT: Y 282 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7482 (tm-30) REVERT: Y 310 ASN cc_start: 0.8323 (t0) cc_final: 0.7946 (t0) REVERT: Y 316 GLU cc_start: 0.8573 (pm20) cc_final: 0.8012 (pm20) REVERT: Y 317 PHE cc_start: 0.8687 (m-80) cc_final: 0.8380 (m-80) REVERT: Y 337 TYR cc_start: 0.8115 (p90) cc_final: 0.7700 (p90) REVERT: Y 365 LYS cc_start: 0.8502 (ptmt) cc_final: 0.8088 (ttpp) REVERT: Y 385 ASP cc_start: 0.8323 (m-30) cc_final: 0.8103 (m-30) REVERT: Y 389 LYS cc_start: 0.8547 (tppt) cc_final: 0.7948 (tppt) REVERT: Y 404 SER cc_start: 0.9112 (t) cc_final: 0.8657 (m) REVERT: Y 411 MET cc_start: 0.7933 (mmm) cc_final: 0.7536 (mmm) REVERT: Y 421 GLU cc_start: 0.8257 (tt0) cc_final: 0.7985 (tt0) REVERT: Y 438 LYS cc_start: 0.8244 (ttmt) cc_final: 0.8012 (ttmm) REVERT: Y 443 ASN cc_start: 0.7148 (m110) cc_final: 0.6734 (m110) REVERT: Y 444 GLU cc_start: 0.7771 (tp30) cc_final: 0.7517 (tp30) REVERT: Y 446 GLN cc_start: 0.7771 (mt0) cc_final: 0.7414 (mm-40) REVERT: Y 447 TYR cc_start: 0.7853 (m-80) cc_final: 0.7430 (m-80) REVERT: Y 455 GLN cc_start: 0.7955 (pp30) cc_final: 0.6046 (pp30) REVERT: Y 456 ILE cc_start: 0.8838 (mp) cc_final: 0.8338 (mm) REVERT: Z 297 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7608 (mmt90) REVERT: Z 298 ARG cc_start: 0.8243 (ttm110) cc_final: 0.7994 (ttm110) outliers start: 0 outliers final: 0 residues processed: 1225 average time/residue: 0.1830 time to fit residues: 339.1185 Evaluate side-chains 1066 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1066 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1100 ASN R 607 HIS R 610 HIS R 659 GLN S 60 HIS ** S 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 ASN T 250 HIS U 36 GLN U 237 HIS V 94 GLN V 238 HIS W 362 GLN X 256 ASN Y 47 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111971 restraints weight = 55643.888| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.24 r_work: 0.3319 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28942 Z= 0.163 Angle : 0.659 14.317 39175 Z= 0.330 Chirality : 0.045 0.214 4610 Planarity : 0.005 0.069 5022 Dihedral : 8.337 169.200 4000 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.15 % Allowed : 21.32 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.13), residues: 3618 helix: 0.19 (0.13), residues: 1496 sheet: 0.08 (0.22), residues: 553 loop : -0.97 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 180 TYR 0.021 0.002 TYR V 462 PHE 0.021 0.002 PHE S 124 TRP 0.022 0.001 TRP Y 280 HIS 0.007 0.001 HIS V 27 Details of bonding type rmsd covalent geometry : bond 0.00344 (28941) covalent geometry : angle 0.65942 (39175) hydrogen bonds : bond 0.04168 ( 1093) hydrogen bonds : angle 4.68294 ( 3156) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1124 time to evaluate : 0.832 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: Q 1027 SER cc_start: 0.9063 (m) cc_final: 0.8495 (p) REVERT: Q 1033 LYS cc_start: 0.8540 (ptmt) cc_final: 0.7938 (ptpp) REVERT: Q 1075 TYR cc_start: 0.8223 (t80) cc_final: 0.7857 (t80) REVERT: Q 1077 SER cc_start: 0.8340 (m) cc_final: 0.7726 (p) REVERT: Q 1109 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7777 (mtpp) REVERT: Q 1112 LYS cc_start: 0.8717 (mttt) cc_final: 0.8447 (ttmt) REVERT: Q 1127 PHE cc_start: 0.8741 (t80) cc_final: 0.8380 (t80) REVERT: Q 1128 LEU cc_start: 0.8782 (mm) cc_final: 0.8488 (mp) REVERT: Q 1130 LYS cc_start: 0.8645 (tptp) cc_final: 0.8338 (tptp) REVERT: Q 1138 ASN cc_start: 0.8083 (m110) cc_final: 0.7606 (p0) REVERT: Q 1150 LYS cc_start: 0.8348 (tttp) cc_final: 0.7941 (tttp) REVERT: Q 1154 GLU cc_start: 0.7774 (pt0) cc_final: 0.7147 (pt0) REVERT: Q 1172 GLN cc_start: 0.7713 (mp10) cc_final: 0.7420 (mp10) REVERT: Q 1176 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7781 (mt-10) REVERT: Q 1187 MET cc_start: 0.8350 (pmm) cc_final: 0.8028 (pmm) REVERT: Q 1190 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8461 (mp) REVERT: Q 1192 ASN cc_start: 0.8270 (p0) cc_final: 0.8003 (p0) REVERT: Q 1200 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7857 (ttp-110) REVERT: Q 1213 ASN cc_start: 0.8306 (m-40) cc_final: 0.8027 (m-40) REVERT: Q 1230 THR cc_start: 0.8720 (m) cc_final: 0.8467 (p) REVERT: Q 1239 ASP cc_start: 0.7268 (t70) cc_final: 0.6998 (t70) REVERT: Q 1241 LEU cc_start: 0.9009 (mm) cc_final: 0.8612 (mp) REVERT: Q 1266 GLU cc_start: 0.8085 (pm20) cc_final: 0.7650 (pm20) REVERT: Q 1327 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6871 (mpp) REVERT: Q 1331 MET cc_start: 0.7466 (tpp) cc_final: 0.6908 (tpp) REVERT: Q 1405 MET cc_start: 0.6627 (ptm) cc_final: 0.6238 (ptm) REVERT: R 81 PHE cc_start: 0.6212 (m-10) cc_final: 0.5976 (m-10) REVERT: R 97 ARG cc_start: 0.7133 (mtm-85) cc_final: 0.6831 (mtm-85) REVERT: R 121 HIS cc_start: 0.7880 (m-70) cc_final: 0.7372 (m-70) REVERT: R 192 GLU cc_start: 0.7536 (mp0) cc_final: 0.7288 (mp0) REVERT: R 193 ASP cc_start: 0.6258 (p0) cc_final: 0.5940 (p0) REVERT: R 218 GLN cc_start: 0.7917 (mp10) cc_final: 0.7620 (mp10) REVERT: R 229 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.7931 (mp) REVERT: R 252 TYR cc_start: 0.7532 (p90) cc_final: 0.7168 (p90) REVERT: R 261 ILE cc_start: 0.8651 (tp) cc_final: 0.8393 (tp) REVERT: R 609 GLN cc_start: 0.8392 (tp-100) cc_final: 0.8072 (tp-100) REVERT: R 618 ARG cc_start: 0.8359 (ptm160) cc_final: 0.8095 (ptm160) REVERT: R 645 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8188 (tp) REVERT: R 656 LYS cc_start: 0.7904 (pptt) cc_final: 0.7500 (pptt) REVERT: R 681 LYS cc_start: 0.8332 (ptmt) cc_final: 0.7979 (ptmm) REVERT: R 711 TRP cc_start: 0.7409 (t60) cc_final: 0.6061 (t60) REVERT: R 724 TYR cc_start: 0.8386 (t80) cc_final: 0.8082 (t80) REVERT: R 725 ARG cc_start: 0.7996 (tpp-160) cc_final: 0.7487 (tpp-160) REVERT: R 729 ILE cc_start: 0.6313 (tp) cc_final: 0.5824 (tt) REVERT: R 733 GLU cc_start: 0.7650 (mp0) cc_final: 0.7232 (pm20) REVERT: R 735 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8538 (pt0) REVERT: R 743 LYS cc_start: 0.8408 (mmtm) cc_final: 0.8182 (mmtm) REVERT: R 744 GLU cc_start: 0.8218 (mp0) cc_final: 0.7705 (mp0) REVERT: R 751 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6762 (mmmt) REVERT: R 754 GLU cc_start: 0.6133 (mp0) cc_final: 0.5842 (mp0) REVERT: S 145 LYS cc_start: 0.8397 (tppt) cc_final: 0.7662 (tppt) REVERT: S 155 TYR cc_start: 0.6665 (m-80) cc_final: 0.6341 (m-10) REVERT: S 157 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7759 (ttpt) REVERT: T 37 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7660 (tm-30) REVERT: T 42 LYS cc_start: 0.7972 (tptp) cc_final: 0.7629 (tppp) REVERT: T 49 VAL cc_start: 0.7640 (p) cc_final: 0.7438 (m) REVERT: T 66 LYS cc_start: 0.8002 (mttt) cc_final: 0.7712 (mttp) REVERT: T 75 ILE cc_start: 0.8294 (mm) cc_final: 0.7788 (tt) REVERT: T 108 SER cc_start: 0.8379 (p) cc_final: 0.8100 (m) REVERT: T 123 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8003 (tt0) REVERT: T 137 LYS cc_start: 0.8250 (tttp) cc_final: 0.8047 (ttmm) REVERT: T 146 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7275 (mm-30) REVERT: T 150 GLU cc_start: 0.7962 (tp30) cc_final: 0.7718 (tp30) REVERT: T 190 GLN cc_start: 0.8313 (mt0) cc_final: 0.8022 (mt0) REVERT: T 209 VAL cc_start: 0.8857 (t) cc_final: 0.8538 (m) REVERT: T 221 GLU cc_start: 0.8014 (pt0) cc_final: 0.7456 (pm20) REVERT: T 225 GLU cc_start: 0.7775 (tp30) cc_final: 0.7459 (tp30) REVERT: T 229 TYR cc_start: 0.9063 (m-10) cc_final: 0.8762 (m-10) REVERT: T 269 MET cc_start: 0.7393 (mmm) cc_final: 0.6733 (mtm) REVERT: T 273 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7951 (mm) REVERT: T 282 GLU cc_start: 0.8038 (tp30) cc_final: 0.7385 (tp30) REVERT: T 287 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7956 (mm-30) REVERT: T 289 ASN cc_start: 0.8701 (m-40) cc_final: 0.8451 (m110) REVERT: T 302 GLU cc_start: 0.8228 (tt0) cc_final: 0.7873 (tm-30) REVERT: T 303 LEU cc_start: 0.8778 (tt) cc_final: 0.8374 (tt) REVERT: T 323 TYR cc_start: 0.8593 (t80) cc_final: 0.8160 (t80) REVERT: T 329 GLU cc_start: 0.7759 (pp20) cc_final: 0.7372 (pp20) REVERT: T 366 ARG cc_start: 0.7993 (mtt-85) cc_final: 0.7683 (mtt90) REVERT: T 376 ASP cc_start: 0.8081 (p0) cc_final: 0.7690 (p0) REVERT: T 398 SER cc_start: 0.8621 (t) cc_final: 0.8208 (p) REVERT: T 401 ASP cc_start: 0.8228 (m-30) cc_final: 0.7977 (m-30) REVERT: T 417 GLN cc_start: 0.8598 (mt0) cc_final: 0.8294 (mt0) REVERT: T 418 LEU cc_start: 0.8527 (tp) cc_final: 0.8038 (tt) REVERT: T 436 VAL cc_start: 0.8272 (p) cc_final: 0.7964 (m) REVERT: T 439 VAL cc_start: 0.8663 (t) cc_final: 0.8438 (t) REVERT: T 441 GLU cc_start: 0.7795 (tt0) cc_final: 0.7422 (tt0) REVERT: T 454 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8193 (mtpt) REVERT: U 73 VAL cc_start: 0.8454 (t) cc_final: 0.8030 (m) REVERT: U 107 PHE cc_start: 0.8609 (m-80) cc_final: 0.8361 (m-80) REVERT: U 113 LYS cc_start: 0.8781 (mttp) cc_final: 0.8493 (mtmt) REVERT: U 128 LYS cc_start: 0.8237 (ttpt) cc_final: 0.8017 (ttmm) REVERT: U 132 GLU cc_start: 0.6983 (tp30) cc_final: 0.6625 (mm-30) REVERT: U 157 LYS cc_start: 0.8532 (mtpp) cc_final: 0.8249 (mtpp) REVERT: U 161 LYS cc_start: 0.8771 (tmmt) cc_final: 0.8222 (tmtt) REVERT: U 166 GLU cc_start: 0.7780 (tp30) cc_final: 0.6988 (tp30) REVERT: U 175 MET cc_start: 0.8518 (tpp) cc_final: 0.8273 (tpp) REVERT: U 189 VAL cc_start: 0.8646 (t) cc_final: 0.8357 (p) REVERT: U 193 ASP cc_start: 0.8322 (t0) cc_final: 0.7823 (p0) REVERT: U 223 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7430 (tm-30) REVERT: U 226 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7310 (mm-30) REVERT: U 233 LYS cc_start: 0.8197 (ptmm) cc_final: 0.7847 (ptmm) REVERT: U 235 VAL cc_start: 0.8768 (t) cc_final: 0.8409 (m) REVERT: U 279 GLU cc_start: 0.8333 (tt0) cc_final: 0.8057 (tt0) REVERT: U 287 GLU cc_start: 0.7929 (tp30) cc_final: 0.7657 (tm-30) REVERT: U 288 ILE cc_start: 0.8735 (tt) cc_final: 0.8165 (mt) REVERT: U 302 ASP cc_start: 0.7972 (m-30) cc_final: 0.7737 (m-30) REVERT: U 307 SER cc_start: 0.9027 (m) cc_final: 0.8809 (p) REVERT: U 316 GLU cc_start: 0.8135 (tt0) cc_final: 0.7698 (tp30) REVERT: U 323 MET cc_start: 0.8420 (mtm) cc_final: 0.8149 (mtm) REVERT: U 339 SER cc_start: 0.8804 (m) cc_final: 0.8584 (m) REVERT: U 346 ASP cc_start: 0.8252 (p0) cc_final: 0.7975 (p0) REVERT: U 357 LYS cc_start: 0.7929 (mppt) cc_final: 0.7666 (mppt) REVERT: U 365 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8562 (tttp) REVERT: U 373 GLN cc_start: 0.8414 (tt0) cc_final: 0.8088 (tm-30) REVERT: U 374 GLU cc_start: 0.8112 (tt0) cc_final: 0.7767 (tt0) REVERT: U 384 LEU cc_start: 0.8089 (tp) cc_final: 0.7682 (tt) REVERT: U 407 GLN cc_start: 0.8505 (tm-30) cc_final: 0.7741 (tm-30) REVERT: U 417 THR cc_start: 0.8633 (p) cc_final: 0.8268 (t) REVERT: U 419 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7574 (mm-30) REVERT: V 63 ASP cc_start: 0.7953 (t0) cc_final: 0.7690 (t0) REVERT: V 69 LYS cc_start: 0.8557 (mtmm) cc_final: 0.8331 (mtmm) REVERT: V 75 ILE cc_start: 0.8443 (pt) cc_final: 0.7997 (mm) REVERT: V 95 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7673 (mm-30) REVERT: V 103 CYS cc_start: 0.8525 (t) cc_final: 0.8142 (t) REVERT: V 112 SER cc_start: 0.8196 (p) cc_final: 0.7604 (t) REVERT: V 114 GLU cc_start: 0.7690 (pm20) cc_final: 0.6923 (pm20) REVERT: V 119 GLU cc_start: 0.7876 (tp30) cc_final: 0.7243 (tm-30) REVERT: V 179 LEU cc_start: 0.8356 (mm) cc_final: 0.8142 (mt) REVERT: V 180 ARG cc_start: 0.8426 (ttp80) cc_final: 0.7733 (ttm-80) REVERT: V 182 ASP cc_start: 0.8084 (t70) cc_final: 0.7712 (t70) REVERT: V 193 LYS cc_start: 0.8484 (mmmt) cc_final: 0.8047 (mmmt) REVERT: V 205 ASN cc_start: 0.8456 (m-40) cc_final: 0.8138 (m-40) REVERT: V 206 THR cc_start: 0.8630 (p) cc_final: 0.8364 (p) REVERT: V 276 LYS cc_start: 0.8349 (mptt) cc_final: 0.7857 (mptt) REVERT: V 278 THR cc_start: 0.8872 (p) cc_final: 0.8667 (p) REVERT: V 286 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7903 (mm-40) REVERT: V 298 GLN cc_start: 0.8379 (tm130) cc_final: 0.8098 (pp30) REVERT: V 342 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8095 (mmt180) REVERT: V 344 MET cc_start: 0.8489 (mmm) cc_final: 0.8281 (mmm) REVERT: V 355 SER cc_start: 0.8321 (t) cc_final: 0.7738 (t) REVERT: V 381 ARG cc_start: 0.8199 (ttp80) cc_final: 0.7959 (ttt90) REVERT: V 385 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7736 (tm-30) REVERT: V 391 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8003 (mt-10) REVERT: V 396 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6518 (tp30) REVERT: V 401 ASP cc_start: 0.7885 (m-30) cc_final: 0.7670 (m-30) REVERT: V 414 TYR cc_start: 0.8823 (t80) cc_final: 0.8489 (t80) REVERT: V 418 LEU cc_start: 0.8959 (tp) cc_final: 0.8719 (tp) REVERT: V 425 LEU cc_start: 0.9275 (mt) cc_final: 0.8953 (mt) REVERT: V 429 SER cc_start: 0.8702 (t) cc_final: 0.8475 (t) REVERT: V 454 LYS cc_start: 0.8558 (tttt) cc_final: 0.8161 (tttt) REVERT: W 23 HIS cc_start: 0.8392 (m90) cc_final: 0.8138 (m-70) REVERT: W 73 VAL cc_start: 0.8419 (t) cc_final: 0.8120 (m) REVERT: W 78 SER cc_start: 0.8547 (t) cc_final: 0.8255 (p) REVERT: W 81 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8091 (mtmm) REVERT: W 82 THR cc_start: 0.7966 (m) cc_final: 0.7725 (p) REVERT: W 110 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7043 (tm-30) REVERT: W 113 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8472 (mtmm) REVERT: W 115 GLU cc_start: 0.8570 (tp30) cc_final: 0.8254 (tp30) REVERT: W 123 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7896 (mttp) REVERT: W 170 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7883 (mm-30) REVERT: W 189 VAL cc_start: 0.7840 (t) cc_final: 0.7311 (m) REVERT: W 201 LYS cc_start: 0.8719 (tttt) cc_final: 0.8471 (tttt) REVERT: W 211 ASP cc_start: 0.8546 (t0) cc_final: 0.8307 (t70) REVERT: W 233 LYS cc_start: 0.7950 (tppt) cc_final: 0.7648 (tppt) REVERT: W 258 PHE cc_start: 0.8539 (m-80) cc_final: 0.8338 (m-10) REVERT: W 261 ASP cc_start: 0.8137 (t0) cc_final: 0.7748 (t0) REVERT: W 273 ILE cc_start: 0.8905 (mt) cc_final: 0.8570 (mt) REVERT: W 274 ASN cc_start: 0.8723 (m-40) cc_final: 0.8203 (m-40) REVERT: W 276 LYS cc_start: 0.8436 (tptt) cc_final: 0.8068 (tptm) REVERT: W 279 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7647 (mt-10) REVERT: W 281 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8311 (ttpp) REVERT: W 283 GLU cc_start: 0.7715 (pt0) cc_final: 0.7446 (tm-30) REVERT: W 316 GLU cc_start: 0.7879 (tt0) cc_final: 0.7501 (tp30) REVERT: W 326 ASN cc_start: 0.7843 (p0) cc_final: 0.7597 (p0) REVERT: W 349 ASP cc_start: 0.8078 (t0) cc_final: 0.7862 (t0) REVERT: W 362 GLN cc_start: 0.8581 (mm-40) cc_final: 0.8231 (tp-100) REVERT: W 365 LYS cc_start: 0.8692 (tmmt) cc_final: 0.8232 (tmmt) REVERT: W 374 GLU cc_start: 0.8219 (mm-30) cc_final: 0.8011 (tp30) REVERT: W 384 LEU cc_start: 0.8440 (tp) cc_final: 0.8117 (tp) REVERT: W 398 TYR cc_start: 0.8072 (t80) cc_final: 0.7869 (t80) REVERT: W 412 LYS cc_start: 0.8676 (mtpp) cc_final: 0.8347 (mmmt) REVERT: W 413 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7781 (ptm160) REVERT: W 424 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8665 (mmmm) REVERT: W 449 ASP cc_start: 0.6851 (t0) cc_final: 0.6271 (t70) REVERT: W 451 GLN cc_start: 0.7896 (mm110) cc_final: 0.7688 (mp10) REVERT: X 68 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8339 (mtmm) REVERT: X 95 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7686 (mm-30) REVERT: X 103 CYS cc_start: 0.8684 (t) cc_final: 0.8466 (t) REVERT: X 114 GLU cc_start: 0.8172 (tt0) cc_final: 0.7800 (tt0) REVERT: X 117 LYS cc_start: 0.8086 (ptmt) cc_final: 0.7736 (mtmt) REVERT: X 119 GLU cc_start: 0.8113 (tp30) cc_final: 0.7640 (tm-30) REVERT: X 153 GLU cc_start: 0.7781 (pp20) cc_final: 0.7537 (pp20) REVERT: X 165 HIS cc_start: 0.8654 (p90) cc_final: 0.8210 (p-80) REVERT: X 171 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8235 (tptt) REVERT: X 177 LYS cc_start: 0.8710 (tptp) cc_final: 0.8440 (tptp) REVERT: X 190 GLN cc_start: 0.8802 (tt0) cc_final: 0.8569 (tt0) REVERT: X 201 TYR cc_start: 0.7097 (t80) cc_final: 0.6680 (t80) REVERT: X 210 LYS cc_start: 0.8064 (mtmm) cc_final: 0.7240 (mtmm) REVERT: X 211 ARG cc_start: 0.8331 (ttp80) cc_final: 0.7965 (ttt-90) REVERT: X 214 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7607 (tpp-160) REVERT: X 251 ASP cc_start: 0.8183 (m-30) cc_final: 0.7827 (m-30) REVERT: X 276 LYS cc_start: 0.8214 (tppp) cc_final: 0.7721 (tppp) REVERT: X 282 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: X 283 LYS cc_start: 0.9050 (tttm) cc_final: 0.8840 (tttm) REVERT: X 289 ASN cc_start: 0.8368 (m110) cc_final: 0.8125 (m110) REVERT: X 312 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7843 (mm-30) REVERT: X 315 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7302 (mtm) REVERT: X 319 GLU cc_start: 0.8371 (pm20) cc_final: 0.8015 (pm20) REVERT: X 348 ARG cc_start: 0.7991 (mtp-110) cc_final: 0.7539 (mtp85) REVERT: X 350 THR cc_start: 0.8216 (t) cc_final: 0.7819 (p) REVERT: X 386 ARG cc_start: 0.8327 (tpp80) cc_final: 0.8012 (mmm-85) REVERT: X 387 ARG cc_start: 0.8802 (mmm160) cc_final: 0.8517 (tpt90) REVERT: X 409 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7897 (tm-30) REVERT: X 414 TYR cc_start: 0.8871 (t80) cc_final: 0.8486 (t80) REVERT: X 447 LEU cc_start: 0.8740 (mt) cc_final: 0.8528 (mt) REVERT: X 450 LYS cc_start: 0.8359 (mttt) cc_final: 0.8100 (mtpt) REVERT: X 454 LYS cc_start: 0.8643 (mttt) cc_final: 0.8274 (mptt) REVERT: Y 36 GLN cc_start: 0.8375 (tt0) cc_final: 0.8171 (tt0) REVERT: Y 38 ARG cc_start: 0.8094 (mpt180) cc_final: 0.7804 (mpt-90) REVERT: Y 42 GLU cc_start: 0.7987 (tt0) cc_final: 0.7690 (tt0) REVERT: Y 59 LYS cc_start: 0.8469 (mmmt) cc_final: 0.7968 (mmmt) REVERT: Y 63 ASN cc_start: 0.8773 (m-40) cc_final: 0.8397 (m-40) REVERT: Y 86 MET cc_start: 0.7356 (tpp) cc_final: 0.6410 (tpp) REVERT: Y 96 VAL cc_start: 0.8324 (t) cc_final: 0.8098 (p) REVERT: Y 113 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7990 (mtmm) REVERT: Y 115 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7599 (tm-30) REVERT: Y 130 LYS cc_start: 0.8833 (pttm) cc_final: 0.8273 (pttm) REVERT: Y 131 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6865 (mm-30) REVERT: Y 139 GLU cc_start: 0.7624 (tt0) cc_final: 0.7398 (tt0) REVERT: Y 142 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7064 (tm-30) REVERT: Y 161 LYS cc_start: 0.8419 (pttt) cc_final: 0.7926 (pptt) REVERT: Y 173 ASN cc_start: 0.8464 (p0) cc_final: 0.7746 (p0) REVERT: Y 174 LYS cc_start: 0.8593 (mmtm) cc_final: 0.8107 (mmtm) REVERT: Y 175 MET cc_start: 0.7654 (tpp) cc_final: 0.7181 (tpp) REVERT: Y 179 LEU cc_start: 0.9083 (mm) cc_final: 0.8385 (mt) REVERT: Y 182 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7215 (tp30) REVERT: Y 198 LYS cc_start: 0.8293 (mttm) cc_final: 0.7883 (mttm) REVERT: Y 210 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7973 (mmm160) REVERT: Y 226 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7870 (mp0) REVERT: Y 228 GLU cc_start: 0.8325 (tp30) cc_final: 0.8013 (tp30) REVERT: Y 229 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7259 (mp) REVERT: Y 245 ASP cc_start: 0.7882 (m-30) cc_final: 0.7516 (m-30) REVERT: Y 276 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8259 (mmmm) REVERT: Y 277 VAL cc_start: 0.8988 (t) cc_final: 0.8724 (p) REVERT: Y 279 GLU cc_start: 0.8114 (tt0) cc_final: 0.7712 (tm-30) REVERT: Y 281 LYS cc_start: 0.8803 (tmmt) cc_final: 0.8470 (tmmt) REVERT: Y 282 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7687 (tm-30) REVERT: Y 283 GLU cc_start: 0.7720 (mt-10) cc_final: 0.6546 (mt-10) REVERT: Y 287 GLU cc_start: 0.8477 (pm20) cc_final: 0.7261 (mp0) REVERT: Y 297 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7394 (mt-10) REVERT: Y 310 ASN cc_start: 0.8680 (t0) cc_final: 0.8213 (t0) REVERT: Y 311 ARG cc_start: 0.8275 (tpp-160) cc_final: 0.7990 (tpp-160) REVERT: Y 323 MET cc_start: 0.8213 (mtm) cc_final: 0.7968 (mtm) REVERT: Y 337 TYR cc_start: 0.8295 (p90) cc_final: 0.7979 (p90) REVERT: Y 374 GLU cc_start: 0.7926 (tp30) cc_final: 0.7699 (mm-30) REVERT: Y 376 GLU cc_start: 0.8233 (tp30) cc_final: 0.7929 (tp30) REVERT: Y 378 GLU cc_start: 0.7958 (pm20) cc_final: 0.7287 (pm20) REVERT: Y 389 LYS cc_start: 0.8625 (tppt) cc_final: 0.8168 (tppt) REVERT: Y 404 SER cc_start: 0.9047 (t) cc_final: 0.8833 (m) REVERT: Y 438 LYS cc_start: 0.8599 (ttmt) cc_final: 0.8346 (ttmm) REVERT: Y 443 ASN cc_start: 0.7879 (m110) cc_final: 0.7525 (m110) REVERT: Y 447 TYR cc_start: 0.8210 (m-80) cc_final: 0.7994 (m-80) REVERT: Y 455 GLN cc_start: 0.8176 (pp30) cc_final: 0.6653 (pp30) REVERT: Y 456 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8612 (mm) REVERT: Z 297 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7896 (mmt90) outliers start: 98 outliers final: 45 residues processed: 1171 average time/residue: 0.1880 time to fit residues: 332.4626 Evaluate side-chains 1098 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 1044 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 971 ILE Chi-restraints excluded: chain Q residue 1153 ILE Chi-restraints excluded: chain Q residue 1186 VAL Chi-restraints excluded: chain Q residue 1190 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1229 VAL Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1327 MET Chi-restraints excluded: chain Q residue 1337 TYR Chi-restraints excluded: chain Q residue 1367 ILE Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 650 PHE Chi-restraints excluded: chain R residue 747 LEU Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 419 LEU Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 196 SER Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain U residue 379 LEU Chi-restraints excluded: chain U residue 433 SER Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain W residue 31 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 300 MET Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 273 LEU Chi-restraints excluded: chain X residue 282 GLU Chi-restraints excluded: chain X residue 296 ILE Chi-restraints excluded: chain X residue 304 ILE Chi-restraints excluded: chain X residue 315 MET Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 455 ILE Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 25 optimal weight: 0.9980 chunk 290 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 258 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 GLN ** R 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN U 173 ASN U 242 HIS U 272 GLN U 401 ASN U 408 GLN V 51 GLN V 440 ASN X 29 HIS X 124 ASN Y 223 GLN Y 443 ASN ** Y 446 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 = 0.3750 r_free = 0.3750 target = 0.129010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108383 restraints weight = 55662.315| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.21 r_work: 0.3274 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28942 Z= 0.210 Angle : 0.670 12.766 39175 Z= 0.337 Chirality : 0.046 0.183 4610 Planarity : 0.004 0.068 5022 Dihedral : 8.245 161.349 4000 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.92 % Allowed : 23.41 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.14), residues: 3618 helix: 0.70 (0.13), residues: 1498 sheet: -0.10 (0.22), residues: 569 loop : -0.85 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG T 431 TYR 0.024 0.002 TYR R 34 PHE 0.022 0.002 PHE Q1127 TRP 0.013 0.001 TRP Y 280 HIS 0.008 0.001 HIS U 153 Details of bonding type rmsd covalent geometry : bond 0.00430 (28941) covalent geometry : angle 0.67031 (39175) hydrogen bonds : bond 0.04283 ( 1093) hydrogen bonds : angle 4.57246 ( 3156) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1088 time to evaluate : 0.940 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: Q 1027 SER cc_start: 0.9016 (m) cc_final: 0.8394 (p) REVERT: Q 1031 PHE cc_start: 0.8615 (p90) cc_final: 0.8312 (p90) REVERT: Q 1075 TYR cc_start: 0.8380 (t80) cc_final: 0.8097 (t80) REVERT: Q 1077 SER cc_start: 0.8369 (m) cc_final: 0.7830 (p) REVERT: Q 1109 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7813 (mtpp) REVERT: Q 1112 LYS cc_start: 0.8768 (mttt) cc_final: 0.8562 (mtmt) REVERT: Q 1127 PHE cc_start: 0.8739 (t80) cc_final: 0.8360 (t80) REVERT: Q 1128 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8475 (mp) REVERT: Q 1138 ASN cc_start: 0.8069 (m110) cc_final: 0.7695 (p0) REVERT: Q 1142 ARG cc_start: 0.8281 (ttm110) cc_final: 0.7901 (ttm110) REVERT: Q 1150 LYS cc_start: 0.8393 (tttp) cc_final: 0.7928 (tttp) REVERT: Q 1154 GLU cc_start: 0.7604 (pt0) cc_final: 0.6779 (pt0) REVERT: Q 1168 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8301 (mtpp) REVERT: Q 1176 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7778 (mt-10) REVERT: Q 1187 MET cc_start: 0.8333 (pmm) cc_final: 0.7999 (pmm) REVERT: Q 1190 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8609 (mt) REVERT: Q 1192 ASN cc_start: 0.8248 (p0) cc_final: 0.7844 (p0) REVERT: Q 1193 VAL cc_start: 0.8720 (m) cc_final: 0.8300 (p) REVERT: Q 1200 ARG cc_start: 0.8328 (ttp-110) cc_final: 0.7900 (ttp-110) REVERT: Q 1213 ASN cc_start: 0.8389 (m-40) cc_final: 0.8184 (m-40) REVERT: Q 1230 THR cc_start: 0.8723 (m) cc_final: 0.8472 (p) REVERT: Q 1239 ASP cc_start: 0.7227 (t70) cc_final: 0.7013 (t70) REVERT: Q 1241 LEU cc_start: 0.9029 (mm) cc_final: 0.8791 (mm) REVERT: Q 1266 GLU cc_start: 0.8099 (pm20) cc_final: 0.7670 (pm20) REVERT: Q 1327 MET cc_start: 0.7165 (OUTLIER) cc_final: 0.6954 (mpp) REVERT: Q 1331 MET cc_start: 0.7464 (tpp) cc_final: 0.6953 (tpp) REVERT: Q 1405 MET cc_start: 0.6664 (ptm) cc_final: 0.6297 (ptm) REVERT: R 155 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6881 (m-10) REVERT: R 193 ASP cc_start: 0.6228 (p0) cc_final: 0.5891 (p0) REVERT: R 218 GLN cc_start: 0.7951 (mp10) cc_final: 0.7639 (mp10) REVERT: R 229 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8107 (mt) REVERT: R 252 TYR cc_start: 0.7744 (p90) cc_final: 0.7299 (p90) REVERT: R 257 TYR cc_start: 0.8630 (t80) cc_final: 0.8389 (t80) REVERT: R 261 ILE cc_start: 0.8647 (tp) cc_final: 0.8333 (tp) REVERT: R 587 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7653 (mtm-85) REVERT: R 609 GLN cc_start: 0.8391 (tp-100) cc_final: 0.8078 (tp-100) REVERT: R 618 ARG cc_start: 0.8378 (ptm160) cc_final: 0.8173 (ptm160) REVERT: R 645 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8256 (tp) REVERT: R 656 LYS cc_start: 0.8164 (pptt) cc_final: 0.7792 (pptt) REVERT: R 659 GLN cc_start: 0.8032 (tp40) cc_final: 0.7804 (tp40) REVERT: R 699 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7652 (p) REVERT: R 711 TRP cc_start: 0.7479 (t60) cc_final: 0.6073 (t60) REVERT: R 724 TYR cc_start: 0.8387 (t80) cc_final: 0.8049 (t80) REVERT: R 725 ARG cc_start: 0.8016 (tpp-160) cc_final: 0.7466 (tpp-160) REVERT: R 744 GLU cc_start: 0.8166 (mp0) cc_final: 0.7805 (mp0) REVERT: R 749 ASN cc_start: 0.8478 (t0) cc_final: 0.8240 (t0) REVERT: R 751 LYS cc_start: 0.7389 (mmmt) cc_final: 0.6989 (mmmt) REVERT: S 145 LYS cc_start: 0.8461 (tppt) cc_final: 0.7736 (tppt) REVERT: S 157 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7771 (ttpt) REVERT: T 37 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7660 (tm-30) REVERT: T 42 LYS cc_start: 0.8065 (tptp) cc_final: 0.7771 (tppp) REVERT: T 49 VAL cc_start: 0.7685 (p) cc_final: 0.7401 (m) REVERT: T 108 SER cc_start: 0.8391 (p) cc_final: 0.8160 (m) REVERT: T 123 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8011 (tt0) REVERT: T 150 GLU cc_start: 0.7982 (tp30) cc_final: 0.7761 (tp30) REVERT: T 174 LYS cc_start: 0.8525 (mmtp) cc_final: 0.8253 (mmmm) REVERT: T 182 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.6900 (m-30) REVERT: T 190 GLN cc_start: 0.8383 (mt0) cc_final: 0.8176 (mt0) REVERT: T 209 VAL cc_start: 0.8946 (t) cc_final: 0.8632 (m) REVERT: T 221 GLU cc_start: 0.8100 (pt0) cc_final: 0.7490 (pm20) REVERT: T 225 GLU cc_start: 0.7788 (tp30) cc_final: 0.7402 (tp30) REVERT: T 273 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8010 (mm) REVERT: T 282 GLU cc_start: 0.8049 (tp30) cc_final: 0.7557 (tp30) REVERT: T 289 ASN cc_start: 0.8658 (m-40) cc_final: 0.8355 (m110) REVERT: T 302 GLU cc_start: 0.8261 (tt0) cc_final: 0.8006 (tt0) REVERT: T 304 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8069 (mm) REVERT: T 319 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7696 (mt-10) REVERT: T 323 TYR cc_start: 0.8546 (t80) cc_final: 0.8200 (t80) REVERT: T 325 ASN cc_start: 0.8524 (t0) cc_final: 0.7802 (t0) REVERT: T 329 GLU cc_start: 0.7833 (pp20) cc_final: 0.7391 (pp20) REVERT: T 366 ARG cc_start: 0.8036 (mtt-85) cc_final: 0.7795 (mtt-85) REVERT: T 376 ASP cc_start: 0.7968 (p0) cc_final: 0.7721 (p0) REVERT: T 396 GLU cc_start: 0.8088 (tp30) cc_final: 0.7853 (tp30) REVERT: T 398 SER cc_start: 0.8780 (t) cc_final: 0.8313 (p) REVERT: T 401 ASP cc_start: 0.8261 (m-30) cc_final: 0.8003 (m-30) REVERT: T 417 GLN cc_start: 0.8722 (mt0) cc_final: 0.8417 (mt0) REVERT: T 441 GLU cc_start: 0.7843 (tt0) cc_final: 0.7483 (tt0) REVERT: U 86 MET cc_start: 0.8202 (tpp) cc_final: 0.7993 (tpp) REVERT: U 113 LYS cc_start: 0.8809 (mttp) cc_final: 0.8598 (mttt) REVERT: U 132 GLU cc_start: 0.7055 (tp30) cc_final: 0.6668 (mm-30) REVERT: U 140 VAL cc_start: 0.8350 (m) cc_final: 0.7982 (p) REVERT: U 157 LYS cc_start: 0.8535 (mtpp) cc_final: 0.8253 (mtpp) REVERT: U 161 LYS cc_start: 0.8775 (tmmt) cc_final: 0.8515 (tttm) REVERT: U 166 GLU cc_start: 0.7821 (tp30) cc_final: 0.7060 (tp30) REVERT: U 175 MET cc_start: 0.8506 (tpp) cc_final: 0.8196 (tpp) REVERT: U 176 ILE cc_start: 0.8224 (mm) cc_final: 0.7985 (tp) REVERT: U 179 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8539 (mp) REVERT: U 189 VAL cc_start: 0.8601 (t) cc_final: 0.8364 (p) REVERT: U 193 ASP cc_start: 0.8271 (t0) cc_final: 0.7872 (p0) REVERT: U 223 GLN cc_start: 0.7822 (tm-30) cc_final: 0.7409 (tm-30) REVERT: U 226 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7423 (mm-30) REVERT: U 233 LYS cc_start: 0.8255 (ptmm) cc_final: 0.7746 (ptmm) REVERT: U 235 VAL cc_start: 0.8778 (t) cc_final: 0.8377 (m) REVERT: U 249 SER cc_start: 0.8623 (t) cc_final: 0.8120 (p) REVERT: U 276 LYS cc_start: 0.8722 (ttmm) cc_final: 0.8363 (ttmm) REVERT: U 279 GLU cc_start: 0.8277 (tt0) cc_final: 0.7996 (tt0) REVERT: U 281 LYS cc_start: 0.8922 (tttt) cc_final: 0.8613 (tptp) REVERT: U 288 ILE cc_start: 0.8734 (tt) cc_final: 0.8149 (mt) REVERT: U 307 SER cc_start: 0.9010 (m) cc_final: 0.8810 (p) REVERT: U 316 GLU cc_start: 0.8211 (tt0) cc_final: 0.7843 (tp30) REVERT: U 323 MET cc_start: 0.8493 (mtm) cc_final: 0.8238 (mtp) REVERT: U 346 ASP cc_start: 0.8361 (p0) cc_final: 0.8140 (p0) REVERT: U 357 LYS cc_start: 0.7951 (mppt) cc_final: 0.7686 (mppt) REVERT: U 368 LEU cc_start: 0.8983 (mt) cc_final: 0.8699 (mm) REVERT: U 373 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8104 (tm-30) REVERT: U 407 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8063 (tp40) REVERT: U 411 MET cc_start: 0.7990 (mmm) cc_final: 0.7581 (mtt) REVERT: U 417 THR cc_start: 0.8647 (p) cc_final: 0.7942 (t) REVERT: U 419 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7632 (mp0) REVERT: U 435 ARG cc_start: 0.8598 (ttp-170) cc_final: 0.7900 (ttp-170) REVERT: U 438 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8013 (tptp) REVERT: U 439 TYR cc_start: 0.8358 (m-80) cc_final: 0.7643 (m-80) REVERT: V 75 ILE cc_start: 0.8476 (pt) cc_final: 0.8154 (mp) REVERT: V 90 LEU cc_start: 0.7775 (mt) cc_final: 0.7499 (tt) REVERT: V 93 SER cc_start: 0.8493 (t) cc_final: 0.7822 (p) REVERT: V 103 CYS cc_start: 0.8388 (t) cc_final: 0.8013 (t) REVERT: V 114 GLU cc_start: 0.7782 (pm20) cc_final: 0.7503 (mp0) REVERT: V 119 GLU cc_start: 0.7997 (tp30) cc_final: 0.7460 (tp30) REVERT: V 143 GLU cc_start: 0.7717 (tt0) cc_final: 0.7444 (tt0) REVERT: V 179 LEU cc_start: 0.8392 (mm) cc_final: 0.8144 (mt) REVERT: V 193 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8077 (mmmt) REVERT: V 205 ASN cc_start: 0.8479 (m-40) cc_final: 0.7932 (m-40) REVERT: V 236 GLU cc_start: 0.7396 (pm20) cc_final: 0.7188 (pm20) REVERT: V 251 ASP cc_start: 0.7883 (m-30) cc_final: 0.7361 (m-30) REVERT: V 267 SER cc_start: 0.7898 (t) cc_final: 0.7660 (p) REVERT: V 268 MET cc_start: 0.8178 (mtm) cc_final: 0.7920 (mtm) REVERT: V 276 LYS cc_start: 0.8379 (mptt) cc_final: 0.7811 (mptt) REVERT: V 286 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7814 (mm-40) REVERT: V 290 LYS cc_start: 0.8499 (mppt) cc_final: 0.7984 (mttm) REVERT: V 311 ASP cc_start: 0.8150 (t0) cc_final: 0.7794 (t0) REVERT: V 325 ASN cc_start: 0.8043 (p0) cc_final: 0.7786 (p0) REVERT: V 336 VAL cc_start: 0.8452 (p) cc_final: 0.8154 (m) REVERT: V 342 ARG cc_start: 0.8605 (mtt-85) cc_final: 0.8108 (mmt180) REVERT: V 344 MET cc_start: 0.8388 (mmm) cc_final: 0.8183 (mmm) REVERT: V 365 ASP cc_start: 0.8460 (m-30) cc_final: 0.8246 (m-30) REVERT: V 381 ARG cc_start: 0.8287 (ttp80) cc_final: 0.8042 (ttt90) REVERT: V 385 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7823 (tm-30) REVERT: V 387 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8274 (mmm160) REVERT: V 391 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7996 (mt-10) REVERT: V 414 TYR cc_start: 0.8910 (t80) cc_final: 0.8657 (t80) REVERT: V 425 LEU cc_start: 0.9197 (mt) cc_final: 0.8962 (mt) REVERT: V 429 SER cc_start: 0.8673 (t) cc_final: 0.8212 (p) REVERT: V 454 LYS cc_start: 0.8578 (tttt) cc_final: 0.8236 (tttt) REVERT: W 23 HIS cc_start: 0.8426 (m90) cc_final: 0.8103 (m-70) REVERT: W 44 MET cc_start: 0.8586 (ttt) cc_final: 0.8300 (mtp) REVERT: W 73 VAL cc_start: 0.8558 (t) cc_final: 0.8256 (m) REVERT: W 78 SER cc_start: 0.8586 (t) cc_final: 0.8289 (p) REVERT: W 82 THR cc_start: 0.7975 (m) cc_final: 0.7635 (p) REVERT: W 113 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8434 (mtmm) REVERT: W 115 GLU cc_start: 0.8544 (tp30) cc_final: 0.8116 (tp30) REVERT: W 123 LYS cc_start: 0.8350 (mtmt) cc_final: 0.7986 (mtmm) REVERT: W 131 GLU cc_start: 0.7959 (tp30) cc_final: 0.7046 (mm-30) REVERT: W 154 LYS cc_start: 0.8397 (mttp) cc_final: 0.8078 (mttp) REVERT: W 170 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7920 (mm-30) REVERT: W 189 VAL cc_start: 0.7936 (t) cc_final: 0.7425 (m) REVERT: W 201 LYS cc_start: 0.8668 (tttt) cc_final: 0.8449 (tttt) REVERT: W 233 LYS cc_start: 0.8083 (tppt) cc_final: 0.7741 (tppt) REVERT: W 261 ASP cc_start: 0.8161 (t0) cc_final: 0.7843 (t0) REVERT: W 273 ILE cc_start: 0.8928 (mt) cc_final: 0.8666 (mt) REVERT: W 276 LYS cc_start: 0.8408 (tptt) cc_final: 0.8078 (tptm) REVERT: W 279 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7635 (mt-10) REVERT: W 281 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8385 (ttpp) REVERT: W 316 GLU cc_start: 0.7854 (tt0) cc_final: 0.7412 (tp30) REVERT: W 322 MET cc_start: 0.8183 (mmm) cc_final: 0.7956 (mtp) REVERT: W 323 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7837 (mtm) REVERT: W 338 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7826 (ttmm) REVERT: W 374 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7936 (tp30) REVERT: W 376 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: W 384 LEU cc_start: 0.8501 (tp) cc_final: 0.8190 (tp) REVERT: W 407 GLN cc_start: 0.8638 (tp40) cc_final: 0.7893 (tm-30) REVERT: W 409 ILE cc_start: 0.8326 (mt) cc_final: 0.8100 (mm) REVERT: W 412 LYS cc_start: 0.8766 (mtpp) cc_final: 0.8517 (mmmt) REVERT: W 413 ARG cc_start: 0.8500 (mtp-110) cc_final: 0.7988 (ptm160) REVERT: W 451 GLN cc_start: 0.7940 (mm110) cc_final: 0.7588 (mp10) REVERT: X 35 LEU cc_start: 0.9168 (tp) cc_final: 0.8719 (tp) REVERT: X 56 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7541 (mm-30) REVERT: X 68 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8274 (mtmm) REVERT: X 70 MET cc_start: 0.6853 (mmt) cc_final: 0.6531 (mmt) REVERT: X 95 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7300 (mm-30) REVERT: X 103 CYS cc_start: 0.8777 (t) cc_final: 0.8575 (t) REVERT: X 114 GLU cc_start: 0.8233 (tt0) cc_final: 0.7846 (tt0) REVERT: X 119 GLU cc_start: 0.8121 (tp30) cc_final: 0.7846 (tp30) REVERT: X 124 ASN cc_start: 0.8983 (m-40) cc_final: 0.8753 (m110) REVERT: X 153 GLU cc_start: 0.7816 (pp20) cc_final: 0.7465 (pp20) REVERT: X 171 LYS cc_start: 0.8695 (ttpt) cc_final: 0.8188 (ttpp) REVERT: X 177 LYS cc_start: 0.8749 (tptp) cc_final: 0.8437 (tptp) REVERT: X 190 GLN cc_start: 0.8837 (tt0) cc_final: 0.8473 (mt0) REVERT: X 201 TYR cc_start: 0.7219 (t80) cc_final: 0.6578 (t80) REVERT: X 210 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7216 (mtmm) REVERT: X 227 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7609 (tp30) REVERT: X 240 LYS cc_start: 0.8157 (mptt) cc_final: 0.7543 (mmtp) REVERT: X 251 ASP cc_start: 0.8284 (m-30) cc_final: 0.7942 (m-30) REVERT: X 269 MET cc_start: 0.8140 (mmm) cc_final: 0.7523 (mmm) REVERT: X 276 LYS cc_start: 0.8306 (tppp) cc_final: 0.7823 (tppp) REVERT: X 277 LYS cc_start: 0.8589 (mtpp) cc_final: 0.7435 (mtpp) REVERT: X 282 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7221 (tp30) REVERT: X 289 ASN cc_start: 0.8447 (m110) cc_final: 0.8202 (m110) REVERT: X 294 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8506 (ttmt) REVERT: X 311 ASP cc_start: 0.8187 (t0) cc_final: 0.7459 (t0) REVERT: X 312 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7951 (mm-30) REVERT: X 315 MET cc_start: 0.7856 (OUTLIER) cc_final: 0.7539 (ttm) REVERT: X 319 GLU cc_start: 0.8392 (pm20) cc_final: 0.8118 (pm20) REVERT: X 348 ARG cc_start: 0.7968 (mtp-110) cc_final: 0.7383 (mtp85) REVERT: X 350 THR cc_start: 0.8286 (t) cc_final: 0.7876 (p) REVERT: X 377 LYS cc_start: 0.8489 (tttm) cc_final: 0.8164 (ttmm) REVERT: X 386 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7927 (mmm-85) REVERT: X 387 ARG cc_start: 0.8798 (mmm160) cc_final: 0.8515 (tpt90) REVERT: X 409 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7951 (tm-30) REVERT: X 414 TYR cc_start: 0.8931 (t80) cc_final: 0.8653 (t80) REVERT: X 450 LYS cc_start: 0.8425 (mttt) cc_final: 0.7901 (mtpp) REVERT: X 454 LYS cc_start: 0.8560 (mttt) cc_final: 0.8162 (mptt) REVERT: Y 20 ILE cc_start: 0.8110 (mt) cc_final: 0.7781 (mm) REVERT: Y 36 GLN cc_start: 0.8427 (tt0) cc_final: 0.7999 (tt0) REVERT: Y 49 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7573 (mm-40) REVERT: Y 59 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8191 (mmmt) REVERT: Y 86 MET cc_start: 0.7357 (tpp) cc_final: 0.6783 (tpp) REVERT: Y 96 VAL cc_start: 0.8370 (t) cc_final: 0.8143 (p) REVERT: Y 113 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8203 (mtmm) REVERT: Y 115 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7483 (tm-30) REVERT: Y 130 LYS cc_start: 0.8820 (pttm) cc_final: 0.8318 (pttm) REVERT: Y 142 GLU cc_start: 0.7425 (tm-30) cc_final: 0.6968 (tm-30) REVERT: Y 161 LYS cc_start: 0.8348 (pttt) cc_final: 0.7855 (pptt) REVERT: Y 165 MET cc_start: 0.7814 (tmm) cc_final: 0.7490 (tmm) REVERT: Y 173 ASN cc_start: 0.8460 (p0) cc_final: 0.7834 (p0) REVERT: Y 174 LYS cc_start: 0.8675 (mmtm) cc_final: 0.8210 (mmtm) REVERT: Y 175 MET cc_start: 0.7564 (tpp) cc_final: 0.7091 (tpp) REVERT: Y 179 LEU cc_start: 0.9111 (mm) cc_final: 0.8469 (mt) REVERT: Y 182 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7389 (tp30) REVERT: Y 198 LYS cc_start: 0.8412 (mttm) cc_final: 0.7989 (mttm) REVERT: Y 206 PHE cc_start: 0.7938 (t80) cc_final: 0.7455 (m-80) REVERT: Y 208 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8037 (mtm180) REVERT: Y 210 ARG cc_start: 0.8264 (mmm160) cc_final: 0.8029 (mmm160) REVERT: Y 226 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7876 (mp0) REVERT: Y 229 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7516 (mp) REVERT: Y 276 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8190 (mmmm) REVERT: Y 279 GLU cc_start: 0.8247 (tt0) cc_final: 0.7907 (tm-30) REVERT: Y 280 TRP cc_start: 0.7852 (m100) cc_final: 0.7535 (m100) REVERT: Y 281 LYS cc_start: 0.8807 (tmmt) cc_final: 0.8492 (tmmt) REVERT: Y 282 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7723 (tm-30) REVERT: Y 283 GLU cc_start: 0.7730 (mt-10) cc_final: 0.6622 (mt-10) REVERT: Y 296 ASP cc_start: 0.8004 (t0) cc_final: 0.7678 (t0) REVERT: Y 297 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7423 (mp0) REVERT: Y 310 ASN cc_start: 0.8687 (t0) cc_final: 0.8360 (t0) REVERT: Y 311 ARG cc_start: 0.8269 (tpp-160) cc_final: 0.8006 (tpp-160) REVERT: Y 323 MET cc_start: 0.8234 (mtm) cc_final: 0.7973 (mtm) REVERT: Y 337 TYR cc_start: 0.8314 (p90) cc_final: 0.8079 (p90) REVERT: Y 376 GLU cc_start: 0.8286 (tp30) cc_final: 0.7864 (tp30) REVERT: Y 389 LYS cc_start: 0.8683 (tppt) cc_final: 0.8166 (tppt) REVERT: Y 392 VAL cc_start: 0.8232 (t) cc_final: 0.8016 (p) REVERT: Y 443 ASN cc_start: 0.7845 (m-40) cc_final: 0.7583 (m110) REVERT: Y 444 GLU cc_start: 0.7709 (tp30) cc_final: 0.7447 (tp30) REVERT: Y 455 GLN cc_start: 0.8271 (pp30) cc_final: 0.7278 (pp30) REVERT: Y 456 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8603 (mm) REVERT: Z 309 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8019 (tt) outliers start: 122 outliers final: 58 residues processed: 1154 average time/residue: 0.1907 time to fit residues: 331.9296 Evaluate side-chains 1117 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1040 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 971 ILE Chi-restraints excluded: chain Q residue 1128 LEU Chi-restraints excluded: chain Q residue 1190 LEU Chi-restraints excluded: chain Q residue 1221 ILE Chi-restraints excluded: chain Q residue 1257 MET Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1285 ASN Chi-restraints excluded: chain Q residue 1309 VAL Chi-restraints excluded: chain Q residue 1327 MET Chi-restraints excluded: chain Q residue 1328 MET Chi-restraints excluded: chain Q residue 1337 TYR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 607 HIS Chi-restraints excluded: chain R residue 623 GLU Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 699 THR Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 162 ASN Chi-restraints excluded: chain T residue 63 ASP Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 244 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 379 GLU Chi-restraints excluded: chain T residue 419 LEU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 196 SER Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain U residue 379 LEU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 387 ARG Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 277 VAL Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 273 LEU Chi-restraints excluded: chain X residue 282 GLU Chi-restraints excluded: chain X residue 315 MET Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 455 ILE Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 437 VAL Chi-restraints excluded: chain Y residue 456 ILE Chi-restraints excluded: chain Z residue 309 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 282 optimal weight: 0.9980 chunk 262 optimal weight: 0.5980 chunk 358 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 chunk 197 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 311 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN Q1342 HIS ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN ** R 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN U 401 ASN V 256 ASN V 289 ASN ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 256 ASN Y 274 ASN ** Y 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.130718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110164 restraints weight = 54988.423| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.21 r_work: 0.3290 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28942 Z= 0.162 Angle : 0.640 11.577 39175 Z= 0.320 Chirality : 0.045 0.170 4610 Planarity : 0.004 0.065 5022 Dihedral : 8.103 155.206 4000 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.37 % Allowed : 24.02 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.14), residues: 3618 helix: 0.90 (0.13), residues: 1508 sheet: -0.13 (0.21), residues: 583 loop : -0.81 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 587 TYR 0.024 0.001 TYR R 34 PHE 0.028 0.002 PHE R 104 TRP 0.014 0.002 TRP R 150 HIS 0.004 0.001 HIS Y 242 Details of bonding type rmsd covalent geometry : bond 0.00340 (28941) covalent geometry : angle 0.63969 (39175) hydrogen bonds : bond 0.03730 ( 1093) hydrogen bonds : angle 4.37251 ( 3156) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1087 time to evaluate : 1.169 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: Q 1027 SER cc_start: 0.9021 (m) cc_final: 0.8440 (p) REVERT: Q 1073 LEU cc_start: 0.8109 (mp) cc_final: 0.7453 (tp) REVERT: Q 1075 TYR cc_start: 0.8376 (t80) cc_final: 0.8095 (t80) REVERT: Q 1077 SER cc_start: 0.8374 (m) cc_final: 0.7810 (p) REVERT: Q 1082 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7779 (mmtt) REVERT: Q 1090 TYR cc_start: 0.7982 (t80) cc_final: 0.7349 (t80) REVERT: Q 1093 LEU cc_start: 0.8654 (mt) cc_final: 0.8414 (mm) REVERT: Q 1097 ASN cc_start: 0.7973 (t0) cc_final: 0.7625 (t0) REVERT: Q 1109 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7775 (mtpp) REVERT: Q 1112 LYS cc_start: 0.8775 (mttt) cc_final: 0.8575 (mtmt) REVERT: Q 1123 GLU cc_start: 0.8331 (pm20) cc_final: 0.8118 (pm20) REVERT: Q 1127 PHE cc_start: 0.8749 (t80) cc_final: 0.8327 (t80) REVERT: Q 1138 ASN cc_start: 0.8065 (m110) cc_final: 0.7671 (p0) REVERT: Q 1142 ARG cc_start: 0.8260 (ttm110) cc_final: 0.7902 (ttm110) REVERT: Q 1150 LYS cc_start: 0.8336 (tttp) cc_final: 0.7906 (tttp) REVERT: Q 1154 GLU cc_start: 0.7508 (pt0) cc_final: 0.6747 (pt0) REVERT: Q 1168 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8216 (mtpp) REVERT: Q 1172 GLN cc_start: 0.7784 (mp10) cc_final: 0.7496 (mp10) REVERT: Q 1176 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7774 (mt-10) REVERT: Q 1187 MET cc_start: 0.8283 (pmm) cc_final: 0.7943 (pmm) REVERT: Q 1190 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8546 (mt) REVERT: Q 1192 ASN cc_start: 0.8250 (p0) cc_final: 0.7840 (p0) REVERT: Q 1193 VAL cc_start: 0.8726 (m) cc_final: 0.8338 (p) REVERT: Q 1200 ARG cc_start: 0.8294 (ttp-110) cc_final: 0.7861 (ttp-110) REVERT: Q 1241 LEU cc_start: 0.9023 (mm) cc_final: 0.8780 (mt) REVERT: Q 1266 GLU cc_start: 0.8084 (pm20) cc_final: 0.7663 (pm20) REVERT: Q 1324 MET cc_start: 0.5767 (mmp) cc_final: 0.5521 (mmp) REVERT: Q 1331 MET cc_start: 0.7447 (tpp) cc_final: 0.6962 (tpp) REVERT: Q 1405 MET cc_start: 0.6623 (ptm) cc_final: 0.6261 (ptm) REVERT: R 93 ARG cc_start: 0.7706 (ttp80) cc_final: 0.7173 (ttp80) REVERT: R 113 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8414 (mm-30) REVERT: R 115 LEU cc_start: 0.9121 (mm) cc_final: 0.8909 (mp) REVERT: R 158 TYR cc_start: 0.7339 (m-80) cc_final: 0.7131 (m-80) REVERT: R 171 PHE cc_start: 0.8092 (m-80) cc_final: 0.7774 (m-80) REVERT: R 193 ASP cc_start: 0.6266 (p0) cc_final: 0.5983 (p0) REVERT: R 218 GLN cc_start: 0.7949 (mp10) cc_final: 0.7638 (mp10) REVERT: R 229 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8018 (mt) REVERT: R 261 ILE cc_start: 0.8603 (tp) cc_final: 0.8304 (tp) REVERT: R 585 ASP cc_start: 0.6586 (t0) cc_final: 0.6336 (t70) REVERT: R 609 GLN cc_start: 0.8389 (tp-100) cc_final: 0.8082 (tp-100) REVERT: R 633 GLN cc_start: 0.8283 (mp10) cc_final: 0.7955 (mt0) REVERT: R 645 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8242 (tp) REVERT: R 656 LYS cc_start: 0.8155 (pptt) cc_final: 0.7818 (pptt) REVERT: R 711 TRP cc_start: 0.7477 (t60) cc_final: 0.6280 (t60) REVERT: R 714 MET cc_start: 0.7595 (mtm) cc_final: 0.7290 (mtm) REVERT: R 719 ARG cc_start: 0.7745 (mmt-90) cc_final: 0.7404 (mmt-90) REVERT: R 724 TYR cc_start: 0.8363 (t80) cc_final: 0.8028 (t80) REVERT: R 725 ARG cc_start: 0.8100 (tpp-160) cc_final: 0.7545 (tpp-160) REVERT: R 744 GLU cc_start: 0.8181 (mp0) cc_final: 0.7747 (mp0) REVERT: R 751 LYS cc_start: 0.7380 (mmmt) cc_final: 0.7002 (mmmt) REVERT: S 70 GLU cc_start: 0.8583 (tp30) cc_final: 0.8019 (tp30) REVERT: S 145 LYS cc_start: 0.8441 (tppt) cc_final: 0.7699 (tppt) REVERT: S 156 LEU cc_start: 0.7653 (tp) cc_final: 0.7281 (tp) REVERT: S 157 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7750 (ttpt) REVERT: T 37 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7768 (tm-30) REVERT: T 42 LYS cc_start: 0.8077 (tptp) cc_final: 0.7720 (tppp) REVERT: T 49 VAL cc_start: 0.7614 (p) cc_final: 0.7347 (m) REVERT: T 66 LYS cc_start: 0.8074 (mttt) cc_final: 0.7777 (mttm) REVERT: T 109 GLU cc_start: 0.7643 (pm20) cc_final: 0.7281 (pm20) REVERT: T 123 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7933 (tt0) REVERT: T 168 VAL cc_start: 0.8476 (t) cc_final: 0.8188 (m) REVERT: T 174 LYS cc_start: 0.8518 (mmtp) cc_final: 0.8244 (mmmm) REVERT: T 182 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7916 (p0) REVERT: T 190 GLN cc_start: 0.8411 (mt0) cc_final: 0.8200 (mt0) REVERT: T 209 VAL cc_start: 0.8920 (t) cc_final: 0.8584 (m) REVERT: T 225 GLU cc_start: 0.7751 (tp30) cc_final: 0.7272 (tp30) REVERT: T 269 MET cc_start: 0.7340 (mtp) cc_final: 0.7118 (mtp) REVERT: T 273 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8005 (mm) REVERT: T 282 GLU cc_start: 0.8113 (tp30) cc_final: 0.7605 (tp30) REVERT: T 302 GLU cc_start: 0.8265 (tt0) cc_final: 0.8015 (tt0) REVERT: T 304 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (mt) REVERT: T 319 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7744 (mt-10) REVERT: T 323 TYR cc_start: 0.8519 (t80) cc_final: 0.8254 (t80) REVERT: T 329 GLU cc_start: 0.7783 (pp20) cc_final: 0.7347 (pp20) REVERT: T 376 ASP cc_start: 0.7884 (p0) cc_final: 0.7678 (p0) REVERT: T 396 GLU cc_start: 0.8127 (tp30) cc_final: 0.7922 (tp30) REVERT: T 398 SER cc_start: 0.8736 (t) cc_final: 0.8275 (p) REVERT: T 401 ASP cc_start: 0.8247 (m-30) cc_final: 0.7961 (m-30) REVERT: T 417 GLN cc_start: 0.8702 (mt0) cc_final: 0.8385 (mt0) REVERT: T 433 GLU cc_start: 0.6659 (pm20) cc_final: 0.6234 (pm20) REVERT: T 441 GLU cc_start: 0.7887 (tt0) cc_final: 0.7612 (tt0) REVERT: U 34 ASN cc_start: 0.8510 (m-40) cc_final: 0.8249 (m-40) REVERT: U 86 MET cc_start: 0.8187 (tpp) cc_final: 0.7974 (tpp) REVERT: U 113 LYS cc_start: 0.8753 (mttp) cc_final: 0.8465 (mtmt) REVERT: U 132 GLU cc_start: 0.7025 (tp30) cc_final: 0.6708 (mm-30) REVERT: U 140 VAL cc_start: 0.8333 (m) cc_final: 0.7974 (p) REVERT: U 157 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8159 (mtpp) REVERT: U 161 LYS cc_start: 0.8784 (tmmt) cc_final: 0.8550 (tttm) REVERT: U 166 GLU cc_start: 0.7854 (tp30) cc_final: 0.7136 (tp30) REVERT: U 168 ILE cc_start: 0.7951 (tp) cc_final: 0.7638 (tt) REVERT: U 170 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7458 (pm20) REVERT: U 175 MET cc_start: 0.8454 (tpp) cc_final: 0.8250 (tpp) REVERT: U 176 ILE cc_start: 0.8210 (mm) cc_final: 0.7895 (tp) REVERT: U 189 VAL cc_start: 0.8585 (t) cc_final: 0.8380 (p) REVERT: U 193 ASP cc_start: 0.8218 (t0) cc_final: 0.7868 (p0) REVERT: U 223 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7420 (tm-30) REVERT: U 226 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7380 (mm-30) REVERT: U 233 LYS cc_start: 0.8250 (ptmm) cc_final: 0.7965 (ptmm) REVERT: U 235 VAL cc_start: 0.8806 (t) cc_final: 0.8389 (m) REVERT: U 249 SER cc_start: 0.8636 (t) cc_final: 0.8106 (p) REVERT: U 276 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8233 (ttmm) REVERT: U 279 GLU cc_start: 0.8253 (tt0) cc_final: 0.7978 (tt0) REVERT: U 281 LYS cc_start: 0.8942 (tttt) cc_final: 0.8503 (tptp) REVERT: U 288 ILE cc_start: 0.8393 (tt) cc_final: 0.8109 (mt) REVERT: U 316 GLU cc_start: 0.8175 (tt0) cc_final: 0.7794 (tp30) REVERT: U 357 LYS cc_start: 0.7950 (mppt) cc_final: 0.7649 (mppt) REVERT: U 362 GLN cc_start: 0.8126 (mp10) cc_final: 0.7743 (mp10) REVERT: U 368 LEU cc_start: 0.8945 (mt) cc_final: 0.8671 (mm) REVERT: U 373 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8097 (tm-30) REVERT: U 407 GLN cc_start: 0.8500 (tm-30) cc_final: 0.8094 (tp40) REVERT: U 417 THR cc_start: 0.8588 (p) cc_final: 0.7866 (t) REVERT: U 419 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7586 (mp0) REVERT: U 435 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.7558 (ttp-170) REVERT: U 438 LYS cc_start: 0.8545 (ttpt) cc_final: 0.7987 (tptp) REVERT: U 439 TYR cc_start: 0.8322 (m-80) cc_final: 0.7521 (m-80) REVERT: V 70 MET cc_start: 0.8394 (mmm) cc_final: 0.8022 (mmm) REVERT: V 75 ILE cc_start: 0.8481 (pt) cc_final: 0.8158 (mp) REVERT: V 103 CYS cc_start: 0.8372 (t) cc_final: 0.7993 (t) REVERT: V 114 GLU cc_start: 0.7549 (pm20) cc_final: 0.7184 (pm20) REVERT: V 119 GLU cc_start: 0.8051 (tp30) cc_final: 0.7501 (tp30) REVERT: V 143 GLU cc_start: 0.7688 (tt0) cc_final: 0.7386 (tt0) REVERT: V 146 GLU cc_start: 0.7518 (tm-30) cc_final: 0.6775 (tm-30) REVERT: V 179 LEU cc_start: 0.8360 (mm) cc_final: 0.8140 (mp) REVERT: V 193 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8071 (mmmt) REVERT: V 205 ASN cc_start: 0.8455 (m-40) cc_final: 0.8161 (m-40) REVERT: V 236 GLU cc_start: 0.7480 (pm20) cc_final: 0.7212 (pm20) REVERT: V 251 ASP cc_start: 0.7868 (m-30) cc_final: 0.7303 (m-30) REVERT: V 274 LYS cc_start: 0.8350 (tttp) cc_final: 0.7927 (tttp) REVERT: V 276 LYS cc_start: 0.8424 (mptt) cc_final: 0.7915 (mptt) REVERT: V 286 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7854 (mm-40) REVERT: V 290 LYS cc_start: 0.8482 (mppt) cc_final: 0.7972 (mttm) REVERT: V 296 ILE cc_start: 0.7934 (mt) cc_final: 0.7670 (pt) REVERT: V 325 ASN cc_start: 0.8036 (p0) cc_final: 0.7576 (p0) REVERT: V 336 VAL cc_start: 0.8476 (p) cc_final: 0.8199 (m) REVERT: V 342 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8288 (mpt90) REVERT: V 355 SER cc_start: 0.8380 (t) cc_final: 0.7662 (t) REVERT: V 373 LEU cc_start: 0.9041 (mt) cc_final: 0.8813 (mm) REVERT: V 381 ARG cc_start: 0.8289 (ttp80) cc_final: 0.8046 (ttt90) REVERT: V 385 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7825 (tm-30) REVERT: V 387 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8238 (mmm160) REVERT: V 391 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7915 (mt-10) REVERT: V 414 TYR cc_start: 0.8887 (t80) cc_final: 0.8408 (t80) REVERT: V 425 LEU cc_start: 0.9161 (mt) cc_final: 0.8925 (mt) REVERT: V 429 SER cc_start: 0.8742 (t) cc_final: 0.8266 (t) REVERT: V 430 ASN cc_start: 0.8662 (t0) cc_final: 0.8461 (t0) REVERT: V 431 ARG cc_start: 0.8082 (mtm-85) cc_final: 0.7772 (mtm-85) REVERT: V 454 LYS cc_start: 0.8604 (tttt) cc_final: 0.8252 (tttt) REVERT: W 23 HIS cc_start: 0.8473 (m90) cc_final: 0.8091 (m-70) REVERT: W 73 VAL cc_start: 0.8573 (t) cc_final: 0.8267 (m) REVERT: W 78 SER cc_start: 0.8562 (t) cc_final: 0.8246 (p) REVERT: W 81 LYS cc_start: 0.8399 (mtmm) cc_final: 0.7799 (mtmm) REVERT: W 82 THR cc_start: 0.7892 (m) cc_final: 0.7490 (p) REVERT: W 115 GLU cc_start: 0.8505 (tp30) cc_final: 0.8019 (tp30) REVERT: W 123 LYS cc_start: 0.8360 (mtmt) cc_final: 0.8024 (mttp) REVERT: W 131 GLU cc_start: 0.7908 (tp30) cc_final: 0.7077 (mm-30) REVERT: W 170 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8010 (mm-30) REVERT: W 189 VAL cc_start: 0.7863 (t) cc_final: 0.7389 (m) REVERT: W 233 LYS cc_start: 0.8058 (tppt) cc_final: 0.7724 (tppt) REVERT: W 261 ASP cc_start: 0.8083 (t0) cc_final: 0.7771 (t0) REVERT: W 273 ILE cc_start: 0.8910 (mt) cc_final: 0.8703 (mt) REVERT: W 276 LYS cc_start: 0.8405 (tptt) cc_final: 0.8081 (tptm) REVERT: W 279 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7650 (mt-10) REVERT: W 281 LYS cc_start: 0.8645 (ttpp) cc_final: 0.8354 (ttpp) REVERT: W 316 GLU cc_start: 0.7806 (tt0) cc_final: 0.7400 (tp30) REVERT: W 323 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7835 (mtm) REVERT: W 338 LYS cc_start: 0.8015 (ttpp) cc_final: 0.7805 (ttmm) REVERT: W 407 GLN cc_start: 0.8609 (tp40) cc_final: 0.7867 (tm-30) REVERT: W 413 ARG cc_start: 0.8552 (mtp-110) cc_final: 0.8047 (ptm160) REVERT: W 449 ASP cc_start: 0.6963 (t0) cc_final: 0.6258 (t70) REVERT: W 451 GLN cc_start: 0.7996 (mm110) cc_final: 0.7730 (mp10) REVERT: X 31 LYS cc_start: 0.8551 (mmmt) cc_final: 0.8134 (mmmt) REVERT: X 35 LEU cc_start: 0.9144 (tp) cc_final: 0.8706 (tp) REVERT: X 68 LYS cc_start: 0.8600 (mtmm) cc_final: 0.8313 (mtmm) REVERT: X 95 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7483 (mm-30) REVERT: X 103 CYS cc_start: 0.8760 (t) cc_final: 0.8534 (t) REVERT: X 114 GLU cc_start: 0.8189 (tt0) cc_final: 0.7774 (tt0) REVERT: X 116 LYS cc_start: 0.8607 (ptpt) cc_final: 0.8403 (pttt) REVERT: X 117 LYS cc_start: 0.8233 (ptmt) cc_final: 0.7922 (mtmt) REVERT: X 119 GLU cc_start: 0.8113 (tp30) cc_final: 0.7615 (tp30) REVERT: X 153 GLU cc_start: 0.7751 (pp20) cc_final: 0.7421 (pp20) REVERT: X 165 HIS cc_start: 0.8685 (p90) cc_final: 0.8368 (p-80) REVERT: X 171 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8256 (tptt) REVERT: X 177 LYS cc_start: 0.8697 (tptp) cc_final: 0.8395 (tptp) REVERT: X 190 GLN cc_start: 0.8797 (tt0) cc_final: 0.8496 (mt0) REVERT: X 201 TYR cc_start: 0.7239 (t80) cc_final: 0.6486 (t80) REVERT: X 210 LYS cc_start: 0.8238 (mtmm) cc_final: 0.7275 (mtmm) REVERT: X 227 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7758 (tp30) REVERT: X 251 ASP cc_start: 0.8291 (m-30) cc_final: 0.7980 (m-30) REVERT: X 269 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7537 (mmm) REVERT: X 276 LYS cc_start: 0.8325 (tppp) cc_final: 0.7797 (tppp) REVERT: X 282 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: X 283 LYS cc_start: 0.9074 (tttm) cc_final: 0.8855 (tttm) REVERT: X 289 ASN cc_start: 0.8376 (m110) cc_final: 0.8111 (m110) REVERT: X 311 ASP cc_start: 0.8237 (t0) cc_final: 0.7755 (t0) REVERT: X 312 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7951 (mm-30) REVERT: X 319 GLU cc_start: 0.8475 (pm20) cc_final: 0.8082 (pm20) REVERT: X 348 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7588 (mtp85) REVERT: X 350 THR cc_start: 0.8276 (t) cc_final: 0.7887 (p) REVERT: X 365 ASP cc_start: 0.8723 (m-30) cc_final: 0.8422 (t0) REVERT: X 386 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7941 (mmm-85) REVERT: X 387 ARG cc_start: 0.8775 (mmm160) cc_final: 0.8475 (tpt90) REVERT: X 391 GLU cc_start: 0.8777 (tt0) cc_final: 0.8557 (tm-30) REVERT: X 409 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7884 (tm-30) REVERT: X 414 TYR cc_start: 0.8935 (t80) cc_final: 0.8711 (t80) REVERT: X 443 LYS cc_start: 0.7956 (mmmm) cc_final: 0.7717 (mmmm) REVERT: X 450 LYS cc_start: 0.8455 (mttt) cc_final: 0.8091 (mtpt) REVERT: X 454 LYS cc_start: 0.8567 (mttt) cc_final: 0.8187 (mptt) REVERT: Y 20 ILE cc_start: 0.8118 (mt) cc_final: 0.7820 (mm) REVERT: Y 49 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7574 (mm-40) REVERT: Y 86 MET cc_start: 0.7293 (tpp) cc_final: 0.6724 (tpp) REVERT: Y 96 VAL cc_start: 0.8371 (t) cc_final: 0.8143 (p) REVERT: Y 113 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8126 (mtmm) REVERT: Y 115 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7452 (tm-30) REVERT: Y 142 GLU cc_start: 0.7331 (tm-30) cc_final: 0.6920 (tm-30) REVERT: Y 161 LYS cc_start: 0.8375 (pttt) cc_final: 0.7865 (pttm) REVERT: Y 173 ASN cc_start: 0.8336 (p0) cc_final: 0.6990 (p0) REVERT: Y 174 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8161 (mmtm) REVERT: Y 175 MET cc_start: 0.7581 (tpp) cc_final: 0.7076 (tpp) REVERT: Y 179 LEU cc_start: 0.9109 (mm) cc_final: 0.8427 (mt) REVERT: Y 182 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7301 (tp30) REVERT: Y 206 PHE cc_start: 0.8028 (t80) cc_final: 0.7503 (m-80) REVERT: Y 208 ARG cc_start: 0.8382 (mtt180) cc_final: 0.8142 (mtp85) REVERT: Y 226 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7752 (mp0) REVERT: Y 274 ASN cc_start: 0.8745 (m110) cc_final: 0.8516 (m-40) REVERT: Y 276 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8367 (tppp) REVERT: Y 279 GLU cc_start: 0.8190 (tt0) cc_final: 0.7890 (tm-30) REVERT: Y 281 LYS cc_start: 0.8787 (tmmt) cc_final: 0.8450 (tmmt) REVERT: Y 282 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7839 (tm-30) REVERT: Y 283 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6619 (mt-10) REVERT: Y 296 ASP cc_start: 0.8009 (t0) cc_final: 0.7692 (t0) REVERT: Y 297 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7465 (mp0) REVERT: Y 304 GLU cc_start: 0.7621 (mp0) cc_final: 0.7318 (mp0) REVERT: Y 310 ASN cc_start: 0.8665 (t0) cc_final: 0.8298 (t0) REVERT: Y 311 ARG cc_start: 0.8214 (tpp-160) cc_final: 0.7997 (tpp-160) REVERT: Y 323 MET cc_start: 0.8210 (mtm) cc_final: 0.7936 (mtm) REVERT: Y 337 TYR cc_start: 0.8319 (p90) cc_final: 0.8069 (p90) REVERT: Y 376 GLU cc_start: 0.8233 (tp30) cc_final: 0.7843 (tp30) REVERT: Y 378 GLU cc_start: 0.7849 (pm20) cc_final: 0.7595 (pm20) REVERT: Y 443 ASN cc_start: 0.7820 (m-40) cc_final: 0.7586 (m110) REVERT: Y 444 GLU cc_start: 0.7685 (tp30) cc_final: 0.7421 (tp30) REVERT: Y 455 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7298 (pp30) REVERT: Y 456 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8626 (mm) outliers start: 136 outliers final: 80 residues processed: 1149 average time/residue: 0.1941 time to fit residues: 336.2074 Evaluate side-chains 1153 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1061 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 971 ILE Chi-restraints excluded: chain Q residue 1190 LEU Chi-restraints excluded: chain Q residue 1257 MET Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1285 ASN Chi-restraints excluded: chain Q residue 1328 MET Chi-restraints excluded: chain Q residue 1337 TYR Chi-restraints excluded: chain Q residue 1367 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 623 GLU Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 650 PHE Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 99 LYS Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 244 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 276 LYS Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 379 GLU Chi-restraints excluded: chain T residue 419 LEU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 196 SER Chi-restraints excluded: chain U residue 305 CYS Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain U residue 374 GLU Chi-restraints excluded: chain U residue 379 LEU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 387 ARG Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 167 THR Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 277 VAL Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 269 MET Chi-restraints excluded: chain X residue 273 LEU Chi-restraints excluded: chain X residue 282 GLU Chi-restraints excluded: chain X residue 297 ASP Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 455 ILE Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 455 GLN Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 230 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 313 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 121 optimal weight: 0.0470 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN ** U 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 256 ASN ** Y 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109396 restraints weight = 55188.715| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 3.21 r_work: 0.3296 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28942 Z= 0.148 Angle : 0.639 10.855 39175 Z= 0.316 Chirality : 0.045 0.182 4610 Planarity : 0.004 0.087 5022 Dihedral : 7.967 148.654 4000 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.72 % Allowed : 24.98 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.14), residues: 3618 helix: 1.06 (0.13), residues: 1502 sheet: -0.01 (0.22), residues: 560 loop : -0.82 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 22 TYR 0.025 0.001 TYR R 34 PHE 0.026 0.002 PHE R 104 TRP 0.014 0.001 TRP Y 280 HIS 0.005 0.001 HIS X 29 Details of bonding type rmsd covalent geometry : bond 0.00319 (28941) covalent geometry : angle 0.63892 (39175) hydrogen bonds : bond 0.03576 ( 1093) hydrogen bonds : angle 4.27201 ( 3156) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 1076 time to evaluate : 0.774 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 1027 SER cc_start: 0.9028 (m) cc_final: 0.8429 (p) REVERT: Q 1073 LEU cc_start: 0.8128 (mp) cc_final: 0.7604 (tt) REVERT: Q 1075 TYR cc_start: 0.8346 (t80) cc_final: 0.8063 (t80) REVERT: Q 1077 SER cc_start: 0.8371 (m) cc_final: 0.7794 (p) REVERT: Q 1082 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7781 (mmtt) REVERT: Q 1092 ASP cc_start: 0.7976 (m-30) cc_final: 0.7762 (m-30) REVERT: Q 1097 ASN cc_start: 0.8009 (t0) cc_final: 0.7637 (t0) REVERT: Q 1109 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7765 (mtpp) REVERT: Q 1127 PHE cc_start: 0.8726 (t80) cc_final: 0.8329 (t80) REVERT: Q 1128 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8417 (mp) REVERT: Q 1138 ASN cc_start: 0.8052 (m110) cc_final: 0.7660 (p0) REVERT: Q 1142 ARG cc_start: 0.8279 (ttm110) cc_final: 0.7955 (ttm110) REVERT: Q 1150 LYS cc_start: 0.8380 (tttp) cc_final: 0.7902 (tttp) REVERT: Q 1154 GLU cc_start: 0.7478 (pt0) cc_final: 0.6740 (pt0) REVERT: Q 1168 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8318 (mtpp) REVERT: Q 1176 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7894 (mt-10) REVERT: Q 1187 MET cc_start: 0.8213 (pmm) cc_final: 0.7870 (pmm) REVERT: Q 1190 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8558 (mt) REVERT: Q 1193 VAL cc_start: 0.8760 (m) cc_final: 0.8479 (p) REVERT: Q 1213 ASN cc_start: 0.8359 (m-40) cc_final: 0.8154 (m-40) REVERT: Q 1266 GLU cc_start: 0.8068 (pm20) cc_final: 0.7617 (pm20) REVERT: Q 1273 LEU cc_start: 0.8401 (mp) cc_final: 0.8187 (mt) REVERT: Q 1324 MET cc_start: 0.5758 (mmp) cc_final: 0.5529 (mmp) REVERT: Q 1327 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6904 (mpp) REVERT: Q 1331 MET cc_start: 0.7406 (tpp) cc_final: 0.6894 (tpp) REVERT: Q 1405 MET cc_start: 0.6629 (ptm) cc_final: 0.6248 (ptm) REVERT: R 113 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8442 (mm-30) REVERT: R 121 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7332 (m-70) REVERT: R 149 ASN cc_start: 0.8722 (m-40) cc_final: 0.8441 (m110) REVERT: R 155 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7023 (m-10) REVERT: R 193 ASP cc_start: 0.6265 (p0) cc_final: 0.6034 (p0) REVERT: R 210 LYS cc_start: 0.6858 (mmtp) cc_final: 0.6472 (mmtp) REVERT: R 218 GLN cc_start: 0.7967 (mp10) cc_final: 0.7656 (mp10) REVERT: R 229 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.7776 (mp) REVERT: R 261 ILE cc_start: 0.8563 (tp) cc_final: 0.8187 (tp) REVERT: R 585 ASP cc_start: 0.6672 (t70) cc_final: 0.5645 (t70) REVERT: R 609 GLN cc_start: 0.8401 (tp-100) cc_final: 0.8098 (tp-100) REVERT: R 645 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8254 (tp) REVERT: R 656 LYS cc_start: 0.8185 (pptt) cc_final: 0.7964 (pptt) REVERT: R 697 ASN cc_start: 0.8359 (t0) cc_final: 0.7926 (t0) REVERT: R 724 TYR cc_start: 0.8391 (t80) cc_final: 0.8086 (t80) REVERT: R 725 ARG cc_start: 0.8116 (tpp-160) cc_final: 0.7548 (tpp-160) REVERT: R 743 LYS cc_start: 0.8476 (mmtm) cc_final: 0.8230 (mmmm) REVERT: R 744 GLU cc_start: 0.8160 (mp0) cc_final: 0.7722 (mp0) REVERT: R 749 ASN cc_start: 0.8396 (t0) cc_final: 0.8157 (t0) REVERT: R 751 LYS cc_start: 0.7251 (mmmt) cc_final: 0.6913 (mmmt) REVERT: S 70 GLU cc_start: 0.8484 (tp30) cc_final: 0.8041 (tp30) REVERT: S 145 LYS cc_start: 0.8481 (tppt) cc_final: 0.7740 (tppt) REVERT: S 157 LYS cc_start: 0.8186 (ttpt) cc_final: 0.7744 (ttpt) REVERT: T 37 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7727 (tm-30) REVERT: T 42 LYS cc_start: 0.8082 (tptp) cc_final: 0.7754 (tppp) REVERT: T 49 VAL cc_start: 0.7568 (p) cc_final: 0.7350 (m) REVERT: T 66 LYS cc_start: 0.8044 (mttt) cc_final: 0.7824 (mttm) REVERT: T 109 GLU cc_start: 0.7560 (pm20) cc_final: 0.7229 (pm20) REVERT: T 123 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7967 (tt0) REVERT: T 168 VAL cc_start: 0.8441 (t) cc_final: 0.8161 (m) REVERT: T 174 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8259 (mmmm) REVERT: T 182 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7941 (p0) REVERT: T 190 GLN cc_start: 0.8421 (mt0) cc_final: 0.8203 (mt0) REVERT: T 209 VAL cc_start: 0.8919 (t) cc_final: 0.8584 (m) REVERT: T 225 GLU cc_start: 0.7644 (tp30) cc_final: 0.7221 (tp30) REVERT: T 282 GLU cc_start: 0.8100 (tp30) cc_final: 0.7602 (tp30) REVERT: T 302 GLU cc_start: 0.8262 (tt0) cc_final: 0.8013 (tt0) REVERT: T 304 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8202 (mt) REVERT: T 319 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7734 (mt-10) REVERT: T 329 GLU cc_start: 0.7807 (pp20) cc_final: 0.7359 (pp20) REVERT: T 366 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7723 (mtt-85) REVERT: T 401 ASP cc_start: 0.8244 (m-30) cc_final: 0.7934 (m-30) REVERT: T 417 GLN cc_start: 0.8696 (mt0) cc_final: 0.8370 (mt0) REVERT: T 431 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7460 (mtm-85) REVERT: T 433 GLU cc_start: 0.6855 (pm20) cc_final: 0.6436 (pm20) REVERT: T 441 GLU cc_start: 0.7996 (tt0) cc_final: 0.7581 (tt0) REVERT: U 34 ASN cc_start: 0.8591 (m-40) cc_final: 0.8199 (m-40) REVERT: U 132 GLU cc_start: 0.7071 (tp30) cc_final: 0.6776 (mm-30) REVERT: U 140 VAL cc_start: 0.8304 (m) cc_final: 0.7971 (p) REVERT: U 157 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8201 (mtpp) REVERT: U 159 THR cc_start: 0.8155 (OUTLIER) cc_final: 0.7394 (p) REVERT: U 161 LYS cc_start: 0.8769 (tmmt) cc_final: 0.8524 (tttm) REVERT: U 166 GLU cc_start: 0.7883 (tp30) cc_final: 0.7188 (tp30) REVERT: U 168 ILE cc_start: 0.7951 (tp) cc_final: 0.7707 (tt) REVERT: U 176 ILE cc_start: 0.8226 (mm) cc_final: 0.7887 (tp) REVERT: U 193 ASP cc_start: 0.8195 (t0) cc_final: 0.7932 (p0) REVERT: U 223 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7411 (tm-30) REVERT: U 226 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7394 (mm-30) REVERT: U 233 LYS cc_start: 0.8267 (ptmm) cc_final: 0.7988 (ptmm) REVERT: U 235 VAL cc_start: 0.8783 (t) cc_final: 0.8349 (m) REVERT: U 249 SER cc_start: 0.8620 (t) cc_final: 0.8074 (p) REVERT: U 276 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8283 (ttmm) REVERT: U 279 GLU cc_start: 0.8242 (tt0) cc_final: 0.7960 (tt0) REVERT: U 281 LYS cc_start: 0.8929 (tttt) cc_final: 0.8487 (tptp) REVERT: U 316 GLU cc_start: 0.8226 (tt0) cc_final: 0.7836 (tp30) REVERT: U 323 MET cc_start: 0.8510 (mtp) cc_final: 0.8222 (mtm) REVERT: U 357 LYS cc_start: 0.7929 (mppt) cc_final: 0.7654 (mppt) REVERT: U 362 GLN cc_start: 0.8141 (mp10) cc_final: 0.7758 (mp10) REVERT: U 368 LEU cc_start: 0.8931 (mt) cc_final: 0.8680 (mm) REVERT: U 373 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: U 407 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8185 (tp40) REVERT: U 411 MET cc_start: 0.8079 (mtt) cc_final: 0.7847 (mtt) REVERT: U 417 THR cc_start: 0.8577 (p) cc_final: 0.7770 (t) REVERT: U 419 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7529 (mp0) REVERT: U 435 ARG cc_start: 0.8606 (ttp-170) cc_final: 0.7592 (ttp-170) REVERT: U 438 LYS cc_start: 0.8513 (ttpt) cc_final: 0.7961 (tptp) REVERT: U 439 TYR cc_start: 0.8288 (m-80) cc_final: 0.7573 (m-80) REVERT: V 45 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6902 (mm-30) REVERT: V 70 MET cc_start: 0.8332 (mmm) cc_final: 0.8026 (mmm) REVERT: V 75 ILE cc_start: 0.8484 (pt) cc_final: 0.8163 (mp) REVERT: V 103 CYS cc_start: 0.8318 (t) cc_final: 0.7945 (t) REVERT: V 114 GLU cc_start: 0.7532 (pm20) cc_final: 0.7254 (pm20) REVERT: V 119 GLU cc_start: 0.8085 (tp30) cc_final: 0.7455 (tp30) REVERT: V 143 GLU cc_start: 0.7663 (tt0) cc_final: 0.7346 (tt0) REVERT: V 146 GLU cc_start: 0.7565 (tm-30) cc_final: 0.6748 (tm-30) REVERT: V 179 LEU cc_start: 0.8358 (mm) cc_final: 0.8140 (mp) REVERT: V 193 LYS cc_start: 0.8532 (mmmt) cc_final: 0.8084 (mmmt) REVERT: V 205 ASN cc_start: 0.8442 (m-40) cc_final: 0.8167 (m-40) REVERT: V 224 LEU cc_start: 0.8491 (mt) cc_final: 0.8274 (mt) REVERT: V 251 ASP cc_start: 0.7880 (m-30) cc_final: 0.7366 (m-30) REVERT: V 276 LYS cc_start: 0.8449 (mptt) cc_final: 0.7934 (mptt) REVERT: V 286 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7879 (mm-40) REVERT: V 290 LYS cc_start: 0.8468 (mppt) cc_final: 0.7985 (mttm) REVERT: V 296 ILE cc_start: 0.7934 (mt) cc_final: 0.7705 (pt) REVERT: V 298 GLN cc_start: 0.8488 (tm130) cc_final: 0.8176 (pp30) REVERT: V 336 VAL cc_start: 0.8480 (p) cc_final: 0.8201 (m) REVERT: V 342 ARG cc_start: 0.8593 (mtt-85) cc_final: 0.8199 (mpt90) REVERT: V 355 SER cc_start: 0.8351 (t) cc_final: 0.7929 (t) REVERT: V 373 LEU cc_start: 0.9026 (mt) cc_final: 0.8796 (mm) REVERT: V 381 ARG cc_start: 0.8302 (ttp80) cc_final: 0.8049 (ttt90) REVERT: V 385 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7806 (tm-30) REVERT: V 387 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8294 (mmm160) REVERT: V 391 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7908 (mt-10) REVERT: V 414 TYR cc_start: 0.8883 (t80) cc_final: 0.8364 (t80) REVERT: V 425 LEU cc_start: 0.9135 (mt) cc_final: 0.8881 (mt) REVERT: V 429 SER cc_start: 0.8723 (t) cc_final: 0.8380 (t) REVERT: V 430 ASN cc_start: 0.8676 (t0) cc_final: 0.8365 (t0) REVERT: V 454 LYS cc_start: 0.8611 (tttt) cc_final: 0.8266 (tttt) REVERT: W 23 HIS cc_start: 0.8508 (m90) cc_final: 0.8099 (m-70) REVERT: W 73 VAL cc_start: 0.8572 (t) cc_final: 0.8263 (m) REVERT: W 78 SER cc_start: 0.8561 (t) cc_final: 0.8252 (p) REVERT: W 82 THR cc_start: 0.7938 (m) cc_final: 0.7455 (p) REVERT: W 115 GLU cc_start: 0.8474 (tp30) cc_final: 0.8184 (tp30) REVERT: W 119 GLN cc_start: 0.8531 (mt0) cc_final: 0.8328 (mt0) REVERT: W 123 LYS cc_start: 0.8375 (mtmt) cc_final: 0.8014 (mtmm) REVERT: W 131 GLU cc_start: 0.7889 (tp30) cc_final: 0.7062 (mm-30) REVERT: W 170 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7886 (mm-30) REVERT: W 189 VAL cc_start: 0.7879 (t) cc_final: 0.7397 (m) REVERT: W 201 LYS cc_start: 0.8696 (tttt) cc_final: 0.8387 (ttmt) REVERT: W 233 LYS cc_start: 0.8077 (tppt) cc_final: 0.7734 (tppt) REVERT: W 273 ILE cc_start: 0.8916 (mt) cc_final: 0.8663 (mt) REVERT: W 276 LYS cc_start: 0.8400 (tptt) cc_final: 0.8072 (tptm) REVERT: W 279 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7609 (mt-10) REVERT: W 281 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8354 (ttpp) REVERT: W 316 GLU cc_start: 0.7821 (tt0) cc_final: 0.7405 (tp30) REVERT: W 323 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7790 (mtm) REVERT: W 331 LYS cc_start: 0.8253 (ttpp) cc_final: 0.7936 (ttpp) REVERT: W 407 GLN cc_start: 0.8598 (tp40) cc_final: 0.7880 (tm-30) REVERT: W 413 ARG cc_start: 0.8530 (mtp-110) cc_final: 0.8013 (ptm160) REVERT: W 449 ASP cc_start: 0.6981 (t0) cc_final: 0.6295 (t70) REVERT: W 451 GLN cc_start: 0.7955 (mm110) cc_final: 0.7737 (mp10) REVERT: X 31 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8115 (mmmt) REVERT: X 35 LEU cc_start: 0.9058 (tp) cc_final: 0.8732 (tp) REVERT: X 68 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8285 (mtmm) REVERT: X 103 CYS cc_start: 0.8766 (t) cc_final: 0.8558 (t) REVERT: X 114 GLU cc_start: 0.8222 (tt0) cc_final: 0.7799 (tt0) REVERT: X 117 LYS cc_start: 0.8248 (ptmt) cc_final: 0.7949 (mtmt) REVERT: X 119 GLU cc_start: 0.8107 (tp30) cc_final: 0.7637 (tp30) REVERT: X 153 GLU cc_start: 0.7684 (pp20) cc_final: 0.7357 (pp20) REVERT: X 165 HIS cc_start: 0.8478 (p90) cc_final: 0.8211 (p-80) REVERT: X 171 LYS cc_start: 0.8698 (ttpt) cc_final: 0.8259 (tptt) REVERT: X 177 LYS cc_start: 0.8709 (tptp) cc_final: 0.8441 (tptp) REVERT: X 190 GLN cc_start: 0.8781 (tt0) cc_final: 0.8505 (mt0) REVERT: X 201 TYR cc_start: 0.7219 (t80) cc_final: 0.6428 (t80) REVERT: X 210 LYS cc_start: 0.8251 (mtmm) cc_final: 0.7278 (mtmm) REVERT: X 227 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7598 (tp30) REVERT: X 251 ASP cc_start: 0.8270 (m-30) cc_final: 0.7997 (m-30) REVERT: X 252 LEU cc_start: 0.8343 (mt) cc_final: 0.7966 (mt) REVERT: X 256 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8060 (m-40) REVERT: X 269 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7560 (mmm) REVERT: X 276 LYS cc_start: 0.8333 (tppp) cc_final: 0.7806 (tppp) REVERT: X 282 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7143 (tp30) REVERT: X 283 LYS cc_start: 0.9070 (tttm) cc_final: 0.8860 (tttm) REVERT: X 289 ASN cc_start: 0.8378 (m110) cc_final: 0.8100 (m110) REVERT: X 311 ASP cc_start: 0.8257 (t0) cc_final: 0.7632 (t0) REVERT: X 312 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7918 (mm-30) REVERT: X 315 MET cc_start: 0.7953 (mtm) cc_final: 0.7672 (mtm) REVERT: X 319 GLU cc_start: 0.8470 (pm20) cc_final: 0.8010 (pm20) REVERT: X 348 ARG cc_start: 0.7969 (mtp-110) cc_final: 0.7510 (mtp85) REVERT: X 350 THR cc_start: 0.8279 (t) cc_final: 0.7885 (p) REVERT: X 365 ASP cc_start: 0.8707 (m-30) cc_final: 0.8404 (t0) REVERT: X 386 ARG cc_start: 0.8354 (tpp80) cc_final: 0.7911 (mmm-85) REVERT: X 387 ARG cc_start: 0.8780 (mmm160) cc_final: 0.8492 (tpt90) REVERT: X 391 GLU cc_start: 0.8784 (tt0) cc_final: 0.8569 (tm-30) REVERT: X 409 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7805 (tm-30) REVERT: X 414 TYR cc_start: 0.8913 (t80) cc_final: 0.8675 (t80) REVERT: X 443 LYS cc_start: 0.7949 (mmmm) cc_final: 0.7709 (mmmm) REVERT: Y 20 ILE cc_start: 0.8127 (mt) cc_final: 0.7850 (mm) REVERT: Y 49 GLN cc_start: 0.7830 (mm-40) cc_final: 0.7513 (mm-40) REVERT: Y 59 LYS cc_start: 0.8653 (tptt) cc_final: 0.8384 (tppt) REVERT: Y 86 MET cc_start: 0.7333 (tpp) cc_final: 0.6756 (tpp) REVERT: Y 96 VAL cc_start: 0.8349 (t) cc_final: 0.8145 (p) REVERT: Y 113 LYS cc_start: 0.8508 (mtmt) cc_final: 0.8151 (mtmm) REVERT: Y 115 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7473 (tm-30) REVERT: Y 128 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7686 (ttpp) REVERT: Y 142 GLU cc_start: 0.7294 (tm-30) cc_final: 0.7003 (tm-30) REVERT: Y 153 HIS cc_start: 0.6624 (OUTLIER) cc_final: 0.6284 (t-90) REVERT: Y 173 ASN cc_start: 0.8391 (p0) cc_final: 0.7479 (p0) REVERT: Y 175 MET cc_start: 0.7644 (tpp) cc_final: 0.7117 (tpp) REVERT: Y 179 LEU cc_start: 0.9097 (mm) cc_final: 0.8420 (mt) REVERT: Y 182 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7292 (tp30) REVERT: Y 206 PHE cc_start: 0.8005 (t80) cc_final: 0.7458 (m-80) REVERT: Y 223 GLN cc_start: 0.7984 (mm110) cc_final: 0.7710 (mm110) REVERT: Y 226 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7734 (mp0) REVERT: Y 229 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7678 (mp) REVERT: Y 276 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8363 (tppp) REVERT: Y 279 GLU cc_start: 0.8207 (tt0) cc_final: 0.7842 (tm-30) REVERT: Y 281 LYS cc_start: 0.8760 (tmmt) cc_final: 0.8407 (tmmt) REVERT: Y 282 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7894 (tm-30) REVERT: Y 283 GLU cc_start: 0.7851 (mt-10) cc_final: 0.6610 (mt-10) REVERT: Y 287 GLU cc_start: 0.8413 (pm20) cc_final: 0.7902 (pm20) REVERT: Y 296 ASP cc_start: 0.7999 (t0) cc_final: 0.7718 (t0) REVERT: Y 310 ASN cc_start: 0.8660 (t0) cc_final: 0.8281 (t0) REVERT: Y 311 ARG cc_start: 0.8210 (tpp-160) cc_final: 0.7905 (tpp-160) REVERT: Y 323 MET cc_start: 0.8221 (mtm) cc_final: 0.7960 (mtm) REVERT: Y 337 TYR cc_start: 0.8342 (p90) cc_final: 0.8118 (p90) REVERT: Y 376 GLU cc_start: 0.8219 (tp30) cc_final: 0.7838 (tp30) REVERT: Y 378 GLU cc_start: 0.7768 (pm20) cc_final: 0.7469 (pm20) REVERT: Y 443 ASN cc_start: 0.7797 (m-40) cc_final: 0.7588 (m110) REVERT: Y 455 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7484 (pp30) REVERT: Y 456 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8619 (mm) outliers start: 147 outliers final: 96 residues processed: 1145 average time/residue: 0.1959 time to fit residues: 338.3442 Evaluate side-chains 1178 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1062 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 971 ILE Chi-restraints excluded: chain Q residue 1128 LEU Chi-restraints excluded: chain Q residue 1190 LEU Chi-restraints excluded: chain Q residue 1257 MET Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1285 ASN Chi-restraints excluded: chain Q residue 1327 MET Chi-restraints excluded: chain Q residue 1337 TYR Chi-restraints excluded: chain R residue 121 HIS Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 664 MET Chi-restraints excluded: chain R residue 669 LEU Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 732 LYS Chi-restraints excluded: chain R residue 733 GLU Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 63 ASP Chi-restraints excluded: chain T residue 99 LYS Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 244 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 276 LYS Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 379 GLU Chi-restraints excluded: chain T residue 419 LEU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 159 THR Chi-restraints excluded: chain U residue 196 SER Chi-restraints excluded: chain U residue 307 SER Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain U residue 373 GLN Chi-restraints excluded: chain U residue 374 GLU Chi-restraints excluded: chain U residue 379 LEU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 387 ARG Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 262 THR Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 277 VAL Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 425 ARG Chi-restraints excluded: chain X residue 29 HIS Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 228 GLU Chi-restraints excluded: chain X residue 256 ASN Chi-restraints excluded: chain X residue 269 MET Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 273 LEU Chi-restraints excluded: chain X residue 282 GLU Chi-restraints excluded: chain X residue 297 ASP Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 153 HIS Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 300 MET Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 405 VAL Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 455 GLN Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 48 optimal weight: 0.9980 chunk 347 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 308 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 287 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1192 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS R 177 ASN ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 592 HIS ** R 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 667 ASN U 36 GLN U 274 ASN U 299 HIS ** U 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 453 ASN ** X 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 274 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.128429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107600 restraints weight = 54967.063| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.20 r_work: 0.3247 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 28942 Z= 0.299 Angle : 0.730 12.533 39175 Z= 0.372 Chirality : 0.049 0.175 4610 Planarity : 0.005 0.070 5022 Dihedral : 8.228 149.470 4000 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.42 % Favored : 95.55 % Rotamer: Outliers : 5.07 % Allowed : 25.31 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.14), residues: 3618 helix: 0.75 (0.13), residues: 1509 sheet: -0.23 (0.20), residues: 605 loop : -0.91 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG V 180 TYR 0.026 0.002 TYR Y 427 PHE 0.026 0.002 PHE R 104 TRP 0.035 0.003 TRP R 586 HIS 0.007 0.001 HIS X 29 Details of bonding type rmsd covalent geometry : bond 0.00611 (28941) covalent geometry : angle 0.73020 (39175) hydrogen bonds : bond 0.04658 ( 1093) hydrogen bonds : angle 4.64287 ( 3156) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1083 time to evaluate : 1.022 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: Q 1027 SER cc_start: 0.8969 (m) cc_final: 0.8330 (p) REVERT: Q 1070 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7767 (p90) REVERT: Q 1073 LEU cc_start: 0.8232 (mp) cc_final: 0.7772 (tp) REVERT: Q 1075 TYR cc_start: 0.8414 (t80) cc_final: 0.8170 (t80) REVERT: Q 1077 SER cc_start: 0.8445 (m) cc_final: 0.7959 (p) REVERT: Q 1087 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7755 (ttm110) REVERT: Q 1090 TYR cc_start: 0.7925 (t80) cc_final: 0.7644 (t80) REVERT: Q 1097 ASN cc_start: 0.8048 (t0) cc_final: 0.7617 (t0) REVERT: Q 1109 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7861 (mtpp) REVERT: Q 1127 PHE cc_start: 0.8728 (t80) cc_final: 0.8404 (t80) REVERT: Q 1128 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8537 (mp) REVERT: Q 1134 GLU cc_start: 0.7925 (tp30) cc_final: 0.7710 (tp30) REVERT: Q 1138 ASN cc_start: 0.7980 (m110) cc_final: 0.7465 (p0) REVERT: Q 1142 ARG cc_start: 0.8284 (ttm110) cc_final: 0.7958 (ttm110) REVERT: Q 1150 LYS cc_start: 0.8435 (tttp) cc_final: 0.7952 (tttp) REVERT: Q 1152 VAL cc_start: 0.8130 (t) cc_final: 0.6994 (m) REVERT: Q 1154 GLU cc_start: 0.7635 (pt0) cc_final: 0.6901 (pt0) REVERT: Q 1168 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8306 (mtpp) REVERT: Q 1172 GLN cc_start: 0.7903 (mp10) cc_final: 0.7663 (mp10) REVERT: Q 1173 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7473 (mp0) REVERT: Q 1176 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8054 (mt-10) REVERT: Q 1187 MET cc_start: 0.8268 (pmm) cc_final: 0.7946 (pmm) REVERT: Q 1190 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8555 (mt) REVERT: Q 1192 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7801 (p0) REVERT: Q 1193 VAL cc_start: 0.8847 (m) cc_final: 0.8433 (p) REVERT: Q 1266 GLU cc_start: 0.8036 (pm20) cc_final: 0.7619 (pm20) REVERT: Q 1324 MET cc_start: 0.5982 (mmp) cc_final: 0.5757 (mmp) REVERT: Q 1327 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.7058 (mpp) REVERT: Q 1331 MET cc_start: 0.7440 (tpp) cc_final: 0.6962 (tpp) REVERT: Q 1337 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.7436 (m-80) REVERT: Q 1405 MET cc_start: 0.6558 (ptm) cc_final: 0.6229 (ptm) REVERT: R 93 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7185 (ttp80) REVERT: R 113 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8438 (mm-30) REVERT: R 117 TYR cc_start: 0.8239 (t80) cc_final: 0.8019 (t80) REVERT: R 149 ASN cc_start: 0.8753 (m-40) cc_final: 0.8523 (m110) REVERT: R 155 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7128 (m-10) REVERT: R 193 ASP cc_start: 0.6317 (p0) cc_final: 0.6018 (p0) REVERT: R 210 LYS cc_start: 0.6857 (mmtp) cc_final: 0.6557 (mmtp) REVERT: R 218 GLN cc_start: 0.8004 (mp10) cc_final: 0.7648 (mp10) REVERT: R 261 ILE cc_start: 0.8606 (tp) cc_final: 0.8310 (tp) REVERT: R 609 GLN cc_start: 0.8478 (tp-100) cc_final: 0.8153 (tp-100) REVERT: R 645 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8265 (tp) REVERT: R 656 LYS cc_start: 0.8318 (pptt) cc_final: 0.8094 (pptt) REVERT: R 697 ASN cc_start: 0.8402 (t0) cc_final: 0.8085 (t0) REVERT: R 719 ARG cc_start: 0.7932 (mmt-90) cc_final: 0.7685 (mmt-90) REVERT: R 724 TYR cc_start: 0.8356 (t80) cc_final: 0.8070 (t80) REVERT: R 725 ARG cc_start: 0.8102 (tpp-160) cc_final: 0.7566 (tpp-160) REVERT: R 744 GLU cc_start: 0.8313 (mp0) cc_final: 0.8032 (mp0) REVERT: R 749 ASN cc_start: 0.8403 (t0) cc_final: 0.8145 (t0) REVERT: R 751 LYS cc_start: 0.7625 (mmmt) cc_final: 0.7182 (mmmt) REVERT: S 65 GLN cc_start: 0.8247 (mm110) cc_final: 0.7992 (mm110) REVERT: S 157 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7808 (ttpt) REVERT: T 37 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7747 (tm-30) REVERT: T 42 LYS cc_start: 0.8027 (tptp) cc_final: 0.7707 (tppp) REVERT: T 49 VAL cc_start: 0.7882 (p) cc_final: 0.7668 (m) REVERT: T 69 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8649 (mtpp) REVERT: T 70 MET cc_start: 0.8761 (mtm) cc_final: 0.8527 (mtp) REVERT: T 109 GLU cc_start: 0.7689 (pm20) cc_final: 0.7372 (pm20) REVERT: T 123 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8012 (tt0) REVERT: T 168 VAL cc_start: 0.8409 (t) cc_final: 0.8129 (m) REVERT: T 174 LYS cc_start: 0.8533 (mmtp) cc_final: 0.8324 (mmmm) REVERT: T 182 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8126 (p0) REVERT: T 185 ILE cc_start: 0.8906 (tt) cc_final: 0.8635 (tp) REVERT: T 209 VAL cc_start: 0.9014 (t) cc_final: 0.8711 (m) REVERT: T 221 GLU cc_start: 0.8172 (pt0) cc_final: 0.7541 (pm20) REVERT: T 225 GLU cc_start: 0.7700 (tp30) cc_final: 0.7408 (tp30) REVERT: T 268 MET cc_start: 0.7647 (tpp) cc_final: 0.6877 (mpp) REVERT: T 282 GLU cc_start: 0.8104 (tp30) cc_final: 0.7687 (tp30) REVERT: T 302 GLU cc_start: 0.8332 (tt0) cc_final: 0.8058 (tt0) REVERT: T 304 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8110 (mm) REVERT: T 319 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7857 (mt-10) REVERT: T 329 GLU cc_start: 0.7804 (pp20) cc_final: 0.7335 (pp20) REVERT: T 348 ARG cc_start: 0.8102 (mtp-110) cc_final: 0.7703 (mmm-85) REVERT: T 366 ARG cc_start: 0.7973 (mtt-85) cc_final: 0.7749 (mtt-85) REVERT: T 367 LEU cc_start: 0.8760 (mm) cc_final: 0.8461 (mt) REVERT: T 396 GLU cc_start: 0.8043 (tp30) cc_final: 0.7609 (tp30) REVERT: T 401 ASP cc_start: 0.8296 (m-30) cc_final: 0.8005 (m-30) REVERT: T 417 GLN cc_start: 0.8736 (mt0) cc_final: 0.8463 (mt0) REVERT: T 431 ARG cc_start: 0.8010 (mtm-85) cc_final: 0.7628 (mtm-85) REVERT: T 441 GLU cc_start: 0.8062 (tt0) cc_final: 0.7677 (tt0) REVERT: U 99 THR cc_start: 0.8345 (m) cc_final: 0.8025 (p) REVERT: U 128 LYS cc_start: 0.8202 (ttpt) cc_final: 0.7991 (mttm) REVERT: U 132 GLU cc_start: 0.7138 (tp30) cc_final: 0.6770 (mm-30) REVERT: U 140 VAL cc_start: 0.8348 (m) cc_final: 0.8016 (p) REVERT: U 157 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8254 (mtpp) REVERT: U 159 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7477 (p) REVERT: U 161 LYS cc_start: 0.8789 (tmmt) cc_final: 0.8587 (tttm) REVERT: U 166 GLU cc_start: 0.7946 (tp30) cc_final: 0.7361 (tp30) REVERT: U 168 ILE cc_start: 0.7996 (tp) cc_final: 0.7761 (tt) REVERT: U 193 ASP cc_start: 0.8205 (t0) cc_final: 0.7903 (p0) REVERT: U 223 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7483 (tm-30) REVERT: U 226 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7452 (mm-30) REVERT: U 233 LYS cc_start: 0.8271 (ptmm) cc_final: 0.7955 (ptmm) REVERT: U 235 VAL cc_start: 0.8755 (t) cc_final: 0.8386 (m) REVERT: U 249 SER cc_start: 0.8704 (t) cc_final: 0.8157 (p) REVERT: U 276 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8289 (ttmm) REVERT: U 279 GLU cc_start: 0.8231 (tt0) cc_final: 0.7959 (tt0) REVERT: U 281 LYS cc_start: 0.8901 (tttt) cc_final: 0.8503 (tptp) REVERT: U 316 GLU cc_start: 0.8213 (tt0) cc_final: 0.7852 (tp30) REVERT: U 323 MET cc_start: 0.8475 (mtp) cc_final: 0.8135 (mtm) REVERT: U 357 LYS cc_start: 0.7960 (mppt) cc_final: 0.7659 (mppt) REVERT: U 362 GLN cc_start: 0.8186 (mp10) cc_final: 0.7740 (mp10) REVERT: U 368 LEU cc_start: 0.8986 (mt) cc_final: 0.8705 (mm) REVERT: U 373 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8058 (tm-30) REVERT: U 407 GLN cc_start: 0.8613 (tm-30) cc_final: 0.8185 (tp40) REVERT: U 417 THR cc_start: 0.8554 (p) cc_final: 0.7713 (t) REVERT: U 419 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7585 (mp0) REVERT: U 435 ARG cc_start: 0.8614 (ttp-170) cc_final: 0.7480 (ttp-170) REVERT: U 438 LYS cc_start: 0.8541 (ttpt) cc_final: 0.8042 (tptp) REVERT: U 439 TYR cc_start: 0.8209 (m-80) cc_final: 0.7537 (m-80) REVERT: V 31 LYS cc_start: 0.8554 (mptt) cc_final: 0.8310 (mtpp) REVERT: V 45 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7031 (mm-30) REVERT: V 75 ILE cc_start: 0.8465 (pt) cc_final: 0.8169 (mp) REVERT: V 103 CYS cc_start: 0.8297 (t) cc_final: 0.7948 (t) REVERT: V 112 SER cc_start: 0.8258 (t) cc_final: 0.7919 (p) REVERT: V 119 GLU cc_start: 0.8121 (tp30) cc_final: 0.7603 (tp30) REVERT: V 143 GLU cc_start: 0.7693 (tt0) cc_final: 0.7368 (tt0) REVERT: V 146 GLU cc_start: 0.7535 (tm-30) cc_final: 0.6676 (tm-30) REVERT: V 179 LEU cc_start: 0.8364 (mm) cc_final: 0.8153 (mp) REVERT: V 193 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8115 (mmmt) REVERT: V 205 ASN cc_start: 0.8532 (m-40) cc_final: 0.8277 (m-40) REVERT: V 214 ARG cc_start: 0.8541 (mtt-85) cc_final: 0.8327 (mmm-85) REVERT: V 224 LEU cc_start: 0.8616 (mt) cc_final: 0.8402 (mt) REVERT: V 251 ASP cc_start: 0.7955 (m-30) cc_final: 0.7444 (m-30) REVERT: V 269 MET cc_start: 0.8382 (tpp) cc_final: 0.8101 (tpp) REVERT: V 276 LYS cc_start: 0.8486 (mptt) cc_final: 0.8254 (tptt) REVERT: V 290 LYS cc_start: 0.8459 (mppt) cc_final: 0.7968 (mttm) REVERT: V 325 ASN cc_start: 0.7977 (p0) cc_final: 0.7699 (p0) REVERT: V 336 VAL cc_start: 0.8530 (p) cc_final: 0.8255 (m) REVERT: V 342 ARG cc_start: 0.8558 (mtt-85) cc_final: 0.8129 (mpt90) REVERT: V 373 LEU cc_start: 0.9036 (mt) cc_final: 0.8817 (mm) REVERT: V 385 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7796 (tm-30) REVERT: V 387 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8246 (mmm160) REVERT: V 391 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7876 (mt-10) REVERT: V 414 TYR cc_start: 0.8958 (t80) cc_final: 0.8526 (t80) REVERT: V 425 LEU cc_start: 0.9129 (mt) cc_final: 0.8714 (mt) REVERT: V 429 SER cc_start: 0.8753 (t) cc_final: 0.8367 (p) REVERT: V 454 LYS cc_start: 0.8588 (tttt) cc_final: 0.8256 (tttt) REVERT: W 23 HIS cc_start: 0.8578 (m90) cc_final: 0.8288 (m-70) REVERT: W 73 VAL cc_start: 0.8611 (t) cc_final: 0.8300 (m) REVERT: W 78 SER cc_start: 0.8693 (t) cc_final: 0.8361 (p) REVERT: W 110 GLU cc_start: 0.7520 (mp0) cc_final: 0.7229 (mp0) REVERT: W 115 GLU cc_start: 0.8454 (tp30) cc_final: 0.8128 (tp30) REVERT: W 119 GLN cc_start: 0.8566 (mt0) cc_final: 0.8345 (mt0) REVERT: W 123 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8076 (mtmm) REVERT: W 131 GLU cc_start: 0.7902 (tp30) cc_final: 0.7135 (mm-30) REVERT: W 157 LYS cc_start: 0.8489 (mttt) cc_final: 0.7554 (ttmm) REVERT: W 170 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7792 (mm-30) REVERT: W 189 VAL cc_start: 0.7902 (t) cc_final: 0.7438 (m) REVERT: W 194 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8336 (mtpp) REVERT: W 201 LYS cc_start: 0.8708 (tttt) cc_final: 0.8427 (ttmt) REVERT: W 233 LYS cc_start: 0.8137 (tppt) cc_final: 0.7804 (tppt) REVERT: W 267 SER cc_start: 0.7230 (OUTLIER) cc_final: 0.7016 (t) REVERT: W 273 ILE cc_start: 0.8946 (mt) cc_final: 0.8718 (mt) REVERT: W 276 LYS cc_start: 0.8418 (tptt) cc_final: 0.8105 (tptm) REVERT: W 279 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7636 (mt-10) REVERT: W 281 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8504 (ttpp) REVERT: W 287 GLU cc_start: 0.7713 (tp30) cc_final: 0.7494 (tp30) REVERT: W 315 ASP cc_start: 0.8304 (t0) cc_final: 0.7961 (t0) REVERT: W 316 GLU cc_start: 0.7911 (tt0) cc_final: 0.7491 (tp30) REVERT: W 338 LYS cc_start: 0.8054 (ttpp) cc_final: 0.7850 (ttmm) REVERT: W 358 SER cc_start: 0.9054 (m) cc_final: 0.8756 (p) REVERT: W 412 LYS cc_start: 0.8932 (tppt) cc_final: 0.8679 (mmmt) REVERT: W 413 ARG cc_start: 0.8594 (mtp-110) cc_final: 0.8018 (ttp80) REVERT: W 449 ASP cc_start: 0.7121 (t0) cc_final: 0.6641 (t0) REVERT: W 451 GLN cc_start: 0.7986 (mm110) cc_final: 0.7731 (mp10) REVERT: X 31 LYS cc_start: 0.8585 (mmmt) cc_final: 0.8173 (mmmt) REVERT: X 35 LEU cc_start: 0.9155 (tp) cc_final: 0.8890 (tp) REVERT: X 68 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8291 (mtmm) REVERT: X 70 MET cc_start: 0.6781 (mmt) cc_final: 0.6542 (mmt) REVERT: X 103 CYS cc_start: 0.8833 (t) cc_final: 0.8598 (t) REVERT: X 114 GLU cc_start: 0.8289 (tt0) cc_final: 0.7630 (tt0) REVERT: X 117 LYS cc_start: 0.8356 (ptmt) cc_final: 0.7959 (mtmt) REVERT: X 119 GLU cc_start: 0.8150 (tp30) cc_final: 0.7636 (tp30) REVERT: X 134 LYS cc_start: 0.8147 (ptpt) cc_final: 0.7851 (pttm) REVERT: X 150 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6877 (tm-30) REVERT: X 165 HIS cc_start: 0.8600 (p90) cc_final: 0.8208 (p-80) REVERT: X 171 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8282 (tptt) REVERT: X 177 LYS cc_start: 0.8715 (tptp) cc_final: 0.8435 (tptp) REVERT: X 190 GLN cc_start: 0.8842 (tt0) cc_final: 0.8503 (mt0) REVERT: X 201 TYR cc_start: 0.7314 (t80) cc_final: 0.6594 (t80) REVERT: X 210 LYS cc_start: 0.8284 (mtmm) cc_final: 0.7383 (mtmm) REVERT: X 227 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7626 (tp30) REVERT: X 251 ASP cc_start: 0.8308 (m-30) cc_final: 0.8011 (m-30) REVERT: X 252 LEU cc_start: 0.8446 (mt) cc_final: 0.8176 (mt) REVERT: X 269 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7618 (mmm) REVERT: X 276 LYS cc_start: 0.8345 (tppp) cc_final: 0.7831 (tppp) REVERT: X 282 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7248 (tp30) REVERT: X 283 LYS cc_start: 0.9154 (tttm) cc_final: 0.8936 (tptm) REVERT: X 289 ASN cc_start: 0.8495 (m110) cc_final: 0.8228 (m110) REVERT: X 311 ASP cc_start: 0.8264 (t0) cc_final: 0.7707 (t0) REVERT: X 312 GLU cc_start: 0.8221 (mm-30) cc_final: 0.8006 (mm-30) REVERT: X 315 MET cc_start: 0.8047 (mtm) cc_final: 0.7827 (mtp) REVERT: X 319 GLU cc_start: 0.8470 (pm20) cc_final: 0.8006 (pm20) REVERT: X 348 ARG cc_start: 0.7998 (mtp-110) cc_final: 0.7521 (mtp85) REVERT: X 350 THR cc_start: 0.8285 (t) cc_final: 0.7894 (p) REVERT: X 365 ASP cc_start: 0.8731 (m-30) cc_final: 0.8458 (t0) REVERT: X 386 ARG cc_start: 0.8425 (tpp80) cc_final: 0.7982 (mmm-85) REVERT: X 387 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8212 (tpp80) REVERT: X 409 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7822 (tm-30) REVERT: X 433 GLU cc_start: 0.6961 (tp30) cc_final: 0.6533 (tp30) REVERT: X 443 LYS cc_start: 0.8044 (mmmm) cc_final: 0.7820 (mmmm) REVERT: X 454 LYS cc_start: 0.8582 (mttt) cc_final: 0.8357 (mttt) REVERT: Y 20 ILE cc_start: 0.8155 (mt) cc_final: 0.7900 (mm) REVERT: Y 49 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7716 (mm-40) REVERT: Y 86 MET cc_start: 0.7355 (tpp) cc_final: 0.6781 (tpp) REVERT: Y 96 VAL cc_start: 0.8399 (t) cc_final: 0.8182 (p) REVERT: Y 113 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8244 (mtmm) REVERT: Y 115 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7406 (tm-30) REVERT: Y 132 GLU cc_start: 0.7940 (tp30) cc_final: 0.7361 (tp30) REVERT: Y 142 GLU cc_start: 0.7423 (tm-30) cc_final: 0.7033 (tm-30) REVERT: Y 153 HIS cc_start: 0.6740 (OUTLIER) cc_final: 0.6357 (t-90) REVERT: Y 173 ASN cc_start: 0.8556 (p0) cc_final: 0.7324 (p0) REVERT: Y 174 LYS cc_start: 0.8732 (mmtm) cc_final: 0.8238 (mmtm) REVERT: Y 175 MET cc_start: 0.7644 (tpp) cc_final: 0.7081 (tpp) REVERT: Y 179 LEU cc_start: 0.9088 (mm) cc_final: 0.8394 (mt) REVERT: Y 182 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7525 (mm-30) REVERT: Y 206 PHE cc_start: 0.7997 (t80) cc_final: 0.7399 (m-80) REVERT: Y 208 ARG cc_start: 0.8386 (mtm180) cc_final: 0.7923 (mtm180) REVERT: Y 223 GLN cc_start: 0.8099 (mm110) cc_final: 0.7854 (mm110) REVERT: Y 226 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7752 (mp0) REVERT: Y 229 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7641 (mp) REVERT: Y 276 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8389 (tppp) REVERT: Y 279 GLU cc_start: 0.8267 (tt0) cc_final: 0.7948 (tm-30) REVERT: Y 281 LYS cc_start: 0.8771 (tmmt) cc_final: 0.8476 (tmmt) REVERT: Y 282 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8078 (tm-30) REVERT: Y 283 GLU cc_start: 0.7980 (mt-10) cc_final: 0.6796 (mt-10) REVERT: Y 297 GLU cc_start: 0.7567 (mp0) cc_final: 0.7312 (mp0) REVERT: Y 310 ASN cc_start: 0.8675 (t0) cc_final: 0.8328 (t0) REVERT: Y 311 ARG cc_start: 0.8211 (tpp-160) cc_final: 0.7846 (tpp-160) REVERT: Y 323 MET cc_start: 0.8233 (mtm) cc_final: 0.7985 (mtm) REVERT: Y 337 TYR cc_start: 0.8354 (p90) cc_final: 0.8143 (p90) REVERT: Y 376 GLU cc_start: 0.8244 (tp30) cc_final: 0.7803 (tp30) REVERT: Y 444 GLU cc_start: 0.7793 (tp30) cc_final: 0.7544 (tp30) REVERT: Y 455 GLN cc_start: 0.8315 (pp30) cc_final: 0.7462 (pp30) REVERT: Y 456 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8567 (mm) REVERT: Z 306 THR cc_start: 0.8531 (p) cc_final: 0.8256 (t) outliers start: 158 outliers final: 104 residues processed: 1153 average time/residue: 0.1871 time to fit residues: 326.4488 Evaluate side-chains 1176 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 1054 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 971 ILE Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1070 PHE Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1128 LEU Chi-restraints excluded: chain Q residue 1190 LEU Chi-restraints excluded: chain Q residue 1192 ASN Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1285 ASN Chi-restraints excluded: chain Q residue 1292 ASP Chi-restraints excluded: chain Q residue 1305 ASP Chi-restraints excluded: chain Q residue 1327 MET Chi-restraints excluded: chain Q residue 1337 TYR Chi-restraints excluded: chain Q residue 1367 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 587 ARG Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 607 HIS Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 667 ASN Chi-restraints excluded: chain R residue 677 VAL Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain R residue 732 LYS Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain T residue 63 ASP Chi-restraints excluded: chain T residue 99 LYS Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 244 VAL Chi-restraints excluded: chain T residue 246 ASP Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 256 ASN Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 276 LYS Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 379 GLU Chi-restraints excluded: chain T residue 419 LEU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 159 THR Chi-restraints excluded: chain U residue 196 SER Chi-restraints excluded: chain U residue 237 HIS Chi-restraints excluded: chain U residue 307 SER Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain U residue 374 GLU Chi-restraints excluded: chain U residue 379 LEU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 93 SER Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 387 ARG Chi-restraints excluded: chain V residue 418 LEU Chi-restraints excluded: chain V residue 437 ASN Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 267 SER Chi-restraints excluded: chain W residue 277 VAL Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain X residue 29 HIS Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 269 MET Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 273 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 326 LYS Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 383 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 125 ILE Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Y residue 153 HIS Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 437 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 25 optimal weight: 0.3980 chunk 119 optimal weight: 0.5980 chunk 319 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 323 optimal weight: 0.6980 chunk 289 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1192 ASN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 177 ASN ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN ** U 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 HIS X 256 ASN Y 119 GLN Y 274 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.129636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.108941 restraints weight = 54985.003| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 3.20 r_work: 0.3281 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28942 Z= 0.145 Angle : 0.673 11.913 39175 Z= 0.334 Chirality : 0.045 0.179 4610 Planarity : 0.004 0.096 5022 Dihedral : 8.025 141.670 4000 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 4.46 % Allowed : 27.20 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.14), residues: 3618 helix: 1.01 (0.13), residues: 1499 sheet: -0.07 (0.21), residues: 579 loop : -0.88 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 22 TYR 0.025 0.002 TYR R 34 PHE 0.025 0.001 PHE R 104 TRP 0.015 0.001 TRP Y 280 HIS 0.006 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00315 (28941) covalent geometry : angle 0.67336 (39175) hydrogen bonds : bond 0.03724 ( 1093) hydrogen bonds : angle 4.33810 ( 3156) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1053 time to evaluate : 0.806 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 1027 SER cc_start: 0.8991 (m) cc_final: 0.8349 (p) REVERT: Q 1070 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7815 (p90) REVERT: Q 1073 LEU cc_start: 0.8051 (mp) cc_final: 0.7336 (mm) REVERT: Q 1075 TYR cc_start: 0.8381 (t80) cc_final: 0.8101 (t80) REVERT: Q 1077 SER cc_start: 0.8415 (m) cc_final: 0.7883 (p) REVERT: Q 1097 ASN cc_start: 0.8037 (t0) cc_final: 0.7608 (t0) REVERT: Q 1109 LYS cc_start: 0.8107 (mtpp) cc_final: 0.7828 (mtpp) REVERT: Q 1127 PHE cc_start: 0.8717 (t80) cc_final: 0.8351 (t80) REVERT: Q 1128 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8422 (mp) REVERT: Q 1134 GLU cc_start: 0.7938 (tp30) cc_final: 0.7690 (tp30) REVERT: Q 1142 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7980 (ttm110) REVERT: Q 1150 LYS cc_start: 0.8316 (tttp) cc_final: 0.7834 (tttp) REVERT: Q 1154 GLU cc_start: 0.7495 (pt0) cc_final: 0.6848 (pt0) REVERT: Q 1168 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8312 (mtpp) REVERT: Q 1187 MET cc_start: 0.8140 (pmm) cc_final: 0.7761 (pmm) REVERT: Q 1190 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8459 (mt) REVERT: Q 1192 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7686 (p0) REVERT: Q 1193 VAL cc_start: 0.8809 (m) cc_final: 0.8367 (p) REVERT: Q 1260 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8591 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7979 (pm20) cc_final: 0.7547 (pm20) REVERT: Q 1324 MET cc_start: 0.5817 (mmp) cc_final: 0.5580 (mmp) REVERT: Q 1327 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.6924 (mpp) REVERT: Q 1331 MET cc_start: 0.7443 (tpp) cc_final: 0.6855 (tpp) REVERT: Q 1405 MET cc_start: 0.6632 (ptm) cc_final: 0.6231 (ptm) REVERT: R 18 ASP cc_start: 0.7643 (m-30) cc_final: 0.7371 (m-30) REVERT: R 113 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8396 (mm-30) REVERT: R 149 ASN cc_start: 0.8691 (m-40) cc_final: 0.8451 (m110) REVERT: R 193 ASP cc_start: 0.6244 (p0) cc_final: 0.5812 (p0) REVERT: R 210 LYS cc_start: 0.6757 (mmtp) cc_final: 0.6455 (mmtp) REVERT: R 218 GLN cc_start: 0.7986 (mp10) cc_final: 0.7681 (mp10) REVERT: R 229 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.7798 (mp) REVERT: R 261 ILE cc_start: 0.8550 (tp) cc_final: 0.8235 (tp) REVERT: R 609 GLN cc_start: 0.8398 (tp-100) cc_final: 0.8072 (tp-100) REVERT: R 633 GLN cc_start: 0.8365 (mp10) cc_final: 0.8047 (mt0) REVERT: R 645 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8261 (tp) REVERT: R 656 LYS cc_start: 0.8233 (pptt) cc_final: 0.8018 (pptt) REVERT: R 683 ARG cc_start: 0.8829 (tpt90) cc_final: 0.8500 (tpt90) REVERT: R 697 ASN cc_start: 0.8374 (t0) cc_final: 0.8047 (t0) REVERT: R 722 GLU cc_start: 0.8239 (tm-30) cc_final: 0.8004 (pp20) REVERT: R 724 TYR cc_start: 0.8341 (t80) cc_final: 0.8053 (t80) REVERT: R 725 ARG cc_start: 0.8109 (tpp-160) cc_final: 0.7532 (tpp-160) REVERT: R 744 GLU cc_start: 0.8262 (mp0) cc_final: 0.7969 (mp0) REVERT: R 749 ASN cc_start: 0.8410 (t0) cc_final: 0.8148 (t0) REVERT: R 751 LYS cc_start: 0.7401 (mmmt) cc_final: 0.6995 (mmmt) REVERT: S 65 GLN cc_start: 0.8200 (mm110) cc_final: 0.7944 (mm110) REVERT: S 70 GLU cc_start: 0.8459 (tp30) cc_final: 0.7866 (tp30) REVERT: S 73 ARG cc_start: 0.7717 (mtm110) cc_final: 0.7479 (mtm110) REVERT: S 157 LYS cc_start: 0.8185 (ttpt) cc_final: 0.7734 (ttpt) REVERT: T 37 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7704 (tm-30) REVERT: T 42 LYS cc_start: 0.7895 (tptp) cc_final: 0.7586 (tppp) REVERT: T 49 VAL cc_start: 0.7728 (p) cc_final: 0.7502 (m) REVERT: T 69 LYS cc_start: 0.8848 (mtmm) cc_final: 0.8565 (mtpp) REVERT: T 70 MET cc_start: 0.8753 (mtm) cc_final: 0.8507 (mtp) REVERT: T 109 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: T 123 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7949 (tt0) REVERT: T 168 VAL cc_start: 0.8375 (t) cc_final: 0.8130 (m) REVERT: T 174 LYS cc_start: 0.8517 (mmtp) cc_final: 0.8307 (mmmm) REVERT: T 182 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8155 (p0) REVERT: T 190 GLN cc_start: 0.8380 (mt0) cc_final: 0.8031 (mt0) REVERT: T 209 VAL cc_start: 0.8935 (t) cc_final: 0.8596 (m) REVERT: T 221 GLU cc_start: 0.8145 (pt0) cc_final: 0.7535 (pm20) REVERT: T 225 GLU cc_start: 0.7680 (tp30) cc_final: 0.7296 (tp30) REVERT: T 268 MET cc_start: 0.7631 (tpp) cc_final: 0.7015 (mpp) REVERT: T 282 GLU cc_start: 0.8078 (tp30) cc_final: 0.7647 (tp30) REVERT: T 302 GLU cc_start: 0.8212 (tt0) cc_final: 0.7981 (tt0) REVERT: T 319 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7830 (mt-10) REVERT: T 329 GLU cc_start: 0.7776 (pp20) cc_final: 0.7332 (pp20) REVERT: T 348 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.7625 (mmm-85) REVERT: T 366 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7708 (mtt-85) REVERT: T 401 ASP cc_start: 0.8246 (m-30) cc_final: 0.7937 (m-30) REVERT: T 417 GLN cc_start: 0.8711 (mt0) cc_final: 0.8241 (mt0) REVERT: T 433 GLU cc_start: 0.7226 (pm20) cc_final: 0.6850 (pm20) REVERT: T 441 GLU cc_start: 0.7972 (tt0) cc_final: 0.7611 (tt0) REVERT: U 99 THR cc_start: 0.8346 (m) cc_final: 0.8082 (p) REVERT: U 132 GLU cc_start: 0.7112 (tp30) cc_final: 0.6749 (mm-30) REVERT: U 140 VAL cc_start: 0.8338 (m) cc_final: 0.8039 (p) REVERT: U 157 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8249 (mtpp) REVERT: U 159 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7452 (p) REVERT: U 161 LYS cc_start: 0.8744 (tmmt) cc_final: 0.8515 (tttm) REVERT: U 166 GLU cc_start: 0.7886 (tp30) cc_final: 0.7199 (tp30) REVERT: U 168 ILE cc_start: 0.7905 (tp) cc_final: 0.7646 (tt) REVERT: U 193 ASP cc_start: 0.8170 (t0) cc_final: 0.7930 (p0) REVERT: U 223 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7509 (tm-30) REVERT: U 226 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7485 (mm-30) REVERT: U 233 LYS cc_start: 0.8279 (ptmm) cc_final: 0.7778 (ptmm) REVERT: U 235 VAL cc_start: 0.8761 (t) cc_final: 0.8428 (t) REVERT: U 249 SER cc_start: 0.8694 (t) cc_final: 0.8151 (p) REVERT: U 276 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8237 (ttmm) REVERT: U 279 GLU cc_start: 0.8210 (tt0) cc_final: 0.7926 (tt0) REVERT: U 281 LYS cc_start: 0.8934 (tttt) cc_final: 0.8611 (tptp) REVERT: U 316 GLU cc_start: 0.8179 (tt0) cc_final: 0.7834 (tp30) REVERT: U 323 MET cc_start: 0.8401 (mtp) cc_final: 0.8092 (mtm) REVERT: U 357 LYS cc_start: 0.7918 (mppt) cc_final: 0.7653 (mppt) REVERT: U 362 GLN cc_start: 0.8139 (mp10) cc_final: 0.7733 (mp10) REVERT: U 368 LEU cc_start: 0.8926 (mt) cc_final: 0.8681 (mm) REVERT: U 373 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7989 (tm-30) REVERT: U 407 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8121 (tp40) REVERT: U 414 LYS cc_start: 0.8747 (tppt) cc_final: 0.8542 (tppt) REVERT: U 417 THR cc_start: 0.8573 (p) cc_final: 0.7575 (t) REVERT: U 419 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7572 (mp0) REVERT: U 435 ARG cc_start: 0.8570 (ttp-170) cc_final: 0.7502 (ttp-170) REVERT: U 438 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8008 (tptp) REVERT: U 439 TYR cc_start: 0.8190 (m-80) cc_final: 0.7556 (m-80) REVERT: U 442 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7537 (tp30) REVERT: V 31 LYS cc_start: 0.8512 (mptt) cc_final: 0.8093 (mtmm) REVERT: V 44 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.6658 (p) REVERT: V 45 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7002 (mm-30) REVERT: V 75 ILE cc_start: 0.8446 (pt) cc_final: 0.8136 (mp) REVERT: V 103 CYS cc_start: 0.8228 (t) cc_final: 0.7837 (t) REVERT: V 119 GLU cc_start: 0.8060 (tp30) cc_final: 0.7400 (tp30) REVERT: V 143 GLU cc_start: 0.7660 (tt0) cc_final: 0.7344 (tt0) REVERT: V 146 GLU cc_start: 0.7550 (tm-30) cc_final: 0.6663 (tm-30) REVERT: V 193 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8101 (mmmt) REVERT: V 205 ASN cc_start: 0.8431 (m-40) cc_final: 0.8153 (m-40) REVERT: V 251 ASP cc_start: 0.7797 (m-30) cc_final: 0.7332 (m-30) REVERT: V 269 MET cc_start: 0.8359 (tpp) cc_final: 0.8091 (tpp) REVERT: V 276 LYS cc_start: 0.8440 (mptt) cc_final: 0.8230 (tptt) REVERT: V 286 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7886 (mm-40) REVERT: V 290 LYS cc_start: 0.8466 (mppt) cc_final: 0.8006 (mttm) REVERT: V 296 ILE cc_start: 0.7981 (mt) cc_final: 0.7755 (pt) REVERT: V 298 GLN cc_start: 0.8438 (tm130) cc_final: 0.8174 (pp30) REVERT: V 336 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8221 (m) REVERT: V 342 ARG cc_start: 0.8544 (mtt-85) cc_final: 0.8069 (mpt90) REVERT: V 373 LEU cc_start: 0.9027 (mt) cc_final: 0.8804 (mm) REVERT: V 381 ARG cc_start: 0.8289 (ttp80) cc_final: 0.7951 (ttt90) REVERT: V 385 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7800 (tm-30) REVERT: V 387 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.8306 (mmm160) REVERT: V 391 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7888 (mt-10) REVERT: V 414 TYR cc_start: 0.8912 (t80) cc_final: 0.8441 (t80) REVERT: V 425 LEU cc_start: 0.9122 (mt) cc_final: 0.8707 (mt) REVERT: V 429 SER cc_start: 0.8704 (t) cc_final: 0.8399 (p) REVERT: V 432 LYS cc_start: 0.8356 (ptmt) cc_final: 0.7874 (ptmt) REVERT: V 454 LYS cc_start: 0.8594 (tttt) cc_final: 0.8262 (tttt) REVERT: W 23 HIS cc_start: 0.8559 (m90) cc_final: 0.8163 (m-70) REVERT: W 42 GLU cc_start: 0.8239 (tt0) cc_final: 0.7910 (tt0) REVERT: W 73 VAL cc_start: 0.8601 (t) cc_final: 0.8295 (m) REVERT: W 78 SER cc_start: 0.8637 (t) cc_final: 0.8308 (p) REVERT: W 82 THR cc_start: 0.7949 (m) cc_final: 0.7464 (p) REVERT: W 115 GLU cc_start: 0.8393 (tp30) cc_final: 0.8084 (tp30) REVERT: W 119 GLN cc_start: 0.8497 (mt0) cc_final: 0.8295 (mt0) REVERT: W 123 LYS cc_start: 0.8360 (mtmt) cc_final: 0.7994 (mtmm) REVERT: W 131 GLU cc_start: 0.7865 (tp30) cc_final: 0.7122 (mm-30) REVERT: W 154 LYS cc_start: 0.8376 (mtmm) cc_final: 0.8165 (mttm) REVERT: W 157 LYS cc_start: 0.8406 (mttt) cc_final: 0.7557 (mttp) REVERT: W 170 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7771 (mm-30) REVERT: W 189 VAL cc_start: 0.7868 (t) cc_final: 0.7374 (m) REVERT: W 201 LYS cc_start: 0.8697 (tttt) cc_final: 0.8369 (ttmt) REVERT: W 222 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8834 (m) REVERT: W 233 LYS cc_start: 0.8130 (tppt) cc_final: 0.7799 (tppt) REVERT: W 273 ILE cc_start: 0.8901 (mt) cc_final: 0.8699 (mt) REVERT: W 276 LYS cc_start: 0.8397 (tptt) cc_final: 0.8065 (tptm) REVERT: W 279 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7612 (mt-10) REVERT: W 281 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8410 (ttpp) REVERT: W 297 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8092 (mt-10) REVERT: W 311 ARG cc_start: 0.8182 (tpp-160) cc_final: 0.7929 (tpp-160) REVERT: W 315 ASP cc_start: 0.8296 (t0) cc_final: 0.7894 (t0) REVERT: W 316 GLU cc_start: 0.7851 (tt0) cc_final: 0.7474 (tp30) REVERT: W 323 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7779 (mtm) REVERT: W 338 LYS cc_start: 0.8000 (ttpp) cc_final: 0.7767 (ttmm) REVERT: W 358 SER cc_start: 0.9019 (m) cc_final: 0.8664 (p) REVERT: W 407 GLN cc_start: 0.8558 (tp40) cc_final: 0.7843 (tm-30) REVERT: W 412 LYS cc_start: 0.8840 (tppt) cc_final: 0.8547 (mttm) REVERT: W 413 ARG cc_start: 0.8582 (mtp-110) cc_final: 0.8048 (ptm160) REVERT: W 449 ASP cc_start: 0.6975 (t0) cc_final: 0.6429 (t70) REVERT: X 31 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8099 (mmmt) REVERT: X 35 LEU cc_start: 0.9125 (tp) cc_final: 0.8815 (tp) REVERT: X 68 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8200 (mtmm) REVERT: X 70 MET cc_start: 0.6788 (mmt) cc_final: 0.6531 (mmt) REVERT: X 103 CYS cc_start: 0.8769 (t) cc_final: 0.8550 (t) REVERT: X 114 GLU cc_start: 0.8199 (tt0) cc_final: 0.7861 (tt0) REVERT: X 119 GLU cc_start: 0.8066 (tp30) cc_final: 0.7577 (tp30) REVERT: X 134 LYS cc_start: 0.8103 (ptpt) cc_final: 0.7827 (pttm) REVERT: X 171 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8245 (tptt) REVERT: X 177 LYS cc_start: 0.8739 (tptp) cc_final: 0.8478 (tptp) REVERT: X 190 GLN cc_start: 0.8844 (tt0) cc_final: 0.8529 (mt0) REVERT: X 201 TYR cc_start: 0.7245 (t80) cc_final: 0.6532 (t80) REVERT: X 210 LYS cc_start: 0.8215 (mtmm) cc_final: 0.7334 (mtmm) REVERT: X 227 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7508 (tp30) REVERT: X 251 ASP cc_start: 0.8284 (m-30) cc_final: 0.8080 (m-30) REVERT: X 269 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7507 (mmm) REVERT: X 282 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7128 (tp30) REVERT: X 289 ASN cc_start: 0.8382 (m110) cc_final: 0.8082 (m110) REVERT: X 294 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8477 (ttmt) REVERT: X 311 ASP cc_start: 0.8261 (t0) cc_final: 0.7694 (t0) REVERT: X 312 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7876 (mm-30) REVERT: X 348 ARG cc_start: 0.7935 (mtp-110) cc_final: 0.7385 (mtp85) REVERT: X 350 THR cc_start: 0.8304 (t) cc_final: 0.7927 (p) REVERT: X 365 ASP cc_start: 0.8733 (m-30) cc_final: 0.8457 (t0) REVERT: X 386 ARG cc_start: 0.8352 (tpp80) cc_final: 0.7886 (mmm-85) REVERT: X 387 ARG cc_start: 0.8806 (mmm160) cc_final: 0.8533 (tpt90) REVERT: X 409 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7749 (tm-30) REVERT: X 433 GLU cc_start: 0.6774 (tp30) cc_final: 0.6317 (tp30) REVERT: Y 20 ILE cc_start: 0.8153 (mt) cc_final: 0.7895 (mm) REVERT: Y 49 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7556 (mm-40) REVERT: Y 86 MET cc_start: 0.7294 (tpp) cc_final: 0.6735 (tpp) REVERT: Y 96 VAL cc_start: 0.8333 (t) cc_final: 0.8127 (p) REVERT: Y 113 LYS cc_start: 0.8531 (mtmt) cc_final: 0.8190 (mtmm) REVERT: Y 115 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7541 (tm-30) REVERT: Y 128 LYS cc_start: 0.7969 (ttmm) cc_final: 0.7682 (ttpp) REVERT: Y 132 GLU cc_start: 0.7714 (tp30) cc_final: 0.6763 (mm-30) REVERT: Y 142 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7125 (tm-30) REVERT: Y 153 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.6337 (t-90) REVERT: Y 161 LYS cc_start: 0.8302 (pttt) cc_final: 0.7824 (pttm) REVERT: Y 174 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8485 (mmtm) REVERT: Y 175 MET cc_start: 0.7537 (tpp) cc_final: 0.7019 (tpp) REVERT: Y 179 LEU cc_start: 0.9086 (mm) cc_final: 0.8414 (mt) REVERT: Y 182 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7983 (mm-30) REVERT: Y 206 PHE cc_start: 0.8019 (t80) cc_final: 0.7401 (m-80) REVERT: Y 208 ARG cc_start: 0.8361 (mtm180) cc_final: 0.7904 (mtm180) REVERT: Y 223 GLN cc_start: 0.8103 (mm110) cc_final: 0.7844 (mm110) REVERT: Y 226 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7753 (mp0) REVERT: Y 229 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7461 (mp) REVERT: Y 276 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8328 (tppp) REVERT: Y 279 GLU cc_start: 0.8175 (tt0) cc_final: 0.7858 (tm-30) REVERT: Y 281 LYS cc_start: 0.8750 (tmmt) cc_final: 0.8385 (tmmt) REVERT: Y 282 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7976 (tm-30) REVERT: Y 283 GLU cc_start: 0.7853 (mt-10) cc_final: 0.6661 (mt-10) REVERT: Y 287 GLU cc_start: 0.8239 (pm20) cc_final: 0.7895 (pm20) REVERT: Y 310 ASN cc_start: 0.8674 (t0) cc_final: 0.8336 (t0) REVERT: Y 311 ARG cc_start: 0.8189 (tpp-160) cc_final: 0.7898 (tpp-160) REVERT: Y 323 MET cc_start: 0.8181 (mtm) cc_final: 0.7978 (mtm) REVERT: Y 337 TYR cc_start: 0.8350 (p90) cc_final: 0.8122 (p90) REVERT: Y 376 GLU cc_start: 0.8171 (tp30) cc_final: 0.7779 (tp30) REVERT: Y 378 GLU cc_start: 0.7721 (pm20) cc_final: 0.6986 (pm20) REVERT: Y 455 GLN cc_start: 0.8288 (pp30) cc_final: 0.7409 (pp30) REVERT: Y 456 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8535 (mm) REVERT: Z 306 THR cc_start: 0.8515 (p) cc_final: 0.8234 (t) outliers start: 139 outliers final: 93 residues processed: 1118 average time/residue: 0.1882 time to fit residues: 317.9228 Evaluate side-chains 1149 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 1035 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 971 ILE Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1070 PHE Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1128 LEU Chi-restraints excluded: chain Q residue 1190 LEU Chi-restraints excluded: chain Q residue 1192 ASN Chi-restraints excluded: chain Q residue 1260 LYS Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1285 ASN Chi-restraints excluded: chain Q residue 1305 ASP Chi-restraints excluded: chain Q residue 1327 MET Chi-restraints excluded: chain Q residue 1367 ILE Chi-restraints excluded: chain R residue 44 PHE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 587 ARG Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 669 LEU Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain T residue 63 ASP Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 244 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 256 ASN Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 276 LYS Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 379 GLU Chi-restraints excluded: chain T residue 419 LEU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 159 THR Chi-restraints excluded: chain U residue 196 SER Chi-restraints excluded: chain U residue 305 CYS Chi-restraints excluded: chain U residue 307 SER Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain U residue 373 GLN Chi-restraints excluded: chain U residue 374 GLU Chi-restraints excluded: chain U residue 379 LEU Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 387 ARG Chi-restraints excluded: chain V residue 444 LEU Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 136 ILE Chi-restraints excluded: chain W residue 222 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain X residue 29 HIS Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 269 MET Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 273 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 153 HIS Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 274 ASN Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 456 ILE Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 311 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 4 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 316 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 246 optimal weight: 0.0970 chunk 178 optimal weight: 0.9990 chunk 318 optimal weight: 2.9990 chunk 355 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q1192 ASN R 121 HIS ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 237 HIS U 274 ASN ** U 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 451 GLN Y 274 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.130016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109156 restraints weight = 55165.866| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.22 r_work: 0.3288 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28942 Z= 0.147 Angle : 0.677 11.761 39175 Z= 0.336 Chirality : 0.045 0.194 4610 Planarity : 0.004 0.063 5022 Dihedral : 7.898 137.791 4000 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.08 % Rotamer: Outliers : 4.21 % Allowed : 27.62 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.14), residues: 3618 helix: 1.08 (0.13), residues: 1501 sheet: -0.05 (0.21), residues: 584 loop : -0.86 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 22 TYR 0.030 0.002 TYR X 414 PHE 0.023 0.001 PHE R 104 TRP 0.013 0.001 TRP Y 280 HIS 0.007 0.001 HIS X 165 Details of bonding type rmsd covalent geometry : bond 0.00321 (28941) covalent geometry : angle 0.67652 (39175) hydrogen bonds : bond 0.03656 ( 1093) hydrogen bonds : angle 4.28227 ( 3156) Misc. bond : bond 0.00017 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1051 time to evaluate : 0.758 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: Q 1027 SER cc_start: 0.8998 (m) cc_final: 0.8378 (p) REVERT: Q 1070 PHE cc_start: 0.8155 (p90) cc_final: 0.7682 (p90) REVERT: Q 1073 LEU cc_start: 0.7974 (mp) cc_final: 0.7582 (tp) REVERT: Q 1075 TYR cc_start: 0.8383 (t80) cc_final: 0.8104 (t80) REVERT: Q 1077 SER cc_start: 0.8415 (m) cc_final: 0.7881 (p) REVERT: Q 1097 ASN cc_start: 0.8037 (t0) cc_final: 0.7597 (t0) REVERT: Q 1109 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7833 (mtpp) REVERT: Q 1127 PHE cc_start: 0.8700 (t80) cc_final: 0.8344 (t80) REVERT: Q 1128 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8395 (mp) REVERT: Q 1134 GLU cc_start: 0.8006 (tp30) cc_final: 0.7694 (tp30) REVERT: Q 1138 ASN cc_start: 0.8074 (m-40) cc_final: 0.7431 (p0) REVERT: Q 1142 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7975 (ttm110) REVERT: Q 1150 LYS cc_start: 0.8340 (tttp) cc_final: 0.7879 (tttp) REVERT: Q 1154 GLU cc_start: 0.7395 (pt0) cc_final: 0.6735 (pt0) REVERT: Q 1168 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8252 (mtpp) REVERT: Q 1172 GLN cc_start: 0.7795 (mp10) cc_final: 0.7592 (pm20) REVERT: Q 1187 MET cc_start: 0.8151 (pmm) cc_final: 0.7748 (pmm) REVERT: Q 1190 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8448 (mt) REVERT: Q 1192 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7714 (p0) REVERT: Q 1260 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8595 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7926 (pm20) cc_final: 0.7494 (pm20) REVERT: Q 1273 LEU cc_start: 0.8368 (mp) cc_final: 0.8147 (mt) REVERT: Q 1324 MET cc_start: 0.5902 (mmp) cc_final: 0.5666 (mmp) REVERT: Q 1327 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6979 (mpp) REVERT: Q 1331 MET cc_start: 0.7450 (tpp) cc_final: 0.6870 (tpp) REVERT: Q 1337 TYR cc_start: 0.7617 (OUTLIER) cc_final: 0.7116 (m-80) REVERT: Q 1405 MET cc_start: 0.6628 (ptm) cc_final: 0.6239 (ptm) REVERT: R 63 PHE cc_start: 0.7422 (p90) cc_final: 0.7204 (p90) REVERT: R 113 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8396 (mm-30) REVERT: R 149 ASN cc_start: 0.8703 (m-40) cc_final: 0.8468 (m110) REVERT: R 193 ASP cc_start: 0.6260 (p0) cc_final: 0.5895 (p0) REVERT: R 210 LYS cc_start: 0.6761 (mmtp) cc_final: 0.6439 (mmtp) REVERT: R 218 GLN cc_start: 0.7974 (mp10) cc_final: 0.7666 (mp10) REVERT: R 229 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7792 (mp) REVERT: R 261 ILE cc_start: 0.8544 (tp) cc_final: 0.8214 (tp) REVERT: R 263 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8131 (pttp) REVERT: R 586 TRP cc_start: 0.7269 (p90) cc_final: 0.7054 (p90) REVERT: R 609 GLN cc_start: 0.8412 (tp-100) cc_final: 0.8098 (tp-100) REVERT: R 623 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7427 (mp0) REVERT: R 633 GLN cc_start: 0.8286 (mp10) cc_final: 0.8053 (mt0) REVERT: R 645 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8254 (tp) REVERT: R 656 LYS cc_start: 0.8218 (pptt) cc_final: 0.8012 (pptt) REVERT: R 697 ASN cc_start: 0.8358 (t0) cc_final: 0.8038 (t0) REVERT: R 722 GLU cc_start: 0.8239 (tm-30) cc_final: 0.7999 (pp20) REVERT: R 724 TYR cc_start: 0.8375 (t80) cc_final: 0.8072 (t80) REVERT: R 725 ARG cc_start: 0.8120 (tpp-160) cc_final: 0.7556 (tpp-160) REVERT: R 735 GLU cc_start: 0.8863 (pt0) cc_final: 0.8576 (mt-10) REVERT: R 744 GLU cc_start: 0.8239 (mp0) cc_final: 0.7955 (mp0) REVERT: R 751 LYS cc_start: 0.7401 (mmmt) cc_final: 0.7012 (mmmt) REVERT: S 65 GLN cc_start: 0.8207 (mm110) cc_final: 0.7935 (mm110) REVERT: S 70 GLU cc_start: 0.8445 (tp30) cc_final: 0.8022 (tp30) REVERT: S 157 LYS cc_start: 0.8171 (ttpt) cc_final: 0.7762 (ttpt) REVERT: T 37 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7696 (tm-30) REVERT: T 42 LYS cc_start: 0.7806 (tptp) cc_final: 0.7567 (tppp) REVERT: T 49 VAL cc_start: 0.7706 (p) cc_final: 0.7473 (m) REVERT: T 66 LYS cc_start: 0.8032 (mttt) cc_final: 0.7792 (mttm) REVERT: T 69 LYS cc_start: 0.8816 (mtmm) cc_final: 0.8545 (mtpp) REVERT: T 70 MET cc_start: 0.8744 (mtm) cc_final: 0.8501 (mtp) REVERT: T 116 LYS cc_start: 0.7835 (pttt) cc_final: 0.7567 (pttm) REVERT: T 123 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8024 (tt0) REVERT: T 168 VAL cc_start: 0.8379 (t) cc_final: 0.8137 (m) REVERT: T 182 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.7987 (p0) REVERT: T 190 GLN cc_start: 0.8352 (mt0) cc_final: 0.7958 (mt0) REVERT: T 209 VAL cc_start: 0.8921 (t) cc_final: 0.8575 (m) REVERT: T 221 GLU cc_start: 0.8135 (pt0) cc_final: 0.7531 (pm20) REVERT: T 225 GLU cc_start: 0.7658 (tp30) cc_final: 0.7304 (tp30) REVERT: T 268 MET cc_start: 0.7660 (tpp) cc_final: 0.7039 (mpp) REVERT: T 282 GLU cc_start: 0.8088 (tp30) cc_final: 0.7655 (tp30) REVERT: T 302 GLU cc_start: 0.8245 (tt0) cc_final: 0.7964 (tt0) REVERT: T 304 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8037 (mm) REVERT: T 319 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7831 (mt-10) REVERT: T 323 TYR cc_start: 0.8544 (t80) cc_final: 0.8269 (t80) REVERT: T 329 GLU cc_start: 0.7786 (pp20) cc_final: 0.7362 (pp20) REVERT: T 348 ARG cc_start: 0.8025 (mtp-110) cc_final: 0.7619 (mmm-85) REVERT: T 367 LEU cc_start: 0.8666 (mm) cc_final: 0.8397 (mt) REVERT: T 396 GLU cc_start: 0.7998 (tp30) cc_final: 0.7566 (tp30) REVERT: T 401 ASP cc_start: 0.8248 (m-30) cc_final: 0.7959 (m-30) REVERT: T 417 GLN cc_start: 0.8701 (mt0) cc_final: 0.8366 (mt0) REVERT: T 431 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7766 (mtm110) REVERT: T 433 GLU cc_start: 0.7322 (pm20) cc_final: 0.6993 (pm20) REVERT: T 441 GLU cc_start: 0.7976 (tt0) cc_final: 0.7608 (tt0) REVERT: U 34 ASN cc_start: 0.8444 (m-40) cc_final: 0.7926 (m-40) REVERT: U 99 THR cc_start: 0.8353 (m) cc_final: 0.8066 (p) REVERT: U 132 GLU cc_start: 0.7137 (tp30) cc_final: 0.6771 (mm-30) REVERT: U 140 VAL cc_start: 0.8334 (m) cc_final: 0.8054 (p) REVERT: U 157 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8236 (mtpp) REVERT: U 159 THR cc_start: 0.8098 (OUTLIER) cc_final: 0.7488 (p) REVERT: U 161 LYS cc_start: 0.8736 (tmmt) cc_final: 0.8502 (tttm) REVERT: U 166 GLU cc_start: 0.7917 (tp30) cc_final: 0.7232 (tp30) REVERT: U 168 ILE cc_start: 0.7866 (tp) cc_final: 0.7615 (tt) REVERT: U 193 ASP cc_start: 0.8167 (t0) cc_final: 0.7919 (p0) REVERT: U 223 GLN cc_start: 0.7810 (tm-30) cc_final: 0.7477 (tm-30) REVERT: U 226 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7486 (mm-30) REVERT: U 233 LYS cc_start: 0.8293 (ptmm) cc_final: 0.7781 (ptmm) REVERT: U 235 VAL cc_start: 0.8708 (t) cc_final: 0.8400 (t) REVERT: U 249 SER cc_start: 0.8718 (t) cc_final: 0.8187 (p) REVERT: U 276 LYS cc_start: 0.8714 (ttmm) cc_final: 0.8244 (ttmm) REVERT: U 279 GLU cc_start: 0.8213 (tt0) cc_final: 0.7939 (tt0) REVERT: U 281 LYS cc_start: 0.8927 (tttt) cc_final: 0.8500 (tptp) REVERT: U 316 GLU cc_start: 0.8182 (tt0) cc_final: 0.7820 (tp30) REVERT: U 323 MET cc_start: 0.8394 (mtp) cc_final: 0.8093 (mtm) REVERT: U 339 SER cc_start: 0.8651 (m) cc_final: 0.8439 (m) REVERT: U 357 LYS cc_start: 0.7921 (mppt) cc_final: 0.7656 (mppt) REVERT: U 362 GLN cc_start: 0.8155 (mp10) cc_final: 0.7754 (mp10) REVERT: U 368 LEU cc_start: 0.8924 (mt) cc_final: 0.8674 (mm) REVERT: U 373 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8037 (tm-30) REVERT: U 407 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8116 (tp40) REVERT: U 417 THR cc_start: 0.8547 (p) cc_final: 0.7461 (t) REVERT: U 419 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7565 (mp0) REVERT: U 435 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.7544 (ttp-170) REVERT: U 438 LYS cc_start: 0.8518 (ttpt) cc_final: 0.7987 (tptp) REVERT: U 439 TYR cc_start: 0.8179 (m-80) cc_final: 0.7550 (m-80) REVERT: U 442 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7586 (tp30) REVERT: V 31 LYS cc_start: 0.8533 (mptt) cc_final: 0.8083 (mtmm) REVERT: V 44 VAL cc_start: 0.7850 (OUTLIER) cc_final: 0.6758 (p) REVERT: V 45 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7054 (mm-30) REVERT: V 75 ILE cc_start: 0.8453 (pt) cc_final: 0.8151 (mp) REVERT: V 103 CYS cc_start: 0.8226 (t) cc_final: 0.7839 (t) REVERT: V 119 GLU cc_start: 0.8067 (tp30) cc_final: 0.7454 (tp30) REVERT: V 143 GLU cc_start: 0.7647 (tt0) cc_final: 0.7334 (tt0) REVERT: V 146 GLU cc_start: 0.7543 (tm-30) cc_final: 0.6679 (tm-30) REVERT: V 193 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8117 (mmmt) REVERT: V 205 ASN cc_start: 0.8413 (m-40) cc_final: 0.8133 (m-40) REVERT: V 251 ASP cc_start: 0.7849 (m-30) cc_final: 0.7296 (m-30) REVERT: V 269 MET cc_start: 0.8316 (tpp) cc_final: 0.8038 (tpp) REVERT: V 276 LYS cc_start: 0.8460 (mptt) cc_final: 0.7953 (mptt) REVERT: V 286 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7880 (mm-40) REVERT: V 290 LYS cc_start: 0.8430 (mppt) cc_final: 0.7983 (mttm) REVERT: V 296 ILE cc_start: 0.7986 (mt) cc_final: 0.7777 (pt) REVERT: V 336 VAL cc_start: 0.8502 (OUTLIER) cc_final: 0.8217 (m) REVERT: V 373 LEU cc_start: 0.9008 (mt) cc_final: 0.8776 (mm) REVERT: V 381 ARG cc_start: 0.8296 (ttp80) cc_final: 0.7956 (ttt90) REVERT: V 385 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7792 (tm-30) REVERT: V 387 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8247 (mmm160) REVERT: V 391 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7874 (mt-10) REVERT: V 414 TYR cc_start: 0.8904 (t80) cc_final: 0.8445 (t80) REVERT: V 425 LEU cc_start: 0.9116 (mt) cc_final: 0.8690 (mt) REVERT: V 429 SER cc_start: 0.8705 (t) cc_final: 0.8420 (p) REVERT: V 432 LYS cc_start: 0.8371 (ptmt) cc_final: 0.7884 (ptmt) REVERT: V 454 LYS cc_start: 0.8614 (tttt) cc_final: 0.8281 (tttt) REVERT: W 23 HIS cc_start: 0.8551 (m90) cc_final: 0.7959 (m-70) REVERT: W 73 VAL cc_start: 0.8595 (t) cc_final: 0.8299 (m) REVERT: W 78 SER cc_start: 0.8583 (t) cc_final: 0.8259 (p) REVERT: W 82 THR cc_start: 0.7944 (m) cc_final: 0.7465 (p) REVERT: W 110 GLU cc_start: 0.7443 (mp0) cc_final: 0.7103 (mp0) REVERT: W 115 GLU cc_start: 0.8396 (tp30) cc_final: 0.8066 (tp30) REVERT: W 119 GLN cc_start: 0.8490 (mt0) cc_final: 0.8286 (mt0) REVERT: W 123 LYS cc_start: 0.8351 (mtmt) cc_final: 0.8008 (mttp) REVERT: W 131 GLU cc_start: 0.7849 (tp30) cc_final: 0.7106 (mm-30) REVERT: W 157 LYS cc_start: 0.8415 (mttt) cc_final: 0.7562 (mttp) REVERT: W 170 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7778 (mm-30) REVERT: W 189 VAL cc_start: 0.7863 (t) cc_final: 0.7358 (m) REVERT: W 201 LYS cc_start: 0.8694 (tttt) cc_final: 0.8345 (ttmt) REVERT: W 222 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8832 (m) REVERT: W 233 LYS cc_start: 0.8124 (tppt) cc_final: 0.7797 (tppt) REVERT: W 273 ILE cc_start: 0.8902 (mt) cc_final: 0.8646 (mt) REVERT: W 276 LYS cc_start: 0.8400 (tptt) cc_final: 0.8072 (tptm) REVERT: W 279 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7610 (mt-10) REVERT: W 281 LYS cc_start: 0.8694 (ttpp) cc_final: 0.8424 (ttpp) REVERT: W 297 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8038 (mt-10) REVERT: W 303 ILE cc_start: 0.8818 (tp) cc_final: 0.8597 (tt) REVERT: W 311 ARG cc_start: 0.8227 (tpp-160) cc_final: 0.7993 (tpp-160) REVERT: W 315 ASP cc_start: 0.8338 (t0) cc_final: 0.7966 (t0) REVERT: W 316 GLU cc_start: 0.7868 (tt0) cc_final: 0.7487 (tp30) REVERT: W 323 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7746 (mtm) REVERT: W 331 LYS cc_start: 0.8183 (ttmm) cc_final: 0.7950 (ttpp) REVERT: W 338 LYS cc_start: 0.7961 (ttpp) cc_final: 0.7755 (ttmm) REVERT: W 358 SER cc_start: 0.9002 (m) cc_final: 0.8641 (p) REVERT: W 407 GLN cc_start: 0.8549 (tp40) cc_final: 0.7852 (tm-30) REVERT: W 412 LYS cc_start: 0.8858 (tppt) cc_final: 0.8565 (mmmt) REVERT: W 413 ARG cc_start: 0.8613 (mtp-110) cc_final: 0.8053 (ptm160) REVERT: W 415 ASN cc_start: 0.8421 (p0) cc_final: 0.7858 (p0) REVERT: W 449 ASP cc_start: 0.6685 (t0) cc_final: 0.6341 (t0) REVERT: W 450 ASP cc_start: 0.8001 (t70) cc_final: 0.7751 (m-30) REVERT: W 451 GLN cc_start: 0.7760 (mp-120) cc_final: 0.7312 (mp10) REVERT: X 31 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8107 (mmmt) REVERT: X 35 LEU cc_start: 0.9098 (tp) cc_final: 0.8805 (tp) REVERT: X 37 GLU cc_start: 0.8219 (pp20) cc_final: 0.8013 (pp20) REVERT: X 68 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8210 (mtmm) REVERT: X 103 CYS cc_start: 0.8786 (t) cc_final: 0.8568 (t) REVERT: X 114 GLU cc_start: 0.8196 (tt0) cc_final: 0.7863 (tt0) REVERT: X 119 GLU cc_start: 0.8067 (tp30) cc_final: 0.7574 (tp30) REVERT: X 134 LYS cc_start: 0.8069 (ptpt) cc_final: 0.7787 (pttm) REVERT: X 171 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8264 (tptt) REVERT: X 177 LYS cc_start: 0.8729 (tptp) cc_final: 0.8461 (tptp) REVERT: X 190 GLN cc_start: 0.8838 (tt0) cc_final: 0.8554 (mt0) REVERT: X 201 TYR cc_start: 0.7229 (t80) cc_final: 0.6509 (t80) REVERT: X 210 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7354 (mtmm) REVERT: X 227 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7423 (tp30) REVERT: X 251 ASP cc_start: 0.8305 (m-30) cc_final: 0.8080 (m-30) REVERT: X 256 ASN cc_start: 0.8471 (m-40) cc_final: 0.8142 (m-40) REVERT: X 269 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7494 (mmm) REVERT: X 282 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7135 (tp30) REVERT: X 289 ASN cc_start: 0.8388 (m110) cc_final: 0.8111 (m110) REVERT: X 294 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8486 (ttmt) REVERT: X 311 ASP cc_start: 0.8248 (t0) cc_final: 0.7920 (t0) REVERT: X 312 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7847 (mm-30) REVERT: X 315 MET cc_start: 0.8281 (mmm) cc_final: 0.7837 (mtm) REVERT: X 319 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8178 (mm-30) REVERT: X 321 PHE cc_start: 0.8860 (m-80) cc_final: 0.7850 (m-80) REVERT: X 348 ARG cc_start: 0.7979 (mtp-110) cc_final: 0.7458 (mtp85) REVERT: X 350 THR cc_start: 0.8328 (t) cc_final: 0.7925 (p) REVERT: X 359 VAL cc_start: 0.8332 (m) cc_final: 0.8110 (p) REVERT: X 365 ASP cc_start: 0.8701 (m-30) cc_final: 0.8441 (t0) REVERT: X 377 LYS cc_start: 0.8635 (tttp) cc_final: 0.8421 (mtpp) REVERT: X 386 ARG cc_start: 0.8346 (tpp80) cc_final: 0.8054 (tpp-160) REVERT: X 387 ARG cc_start: 0.8798 (mmm160) cc_final: 0.8520 (tpt90) REVERT: X 409 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7754 (tm-30) REVERT: X 433 GLU cc_start: 0.6753 (tp30) cc_final: 0.6401 (mm-30) REVERT: Y 20 ILE cc_start: 0.8176 (mt) cc_final: 0.7918 (mm) REVERT: Y 49 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7550 (mm-40) REVERT: Y 86 MET cc_start: 0.7316 (tpp) cc_final: 0.6756 (tpp) REVERT: Y 96 VAL cc_start: 0.8331 (t) cc_final: 0.8130 (p) REVERT: Y 113 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8197 (mtmm) REVERT: Y 115 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7510 (tm-30) REVERT: Y 128 LYS cc_start: 0.7960 (ttmm) cc_final: 0.7633 (ttpp) REVERT: Y 130 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8542 (ptmm) REVERT: Y 132 GLU cc_start: 0.7681 (tp30) cc_final: 0.7186 (tp30) REVERT: Y 142 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7115 (tm-30) REVERT: Y 153 HIS cc_start: 0.6694 (OUTLIER) cc_final: 0.6359 (t-90) REVERT: Y 161 LYS cc_start: 0.8329 (pttt) cc_final: 0.7902 (pttm) REVERT: Y 174 LYS cc_start: 0.8734 (mmtm) cc_final: 0.8484 (mmtm) REVERT: Y 175 MET cc_start: 0.7497 (tpp) cc_final: 0.6991 (tpp) REVERT: Y 179 LEU cc_start: 0.9088 (mm) cc_final: 0.8435 (mt) REVERT: Y 182 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7598 (mm-30) REVERT: Y 206 PHE cc_start: 0.8025 (t80) cc_final: 0.7404 (m-80) REVERT: Y 208 ARG cc_start: 0.8340 (mtm180) cc_final: 0.7909 (mtm180) REVERT: Y 223 GLN cc_start: 0.8125 (mm110) cc_final: 0.7865 (mm110) REVERT: Y 226 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7804 (mp0) REVERT: Y 229 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7505 (mp) REVERT: Y 276 LYS cc_start: 0.8903 (mmmt) cc_final: 0.8317 (tppp) REVERT: Y 279 GLU cc_start: 0.8155 (tt0) cc_final: 0.7799 (tm-30) REVERT: Y 281 LYS cc_start: 0.8722 (tmmt) cc_final: 0.8384 (tmmt) REVERT: Y 282 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8009 (tm-30) REVERT: Y 283 GLU cc_start: 0.7880 (mt-10) cc_final: 0.6723 (mt-10) REVERT: Y 287 GLU cc_start: 0.8228 (pm20) cc_final: 0.7810 (pm20) REVERT: Y 297 GLU cc_start: 0.7622 (mp0) cc_final: 0.7337 (mp0) REVERT: Y 310 ASN cc_start: 0.8691 (t0) cc_final: 0.8420 (t0) REVERT: Y 337 TYR cc_start: 0.8354 (p90) cc_final: 0.8141 (p90) REVERT: Y 376 GLU cc_start: 0.8152 (tp30) cc_final: 0.7810 (tp30) REVERT: Y 378 GLU cc_start: 0.7734 (pm20) cc_final: 0.7010 (pm20) REVERT: Y 455 GLN cc_start: 0.8318 (pp30) cc_final: 0.7442 (pp30) REVERT: Y 456 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8530 (mm) REVERT: Y 457 SER cc_start: 0.8832 (t) cc_final: 0.8217 (t) REVERT: Z 306 THR cc_start: 0.8515 (p) cc_final: 0.8249 (t) outliers start: 131 outliers final: 92 residues processed: 1115 average time/residue: 0.1996 time to fit residues: 336.1284 Evaluate side-chains 1148 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1032 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 971 ILE Chi-restraints excluded: chain Q residue 1001 ILE Chi-restraints excluded: chain Q residue 1123 GLU Chi-restraints excluded: chain Q residue 1128 LEU Chi-restraints excluded: chain Q residue 1190 LEU Chi-restraints excluded: chain Q residue 1192 ASN Chi-restraints excluded: chain Q residue 1194 GLU Chi-restraints excluded: chain Q residue 1260 LYS Chi-restraints excluded: chain Q residue 1265 VAL Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1285 ASN Chi-restraints excluded: chain Q residue 1305 ASP Chi-restraints excluded: chain Q residue 1327 MET Chi-restraints excluded: chain Q residue 1337 TYR Chi-restraints excluded: chain Q residue 1367 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 183 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 587 ARG Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 623 GLU Chi-restraints excluded: chain R residue 640 GLU Chi-restraints excluded: chain R residue 645 ILE Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 63 ASP Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 244 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 256 ASN Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 276 LYS Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 379 GLU Chi-restraints excluded: chain T residue 419 LEU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 159 THR Chi-restraints excluded: chain U residue 196 SER Chi-restraints excluded: chain U residue 305 CYS Chi-restraints excluded: chain U residue 307 SER Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain U residue 373 GLN Chi-restraints excluded: chain U residue 374 GLU Chi-restraints excluded: chain U residue 379 LEU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 387 ARG Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 222 VAL Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain X residue 29 HIS Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 269 MET Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 273 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Y residue 144 GLN Chi-restraints excluded: chain Y residue 153 HIS Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 238 THR Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 418 VAL Chi-restraints excluded: chain Y residue 456 ILE Chi-restraints excluded: chain Z residue 311 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 28 optimal weight: 0.0970 chunk 117 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 286 optimal weight: 6.9990 chunk 80 optimal weight: 0.0670 chunk 309 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 323 optimal weight: 0.6980 chunk 190 optimal weight: 0.5980 chunk 320 optimal weight: 0.8980 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 237 HIS U 274 ASN ** U 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 289 ASN V 430 ASN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.131072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110001 restraints weight = 54800.782| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.23 r_work: 0.3302 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28942 Z= 0.135 Angle : 0.684 11.636 39175 Z= 0.339 Chirality : 0.045 0.188 4610 Planarity : 0.004 0.086 5022 Dihedral : 7.784 134.879 4000 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 3.85 % Allowed : 28.20 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.14), residues: 3618 helix: 1.11 (0.13), residues: 1501 sheet: -0.06 (0.21), residues: 586 loop : -0.81 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 211 TYR 0.019 0.001 TYR V 186 PHE 0.023 0.001 PHE R 104 TRP 0.014 0.001 TRP Y 280 HIS 0.005 0.001 HIS R 745 Details of bonding type rmsd covalent geometry : bond 0.00301 (28941) covalent geometry : angle 0.68392 (39175) hydrogen bonds : bond 0.03453 ( 1093) hydrogen bonds : angle 4.23009 ( 3156) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1055 time to evaluate : 0.873 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: Q 1027 SER cc_start: 0.9027 (m) cc_final: 0.8451 (t) REVERT: Q 1033 LYS cc_start: 0.8465 (ptmt) cc_final: 0.7903 (pttm) REVERT: Q 1070 PHE cc_start: 0.8196 (p90) cc_final: 0.7698 (p90) REVERT: Q 1073 LEU cc_start: 0.7926 (mp) cc_final: 0.7517 (tp) REVERT: Q 1075 TYR cc_start: 0.8377 (t80) cc_final: 0.8089 (t80) REVERT: Q 1077 SER cc_start: 0.8395 (m) cc_final: 0.7852 (p) REVERT: Q 1097 ASN cc_start: 0.8067 (t0) cc_final: 0.7662 (t0) REVERT: Q 1109 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7782 (mtpp) REVERT: Q 1112 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8507 (ttmt) REVERT: Q 1122 TYR cc_start: 0.8368 (t80) cc_final: 0.8111 (t80) REVERT: Q 1127 PHE cc_start: 0.8711 (t80) cc_final: 0.8386 (t80) REVERT: Q 1130 LYS cc_start: 0.8661 (tptt) cc_final: 0.8398 (tppt) REVERT: Q 1134 GLU cc_start: 0.7965 (tp30) cc_final: 0.7651 (tp30) REVERT: Q 1138 ASN cc_start: 0.8087 (m-40) cc_final: 0.7547 (p0) REVERT: Q 1142 ARG cc_start: 0.8270 (ttm110) cc_final: 0.8006 (ttm110) REVERT: Q 1150 LYS cc_start: 0.8316 (tttp) cc_final: 0.7888 (tttp) REVERT: Q 1154 GLU cc_start: 0.7457 (pt0) cc_final: 0.6604 (pt0) REVERT: Q 1168 LYS cc_start: 0.8565 (mtpp) cc_final: 0.8241 (mtpp) REVERT: Q 1172 GLN cc_start: 0.7737 (mp10) cc_final: 0.7482 (pm20) REVERT: Q 1187 MET cc_start: 0.8128 (pmm) cc_final: 0.7743 (pmm) REVERT: Q 1190 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8424 (mt) REVERT: Q 1192 ASN cc_start: 0.8249 (p0) cc_final: 0.7593 (p0) REVERT: Q 1236 GLU cc_start: 0.8148 (tt0) cc_final: 0.7845 (tt0) REVERT: Q 1260 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8584 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7851 (pm20) cc_final: 0.7418 (pm20) REVERT: Q 1324 MET cc_start: 0.5967 (mmp) cc_final: 0.5766 (mmp) REVERT: Q 1327 MET cc_start: 0.7338 (OUTLIER) cc_final: 0.7008 (mpp) REVERT: Q 1331 MET cc_start: 0.7442 (tpp) cc_final: 0.6865 (tpp) REVERT: Q 1405 MET cc_start: 0.6596 (ptm) cc_final: 0.6218 (ptm) REVERT: R 113 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8400 (mm-30) REVERT: R 149 ASN cc_start: 0.8673 (m-40) cc_final: 0.8462 (m110) REVERT: R 193 ASP cc_start: 0.6319 (p0) cc_final: 0.5906 (p0) REVERT: R 205 ILE cc_start: 0.8810 (mm) cc_final: 0.8452 (pt) REVERT: R 210 LYS cc_start: 0.6726 (mmtp) cc_final: 0.6431 (mmtp) REVERT: R 218 GLN cc_start: 0.7983 (mp10) cc_final: 0.7639 (mp10) REVERT: R 229 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.7792 (mp) REVERT: R 252 TYR cc_start: 0.7622 (p90) cc_final: 0.7225 (p90) REVERT: R 261 ILE cc_start: 0.8528 (tp) cc_final: 0.8211 (tp) REVERT: R 263 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8190 (pttp) REVERT: R 586 TRP cc_start: 0.7283 (p90) cc_final: 0.7064 (p90) REVERT: R 609 GLN cc_start: 0.8418 (tp-100) cc_final: 0.8102 (tp-100) REVERT: R 623 GLU cc_start: 0.7721 (mp0) cc_final: 0.7365 (mp0) REVERT: R 630 MET cc_start: 0.8924 (mtp) cc_final: 0.8636 (mtm) REVERT: R 633 GLN cc_start: 0.8273 (mp10) cc_final: 0.7896 (mt0) REVERT: R 645 ILE cc_start: 0.8485 (mm) cc_final: 0.8248 (tp) REVERT: R 683 ARG cc_start: 0.8847 (tpt90) cc_final: 0.8309 (tpt90) REVERT: R 697 ASN cc_start: 0.8344 (t0) cc_final: 0.8014 (t0) REVERT: R 722 GLU cc_start: 0.8239 (tm-30) cc_final: 0.8004 (pp20) REVERT: R 724 TYR cc_start: 0.8373 (t80) cc_final: 0.8069 (t80) REVERT: R 725 ARG cc_start: 0.8078 (tpp-160) cc_final: 0.7512 (tpp-160) REVERT: R 744 GLU cc_start: 0.8281 (mp0) cc_final: 0.7987 (mp0) REVERT: R 751 LYS cc_start: 0.7307 (mmmt) cc_final: 0.6902 (mmmt) REVERT: S 70 GLU cc_start: 0.8270 (tp30) cc_final: 0.7929 (tp30) REVERT: S 114 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8256 (mtmm) REVERT: S 157 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7763 (ttpt) REVERT: T 37 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7688 (tm-30) REVERT: T 42 LYS cc_start: 0.7701 (tptp) cc_final: 0.7465 (tppp) REVERT: T 49 VAL cc_start: 0.7626 (p) cc_final: 0.7395 (m) REVERT: T 66 LYS cc_start: 0.8032 (mttt) cc_final: 0.7797 (mttm) REVERT: T 69 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8546 (mtpp) REVERT: T 70 MET cc_start: 0.8733 (mtm) cc_final: 0.8503 (mtp) REVERT: T 116 LYS cc_start: 0.7800 (pttt) cc_final: 0.7528 (pttm) REVERT: T 123 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8049 (tt0) REVERT: T 143 GLU cc_start: 0.7981 (tt0) cc_final: 0.7751 (tt0) REVERT: T 168 VAL cc_start: 0.8371 (t) cc_final: 0.8130 (m) REVERT: T 182 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7985 (p0) REVERT: T 190 GLN cc_start: 0.8387 (mt0) cc_final: 0.7995 (mt0) REVERT: T 209 VAL cc_start: 0.8894 (t) cc_final: 0.8535 (m) REVERT: T 221 GLU cc_start: 0.8022 (pt0) cc_final: 0.7441 (pm20) REVERT: T 225 GLU cc_start: 0.7696 (tp30) cc_final: 0.7256 (tp30) REVERT: T 268 MET cc_start: 0.7517 (tpp) cc_final: 0.6890 (mpp) REVERT: T 282 GLU cc_start: 0.8089 (tp30) cc_final: 0.7647 (tp30) REVERT: T 302 GLU cc_start: 0.8283 (tt0) cc_final: 0.7998 (tt0) REVERT: T 303 LEU cc_start: 0.8793 (tt) cc_final: 0.8535 (tp) REVERT: T 304 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8009 (mm) REVERT: T 319 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7759 (mt-10) REVERT: T 325 ASN cc_start: 0.8279 (t0) cc_final: 0.7952 (t0) REVERT: T 329 GLU cc_start: 0.7768 (pp20) cc_final: 0.7347 (pp20) REVERT: T 348 ARG cc_start: 0.8000 (mtp-110) cc_final: 0.7584 (mmm-85) REVERT: T 366 ARG cc_start: 0.7674 (mtt-85) cc_final: 0.7386 (mtt180) REVERT: T 396 GLU cc_start: 0.8027 (tp30) cc_final: 0.7584 (tp30) REVERT: T 401 ASP cc_start: 0.8201 (m-30) cc_final: 0.7904 (m-30) REVERT: T 417 GLN cc_start: 0.8705 (mt0) cc_final: 0.8349 (mt0) REVERT: T 431 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7741 (mtm110) REVERT: T 433 GLU cc_start: 0.7364 (pm20) cc_final: 0.7056 (pm20) REVERT: T 441 GLU cc_start: 0.8036 (tt0) cc_final: 0.7636 (tt0) REVERT: U 34 ASN cc_start: 0.8385 (m-40) cc_final: 0.8011 (m-40) REVERT: U 59 LYS cc_start: 0.8621 (tppp) cc_final: 0.8289 (tppt) REVERT: U 132 GLU cc_start: 0.7169 (tp30) cc_final: 0.6770 (mm-30) REVERT: U 140 VAL cc_start: 0.8304 (m) cc_final: 0.8028 (p) REVERT: U 157 LYS cc_start: 0.8474 (mtpp) cc_final: 0.8216 (mtpp) REVERT: U 159 THR cc_start: 0.8097 (OUTLIER) cc_final: 0.7502 (p) REVERT: U 161 LYS cc_start: 0.8731 (tmmt) cc_final: 0.8505 (tttm) REVERT: U 166 GLU cc_start: 0.7899 (tp30) cc_final: 0.7218 (tp30) REVERT: U 168 ILE cc_start: 0.7871 (tp) cc_final: 0.7618 (tt) REVERT: U 223 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7492 (tm-30) REVERT: U 226 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7439 (mm-30) REVERT: U 233 LYS cc_start: 0.8281 (ptmm) cc_final: 0.7715 (ptmm) REVERT: U 249 SER cc_start: 0.8658 (t) cc_final: 0.8141 (p) REVERT: U 276 LYS cc_start: 0.8706 (ttmm) cc_final: 0.8209 (ttmm) REVERT: U 279 GLU cc_start: 0.8259 (tt0) cc_final: 0.7974 (tt0) REVERT: U 281 LYS cc_start: 0.8924 (tttt) cc_final: 0.8608 (tptp) REVERT: U 310 ASN cc_start: 0.8069 (m-40) cc_final: 0.7461 (m-40) REVERT: U 316 GLU cc_start: 0.8202 (tt0) cc_final: 0.7847 (tp30) REVERT: U 339 SER cc_start: 0.8649 (m) cc_final: 0.8444 (m) REVERT: U 346 ASP cc_start: 0.8075 (p0) cc_final: 0.7847 (p0) REVERT: U 357 LYS cc_start: 0.7897 (mppt) cc_final: 0.7663 (mppt) REVERT: U 362 GLN cc_start: 0.8172 (mp10) cc_final: 0.7787 (mp10) REVERT: U 368 LEU cc_start: 0.8911 (mt) cc_final: 0.8669 (mm) REVERT: U 373 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: U 407 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8077 (tp40) REVERT: U 417 THR cc_start: 0.8518 (p) cc_final: 0.7627 (t) REVERT: U 419 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7502 (mp0) REVERT: U 438 LYS cc_start: 0.8495 (ttpt) cc_final: 0.7969 (tptp) REVERT: U 439 TYR cc_start: 0.8147 (m-80) cc_final: 0.7630 (m-80) REVERT: U 442 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7576 (tp30) REVERT: V 31 LYS cc_start: 0.8530 (mptt) cc_final: 0.8093 (mtmm) REVERT: V 44 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.6897 (p) REVERT: V 45 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7039 (mm-30) REVERT: V 75 ILE cc_start: 0.8453 (pt) cc_final: 0.8148 (mp) REVERT: V 103 CYS cc_start: 0.8212 (t) cc_final: 0.7822 (t) REVERT: V 119 GLU cc_start: 0.8078 (tp30) cc_final: 0.7463 (tp30) REVERT: V 143 GLU cc_start: 0.7641 (tt0) cc_final: 0.7330 (tt0) REVERT: V 146 GLU cc_start: 0.7571 (tm-30) cc_final: 0.6727 (tm-30) REVERT: V 193 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8093 (mmmt) REVERT: V 205 ASN cc_start: 0.8391 (m-40) cc_final: 0.7984 (m-40) REVERT: V 251 ASP cc_start: 0.7823 (m-30) cc_final: 0.7248 (m-30) REVERT: V 269 MET cc_start: 0.8298 (tpp) cc_final: 0.8028 (tpp) REVERT: V 276 LYS cc_start: 0.8437 (mptt) cc_final: 0.7933 (mptt) REVERT: V 286 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7803 (mm-40) REVERT: V 290 LYS cc_start: 0.8417 (mppt) cc_final: 0.7916 (mttm) REVERT: V 296 ILE cc_start: 0.7981 (mt) cc_final: 0.7779 (pt) REVERT: V 298 GLN cc_start: 0.8448 (tm130) cc_final: 0.8155 (pp30) REVERT: V 336 VAL cc_start: 0.8503 (OUTLIER) cc_final: 0.8223 (m) REVERT: V 373 LEU cc_start: 0.8991 (mt) cc_final: 0.8744 (mm) REVERT: V 381 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7993 (ttt90) REVERT: V 385 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7794 (tm-30) REVERT: V 387 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8236 (mmm160) REVERT: V 391 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7842 (mt-10) REVERT: V 414 TYR cc_start: 0.8887 (t80) cc_final: 0.8519 (t80) REVERT: V 425 LEU cc_start: 0.9106 (mt) cc_final: 0.8671 (mt) REVERT: V 429 SER cc_start: 0.8692 (t) cc_final: 0.8404 (p) REVERT: V 432 LYS cc_start: 0.8329 (ptmt) cc_final: 0.7833 (ptmt) REVERT: V 454 LYS cc_start: 0.8612 (tttt) cc_final: 0.8273 (tttt) REVERT: W 23 HIS cc_start: 0.8554 (m90) cc_final: 0.7979 (m-70) REVERT: W 73 VAL cc_start: 0.8583 (t) cc_final: 0.8278 (m) REVERT: W 78 SER cc_start: 0.8557 (t) cc_final: 0.8228 (p) REVERT: W 82 THR cc_start: 0.7939 (m) cc_final: 0.7474 (p) REVERT: W 110 GLU cc_start: 0.7483 (mp0) cc_final: 0.7123 (mp0) REVERT: W 115 GLU cc_start: 0.8424 (tp30) cc_final: 0.8109 (tp30) REVERT: W 119 GLN cc_start: 0.8470 (mt0) cc_final: 0.8248 (mt0) REVERT: W 123 LYS cc_start: 0.8331 (mtmt) cc_final: 0.7969 (mttp) REVERT: W 131 GLU cc_start: 0.7838 (tp30) cc_final: 0.7104 (mm-30) REVERT: W 154 LYS cc_start: 0.8452 (ptpt) cc_final: 0.8176 (ptpt) REVERT: W 157 LYS cc_start: 0.8411 (mttt) cc_final: 0.7562 (mttp) REVERT: W 170 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7792 (mm-30) REVERT: W 189 VAL cc_start: 0.7827 (t) cc_final: 0.7325 (m) REVERT: W 201 LYS cc_start: 0.8684 (tttt) cc_final: 0.8328 (ttmt) REVERT: W 211 ASP cc_start: 0.8379 (t0) cc_final: 0.8174 (t0) REVERT: W 222 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8813 (m) REVERT: W 233 LYS cc_start: 0.8067 (tppt) cc_final: 0.7738 (tppt) REVERT: W 273 ILE cc_start: 0.8891 (mt) cc_final: 0.8635 (mt) REVERT: W 276 LYS cc_start: 0.8395 (tptt) cc_final: 0.8066 (tptm) REVERT: W 279 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7600 (mt-10) REVERT: W 281 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8423 (ttpp) REVERT: W 297 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8057 (mt-10) REVERT: W 303 ILE cc_start: 0.8798 (tp) cc_final: 0.8584 (tt) REVERT: W 309 ILE cc_start: 0.8910 (mm) cc_final: 0.8680 (mt) REVERT: W 311 ARG cc_start: 0.8285 (tpp-160) cc_final: 0.8043 (tpp-160) REVERT: W 315 ASP cc_start: 0.8342 (t0) cc_final: 0.7958 (t0) REVERT: W 316 GLU cc_start: 0.7912 (tt0) cc_final: 0.7517 (tp30) REVERT: W 331 LYS cc_start: 0.8181 (ttmm) cc_final: 0.7924 (ttpp) REVERT: W 338 LYS cc_start: 0.7933 (ttpp) cc_final: 0.7725 (ttmm) REVERT: W 358 SER cc_start: 0.8967 (m) cc_final: 0.8587 (p) REVERT: W 407 GLN cc_start: 0.8528 (tp40) cc_final: 0.7833 (tm-30) REVERT: W 412 LYS cc_start: 0.8858 (tppt) cc_final: 0.8580 (mttm) REVERT: W 413 ARG cc_start: 0.8625 (mtp-110) cc_final: 0.8075 (ptm160) REVERT: W 415 ASN cc_start: 0.8404 (p0) cc_final: 0.7858 (p0) REVERT: X 31 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8083 (mmmt) REVERT: X 35 LEU cc_start: 0.9102 (tp) cc_final: 0.8784 (tp) REVERT: X 37 GLU cc_start: 0.8274 (pp20) cc_final: 0.8046 (pp20) REVERT: X 68 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8197 (mtmm) REVERT: X 103 CYS cc_start: 0.8774 (t) cc_final: 0.8539 (t) REVERT: X 114 GLU cc_start: 0.8145 (tt0) cc_final: 0.7867 (tt0) REVERT: X 119 GLU cc_start: 0.7995 (tp30) cc_final: 0.7531 (tp30) REVERT: X 134 LYS cc_start: 0.7997 (ptpt) cc_final: 0.7731 (pttm) REVERT: X 150 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6998 (tt0) REVERT: X 153 GLU cc_start: 0.7716 (pp20) cc_final: 0.7379 (pp20) REVERT: X 171 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8242 (tptt) REVERT: X 177 LYS cc_start: 0.8725 (tptp) cc_final: 0.8476 (tptp) REVERT: X 190 GLN cc_start: 0.8806 (tt0) cc_final: 0.8530 (mt0) REVERT: X 201 TYR cc_start: 0.7227 (t80) cc_final: 0.6521 (t80) REVERT: X 210 LYS cc_start: 0.8264 (mtmm) cc_final: 0.7411 (mtmm) REVERT: X 227 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7465 (tp30) REVERT: X 251 ASP cc_start: 0.8309 (m-30) cc_final: 0.8039 (m-30) REVERT: X 256 ASN cc_start: 0.8438 (m-40) cc_final: 0.8049 (m-40) REVERT: X 269 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7454 (mmm) REVERT: X 282 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7059 (tp30) REVERT: X 289 ASN cc_start: 0.8388 (m110) cc_final: 0.8101 (m110) REVERT: X 294 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8467 (ttmt) REVERT: X 311 ASP cc_start: 0.8206 (t0) cc_final: 0.7754 (t0) REVERT: X 312 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7829 (mm-30) REVERT: X 315 MET cc_start: 0.8158 (mmm) cc_final: 0.7793 (mtm) REVERT: X 319 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8167 (mm-30) REVERT: X 321 PHE cc_start: 0.8848 (m-80) cc_final: 0.7879 (m-80) REVERT: X 323 TYR cc_start: 0.8208 (t80) cc_final: 0.7971 (t80) REVERT: X 348 ARG cc_start: 0.7950 (mtp-110) cc_final: 0.7430 (mtp85) REVERT: X 350 THR cc_start: 0.8349 (t) cc_final: 0.7941 (p) REVERT: X 365 ASP cc_start: 0.8707 (m-30) cc_final: 0.8461 (t0) REVERT: X 386 ARG cc_start: 0.8332 (tpp80) cc_final: 0.8036 (tpp-160) REVERT: X 387 ARG cc_start: 0.8763 (mmm160) cc_final: 0.8143 (tpp80) REVERT: X 409 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7749 (tm-30) REVERT: X 414 TYR cc_start: 0.8664 (t80) cc_final: 0.8323 (t80) REVERT: X 433 GLU cc_start: 0.6722 (tp30) cc_final: 0.6509 (mm-30) REVERT: Y 20 ILE cc_start: 0.8148 (mt) cc_final: 0.7888 (mm) REVERT: Y 49 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7538 (mm-40) REVERT: Y 86 MET cc_start: 0.7343 (tpp) cc_final: 0.6793 (tpp) REVERT: Y 113 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8173 (mtmm) REVERT: Y 115 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7397 (tm-30) REVERT: Y 128 LYS cc_start: 0.7929 (ttmm) cc_final: 0.7572 (ttpp) REVERT: Y 130 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8559 (ptmm) REVERT: Y 142 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7116 (tm-30) REVERT: Y 144 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: Y 153 HIS cc_start: 0.6762 (OUTLIER) cc_final: 0.6398 (t-90) REVERT: Y 161 LYS cc_start: 0.8310 (pttt) cc_final: 0.8035 (pttp) REVERT: Y 174 LYS cc_start: 0.8722 (mmtm) cc_final: 0.8479 (mmtm) REVERT: Y 175 MET cc_start: 0.7508 (tpp) cc_final: 0.6980 (tpp) REVERT: Y 179 LEU cc_start: 0.9083 (mm) cc_final: 0.8426 (mt) REVERT: Y 182 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7451 (mm-30) REVERT: Y 206 PHE cc_start: 0.8012 (t80) cc_final: 0.7399 (m-80) REVERT: Y 208 ARG cc_start: 0.8317 (mtm180) cc_final: 0.7868 (mtm180) REVERT: Y 223 GLN cc_start: 0.8080 (mm110) cc_final: 0.7817 (mm110) REVERT: Y 226 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7763 (mp0) REVERT: Y 229 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7656 (mp) REVERT: Y 276 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8357 (tppp) REVERT: Y 281 LYS cc_start: 0.8721 (tmmt) cc_final: 0.8400 (tmmt) REVERT: Y 282 GLU cc_start: 0.8331 (tm-30) cc_final: 0.8017 (tm-30) REVERT: Y 287 GLU cc_start: 0.8236 (pm20) cc_final: 0.7904 (pm20) REVERT: Y 297 GLU cc_start: 0.7682 (mp0) cc_final: 0.7350 (mp0) REVERT: Y 300 MET cc_start: 0.8464 (mmm) cc_final: 0.8209 (mmm) REVERT: Y 310 ASN cc_start: 0.8681 (t0) cc_final: 0.8428 (t0) REVERT: Y 311 ARG cc_start: 0.8225 (tpp-160) cc_final: 0.8006 (tpp-160) REVERT: Y 337 TYR cc_start: 0.8368 (p90) cc_final: 0.8146 (p90) REVERT: Y 376 GLU cc_start: 0.8160 (tp30) cc_final: 0.7833 (tp30) REVERT: Y 378 GLU cc_start: 0.7717 (pm20) cc_final: 0.6973 (pm20) REVERT: Y 455 GLN cc_start: 0.8377 (pp30) cc_final: 0.7448 (pp30) REVERT: Y 456 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8512 (mm) REVERT: Y 457 SER cc_start: 0.8838 (t) cc_final: 0.8211 (t) REVERT: Z 306 THR cc_start: 0.8477 (p) cc_final: 0.8203 (t) outliers start: 120 outliers final: 84 residues processed: 1116 average time/residue: 0.1863 time to fit residues: 315.2041 Evaluate side-chains 1139 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 1035 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 971 ILE Chi-restraints excluded: chain Q residue 1190 LEU Chi-restraints excluded: chain Q residue 1194 GLU Chi-restraints excluded: chain Q residue 1260 LYS Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1285 ASN Chi-restraints excluded: chain Q residue 1305 ASP Chi-restraints excluded: chain Q residue 1327 MET Chi-restraints excluded: chain Q residue 1367 ILE Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 587 ARG Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 63 ASP Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 244 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 379 GLU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 159 THR Chi-restraints excluded: chain U residue 188 ASP Chi-restraints excluded: chain U residue 196 SER Chi-restraints excluded: chain U residue 237 HIS Chi-restraints excluded: chain U residue 305 CYS Chi-restraints excluded: chain U residue 373 GLN Chi-restraints excluded: chain U residue 374 GLU Chi-restraints excluded: chain U residue 379 LEU Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 159 TYR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 387 ARG Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 222 VAL Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 269 MET Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 273 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Y residue 144 GLN Chi-restraints excluded: chain Y residue 153 HIS Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 456 ILE Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 311 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 187 optimal weight: 0.6980 chunk 190 optimal weight: 0.7980 chunk 326 optimal weight: 0.6980 chunk 206 optimal weight: 3.9990 chunk 240 optimal weight: 0.4980 chunk 197 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 252 optimal weight: 0.4980 chunk 268 optimal weight: 0.0170 chunk 298 optimal weight: 2.9990 chunk 275 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 274 ASN U 401 ASN ** U 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110419 restraints weight = 54592.681| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.23 r_work: 0.3307 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28942 Z= 0.139 Angle : 0.698 12.501 39175 Z= 0.346 Chirality : 0.045 0.241 4610 Planarity : 0.004 0.076 5022 Dihedral : 7.682 133.249 4000 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Rotamer: Outliers : 3.47 % Allowed : 28.61 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.14), residues: 3618 helix: 1.09 (0.13), residues: 1504 sheet: -0.01 (0.21), residues: 595 loop : -0.81 (0.16), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 431 TYR 0.019 0.001 TYR Y 427 PHE 0.022 0.001 PHE R 104 TRP 0.012 0.001 TRP R 711 HIS 0.013 0.001 HIS U 237 Details of bonding type rmsd covalent geometry : bond 0.00310 (28941) covalent geometry : angle 0.69804 (39175) hydrogen bonds : bond 0.03467 ( 1093) hydrogen bonds : angle 4.22726 ( 3156) Misc. bond : bond 0.00001 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 1048 time to evaluate : 0.857 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 1027 SER cc_start: 0.9025 (m) cc_final: 0.8472 (t) REVERT: Q 1033 LYS cc_start: 0.8498 (ptmt) cc_final: 0.7932 (pttm) REVERT: Q 1070 PHE cc_start: 0.8137 (p90) cc_final: 0.7651 (p90) REVERT: Q 1073 LEU cc_start: 0.7947 (mp) cc_final: 0.7486 (tt) REVERT: Q 1075 TYR cc_start: 0.8388 (t80) cc_final: 0.8098 (t80) REVERT: Q 1077 SER cc_start: 0.8391 (m) cc_final: 0.7843 (p) REVERT: Q 1092 ASP cc_start: 0.8085 (m-30) cc_final: 0.7811 (m-30) REVERT: Q 1097 ASN cc_start: 0.8050 (t0) cc_final: 0.7642 (t0) REVERT: Q 1109 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7805 (mtpp) REVERT: Q 1115 ILE cc_start: 0.8500 (pt) cc_final: 0.8086 (mt) REVERT: Q 1122 TYR cc_start: 0.8374 (t80) cc_final: 0.8137 (t80) REVERT: Q 1127 PHE cc_start: 0.8714 (t80) cc_final: 0.8370 (t80) REVERT: Q 1128 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8364 (mp) REVERT: Q 1130 LYS cc_start: 0.8627 (tptt) cc_final: 0.8379 (tppt) REVERT: Q 1134 GLU cc_start: 0.7957 (tp30) cc_final: 0.7652 (tp30) REVERT: Q 1138 ASN cc_start: 0.8118 (m-40) cc_final: 0.7477 (p0) REVERT: Q 1142 ARG cc_start: 0.8254 (ttm110) cc_final: 0.7921 (ttm110) REVERT: Q 1148 LEU cc_start: 0.8525 (tp) cc_final: 0.8268 (tt) REVERT: Q 1150 LYS cc_start: 0.8262 (tttp) cc_final: 0.7773 (tttp) REVERT: Q 1154 GLU cc_start: 0.7249 (pt0) cc_final: 0.6470 (pt0) REVERT: Q 1168 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8219 (mtpp) REVERT: Q 1172 GLN cc_start: 0.7739 (mp10) cc_final: 0.7477 (pm20) REVERT: Q 1187 MET cc_start: 0.8209 (pmm) cc_final: 0.7816 (pmm) REVERT: Q 1190 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8488 (mt) REVERT: Q 1192 ASN cc_start: 0.8210 (p0) cc_final: 0.7671 (p0) REVERT: Q 1260 LYS cc_start: 0.8861 (mmmm) cc_final: 0.8586 (mtpp) REVERT: Q 1266 GLU cc_start: 0.7839 (pm20) cc_final: 0.7405 (pm20) REVERT: Q 1327 MET cc_start: 0.7350 (OUTLIER) cc_final: 0.7033 (mpp) REVERT: Q 1331 MET cc_start: 0.7430 (tpp) cc_final: 0.6850 (tpp) REVERT: Q 1337 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: Q 1405 MET cc_start: 0.6585 (ptm) cc_final: 0.6206 (ptm) REVERT: R 18 ASP cc_start: 0.7529 (m-30) cc_final: 0.7321 (m-30) REVERT: R 113 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8413 (mm-30) REVERT: R 158 TYR cc_start: 0.7064 (m-80) cc_final: 0.6456 (m-80) REVERT: R 193 ASP cc_start: 0.6286 (p0) cc_final: 0.5864 (p0) REVERT: R 205 ILE cc_start: 0.8784 (mm) cc_final: 0.8519 (pt) REVERT: R 210 LYS cc_start: 0.6810 (mmtp) cc_final: 0.6505 (mmtp) REVERT: R 218 GLN cc_start: 0.7994 (mp10) cc_final: 0.7675 (mp10) REVERT: R 229 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.7812 (mp) REVERT: R 252 TYR cc_start: 0.7566 (p90) cc_final: 0.7162 (p90) REVERT: R 261 ILE cc_start: 0.8529 (tp) cc_final: 0.8238 (tp) REVERT: R 263 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8231 (pttp) REVERT: R 609 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8094 (tp-100) REVERT: R 623 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: R 630 MET cc_start: 0.8925 (mtp) cc_final: 0.8669 (mtm) REVERT: R 633 GLN cc_start: 0.8241 (mp10) cc_final: 0.7885 (mt0) REVERT: R 645 ILE cc_start: 0.8464 (mm) cc_final: 0.8232 (tp) REVERT: R 697 ASN cc_start: 0.8323 (t0) cc_final: 0.7894 (t0) REVERT: R 722 GLU cc_start: 0.8250 (tm-30) cc_final: 0.8014 (pp20) REVERT: R 724 TYR cc_start: 0.8366 (t80) cc_final: 0.8064 (t80) REVERT: R 725 ARG cc_start: 0.8079 (tpp-160) cc_final: 0.7514 (tpp-160) REVERT: R 744 GLU cc_start: 0.8261 (mp0) cc_final: 0.7768 (mp0) REVERT: R 751 LYS cc_start: 0.7321 (mmmt) cc_final: 0.6983 (mmmt) REVERT: S 114 LYS cc_start: 0.8815 (mtmm) cc_final: 0.8278 (mtmm) REVERT: S 157 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7776 (ttpt) REVERT: T 37 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7694 (tm-30) REVERT: T 42 LYS cc_start: 0.7594 (tptp) cc_final: 0.7342 (tmtt) REVERT: T 45 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7227 (mt-10) REVERT: T 49 VAL cc_start: 0.7602 (p) cc_final: 0.7384 (m) REVERT: T 66 LYS cc_start: 0.8015 (mttt) cc_final: 0.7784 (mttm) REVERT: T 69 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8534 (mtpp) REVERT: T 70 MET cc_start: 0.8739 (mtm) cc_final: 0.8514 (mtp) REVERT: T 116 LYS cc_start: 0.7795 (pttt) cc_final: 0.7519 (pttm) REVERT: T 123 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8068 (tt0) REVERT: T 143 GLU cc_start: 0.7979 (tt0) cc_final: 0.7775 (tt0) REVERT: T 168 VAL cc_start: 0.8361 (t) cc_final: 0.8125 (m) REVERT: T 182 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.7983 (p0) REVERT: T 190 GLN cc_start: 0.8373 (mt0) cc_final: 0.7999 (mt0) REVERT: T 209 VAL cc_start: 0.8857 (t) cc_final: 0.8505 (m) REVERT: T 221 GLU cc_start: 0.8039 (pt0) cc_final: 0.7447 (pm20) REVERT: T 225 GLU cc_start: 0.7700 (tp30) cc_final: 0.7278 (tp30) REVERT: T 268 MET cc_start: 0.7525 (tpp) cc_final: 0.6906 (mpp) REVERT: T 282 GLU cc_start: 0.8087 (tp30) cc_final: 0.7635 (tp30) REVERT: T 289 ASN cc_start: 0.8491 (m-40) cc_final: 0.8170 (m110) REVERT: T 303 LEU cc_start: 0.8693 (tt) cc_final: 0.8226 (tp) REVERT: T 304 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7897 (mm) REVERT: T 319 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7744 (mt-10) REVERT: T 325 ASN cc_start: 0.8289 (t0) cc_final: 0.8024 (t0) REVERT: T 329 GLU cc_start: 0.7772 (pp20) cc_final: 0.7356 (pp20) REVERT: T 348 ARG cc_start: 0.8004 (mtp-110) cc_final: 0.7588 (mmm-85) REVERT: T 366 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7448 (mtt180) REVERT: T 396 GLU cc_start: 0.8048 (tp30) cc_final: 0.7648 (tp30) REVERT: T 401 ASP cc_start: 0.8187 (m-30) cc_final: 0.7897 (m-30) REVERT: T 417 GLN cc_start: 0.8729 (mt0) cc_final: 0.8387 (mt0) REVERT: T 433 GLU cc_start: 0.7383 (pm20) cc_final: 0.7113 (pm20) REVERT: T 441 GLU cc_start: 0.8013 (tt0) cc_final: 0.7630 (tt0) REVERT: U 29 LEU cc_start: 0.8271 (mm) cc_final: 0.7664 (mp) REVERT: U 34 ASN cc_start: 0.8379 (m-40) cc_final: 0.8047 (m-40) REVERT: U 42 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8005 (mt-10) REVERT: U 132 GLU cc_start: 0.7202 (tp30) cc_final: 0.6790 (mm-30) REVERT: U 140 VAL cc_start: 0.8307 (m) cc_final: 0.8041 (p) REVERT: U 157 LYS cc_start: 0.8464 (mtpp) cc_final: 0.8208 (mtpp) REVERT: U 159 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7484 (p) REVERT: U 161 LYS cc_start: 0.8732 (tmmt) cc_final: 0.8512 (tttm) REVERT: U 166 GLU cc_start: 0.7895 (tp30) cc_final: 0.7292 (tp30) REVERT: U 168 ILE cc_start: 0.7869 (tp) cc_final: 0.7618 (tt) REVERT: U 223 GLN cc_start: 0.7857 (tm-30) cc_final: 0.7563 (tm-30) REVERT: U 226 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7440 (mm-30) REVERT: U 233 LYS cc_start: 0.8258 (ptmm) cc_final: 0.7703 (ptmm) REVERT: U 249 SER cc_start: 0.8655 (t) cc_final: 0.8144 (p) REVERT: U 276 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8249 (ttmm) REVERT: U 279 GLU cc_start: 0.8224 (tt0) cc_final: 0.7943 (tt0) REVERT: U 281 LYS cc_start: 0.8915 (tttt) cc_final: 0.8608 (tptp) REVERT: U 288 ILE cc_start: 0.8576 (mt) cc_final: 0.8317 (tt) REVERT: U 310 ASN cc_start: 0.8091 (m-40) cc_final: 0.7484 (m-40) REVERT: U 316 GLU cc_start: 0.8212 (tt0) cc_final: 0.7902 (tp30) REVERT: U 339 SER cc_start: 0.8652 (m) cc_final: 0.8433 (m) REVERT: U 346 ASP cc_start: 0.8106 (p0) cc_final: 0.7853 (p0) REVERT: U 357 LYS cc_start: 0.7910 (mppt) cc_final: 0.7638 (mppt) REVERT: U 362 GLN cc_start: 0.8178 (mp10) cc_final: 0.7781 (mp10) REVERT: U 368 LEU cc_start: 0.8904 (mt) cc_final: 0.8667 (mm) REVERT: U 373 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8059 (tm-30) REVERT: U 407 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8059 (tp40) REVERT: U 417 THR cc_start: 0.8501 (p) cc_final: 0.8083 (t) REVERT: U 419 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7461 (mm-30) REVERT: U 438 LYS cc_start: 0.8489 (ttpt) cc_final: 0.7947 (tptp) REVERT: U 439 TYR cc_start: 0.8134 (m-80) cc_final: 0.7661 (m-80) REVERT: U 442 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7596 (tp30) REVERT: V 31 LYS cc_start: 0.8529 (mptt) cc_final: 0.8128 (mtmm) REVERT: V 44 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.6903 (p) REVERT: V 45 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7037 (mm-30) REVERT: V 75 ILE cc_start: 0.8458 (pt) cc_final: 0.8086 (mp) REVERT: V 103 CYS cc_start: 0.8213 (t) cc_final: 0.7838 (t) REVERT: V 119 GLU cc_start: 0.8071 (tp30) cc_final: 0.7456 (tp30) REVERT: V 143 GLU cc_start: 0.7643 (tt0) cc_final: 0.7334 (tt0) REVERT: V 146 GLU cc_start: 0.7603 (tm-30) cc_final: 0.6791 (tm-30) REVERT: V 193 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8080 (mmmt) REVERT: V 205 ASN cc_start: 0.8381 (m-40) cc_final: 0.7969 (m-40) REVERT: V 251 ASP cc_start: 0.7841 (m-30) cc_final: 0.7210 (m-30) REVERT: V 269 MET cc_start: 0.8307 (tpp) cc_final: 0.8035 (tpp) REVERT: V 276 LYS cc_start: 0.8430 (mptt) cc_final: 0.7930 (mptt) REVERT: V 286 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7799 (mm-40) REVERT: V 290 LYS cc_start: 0.8463 (mppt) cc_final: 0.7945 (mttm) REVERT: V 298 GLN cc_start: 0.8444 (tm130) cc_final: 0.8155 (pp30) REVERT: V 325 ASN cc_start: 0.7950 (p0) cc_final: 0.7668 (p0) REVERT: V 336 VAL cc_start: 0.8498 (p) cc_final: 0.8248 (m) REVERT: V 373 LEU cc_start: 0.8978 (mt) cc_final: 0.8740 (mm) REVERT: V 381 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8007 (ttt90) REVERT: V 385 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7794 (tm-30) REVERT: V 387 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8260 (mmm160) REVERT: V 391 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7850 (mt-10) REVERT: V 414 TYR cc_start: 0.8889 (t80) cc_final: 0.8518 (t80) REVERT: V 425 LEU cc_start: 0.9098 (mt) cc_final: 0.8672 (mt) REVERT: V 429 SER cc_start: 0.8705 (t) cc_final: 0.8422 (p) REVERT: V 432 LYS cc_start: 0.8340 (ptmt) cc_final: 0.8027 (ptmt) REVERT: V 454 LYS cc_start: 0.8603 (tttt) cc_final: 0.8274 (tttt) REVERT: W 23 HIS cc_start: 0.8544 (m90) cc_final: 0.7937 (m-70) REVERT: W 44 MET cc_start: 0.8195 (mtp) cc_final: 0.7929 (mmm) REVERT: W 73 VAL cc_start: 0.8572 (t) cc_final: 0.8301 (m) REVERT: W 78 SER cc_start: 0.8549 (t) cc_final: 0.8190 (p) REVERT: W 82 THR cc_start: 0.8009 (m) cc_final: 0.7517 (p) REVERT: W 110 GLU cc_start: 0.7480 (mp0) cc_final: 0.7130 (mp0) REVERT: W 113 LYS cc_start: 0.8672 (mtmt) cc_final: 0.8392 (mtpt) REVERT: W 115 GLU cc_start: 0.8414 (tp30) cc_final: 0.8111 (tp30) REVERT: W 119 GLN cc_start: 0.8469 (mt0) cc_final: 0.8250 (mt0) REVERT: W 123 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7979 (mttp) REVERT: W 131 GLU cc_start: 0.7819 (tp30) cc_final: 0.7045 (mm-30) REVERT: W 157 LYS cc_start: 0.8419 (mttt) cc_final: 0.7642 (mttp) REVERT: W 170 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7795 (mm-30) REVERT: W 189 VAL cc_start: 0.7818 (t) cc_final: 0.7309 (m) REVERT: W 201 LYS cc_start: 0.8693 (tttt) cc_final: 0.8326 (ttmt) REVERT: W 211 ASP cc_start: 0.8379 (t0) cc_final: 0.8174 (t0) REVERT: W 222 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8777 (m) REVERT: W 233 LYS cc_start: 0.8037 (tppt) cc_final: 0.7701 (tppt) REVERT: W 273 ILE cc_start: 0.8893 (mt) cc_final: 0.8585 (mt) REVERT: W 274 ASN cc_start: 0.8746 (m-40) cc_final: 0.8210 (m-40) REVERT: W 276 LYS cc_start: 0.8397 (tptt) cc_final: 0.8081 (tptm) REVERT: W 279 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7578 (mt-10) REVERT: W 281 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8408 (ttpp) REVERT: W 297 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8120 (mt-10) REVERT: W 309 ILE cc_start: 0.8894 (mm) cc_final: 0.8665 (mt) REVERT: W 311 ARG cc_start: 0.8272 (tpp-160) cc_final: 0.8016 (tpp-160) REVERT: W 315 ASP cc_start: 0.8337 (t0) cc_final: 0.7954 (t0) REVERT: W 316 GLU cc_start: 0.7916 (tt0) cc_final: 0.7524 (tp30) REVERT: W 338 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7720 (ttmm) REVERT: W 358 SER cc_start: 0.8962 (m) cc_final: 0.8574 (p) REVERT: W 398 TYR cc_start: 0.8017 (t80) cc_final: 0.7627 (t80) REVERT: W 407 GLN cc_start: 0.8553 (tp40) cc_final: 0.7864 (tm-30) REVERT: W 412 LYS cc_start: 0.8846 (tppt) cc_final: 0.8547 (mmmt) REVERT: W 413 ARG cc_start: 0.8631 (mtp-110) cc_final: 0.8085 (ttp80) REVERT: W 415 ASN cc_start: 0.8382 (p0) cc_final: 0.7620 (p0) REVERT: W 450 ASP cc_start: 0.8064 (m-30) cc_final: 0.7843 (m-30) REVERT: X 31 LYS cc_start: 0.8491 (mmmt) cc_final: 0.8080 (mmmt) REVERT: X 35 LEU cc_start: 0.9107 (tp) cc_final: 0.8815 (tp) REVERT: X 37 GLU cc_start: 0.8281 (pp20) cc_final: 0.8047 (pp20) REVERT: X 68 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8169 (mtmm) REVERT: X 114 GLU cc_start: 0.8158 (tt0) cc_final: 0.7933 (tt0) REVERT: X 119 GLU cc_start: 0.7971 (tp30) cc_final: 0.7506 (tp30) REVERT: X 134 LYS cc_start: 0.7989 (ptpt) cc_final: 0.7708 (pttm) REVERT: X 150 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: X 153 GLU cc_start: 0.7727 (pp20) cc_final: 0.7389 (pp20) REVERT: X 171 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8223 (tptt) REVERT: X 177 LYS cc_start: 0.8710 (tptp) cc_final: 0.8460 (tptp) REVERT: X 190 GLN cc_start: 0.8818 (tt0) cc_final: 0.8528 (mt0) REVERT: X 201 TYR cc_start: 0.7198 (t80) cc_final: 0.6455 (t80) REVERT: X 210 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7367 (mtmm) REVERT: X 227 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7486 (tp30) REVERT: X 251 ASP cc_start: 0.8312 (m-30) cc_final: 0.8103 (m-30) REVERT: X 256 ASN cc_start: 0.8455 (m-40) cc_final: 0.8070 (m-40) REVERT: X 269 MET cc_start: 0.8083 (OUTLIER) cc_final: 0.7422 (mmm) REVERT: X 277 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8048 (mtpp) REVERT: X 282 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7045 (tp30) REVERT: X 289 ASN cc_start: 0.8383 (m110) cc_final: 0.8151 (m110) REVERT: X 294 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8465 (ttmt) REVERT: X 311 ASP cc_start: 0.8220 (t0) cc_final: 0.7744 (t0) REVERT: X 312 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7780 (mm-30) REVERT: X 315 MET cc_start: 0.8086 (mmm) cc_final: 0.7835 (mtm) REVERT: X 319 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8194 (mm-30) REVERT: X 321 PHE cc_start: 0.8824 (m-80) cc_final: 0.7837 (m-80) REVERT: X 323 TYR cc_start: 0.8190 (t80) cc_final: 0.7962 (t80) REVERT: X 348 ARG cc_start: 0.7963 (mtp-110) cc_final: 0.7442 (mtp85) REVERT: X 350 THR cc_start: 0.8334 (t) cc_final: 0.7901 (p) REVERT: X 355 SER cc_start: 0.8749 (t) cc_final: 0.8443 (t) REVERT: X 365 ASP cc_start: 0.8709 (m-30) cc_final: 0.8293 (t70) REVERT: X 377 LYS cc_start: 0.8556 (mmmm) cc_final: 0.8272 (tptt) REVERT: X 378 ASP cc_start: 0.8241 (t0) cc_final: 0.8037 (p0) REVERT: X 386 ARG cc_start: 0.8345 (tpp80) cc_final: 0.8051 (tpp-160) REVERT: X 387 ARG cc_start: 0.8769 (mmm160) cc_final: 0.8151 (tpp80) REVERT: X 406 MET cc_start: 0.7699 (mmp) cc_final: 0.6483 (mmp) REVERT: X 409 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7684 (tm-30) REVERT: X 414 TYR cc_start: 0.8645 (t80) cc_final: 0.8395 (t80) REVERT: X 443 LYS cc_start: 0.7988 (mmmm) cc_final: 0.7741 (mttt) REVERT: Y 20 ILE cc_start: 0.8195 (mt) cc_final: 0.7939 (mm) REVERT: Y 86 MET cc_start: 0.7338 (tpp) cc_final: 0.6773 (tpp) REVERT: Y 113 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8191 (mtmm) REVERT: Y 115 GLU cc_start: 0.8048 (tm-30) cc_final: 0.7505 (tm-30) REVERT: Y 128 LYS cc_start: 0.7944 (ttmm) cc_final: 0.7568 (ttpp) REVERT: Y 142 GLU cc_start: 0.7308 (tm-30) cc_final: 0.7107 (tm-30) REVERT: Y 144 GLN cc_start: 0.7096 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: Y 153 HIS cc_start: 0.6802 (OUTLIER) cc_final: 0.6430 (t-90) REVERT: Y 161 LYS cc_start: 0.8325 (pttt) cc_final: 0.8066 (pttp) REVERT: Y 174 LYS cc_start: 0.8729 (mmtm) cc_final: 0.8518 (mmtm) REVERT: Y 175 MET cc_start: 0.7502 (tpp) cc_final: 0.6999 (tpp) REVERT: Y 179 LEU cc_start: 0.9081 (mm) cc_final: 0.8423 (mt) REVERT: Y 182 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7416 (mm-30) REVERT: Y 206 PHE cc_start: 0.8003 (t80) cc_final: 0.7409 (m-80) REVERT: Y 208 ARG cc_start: 0.8286 (mtm180) cc_final: 0.7834 (mtm180) REVERT: Y 223 GLN cc_start: 0.8088 (mm110) cc_final: 0.7829 (mm110) REVERT: Y 226 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7784 (mp0) REVERT: Y 229 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7561 (mp) REVERT: Y 276 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8316 (tppp) REVERT: Y 281 LYS cc_start: 0.8660 (tmmt) cc_final: 0.8360 (tmmt) REVERT: Y 282 GLU cc_start: 0.8275 (tm-30) cc_final: 0.7983 (tm-30) REVERT: Y 283 GLU cc_start: 0.7782 (mt-10) cc_final: 0.6954 (mt-10) REVERT: Y 287 GLU cc_start: 0.8244 (pm20) cc_final: 0.7903 (pm20) REVERT: Y 297 GLU cc_start: 0.7678 (mp0) cc_final: 0.7344 (mp0) REVERT: Y 300 MET cc_start: 0.8484 (mmm) cc_final: 0.8204 (mmm) REVERT: Y 310 ASN cc_start: 0.8709 (t0) cc_final: 0.8449 (t0) REVERT: Y 311 ARG cc_start: 0.8194 (tpp-160) cc_final: 0.7967 (tpp-160) REVERT: Y 337 TYR cc_start: 0.8324 (p90) cc_final: 0.8074 (p90) REVERT: Y 376 GLU cc_start: 0.8166 (tp30) cc_final: 0.7829 (tp30) REVERT: Y 378 GLU cc_start: 0.7735 (pm20) cc_final: 0.7044 (pm20) REVERT: Y 455 GLN cc_start: 0.8361 (pp30) cc_final: 0.7453 (pp30) REVERT: Y 456 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8538 (mm) REVERT: Y 457 SER cc_start: 0.8810 (t) cc_final: 0.8176 (t) REVERT: Z 306 THR cc_start: 0.8433 (p) cc_final: 0.8165 (t) outliers start: 108 outliers final: 80 residues processed: 1105 average time/residue: 0.1907 time to fit residues: 319.6671 Evaluate side-chains 1136 residues out of total 3172 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1036 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 971 ILE Chi-restraints excluded: chain Q residue 1128 LEU Chi-restraints excluded: chain Q residue 1190 LEU Chi-restraints excluded: chain Q residue 1194 GLU Chi-restraints excluded: chain Q residue 1284 SER Chi-restraints excluded: chain Q residue 1285 ASN Chi-restraints excluded: chain Q residue 1305 ASP Chi-restraints excluded: chain Q residue 1327 MET Chi-restraints excluded: chain Q residue 1337 TYR Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 137 THR Chi-restraints excluded: chain R residue 146 GLN Chi-restraints excluded: chain R residue 150 TRP Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 157 THR Chi-restraints excluded: chain R residue 229 LEU Chi-restraints excluded: chain R residue 263 LYS Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 587 ARG Chi-restraints excluded: chain R residue 606 ILE Chi-restraints excluded: chain R residue 623 GLU Chi-restraints excluded: chain R residue 684 ILE Chi-restraints excluded: chain S residue 61 LYS Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 99 THR Chi-restraints excluded: chain S residue 117 ASP Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain T residue 63 ASP Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 139 VAL Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 179 LEU Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 244 VAL Chi-restraints excluded: chain T residue 248 THR Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 379 GLU Chi-restraints excluded: chain T residue 447 LEU Chi-restraints excluded: chain U residue 159 THR Chi-restraints excluded: chain U residue 188 ASP Chi-restraints excluded: chain U residue 196 SER Chi-restraints excluded: chain U residue 305 CYS Chi-restraints excluded: chain U residue 373 GLN Chi-restraints excluded: chain U residue 374 GLU Chi-restraints excluded: chain U residue 379 LEU Chi-restraints excluded: chain U residue 395 SER Chi-restraints excluded: chain V residue 44 VAL Chi-restraints excluded: chain V residue 125 PHE Chi-restraints excluded: chain V residue 133 ILE Chi-restraints excluded: chain V residue 134 LYS Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 387 ARG Chi-restraints excluded: chain W residue 86 MET Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 222 VAL Chi-restraints excluded: chain W residue 224 CYS Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 257 LEU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 376 GLU Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 96 LEU Chi-restraints excluded: chain X residue 139 VAL Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 168 VAL Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain X residue 269 MET Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 273 LEU Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 364 ILE Chi-restraints excluded: chain X residue 384 ILE Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 400 LEU Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 127 ILE Chi-restraints excluded: chain Y residue 144 GLN Chi-restraints excluded: chain Y residue 153 HIS Chi-restraints excluded: chain Y residue 159 THR Chi-restraints excluded: chain Y residue 213 ASP Chi-restraints excluded: chain Y residue 229 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 279 GLU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 456 ILE Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 311 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 362 random chunks: chunk 236 optimal weight: 0.0870 chunk 316 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 348 optimal weight: 0.0870 chunk 169 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 chunk 213 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS ** R 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 274 ASN ** U 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 441 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 451 GLN X 394 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.131375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110247 restraints weight = 54936.145| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 3.24 r_work: 0.3305 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28942 Z= 0.141 Angle : 0.698 12.422 39175 Z= 0.345 Chirality : 0.045 0.238 4610 Planarity : 0.004 0.073 5022 Dihedral : 7.554 131.536 4000 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 3.60 % Allowed : 29.03 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.14), residues: 3618 helix: 1.06 (0.13), residues: 1516 sheet: -0.02 (0.21), residues: 575 loop : -0.78 (0.16), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 93 TYR 0.029 0.001 TYR R 34 PHE 0.022 0.001 PHE R 104 TRP 0.023 0.002 TRP R 586 HIS 0.005 0.001 HIS R 745 Details of bonding type rmsd covalent geometry : bond 0.00314 (28941) covalent geometry : angle 0.69817 (39175) hydrogen bonds : bond 0.03425 ( 1093) hydrogen bonds : angle 4.22611 ( 3156) Misc. bond : bond 0.00028 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7800.74 seconds wall clock time: 134 minutes 9.48 seconds (8049.48 seconds total)