Starting phenix.real_space_refine on Tue Aug 26 20:23:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cac_45386/08_2025/9cac_45386.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cac_45386/08_2025/9cac_45386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cac_45386/08_2025/9cac_45386.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cac_45386/08_2025/9cac_45386.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cac_45386/08_2025/9cac_45386.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cac_45386/08_2025/9cac_45386.map" } resolution = 3.43 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= 0.002 sd= 0.028 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: 6 Type Number sf(0) Gaussians P 17 5.49 5 Mg 8 5.21 5 S 205 5.16 5 C 25746 2.51 5 N 7131 2.21 5 O 7751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s 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: 40858 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 8242 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 51, 'TRANS': 953} Chain breaks: 6 Chain: "B" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1084 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 13, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 918 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain breaks: 1 Chain: "E" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3249 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 16, 'TRANS': 405} Chain breaks: 1 Chain: "F" Number of atoms: 3381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3381 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 11, 'TRANS': 423} Chain breaks: 1 Chain: "G" Number of atoms: 3308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3308 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 17, 'TRANS': 411} Chain breaks: 2 Chain: "H" Number of atoms: 3327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3327 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 10, 'TRANS': 417} Chain breaks: 1 Chain: "I" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3269 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 16, 'TRANS': 408} Chain breaks: 1 Chain: "J" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3198 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 10, 'TRANS': 401} Chain breaks: 2 Chain: "K" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2884 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "L" Number of atoms: 2824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2824 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 19, 'TRANS': 341} Chain breaks: 1 Chain: "M" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3163 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 22, 'TRANS': 383} Chain breaks: 1 Chain: "N" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1783 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.28, per 1000 atoms: 0.20 Number of scatterers: 40858 At special positions: 0 Unit cell: (209.975, 189.625, 160.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 205 16.00 P 17 15.00 Mg 8 11.99 O 7751 8.00 N 7131 7.00 C 25746 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9626 Finding SS restraints... Secondary structure from input PDB file: 236 helices and 50 sheets defined 51.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 773 through 792 Processing helix chain 'A' and resid 794 through 798 Processing helix chain 'A' and resid 810 through 906 Processing helix chain 'A' and resid 1057 through 1068 Processing helix chain 'A' and resid 1092 through 1108 Processing helix chain 'A' and resid 1121 through 1136 Processing helix chain 'A' and resid 1148 through 1163 removed outlier: 4.698A pdb=" N LEU A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS A1154 " --> pdb=" O CYS A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1184 Processing helix chain 'A' and resid 1198 through 1204 Processing helix chain 'A' and resid 1204 through 1210 removed outlier: 3.685A pdb=" N ARG A1210 " --> pdb=" O THR A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1224 Processing helix chain 'A' and resid 1228 through 1238 removed outlier: 3.677A pdb=" N LEU A1238 " --> pdb=" O ALA A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1266 Processing helix chain 'A' and resid 1282 through 1284 No H-bonds generated for 'chain 'A' and resid 1282 through 1284' Processing helix chain 'A' and resid 1285 through 1301 Processing helix chain 'A' and resid 1312 through 1316 Processing helix chain 'A' and resid 1329 through 1342 Processing helix chain 'A' and resid 1342 through 1352 Processing helix chain 'A' and resid 1353 through 1370 Processing helix chain 'A' and resid 1371 through 1374 Processing helix chain 'A' and resid 1393 through 1399 removed outlier: 4.121A pdb=" N LEU A1397 " --> pdb=" O ALA A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1407 removed outlier: 3.597A pdb=" N GLU A1407 " --> pdb=" O PHE A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1409 through 1414 Processing helix chain 'A' and resid 1415 through 1419 Processing helix chain 'A' and resid 1423 through 1433 Processing helix chain 'A' and resid 1436 through 1447 Processing helix chain 'A' and resid 1459 through 1464 removed outlier: 3.662A pdb=" N LEU A1463 " --> pdb=" O LYS A1459 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1763 removed outlier: 4.086A pdb=" N GLN A1763 " --> pdb=" O ARG A1759 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1776 removed outlier: 3.514A pdb=" N LEU A1772 " --> pdb=" O GLY A1768 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1830 Processing helix chain 'A' and resid 1851 through 1870 Processing helix chain 'A' and resid 1872 through 1881 Processing helix chain 'A' and resid 1890 through 1896 removed outlier: 4.224A pdb=" N GLN A1894 " --> pdb=" O LEU A1890 " (cutoff:3.500A) Processing helix chain 'A' and resid 1897 through 1913 Processing helix chain 'A' and resid 1923 through 1937 Processing helix chain 'A' and resid 1949 through 1963 Processing helix chain 'A' and resid 1976 through 1980 Processing helix chain 'A' and resid 1996 through 2011 Processing helix chain 'A' and resid 2026 through 2035 removed outlier: 4.057A pdb=" N LYS A2030 " --> pdb=" O SER A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2036 through 2046 removed outlier: 3.659A pdb=" N GLN A2046 " --> pdb=" O GLU A2042 " (cutoff:3.500A) Processing helix chain 'A' and resid 2049 through 2053 removed outlier: 3.552A pdb=" N MET A2052 " --> pdb=" O ASP A2049 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2065 Processing helix chain 'A' and resid 2096 through 2119 Proline residue: A2102 - end of helix Processing helix chain 'A' and resid 2147 through 2158 Processing helix chain 'A' and resid 2160 through 2173 Processing helix chain 'A' and resid 2174 through 2177 removed outlier: 4.001A pdb=" N ILE A2177 " --> pdb=" O HIS A2174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2174 through 2177' Processing helix chain 'A' and resid 2184 through 2217 removed outlier: 4.271A pdb=" N ALA A2188 " --> pdb=" O ASN A2184 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A2194 " --> pdb=" O MET A2190 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A2217 " --> pdb=" O LEU A2213 " (cutoff:3.500A) Processing helix chain 'A' and resid 2224 through 2229 Processing helix chain 'A' and resid 2265 through 2269 Processing helix chain 'B' and resid 168 through 192 removed outlier: 4.329A pdb=" N TYR B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 312 through 331 Processing helix chain 'C' and resid 399 through 403 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 435 through 437 No H-bonds generated for 'chain 'C' and resid 435 through 437' Processing helix chain 'C' and resid 474 through 481 Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.619A pdb=" N LYS E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 88 Processing helix chain 'E' and resid 97 through 102 removed outlier: 3.551A pdb=" N TYR E 102 " --> pdb=" O SER E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 Processing helix chain 'E' and resid 173 through 184 Processing helix chain 'E' and resid 208 through 212 removed outlier: 4.251A pdb=" N THR E 211 " --> pdb=" O THR E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 255 through 263 Processing helix chain 'E' and resid 272 through 290 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 308 through 320 removed outlier: 3.787A pdb=" N ARG E 317 " --> pdb=" O THR E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 356 Processing helix chain 'E' and resid 367 through 382 Processing helix chain 'E' and resid 387 through 400 Processing helix chain 'E' and resid 402 through 409 Processing helix chain 'E' and resid 409 through 420 Processing helix chain 'E' and resid 426 through 437 Processing helix chain 'E' and resid 439 through 448 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 Processing helix chain 'F' and resid 106 through 109 removed outlier: 3.593A pdb=" N PHE F 109 " --> pdb=" O SER F 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 106 through 109' Processing helix chain 'F' and resid 114 through 126 Processing helix chain 'F' and resid 175 through 186 Processing helix chain 'F' and resid 244 through 253 removed outlier: 4.161A pdb=" N ARG F 253 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 263 removed outlier: 4.059A pdb=" N ALA F 259 " --> pdb=" O GLN F 255 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE F 261 " --> pdb=" O PHE F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 286 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.686A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 353 removed outlier: 3.712A pdb=" N ARG F 353 " --> pdb=" O ASP F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 379 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.616A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 447 through 450 Processing helix chain 'G' and resid 42 through 59 removed outlier: 3.675A pdb=" N LYS G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 88 Processing helix chain 'G' and resid 99 through 102 removed outlier: 3.563A pdb=" N TYR G 102 " --> pdb=" O SER G 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 99 through 102' Processing helix chain 'G' and resid 107 through 119 removed outlier: 3.546A pdb=" N ALA G 119 " --> pdb=" O ASN G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 183 removed outlier: 4.455A pdb=" N SER G 179 " --> pdb=" O SER G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'G' and resid 240 through 249 Processing helix chain 'G' and resid 257 through 264 Processing helix chain 'G' and resid 272 through 289 Processing helix chain 'G' and resid 303 through 307 Processing helix chain 'G' and resid 308 through 320 removed outlier: 3.585A pdb=" N ARG G 317 " --> pdb=" O THR G 313 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU G 320 " --> pdb=" O HIS G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 367 through 383 Processing helix chain 'G' and resid 387 through 400 Processing helix chain 'G' and resid 402 through 409 Processing helix chain 'G' and resid 409 through 420 Processing helix chain 'G' and resid 426 through 437 Processing helix chain 'G' and resid 439 through 449 Processing helix chain 'H' and resid 49 through 66 Processing helix chain 'H' and resid 82 through 94 Processing helix chain 'H' and resid 106 through 109 removed outlier: 3.565A pdb=" N PHE H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 106 through 109' Processing helix chain 'H' and resid 114 through 126 Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 244 through 253 removed outlier: 4.170A pdb=" N ARG H 253 " --> pdb=" O VAL H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 269 through 287 Processing helix chain 'H' and resid 300 through 304 Processing helix chain 'H' and resid 305 through 316 removed outlier: 3.535A pdb=" N ARG H 314 " --> pdb=" O SER H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 352 Processing helix chain 'H' and resid 363 through 379 Processing helix chain 'H' and resid 383 through 397 Processing helix chain 'H' and resid 398 through 416 removed outlier: 3.814A pdb=" N THR H 407 " --> pdb=" O ILE H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 422 through 433 Processing helix chain 'H' and resid 435 through 446 Processing helix chain 'I' and resid 42 through 59 removed outlier: 3.776A pdb=" N LYS I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 75 through 88 Processing helix chain 'I' and resid 99 through 102 removed outlier: 3.618A pdb=" N TYR I 102 " --> pdb=" O SER I 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 102' Processing helix chain 'I' and resid 107 through 119 Processing helix chain 'I' and resid 174 through 183 removed outlier: 4.142A pdb=" N GLU I 178 " --> pdb=" O PRO I 174 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 240 through 247 Processing helix chain 'I' and resid 255 through 264 Processing helix chain 'I' and resid 272 through 289 Processing helix chain 'I' and resid 303 through 307 Processing helix chain 'I' and resid 308 through 321 removed outlier: 4.104A pdb=" N ARG I 317 " --> pdb=" O THR I 313 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 356 Processing helix chain 'I' and resid 367 through 383 Processing helix chain 'I' and resid 387 through 401 Processing helix chain 'I' and resid 402 through 409 Processing helix chain 'I' and resid 409 through 420 Processing helix chain 'I' and resid 426 through 437 Processing helix chain 'I' and resid 439 through 449 Processing helix chain 'J' and resid 49 through 66 Processing helix chain 'J' and resid 82 through 94 Processing helix chain 'J' and resid 106 through 109 Processing helix chain 'J' and resid 114 through 126 Processing helix chain 'J' and resid 175 through 185 Processing helix chain 'J' and resid 244 through 251 Processing helix chain 'J' and resid 255 through 257 No H-bonds generated for 'chain 'J' and resid 255 through 257' Processing helix chain 'J' and resid 258 through 263 Processing helix chain 'J' and resid 269 through 287 Processing helix chain 'J' and resid 301 through 304 Processing helix chain 'J' and resid 305 through 316 removed outlier: 3.634A pdb=" N ARG J 314 " --> pdb=" O SER J 310 " (cutoff:3.500A) Processing helix chain 'J' and resid 347 through 352 Processing helix chain 'J' and resid 363 through 379 Processing helix chain 'J' and resid 383 through 397 Processing helix chain 'J' and resid 398 through 416 removed outlier: 3.756A pdb=" N THR J 407 " --> pdb=" O ILE J 403 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 433 Processing helix chain 'J' and resid 435 through 446 Processing helix chain 'J' and resid 447 through 450 Processing helix chain 'K' and resid 40 through 46 removed outlier: 3.787A pdb=" N MET K 44 " --> pdb=" O HIS K 40 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLY K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 61 Processing helix chain 'K' and resid 78 through 93 Processing helix chain 'K' and resid 97 through 101 Processing helix chain 'K' and resid 112 through 126 Processing helix chain 'K' and resid 137 through 145 removed outlier: 3.603A pdb=" N SER K 145 " --> pdb=" O SER K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 175 Processing helix chain 'K' and resid 181 through 197 Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 222 through 233 Processing helix chain 'K' and resid 252 through 263 Proline residue: K 258 - end of helix removed outlier: 4.615A pdb=" N LEU K 261 " --> pdb=" O CYS K 257 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE K 262 " --> pdb=" O PRO K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 268 Processing helix chain 'K' and resid 273 through 284 Processing helix chain 'K' and resid 286 through 295 removed outlier: 4.138A pdb=" N LYS K 291 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 306 removed outlier: 4.307A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 349 Processing helix chain 'K' and resid 350 through 355 Processing helix chain 'K' and resid 359 through 366 Processing helix chain 'K' and resid 368 through 374 removed outlier: 3.877A pdb=" N ARG K 372 " --> pdb=" O SER K 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 Processing helix chain 'L' and resid 78 through 93 Processing helix chain 'L' and resid 112 through 126 Processing helix chain 'L' and resid 137 through 146 Processing helix chain 'L' and resid 172 through 175 Processing helix chain 'L' and resid 181 through 197 Processing helix chain 'L' and resid 205 through 217 Processing helix chain 'L' and resid 222 through 233 Processing helix chain 'L' and resid 252 through 263 Proline residue: L 258 - end of helix removed outlier: 4.531A pdb=" N LEU L 261 " --> pdb=" O CYS L 257 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE L 262 " --> pdb=" O PRO L 258 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 268 Processing helix chain 'L' and resid 273 through 284 Processing helix chain 'L' and resid 286 through 296 removed outlier: 4.258A pdb=" N LYS L 291 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP L 292 " --> pdb=" O ASP L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 301 through 305 Processing helix chain 'L' and resid 308 through 321 Processing helix chain 'L' and resid 334 through 336 No H-bonds generated for 'chain 'L' and resid 334 through 336' Processing helix chain 'L' and resid 337 through 349 Processing helix chain 'L' and resid 350 through 356 removed outlier: 3.717A pdb=" N GLN L 354 " --> pdb=" O THR L 351 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP L 356 " --> pdb=" O GLN L 353 " (cutoff:3.500A) Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'L' and resid 368 through 374 removed outlier: 3.562A pdb=" N ARG L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 71 through 76 Processing helix chain 'M' and resid 95 through 110 Processing helix chain 'M' and resid 114 through 118 removed outlier: 3.649A pdb=" N HIS M 118 " --> pdb=" O ALA M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 143 Processing helix chain 'M' and resid 154 through 162 removed outlier: 3.616A pdb=" N ASN M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 192 Processing helix chain 'M' and resid 198 through 213 Processing helix chain 'M' and resid 219 through 221 No H-bonds generated for 'chain 'M' and resid 219 through 221' Processing helix chain 'M' and resid 247 through 266 Processing helix chain 'M' and resid 275 through 282 Processing helix chain 'M' and resid 299 through 307 removed outlier: 3.501A pdb=" N LYS M 303 " --> pdb=" O ALA M 299 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE M 304 " --> pdb=" O GLU M 300 " (cutoff:3.500A) Proline residue: M 305 - end of helix No H-bonds generated for 'chain 'M' and resid 299 through 307' Processing helix chain 'M' and resid 308 through 309 No H-bonds generated for 'chain 'M' and resid 308 through 309' Processing helix chain 'M' and resid 310 through 314 Processing helix chain 'M' and resid 324 through 335 Processing helix chain 'M' and resid 340 through 347 Processing helix chain 'M' and resid 352 through 357 removed outlier: 3.722A pdb=" N ILE M 357 " --> pdb=" O ASN M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 359 through 372 Processing helix chain 'M' and resid 385 through 391 Processing helix chain 'M' and resid 391 through 403 Processing helix chain 'M' and resid 404 through 409 removed outlier: 3.744A pdb=" N GLN M 408 " --> pdb=" O THR M 405 " (cutoff:3.500A) Processing helix chain 'M' and resid 413 through 420 Processing helix chain 'M' and resid 422 through 428 removed outlier: 4.218A pdb=" N ARG M 426 " --> pdb=" O GLN M 422 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 83 through 89 Processing helix chain 'N' and resid 118 through 120 No H-bonds generated for 'chain 'N' and resid 118 through 120' Processing helix chain 'N' and resid 124 through 130 Processing helix chain 'N' and resid 139 through 147 Processing helix chain 'N' and resid 153 through 167 Processing helix chain 'N' and resid 170 through 178 Processing helix chain 'N' and resid 187 through 207 Processing helix chain 'N' and resid 219 through 236 removed outlier: 3.616A pdb=" N ARG N 236 " --> pdb=" O ARG N 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 801 through 802 Processing sheet with id=AA2, first strand: chain 'A' and resid 1168 through 1171 removed outlier: 6.276A pdb=" N LEU A1169 " --> pdb=" O ILE A1195 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N SER A1197 " --> pdb=" O LEU A1169 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N TYR A1171 " --> pdb=" O SER A1197 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N HIS A1143 " --> pdb=" O CYS A1194 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N THR A1196 " --> pdb=" O HIS A1143 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A1145 " --> pdb=" O THR A1196 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS A1214 " --> pdb=" O GLN A1242 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU A1244 " --> pdb=" O LYS A1214 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A1216 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU A1246 " --> pdb=" O LEU A1216 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A1218 " --> pdb=" O LEU A1246 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A1112 " --> pdb=" O ARG A1243 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A1113 " --> pdb=" O LEU A1305 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1319 through 1326 removed outlier: 6.320A pdb=" N TYR A1320 " --> pdb=" O ILE A2018 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ARG A2020 " --> pdb=" O TYR A1320 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N HIS A1322 " --> pdb=" O ARG A2020 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL A2022 " --> pdb=" O HIS A1322 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU A1324 " --> pdb=" O VAL A2022 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LEU A1918 " --> pdb=" O VAL A1989 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A1917 " --> pdb=" O ALA A1969 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU A1971 " --> pdb=" O VAL A1917 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A1919 " --> pdb=" O LEU A1971 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1380 through 1381 Processing sheet with id=AA5, first strand: chain 'A' and resid 1383 through 1385 Processing sheet with id=AA6, first strand: chain 'A' and resid 1390 through 1391 removed outlier: 6.040A pdb=" N TYR A1390 " --> pdb=" O ARG A1846 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1467 through 1468 removed outlier: 6.301A pdb=" N VAL A1467 " --> pdb=" O LYS N 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 2222 through 2223 Processing sheet with id=AA9, first strand: chain 'A' and resid 2232 through 2236 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2242 through 2244 current: chain 'C' and resid 451 through 459 Processing sheet with id=AB1, first strand: chain 'B' and resid 211 through 220 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 260 through 268 current: chain 'F' and resid 158 through 164 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 173 current: chain 'F' and resid 202 through 207 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 202 through 207 current: chain 'G' and resid 153 through 162 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 167 through 172 current: chain 'G' and resid 200 through 206 removed outlier: 4.839A pdb=" N VAL G 221 " --> pdb=" O GLN G 203 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG G 205 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AB3, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AB4, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.321A pdb=" N LEU E 299 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA E 330 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL E 301 " --> pdb=" O ALA E 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 139 removed outlier: 6.442A pdb=" N GLY E 160 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU E 138 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE E 158 " --> pdb=" O LEU E 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 167 through 172 current: chain 'E' and resid 199 through 206 removed outlier: 5.575A pdb=" N VAL E 221 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ARG E 205 " --> pdb=" O VAL E 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AB7, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.550A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY F 77 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR F 359 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ALA F 76 " --> pdb=" O THR F 359 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 332 through 334 Processing sheet with id=AC1, first strand: chain 'G' and resid 35 through 36 Processing sheet with id=AC2, first strand: chain 'G' and resid 93 through 97 removed outlier: 6.353A pdb=" N CYS G 94 " --> pdb=" O PHE G 300 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASP G 302 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET G 96 " --> pdb=" O ASP G 302 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 214 through 215 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 214 through 215 current: chain 'H' and resid 159 through 164 removed outlier: 3.898A pdb=" N GLY H 159 " --> pdb=" O LEU H 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 169 through 174 current: chain 'H' and resid 202 through 207 Processing sheet with id=AC4, first strand: chain 'G' and resid 336 through 337 Processing sheet with id=AC5, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AC6, first strand: chain 'H' and resid 238 through 243 Processing sheet with id=AC7, first strand: chain 'H' and resid 332 through 334 Processing sheet with id=AC8, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AC9, first strand: chain 'I' and resid 93 through 97 removed outlier: 6.349A pdb=" N CYS I 94 " --> pdb=" O PHE I 300 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASP I 302 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET I 96 " --> pdb=" O ASP I 302 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL I 66 " --> pdb=" O PHE I 329 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER I 331 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU I 68 " --> pdb=" O SER I 331 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 120 through 140 removed outlier: 6.449A pdb=" N GLY I 160 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU I 138 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N ILE I 158 " --> pdb=" O LEU I 138 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 166 through 172 current: chain 'I' and resid 200 through 206 removed outlier: 4.849A pdb=" N VAL I 221 " --> pdb=" O GLN I 203 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG I 205 " --> pdb=" O VAL I 221 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 335 through 337 Processing sheet with id=AD3, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AD4, first strand: chain 'J' and resid 100 through 104 removed outlier: 6.445A pdb=" N THR J 101 " --> pdb=" O PHE J 297 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ASP J 299 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE J 103 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU J 296 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ALA J 327 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE J 298 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY J 77 " --> pdb=" O THR J 328 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA J 72 " --> pdb=" O LEU J 355 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N VAL J 357 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU J 74 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N THR J 359 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA J 76 " --> pdb=" O THR J 359 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 127 through 146 removed outlier: 6.678A pdb=" N THR J 162 " --> pdb=" O VAL J 143 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE J 145 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS J 160 " --> pdb=" O ILE J 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 169 through 173 current: chain 'J' and resid 202 through 207 Processing sheet with id=AD6, first strand: chain 'J' and resid 333 through 334 Processing sheet with id=AD7, first strand: chain 'K' and resid 29 through 32 removed outlier: 6.498A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AD9, first strand: chain 'K' and resid 71 through 72 Processing sheet with id=AE1, first strand: chain 'K' and resid 150 through 155 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 169 through 170 current: chain 'K' and resid 329 through 330 Processing sheet with id=AE2, first strand: chain 'K' and resid 238 through 241 Processing sheet with id=AE3, first strand: chain 'L' and resid 29 through 32 removed outlier: 6.473A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AE5, first strand: chain 'L' and resid 71 through 72 Processing sheet with id=AE6, first strand: chain 'L' and resid 150 through 155 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 169 through 170 current: chain 'L' and resid 329 through 330 Processing sheet with id=AE7, first strand: chain 'L' and resid 238 through 241 Processing sheet with id=AE8, first strand: chain 'M' and resid 35 through 38 removed outlier: 6.325A pdb=" N LEU M 14 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N SER M 123 " --> pdb=" O LEU M 14 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N PHE M 16 " --> pdb=" O SER M 123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 67 through 69 Processing sheet with id=AF1, first strand: chain 'M' and resid 88 through 89 Processing sheet with id=AF2, first strand: chain 'M' and resid 167 through 172 Processing sheet with id=AF3, first strand: chain 'M' and resid 223 through 226 removed outlier: 6.605A pdb=" N LYS M 238 " --> pdb=" O ALA M 224 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 286 through 288 Processing sheet with id=AF5, first strand: chain 'N' and resid 95 through 101 removed outlier: 3.638A pdb=" N PHE N 111 " --> pdb=" O PHE N 100 " (cutoff:3.500A) 1947 hydrogen bonds defined for protein. 5517 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: 8.19 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13539 1.34 - 1.46: 5032 1.46 - 1.57: 22634 1.57 - 1.69: 26 1.69 - 1.81: 341 Bond restraints: 41572 Sorted by residual: bond pdb=" C ARG A1849 " pdb=" O ARG A1849 " ideal model delta sigma weight residual 1.235 1.225 0.010 4.70e-03 4.53e+04 4.29e+00 bond pdb=" CA PRO M 219 " pdb=" C PRO M 219 " ideal model delta sigma weight residual 1.514 1.522 -0.008 5.50e-03 3.31e+04 2.11e+00 bond pdb=" C4 ADP J 501 " pdb=" C5 ADP J 501 " ideal model delta sigma weight residual 1.490 1.461 0.029 2.00e-02 2.50e+03 2.09e+00 bond pdb=" C4 ADP H 501 " pdb=" C5 ADP H 501 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C4 ADP G 501 " pdb=" C5 ADP G 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.63e+00 ... (remaining 41567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 55494 1.95 - 3.89: 558 3.89 - 5.84: 89 5.84 - 7.78: 13 7.78 - 9.73: 10 Bond angle restraints: 56164 Sorted by residual: angle pdb=" C2' ADP E 501 " pdb=" C3' ADP E 501 " pdb=" C4' ADP E 501 " ideal model delta sigma weight residual 111.00 101.27 9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C2' ADP F 501 " pdb=" C3' ADP F 501 " pdb=" C4' ADP F 501 " ideal model delta sigma weight residual 111.00 101.49 9.51 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C1' ADP E 501 " pdb=" C2' ADP E 501 " pdb=" C3' ADP E 501 " ideal model delta sigma weight residual 111.00 101.92 9.08 3.00e+00 1.11e-01 9.17e+00 angle pdb=" C1' ADP L 401 " pdb=" C2' ADP L 401 " pdb=" C3' ADP L 401 " ideal model delta sigma weight residual 111.00 102.07 8.93 3.00e+00 1.11e-01 8.85e+00 angle pdb=" C2' ADP G 501 " pdb=" C3' ADP G 501 " pdb=" C4' ADP G 501 " ideal model delta sigma weight residual 111.00 102.08 8.92 3.00e+00 1.11e-01 8.85e+00 ... (remaining 56159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.20: 25020 32.20 - 64.41: 431 64.41 - 96.61: 56 96.61 - 128.82: 3 128.82 - 161.02: 3 Dihedral angle restraints: 25513 sinusoidal: 10615 harmonic: 14898 Sorted by residual: dihedral pdb=" O1B ADP J 501 " pdb=" O3A ADP J 501 " pdb=" PB ADP J 501 " pdb=" PA ADP J 501 " ideal model delta sinusoidal sigma weight residual 300.00 138.98 161.02 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O1B ADP I 501 " pdb=" O3A ADP I 501 " pdb=" PB ADP I 501 " pdb=" PA ADP I 501 " ideal model delta sinusoidal sigma weight residual -60.00 92.06 -152.06 1 2.00e+01 2.50e-03 4.52e+01 dihedral pdb=" O2A ADP L 401 " pdb=" O3A ADP L 401 " pdb=" PA ADP L 401 " pdb=" PB ADP L 401 " ideal model delta sinusoidal sigma weight residual -60.00 84.55 -144.55 1 2.00e+01 2.50e-03 4.36e+01 ... (remaining 25510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 4835 0.043 - 0.086: 1100 0.086 - 0.129: 401 0.129 - 0.172: 21 0.172 - 0.216: 7 Chirality restraints: 6364 Sorted by residual: chirality pdb=" C3' ADP I 501 " pdb=" C2' ADP I 501 " pdb=" C4' ADP I 501 " pdb=" O3' ADP I 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.73 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA THR G 411 " pdb=" N THR G 411 " pdb=" C THR G 411 " pdb=" CB THR G 411 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C2' ADP I 501 " pdb=" C1' ADP I 501 " pdb=" C3' ADP I 501 " pdb=" O2' ADP I 501 " both_signs ideal model delta sigma weight residual False -2.51 -2.70 0.19 2.00e-01 2.50e+01 9.28e-01 ... (remaining 6361 not shown) Planarity restraints: 7187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 314 " 0.220 9.50e-02 1.11e+02 9.95e-02 7.86e+00 pdb=" NE ARG F 314 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG F 314 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG F 314 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG F 314 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 366 " 0.000 2.00e-02 2.50e+03 1.89e-02 7.12e+00 pdb=" CG TYR I 366 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR I 366 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR I 366 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR I 366 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR I 366 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR I 366 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR I 366 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1437 " -0.198 9.50e-02 1.11e+02 8.96e-02 6.51e+00 pdb=" NE ARG A1437 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A1437 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A1437 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A1437 " 0.000 2.00e-02 2.50e+03 ... (remaining 7184 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 184 2.53 - 3.12: 30954 3.12 - 3.72: 63776 3.72 - 4.31: 90331 4.31 - 4.90: 151025 Nonbonded interactions: 336270 Sorted by model distance: nonbonded pdb=" OG1 THR J 84 " pdb="MG MG J 502 " model vdw 1.939 2.170 nonbonded pdb=" O2B ADP F 501 " pdb="MG MG F 502 " model vdw 1.947 2.170 nonbonded pdb=" O1B ADP H 501 " pdb="MG MG H 502 " model vdw 1.974 2.170 nonbonded pdb=" O1B ATP M 501 " pdb="MG MG M 502 " model vdw 1.990 2.170 nonbonded pdb=" O1B ADP G 501 " pdb="MG MG G 502 " model vdw 2.011 2.170 ... (remaining 336265 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 'E' and (resid 12 through 251 or resid 256 through 502)) selection = (chain 'G' and (resid 12 through 140 or resid 156 through 448 or resid 501 throu \ gh 502)) selection = (chain 'I' and (resid 12 through 140 or resid 156 through 251 or resid 256 throu \ gh 448 or resid 501 through 502)) } ncs_group { reference = (chain 'F' and (resid 16 through 147 or resid 159 through 208 or resid 226 throu \ gh 502)) selection = (chain 'H' and (resid 16 through 147 or resid 159 through 208 or resid 226 throu \ gh 502)) selection = (chain 'J' and (resid 16 through 453 or resid 501 through 502)) } ncs_group { reference = (chain 'K' and (resid 6 through 40 or resid 50 through 375)) selection = (chain 'L' and resid 6 through 375) } 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: 5.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 33.140 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 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 : 0.003 0.045 41572 Z= 0.121 Angle : 0.535 9.731 56164 Z= 0.275 Chirality : 0.042 0.216 6364 Planarity : 0.008 0.099 7187 Dihedral : 12.773 161.019 15887 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.14 (0.12), residues: 5082 helix: 0.86 (0.10), residues: 2294 sheet: 0.69 (0.18), residues: 807 loop : 0.93 (0.15), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.003 ARG F 314 TYR 0.027 0.002 TYR I 366 PHE 0.017 0.001 PHE A1404 TRP 0.028 0.002 TRP L 79 HIS 0.013 0.001 HIS N 113 Details of bonding type rmsd covalent geometry : bond 0.00259 (41572) covalent geometry : angle 0.53473 (56164) hydrogen bonds : bond 0.15026 ( 1947) hydrogen bonds : angle 5.60068 ( 5517) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1549 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1549 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 GLN cc_start: 0.8162 (tp-100) cc_final: 0.7703 (tp-100) REVERT: A 820 GLN cc_start: 0.8253 (tt0) cc_final: 0.7744 (mt0) REVERT: A 838 LYS cc_start: 0.8511 (tttt) cc_final: 0.7910 (tttm) REVERT: A 842 ARG cc_start: 0.7780 (mtt-85) cc_final: 0.7452 (mmm-85) REVERT: A 849 GLU cc_start: 0.7631 (tt0) cc_final: 0.7147 (tm-30) REVERT: A 851 LYS cc_start: 0.8251 (tttt) cc_final: 0.7992 (mtpt) REVERT: A 861 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7643 (mt-10) REVERT: A 864 SER cc_start: 0.7638 (m) cc_final: 0.7434 (t) REVERT: A 865 ARG cc_start: 0.8220 (ttt180) cc_final: 0.7981 (ttt180) REVERT: A 889 GLU cc_start: 0.8790 (tt0) cc_final: 0.8296 (tp30) REVERT: A 1169 LEU cc_start: 0.7251 (tp) cc_final: 0.7013 (tp) REVERT: A 1192 HIS cc_start: 0.7323 (m90) cc_final: 0.6751 (m90) REVERT: A 1220 GLU cc_start: 0.6347 (mt-10) cc_final: 0.6106 (mt-10) REVERT: A 1233 GLU cc_start: 0.7908 (tt0) cc_final: 0.6733 (tm-30) REVERT: A 1254 THR cc_start: 0.6338 (p) cc_final: 0.6044 (m) REVERT: A 1261 MET cc_start: 0.3724 (mmp) cc_final: 0.3185 (mmp) REVERT: A 1337 GLU cc_start: 0.7223 (mt-10) cc_final: 0.7023 (tm-30) REVERT: A 1338 ASP cc_start: 0.7535 (t0) cc_final: 0.7114 (t70) REVERT: A 1341 LEU cc_start: 0.7493 (mt) cc_final: 0.6822 (mp) REVERT: A 1346 GLN cc_start: 0.7315 (mm-40) cc_final: 0.6872 (mt0) REVERT: A 1362 VAL cc_start: 0.7579 (t) cc_final: 0.7238 (m) REVERT: A 1363 ARG cc_start: 0.7987 (ttt180) cc_final: 0.7460 (mtp85) REVERT: A 1364 LEU cc_start: 0.8290 (mt) cc_final: 0.8035 (tt) REVERT: A 1369 ASN cc_start: 0.7568 (m-40) cc_final: 0.7296 (m110) REVERT: A 1401 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6971 (tt0) REVERT: A 1402 ARG cc_start: 0.7468 (ptp-110) cc_final: 0.7229 (ptp-170) REVERT: A 1406 LYS cc_start: 0.7679 (mttt) cc_final: 0.6971 (mmmt) REVERT: A 1428 GLU cc_start: 0.7027 (tp30) cc_final: 0.6382 (tp30) REVERT: A 1433 LYS cc_start: 0.7802 (mttt) cc_final: 0.7279 (mtmt) REVERT: A 1442 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7266 (mt-10) REVERT: A 1458 LEU cc_start: 0.8945 (mp) cc_final: 0.8741 (mp) REVERT: A 1464 PHE cc_start: 0.8696 (m-80) cc_final: 0.8472 (m-80) REVERT: A 1468 GLN cc_start: 0.8216 (tt0) cc_final: 0.7935 (tt0) REVERT: A 1472 LYS cc_start: 0.7890 (mmtp) cc_final: 0.7326 (mmtp) REVERT: A 1474 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 1747 LYS cc_start: 0.7734 (tttt) cc_final: 0.7434 (tmtt) REVERT: A 1750 LEU cc_start: 0.7625 (mt) cc_final: 0.7270 (mt) REVERT: A 1758 GLU cc_start: 0.8172 (tt0) cc_final: 0.7949 (tt0) REVERT: A 1762 SER cc_start: 0.7223 (t) cc_final: 0.6926 (p) REVERT: A 1769 ARG cc_start: 0.8080 (mtp-110) cc_final: 0.7587 (mtm110) REVERT: A 1774 ILE cc_start: 0.8475 (tp) cc_final: 0.7978 (mt) REVERT: A 1856 HIS cc_start: 0.7737 (t-90) cc_final: 0.7451 (t-90) REVERT: A 1861 LEU cc_start: 0.8806 (tp) cc_final: 0.8210 (tp) REVERT: A 1863 GLN cc_start: 0.7497 (tp40) cc_final: 0.7247 (tp40) REVERT: A 1894 GLN cc_start: 0.7461 (tt0) cc_final: 0.7034 (tt0) REVERT: A 1897 SER cc_start: 0.7973 (t) cc_final: 0.7698 (p) REVERT: A 1901 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7152 (mm-30) REVERT: A 1908 GLN cc_start: 0.7545 (tt0) cc_final: 0.7277 (tt0) REVERT: A 1909 LYS cc_start: 0.7673 (tttt) cc_final: 0.7461 (ttmm) REVERT: A 1911 LYS cc_start: 0.8260 (tttt) cc_final: 0.8035 (tptm) REVERT: A 1916 ARG cc_start: 0.7283 (mtp180) cc_final: 0.6857 (mtm-85) REVERT: A 1921 SER cc_start: 0.6719 (t) cc_final: 0.6328 (p) REVERT: A 1974 HIS cc_start: 0.7935 (m-70) cc_final: 0.7498 (m-70) REVERT: A 1984 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6344 (tm-30) REVERT: A 1986 ASP cc_start: 0.6713 (p0) cc_final: 0.6122 (p0) REVERT: A 1990 PHE cc_start: 0.8393 (m-80) cc_final: 0.8191 (m-10) REVERT: A 1991 TYR cc_start: 0.7973 (t80) cc_final: 0.7760 (t80) REVERT: A 1996 ASN cc_start: 0.7743 (t0) cc_final: 0.7541 (t0) REVERT: A 1999 MET cc_start: 0.7190 (mmm) cc_final: 0.6882 (mmm) REVERT: A 2000 ASP cc_start: 0.8053 (t70) cc_final: 0.7523 (t0) REVERT: A 2206 GLU cc_start: 0.7334 (tt0) cc_final: 0.6615 (tm-30) REVERT: A 2260 ILE cc_start: 0.8070 (mt) cc_final: 0.7777 (mm) REVERT: A 2263 ASP cc_start: 0.8116 (t0) cc_final: 0.7669 (t0) REVERT: A 2265 VAL cc_start: 0.7997 (t) cc_final: 0.7555 (m) REVERT: A 2266 MET cc_start: 0.7100 (ttp) cc_final: 0.6682 (ttp) REVERT: A 2269 MET cc_start: 0.7191 (mmm) cc_final: 0.6977 (mmm) REVERT: B 277 TRP cc_start: 0.7997 (m100) cc_final: 0.7341 (m100) REVERT: B 294 VAL cc_start: 0.8845 (t) cc_final: 0.8618 (m) REVERT: B 307 ASP cc_start: 0.8254 (t0) cc_final: 0.8006 (t0) REVERT: B 314 ARG cc_start: 0.7742 (mtt180) cc_final: 0.7516 (mtt180) REVERT: B 318 ILE cc_start: 0.8087 (mt) cc_final: 0.7839 (mm) REVERT: E 14 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7791 (mtp180) REVERT: E 15 ILE cc_start: 0.8483 (mm) cc_final: 0.8271 (mt) REVERT: E 101 VAL cc_start: 0.8009 (t) cc_final: 0.7726 (m) REVERT: E 104 THR cc_start: 0.7758 (t) cc_final: 0.7536 (p) REVERT: E 110 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6940 (tp30) REVERT: E 115 ASN cc_start: 0.8000 (m-40) cc_final: 0.7538 (m-40) REVERT: E 118 ARG cc_start: 0.7583 (mtm-85) cc_final: 0.7263 (mtt-85) REVERT: E 123 ARG cc_start: 0.7438 (mtp180) cc_final: 0.7237 (mmm-85) REVERT: E 126 GLU cc_start: 0.7832 (tt0) cc_final: 0.7275 (pt0) REVERT: E 127 THR cc_start: 0.7957 (p) cc_final: 0.7318 (p) REVERT: E 134 GLU cc_start: 0.7667 (tt0) cc_final: 0.7281 (tt0) REVERT: E 161 LEU cc_start: 0.8622 (mt) cc_final: 0.8227 (mt) REVERT: E 176 ILE cc_start: 0.7546 (mm) cc_final: 0.7314 (mt) REVERT: E 209 TYR cc_start: 0.7791 (m-80) cc_final: 0.7569 (m-80) REVERT: E 236 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7436 (mm-40) REVERT: E 243 LEU cc_start: 0.7645 (mt) cc_final: 0.7437 (mp) REVERT: E 258 SER cc_start: 0.7605 (m) cc_final: 0.7163 (p) REVERT: E 264 MET cc_start: 0.6788 (mmm) cc_final: 0.6379 (mmm) REVERT: E 280 ASN cc_start: 0.7625 (m-40) cc_final: 0.7376 (m110) REVERT: E 308 ASP cc_start: 0.7394 (p0) cc_final: 0.6755 (p0) REVERT: E 310 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6699 (pt0) REVERT: E 317 ARG cc_start: 0.7644 (ttt-90) cc_final: 0.7343 (ttt180) REVERT: E 320 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7346 (mt-10) REVERT: E 332 ASN cc_start: 0.7849 (p0) cc_final: 0.7600 (p0) REVERT: E 336 CYS cc_start: 0.7321 (p) cc_final: 0.6965 (p) REVERT: E 337 VAL cc_start: 0.7642 (t) cc_final: 0.7210 (m) REVERT: E 356 ASP cc_start: 0.6868 (t70) cc_final: 0.6648 (t0) REVERT: E 388 GLU cc_start: 0.7588 (tt0) cc_final: 0.7354 (tt0) REVERT: E 396 GLU cc_start: 0.7024 (tm-30) cc_final: 0.6591 (tm-30) REVERT: E 418 LYS cc_start: 0.7866 (ttmm) cc_final: 0.7639 (ttmm) REVERT: F 22 ILE cc_start: 0.8077 (mt) cc_final: 0.7853 (mt) REVERT: F 62 MET cc_start: 0.7594 (ttp) cc_final: 0.7280 (ttp) REVERT: F 65 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7197 (mm-30) REVERT: F 67 LYS cc_start: 0.8391 (mttt) cc_final: 0.8163 (mttt) REVERT: F 88 MET cc_start: 0.7201 (mmp) cc_final: 0.6991 (mmt) REVERT: F 90 MET cc_start: 0.7787 (mtp) cc_final: 0.7449 (mtp) REVERT: F 125 ARG cc_start: 0.7564 (mtm-85) cc_final: 0.7345 (ttm110) REVERT: F 130 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7695 (ttm-80) REVERT: F 136 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7089 (mm-30) REVERT: F 137 ILE cc_start: 0.8571 (mm) cc_final: 0.8305 (tp) REVERT: F 192 VAL cc_start: 0.7939 (t) cc_final: 0.7587 (p) REVERT: F 197 LYS cc_start: 0.8578 (tttt) cc_final: 0.8330 (ttmm) REVERT: F 231 GLU cc_start: 0.7810 (mp0) cc_final: 0.7478 (mp0) REVERT: F 232 LEU cc_start: 0.8198 (mt) cc_final: 0.7735 (mp) REVERT: F 254 THR cc_start: 0.7250 (m) cc_final: 0.6867 (t) REVERT: F 260 LEU cc_start: 0.7791 (mt) cc_final: 0.7351 (mt) REVERT: F 261 PHE cc_start: 0.7594 (m-80) cc_final: 0.7322 (m-80) REVERT: F 279 LYS cc_start: 0.7679 (tttt) cc_final: 0.7465 (ttmm) REVERT: F 291 ILE cc_start: 0.7680 (mm) cc_final: 0.7456 (tp) REVERT: F 313 ASN cc_start: 0.7905 (m-40) cc_final: 0.7484 (m-40) REVERT: F 314 ARG cc_start: 0.7678 (tpt90) cc_final: 0.7348 (tpt90) REVERT: F 349 ASP cc_start: 0.7412 (p0) cc_final: 0.7131 (p0) REVERT: F 411 LEU cc_start: 0.7737 (mt) cc_final: 0.7533 (mm) REVERT: F 414 ARG cc_start: 0.7276 (mtm-85) cc_final: 0.6985 (mtm-85) REVERT: F 427 LYS cc_start: 0.7825 (mmmt) cc_final: 0.7603 (mmmt) REVERT: F 434 LEU cc_start: 0.8290 (mt) cc_final: 0.7999 (mp) REVERT: G 15 ILE cc_start: 0.8197 (mt) cc_final: 0.7923 (mm) REVERT: G 17 SER cc_start: 0.7747 (p) cc_final: 0.7290 (m) REVERT: G 54 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7249 (mm-30) REVERT: G 57 LYS cc_start: 0.8035 (mttt) cc_final: 0.7817 (mtmm) REVERT: G 59 LYS cc_start: 0.7566 (mtmt) cc_final: 0.7275 (mtmm) REVERT: G 61 MET cc_start: 0.8072 (mmm) cc_final: 0.7658 (mmm) REVERT: G 97 VAL cc_start: 0.7952 (p) cc_final: 0.7744 (m) REVERT: G 105 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6914 (mt-10) REVERT: G 107 LYS cc_start: 0.8202 (pttt) cc_final: 0.7900 (ptmt) REVERT: G 110 GLU cc_start: 0.7220 (tp30) cc_final: 0.6746 (tp30) REVERT: G 113 MET cc_start: 0.7411 (tpp) cc_final: 0.7190 (tpp) REVERT: G 116 PHE cc_start: 0.8230 (m-80) cc_final: 0.7948 (m-80) REVERT: G 118 ARG cc_start: 0.7644 (mtt-85) cc_final: 0.7437 (mtt-85) REVERT: G 123 ARG cc_start: 0.7803 (ttt90) cc_final: 0.7344 (mtp85) REVERT: G 125 LYS cc_start: 0.7600 (mttm) cc_final: 0.7215 (mttm) REVERT: G 132 GLU cc_start: 0.7774 (pt0) cc_final: 0.7494 (pt0) REVERT: G 155 SER cc_start: 0.8253 (t) cc_final: 0.8045 (t) REVERT: G 167 THR cc_start: 0.8095 (m) cc_final: 0.7878 (p) REVERT: G 177 PHE cc_start: 0.8450 (p90) cc_final: 0.8122 (p90) REVERT: G 189 ASP cc_start: 0.7259 (m-30) cc_final: 0.7033 (m-30) REVERT: G 215 LEU cc_start: 0.8229 (mt) cc_final: 0.7972 (mt) REVERT: G 227 ASP cc_start: 0.7148 (t0) cc_final: 0.6943 (t0) REVERT: G 230 LYS cc_start: 0.7785 (mttt) cc_final: 0.7576 (mttt) REVERT: G 242 ASP cc_start: 0.7575 (m-30) cc_final: 0.7293 (m-30) REVERT: G 260 MET cc_start: 0.4584 (tmm) cc_final: 0.3657 (tmm) REVERT: G 264 MET cc_start: 0.4894 (mmm) cc_final: 0.4166 (mmm) REVERT: G 268 LYS cc_start: 0.6968 (mttt) cc_final: 0.6731 (mtmt) REVERT: G 278 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7200 (mm-30) REVERT: G 280 ASN cc_start: 0.7947 (m-40) cc_final: 0.7540 (m-40) REVERT: G 306 MET cc_start: 0.7414 (mmp) cc_final: 0.7177 (mmm) REVERT: G 314 TYR cc_start: 0.8279 (t80) cc_final: 0.7935 (t80) REVERT: G 322 SER cc_start: 0.8268 (p) cc_final: 0.7747 (t) REVERT: G 364 MET cc_start: 0.7468 (mtp) cc_final: 0.7255 (mtp) REVERT: G 377 ILE cc_start: 0.7992 (mt) cc_final: 0.7781 (mt) REVERT: G 396 GLU cc_start: 0.6734 (mm-30) cc_final: 0.6082 (mm-30) REVERT: G 409 LEU cc_start: 0.8059 (mt) cc_final: 0.7839 (mt) REVERT: H 46 MET cc_start: 0.7846 (mmm) cc_final: 0.7463 (mmm) REVERT: H 61 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7106 (mm-30) REVERT: H 139 GLU cc_start: 0.7223 (pt0) cc_final: 0.6898 (pt0) REVERT: H 178 MET cc_start: 0.7464 (mmm) cc_final: 0.7217 (tpp) REVERT: H 201 LYS cc_start: 0.7317 (mmmm) cc_final: 0.7049 (mmmm) REVERT: H 207 ARG cc_start: 0.8059 (ptp-170) cc_final: 0.7784 (ptp90) REVERT: H 218 MET cc_start: 0.6887 (mpp) cc_final: 0.6650 (mpp) REVERT: H 241 THR cc_start: 0.7780 (m) cc_final: 0.7360 (t) REVERT: H 246 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6226 (mt-10) REVERT: H 248 ASP cc_start: 0.6401 (m-30) cc_final: 0.6016 (m-30) REVERT: H 275 GLN cc_start: 0.6379 (mt0) cc_final: 0.6164 (mt0) REVERT: H 279 LYS cc_start: 0.7564 (tptt) cc_final: 0.7219 (tptt) REVERT: H 299 ASP cc_start: 0.7795 (t0) cc_final: 0.7564 (t0) REVERT: H 305 ASP cc_start: 0.7132 (p0) cc_final: 0.6749 (p0) REVERT: H 336 ARG cc_start: 0.7417 (mtp180) cc_final: 0.7116 (ttt-90) REVERT: H 352 ASP cc_start: 0.6974 (m-30) cc_final: 0.6592 (m-30) REVERT: H 365 LYS cc_start: 0.7738 (tttt) cc_final: 0.7462 (tttt) REVERT: H 376 GLU cc_start: 0.7110 (tt0) cc_final: 0.6784 (tt0) REVERT: H 392 ARG cc_start: 0.7747 (ttt180) cc_final: 0.7476 (ttt180) REVERT: H 413 CYS cc_start: 0.7774 (t) cc_final: 0.7472 (p) REVERT: H 420 GLU cc_start: 0.6896 (tt0) cc_final: 0.6529 (tt0) REVERT: H 427 LYS cc_start: 0.7968 (mmtm) cc_final: 0.7682 (mmtm) REVERT: H 443 MET cc_start: 0.7062 (ttp) cc_final: 0.6797 (ttm) REVERT: H 444 LYS cc_start: 0.6997 (ttpt) cc_final: 0.6680 (ttpt) REVERT: I 110 GLU cc_start: 0.7476 (tp30) cc_final: 0.7159 (tp30) REVERT: I 125 LYS cc_start: 0.8518 (ttmt) cc_final: 0.8232 (ttpp) REVERT: I 173 ASP cc_start: 0.7416 (t70) cc_final: 0.6976 (t0) REVERT: I 175 SER cc_start: 0.8676 (m) cc_final: 0.8433 (p) REVERT: I 203 GLN cc_start: 0.8215 (pt0) cc_final: 0.8013 (pt0) REVERT: I 234 ILE cc_start: 0.8288 (pt) cc_final: 0.7429 (pt) REVERT: I 247 ASN cc_start: 0.7668 (m-40) cc_final: 0.7380 (m-40) REVERT: I 260 MET cc_start: 0.6001 (mtt) cc_final: 0.5697 (mtt) REVERT: I 262 GLN cc_start: 0.6918 (tt0) cc_final: 0.6515 (tt0) REVERT: I 281 LYS cc_start: 0.7505 (mttt) cc_final: 0.7261 (mttt) REVERT: I 308 ASP cc_start: 0.7061 (p0) cc_final: 0.6806 (p0) REVERT: I 313 THR cc_start: 0.7251 (m) cc_final: 0.7008 (p) REVERT: I 315 LEU cc_start: 0.7899 (mt) cc_final: 0.7658 (mt) REVERT: I 332 ASN cc_start: 0.8062 (p0) cc_final: 0.7823 (p0) REVERT: I 341 THR cc_start: 0.7558 (m) cc_final: 0.7078 (p) REVERT: I 357 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7595 (mtt90) REVERT: I 362 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7654 (ttp-110) REVERT: I 371 MET cc_start: 0.7065 (mtt) cc_final: 0.6813 (mtp) REVERT: I 389 GLU cc_start: 0.7672 (pt0) cc_final: 0.7371 (pt0) REVERT: I 391 LEU cc_start: 0.7743 (tp) cc_final: 0.7512 (tp) REVERT: I 396 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7169 (mt-10) REVERT: I 418 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7466 (mtpt) REVERT: J 50 LEU cc_start: 0.8033 (mt) cc_final: 0.7796 (mm) REVERT: J 100 PHE cc_start: 0.7966 (t80) cc_final: 0.7646 (t80) REVERT: J 134 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6271 (mt-10) REVERT: J 274 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7495 (mt-10) REVERT: J 368 LYS cc_start: 0.7988 (ttmt) cc_final: 0.7590 (ttmm) REVERT: J 377 GLU cc_start: 0.6978 (tp30) cc_final: 0.6646 (tp30) REVERT: J 405 LEU cc_start: 0.8289 (mt) cc_final: 0.8087 (mp) REVERT: J 427 LYS cc_start: 0.8046 (mmtp) cc_final: 0.7791 (mmtp) REVERT: J 436 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6948 (tm-30) REVERT: J 441 GLN cc_start: 0.7342 (mm110) cc_final: 0.7136 (mm110) REVERT: K 119 MET cc_start: 0.2505 (mtp) cc_final: 0.2301 (mtp) REVERT: K 140 LEU cc_start: 0.7441 (mt) cc_final: 0.7136 (mt) REVERT: K 153 MET cc_start: -0.0169 (tmm) cc_final: -0.0904 (tmm) REVERT: K 283 MET cc_start: 0.3739 (mmm) cc_final: 0.3359 (mmm) REVERT: K 355 MET cc_start: 0.5079 (mtp) cc_final: 0.4816 (mtp) REVERT: L 143 TYR cc_start: 0.8102 (m-10) cc_final: 0.7810 (m-10) REVERT: L 166 TYR cc_start: 0.8214 (t80) cc_final: 0.7579 (t80) REVERT: L 167 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7356 (mm-30) REVERT: L 300 SER cc_start: 0.8394 (p) cc_final: 0.8191 (m) REVERT: L 312 ARG cc_start: 0.8615 (tpt90) cc_final: 0.8310 (tpt-90) REVERT: L 328 LYS cc_start: 0.8258 (ttpt) cc_final: 0.7806 (ttpt) REVERT: L 344 SER cc_start: 0.8154 (m) cc_final: 0.7947 (p) REVERT: M 30 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8067 (mm-30) REVERT: M 31 ASP cc_start: 0.7098 (p0) cc_final: 0.6649 (p0) REVERT: M 67 THR cc_start: 0.8654 (m) cc_final: 0.8093 (p) REVERT: M 92 MET cc_start: 0.7702 (mtm) cc_final: 0.7445 (mtm) REVERT: M 128 ASN cc_start: 0.8182 (t0) cc_final: 0.7968 (t0) REVERT: M 134 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7341 (mt-10) REVERT: M 135 LYS cc_start: 0.8625 (tptt) cc_final: 0.8356 (tptt) REVERT: M 138 GLU cc_start: 0.7958 (tt0) cc_final: 0.7570 (tt0) REVERT: M 142 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7892 (mm-30) REVERT: M 202 ILE cc_start: 0.8556 (mm) cc_final: 0.8247 (mt) REVERT: M 226 LYS cc_start: 0.8633 (pttt) cc_final: 0.8005 (ptpt) REVERT: M 227 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7538 (mm-30) REVERT: M 231 GLU cc_start: 0.7506 (pm20) cc_final: 0.7283 (pm20) REVERT: M 238 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8063 (mmtt) REVERT: M 252 ASN cc_start: 0.8258 (m-40) cc_final: 0.7991 (m110) REVERT: M 260 GLN cc_start: 0.8270 (mt0) cc_final: 0.7977 (mt0) REVERT: M 268 GLN cc_start: 0.8468 (tt0) cc_final: 0.8243 (tt0) REVERT: M 285 VAL cc_start: 0.8058 (t) cc_final: 0.7856 (p) REVERT: M 287 TYR cc_start: 0.8344 (t80) cc_final: 0.7997 (t80) REVERT: M 289 PHE cc_start: 0.8179 (m-80) cc_final: 0.7976 (m-80) REVERT: M 296 ASP cc_start: 0.7567 (m-30) cc_final: 0.7313 (m-30) REVERT: M 303 LYS cc_start: 0.8642 (tttp) cc_final: 0.8285 (mtpp) REVERT: M 322 MET cc_start: 0.7522 (mtm) cc_final: 0.7079 (mtm) REVERT: M 347 SER cc_start: 0.7712 (t) cc_final: 0.7180 (p) REVERT: M 348 VAL cc_start: 0.8481 (t) cc_final: 0.8158 (p) REVERT: M 358 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7649 (mm-40) REVERT: M 407 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8058 (mm-40) REVERT: M 416 TYR cc_start: 0.8133 (t80) cc_final: 0.7750 (t80) REVERT: N 62 TYR cc_start: 0.8837 (p90) cc_final: 0.8202 (p90) REVERT: N 91 LYS cc_start: 0.7769 (ptmm) cc_final: 0.7475 (ptmm) REVERT: N 96 LYS cc_start: 0.8343 (tttt) cc_final: 0.7974 (mtpp) REVERT: N 130 ASN cc_start: 0.8321 (t0) cc_final: 0.8051 (t0) REVERT: N 189 GLU cc_start: 0.8263 (mp0) cc_final: 0.8055 (mp0) REVERT: N 191 LEU cc_start: 0.8020 (mt) cc_final: 0.7793 (mm) REVERT: N 192 LYS cc_start: 0.8011 (mttt) cc_final: 0.7750 (mttt) REVERT: N 193 GLU cc_start: 0.7711 (tp30) cc_final: 0.7431 (tp30) REVERT: N 196 TYR cc_start: 0.7841 (m-80) cc_final: 0.7480 (m-80) REVERT: N 202 LEU cc_start: 0.8545 (mt) cc_final: 0.8201 (mt) REVERT: N 228 GLU cc_start: 0.8539 (tp30) cc_final: 0.7868 (tp30) REVERT: N 232 ARG cc_start: 0.8295 (mtp85) cc_final: 0.7813 (ttm170) outliers start: 0 outliers final: 0 residues processed: 1549 average time/residue: 0.2500 time to fit residues: 595.4222 Evaluate side-chains 1363 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1363 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 432 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 50.0000 chunk 455 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 6.9990 chunk 494 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 863 GLN A1330 ASN A1425 HIS A1471 GLN E 316 HIS G 408 GLN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 GLN H 221 GLN H 233 GLN I 305 HIS I 316 HIS I 385 ASN I 408 GLN J 44 GLN J 275 GLN J 302 HIS ** L 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 353 GLN L 354 GLN M 110 HIS M 256 ASN M 327 HIS M 384 ASN ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.175407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142653 restraints weight = 66304.807| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.67 r_work: 0.3497 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41572 Z= 0.139 Angle : 0.562 7.828 56164 Z= 0.284 Chirality : 0.042 0.215 6364 Planarity : 0.004 0.062 7187 Dihedral : 6.926 151.321 5717 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.61 % Allowed : 8.37 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.82 (0.12), residues: 5082 helix: 1.62 (0.11), residues: 2321 sheet: 0.73 (0.18), residues: 821 loop : 1.14 (0.15), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1182 TYR 0.019 0.001 TYR I 314 PHE 0.015 0.001 PHE A1833 TRP 0.023 0.002 TRP A1185 HIS 0.007 0.001 HIS N 113 Details of bonding type rmsd covalent geometry : bond 0.00303 (41572) covalent geometry : angle 0.56163 (56164) hydrogen bonds : bond 0.04253 ( 1947) hydrogen bonds : angle 4.58310 ( 5517) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1457 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1386 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7638 (mtp180) REVERT: A 796 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7425 (tp-100) REVERT: A 819 MET cc_start: 0.7879 (tmm) cc_final: 0.7505 (tmm) REVERT: A 838 LYS cc_start: 0.8398 (tttt) cc_final: 0.7892 (ttpt) REVERT: A 851 LYS cc_start: 0.8232 (tttt) cc_final: 0.7918 (mtpt) REVERT: A 861 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7373 (mt-10) REVERT: A 862 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7801 (mm-30) REVERT: A 863 GLN cc_start: 0.7612 (tt0) cc_final: 0.7162 (tp-100) REVERT: A 864 SER cc_start: 0.7551 (m) cc_final: 0.7299 (t) REVERT: A 865 ARG cc_start: 0.7992 (ttt180) cc_final: 0.7771 (ttt180) REVERT: A 889 GLU cc_start: 0.8699 (tt0) cc_final: 0.8420 (tm-30) REVERT: A 1169 LEU cc_start: 0.6846 (tp) cc_final: 0.6620 (tp) REVERT: A 1192 HIS cc_start: 0.6963 (m170) cc_final: 0.6467 (m90) REVERT: A 1242 GLN cc_start: 0.3060 (pt0) cc_final: 0.1729 (pt0) REVERT: A 1254 THR cc_start: 0.6000 (p) cc_final: 0.5458 (m) REVERT: A 1261 MET cc_start: 0.3360 (mmp) cc_final: 0.2908 (mmp) REVERT: A 1325 LYS cc_start: 0.7866 (tttt) cc_final: 0.7418 (mmmm) REVERT: A 1331 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7711 (mmm160) REVERT: A 1336 TYR cc_start: 0.8214 (t80) cc_final: 0.7942 (t80) REVERT: A 1363 ARG cc_start: 0.8060 (ttt180) cc_final: 0.7545 (mtp85) REVERT: A 1369 ASN cc_start: 0.7516 (m-40) cc_final: 0.7301 (m-40) REVERT: A 1392 SER cc_start: 0.8030 (OUTLIER) cc_final: 0.7768 (m) REVERT: A 1428 GLU cc_start: 0.6862 (tp30) cc_final: 0.6580 (tp30) REVERT: A 1433 LYS cc_start: 0.7790 (mttt) cc_final: 0.7354 (mtmt) REVERT: A 1442 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7232 (mt-10) REVERT: A 1464 PHE cc_start: 0.8637 (m-80) cc_final: 0.8353 (m-80) REVERT: A 1472 LYS cc_start: 0.7860 (mmtp) cc_final: 0.7399 (mmtp) REVERT: A 1758 GLU cc_start: 0.8019 (tt0) cc_final: 0.7709 (mt-10) REVERT: A 1762 SER cc_start: 0.7265 (t) cc_final: 0.7044 (p) REVERT: A 1769 ARG cc_start: 0.7683 (mtp-110) cc_final: 0.7223 (mtm110) REVERT: A 1773 ARG cc_start: 0.7341 (mmm160) cc_final: 0.6978 (mmm160) REVERT: A 1774 ILE cc_start: 0.8465 (tp) cc_final: 0.8239 (tp) REVERT: A 1859 ARG cc_start: 0.7089 (mtm110) cc_final: 0.6791 (mtm110) REVERT: A 1909 LYS cc_start: 0.7657 (tttt) cc_final: 0.7321 (ttmm) REVERT: A 1911 LYS cc_start: 0.8202 (tttt) cc_final: 0.7909 (tptp) REVERT: A 1916 ARG cc_start: 0.7470 (mtp180) cc_final: 0.7150 (mtp85) REVERT: A 1921 SER cc_start: 0.6726 (t) cc_final: 0.6218 (p) REVERT: A 1926 MET cc_start: 0.8105 (tpp) cc_final: 0.7743 (tpt) REVERT: A 1953 ARG cc_start: 0.7469 (mtm180) cc_final: 0.6938 (mtt180) REVERT: A 1958 ARG cc_start: 0.7699 (mtt180) cc_final: 0.7311 (mtt180) REVERT: A 1974 HIS cc_start: 0.7850 (m-70) cc_final: 0.7613 (m-70) REVERT: A 1996 ASN cc_start: 0.7699 (t0) cc_final: 0.7482 (t0) REVERT: A 2000 ASP cc_start: 0.7856 (t70) cc_final: 0.7339 (t0) REVERT: A 2206 GLU cc_start: 0.7269 (tt0) cc_final: 0.6597 (tm-30) REVERT: A 2260 ILE cc_start: 0.8239 (mt) cc_final: 0.8006 (mm) REVERT: A 2263 ASP cc_start: 0.8244 (t0) cc_final: 0.7752 (t0) REVERT: A 2265 VAL cc_start: 0.8202 (t) cc_final: 0.7770 (m) REVERT: A 2266 MET cc_start: 0.7251 (ttp) cc_final: 0.6931 (ttp) REVERT: B 277 TRP cc_start: 0.8155 (m100) cc_final: 0.7594 (m100) REVERT: B 294 VAL cc_start: 0.8891 (t) cc_final: 0.8688 (m) REVERT: B 318 ILE cc_start: 0.8163 (mt) cc_final: 0.7946 (mm) REVERT: E 14 ARG cc_start: 0.7966 (mtp180) cc_final: 0.7525 (mtp180) REVERT: E 15 ILE cc_start: 0.8430 (mm) cc_final: 0.8225 (mt) REVERT: E 90 LYS cc_start: 0.7712 (mmtp) cc_final: 0.7374 (mmtp) REVERT: E 96 MET cc_start: 0.7378 (ttp) cc_final: 0.7026 (ttp) REVERT: E 104 THR cc_start: 0.7691 (t) cc_final: 0.7472 (p) REVERT: E 114 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6951 (mt-10) REVERT: E 115 ASN cc_start: 0.7819 (m-40) cc_final: 0.7605 (m110) REVERT: E 123 ARG cc_start: 0.7347 (mtp180) cc_final: 0.7070 (tpp80) REVERT: E 127 THR cc_start: 0.7868 (p) cc_final: 0.7622 (p) REVERT: E 134 GLU cc_start: 0.7594 (tt0) cc_final: 0.6987 (tt0) REVERT: E 161 LEU cc_start: 0.8523 (mt) cc_final: 0.8055 (mt) REVERT: E 194 GLU cc_start: 0.7216 (tt0) cc_final: 0.6947 (tm-30) REVERT: E 206 CYS cc_start: 0.8210 (t) cc_final: 0.7939 (t) REVERT: E 236 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7107 (mm-40) REVERT: E 262 GLN cc_start: 0.6701 (mt0) cc_final: 0.6470 (mt0) REVERT: E 264 MET cc_start: 0.6481 (mmm) cc_final: 0.6112 (mmm) REVERT: E 274 LYS cc_start: 0.7046 (tttm) cc_final: 0.6719 (ttmm) REVERT: E 317 ARG cc_start: 0.7187 (ttt-90) cc_final: 0.6862 (ttt180) REVERT: E 332 ASN cc_start: 0.7813 (p0) cc_final: 0.7507 (p0) REVERT: E 336 CYS cc_start: 0.6772 (p) cc_final: 0.6457 (p) REVERT: E 337 VAL cc_start: 0.7414 (t) cc_final: 0.7005 (m) REVERT: E 356 ASP cc_start: 0.6855 (t70) cc_final: 0.6634 (t0) REVERT: E 372 LYS cc_start: 0.7484 (mtpp) cc_final: 0.7233 (mttp) REVERT: E 388 GLU cc_start: 0.7629 (tt0) cc_final: 0.7299 (tt0) REVERT: E 393 HIS cc_start: 0.7531 (t-90) cc_final: 0.7257 (t70) REVERT: E 396 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6445 (tm-30) REVERT: E 418 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7631 (ttmm) REVERT: E 438 TYR cc_start: 0.6754 (m-80) cc_final: 0.6365 (m-80) REVERT: E 439 ASP cc_start: 0.6784 (p0) cc_final: 0.6583 (p0) REVERT: E 441 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7301 (mtmm) REVERT: F 20 GLU cc_start: 0.7099 (mp0) cc_final: 0.6726 (mp0) REVERT: F 22 ILE cc_start: 0.8009 (mt) cc_final: 0.7695 (mt) REVERT: F 65 GLU cc_start: 0.7162 (mm-30) cc_final: 0.6896 (mm-30) REVERT: F 67 LYS cc_start: 0.8196 (mttt) cc_final: 0.7917 (mttt) REVERT: F 71 ARG cc_start: 0.7675 (mmm-85) cc_final: 0.7342 (mmm160) REVERT: F 88 MET cc_start: 0.7352 (mmp) cc_final: 0.7138 (mmt) REVERT: F 90 MET cc_start: 0.7680 (mtp) cc_final: 0.7413 (mtp) REVERT: F 115 LYS cc_start: 0.7562 (mtmm) cc_final: 0.7128 (mttp) REVERT: F 125 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.7011 (ttm110) REVERT: F 136 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6989 (mm-30) REVERT: F 148 ASP cc_start: 0.7526 (t0) cc_final: 0.7125 (t0) REVERT: F 192 VAL cc_start: 0.8010 (t) cc_final: 0.7772 (p) REVERT: F 231 GLU cc_start: 0.7521 (mp0) cc_final: 0.7270 (mp0) REVERT: F 232 LEU cc_start: 0.8098 (mt) cc_final: 0.7686 (mp) REVERT: F 254 THR cc_start: 0.7403 (m) cc_final: 0.7013 (t) REVERT: F 261 PHE cc_start: 0.7542 (m-80) cc_final: 0.7181 (m-80) REVERT: F 264 ASP cc_start: 0.7005 (t0) cc_final: 0.6451 (t0) REVERT: F 269 LYS cc_start: 0.7257 (mptt) cc_final: 0.6895 (mttt) REVERT: F 307 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: F 313 ASN cc_start: 0.7812 (m-40) cc_final: 0.7426 (m-40) REVERT: F 314 ARG cc_start: 0.7563 (tpt90) cc_final: 0.7213 (tpt90) REVERT: F 336 ARG cc_start: 0.8099 (mmm160) cc_final: 0.7873 (mtp85) REVERT: F 349 ASP cc_start: 0.7237 (p0) cc_final: 0.7003 (p0) REVERT: F 353 ARG cc_start: 0.6882 (mtt90) cc_final: 0.6541 (mtt90) REVERT: F 379 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6873 (m-30) REVERT: F 411 LEU cc_start: 0.7604 (mt) cc_final: 0.7382 (mm) REVERT: F 414 ARG cc_start: 0.7072 (mtm-85) cc_final: 0.6813 (mtm-85) REVERT: F 415 LYS cc_start: 0.8049 (tptt) cc_final: 0.7825 (tptt) REVERT: F 420 GLU cc_start: 0.6865 (tt0) cc_final: 0.6482 (tt0) REVERT: F 427 LYS cc_start: 0.7730 (mmmt) cc_final: 0.7450 (mmmt) REVERT: G 15 ILE cc_start: 0.8024 (mt) cc_final: 0.7769 (mm) REVERT: G 17 SER cc_start: 0.7722 (p) cc_final: 0.7238 (m) REVERT: G 42 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7482 (mm-40) REVERT: G 54 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7004 (mm-30) REVERT: G 57 LYS cc_start: 0.7877 (mttt) cc_final: 0.7613 (mtmm) REVERT: G 61 MET cc_start: 0.7728 (mmm) cc_final: 0.7251 (mmm) REVERT: G 97 VAL cc_start: 0.7944 (p) cc_final: 0.7609 (m) REVERT: G 107 LYS cc_start: 0.7994 (pttt) cc_final: 0.7652 (ptmt) REVERT: G 110 GLU cc_start: 0.7099 (tp30) cc_final: 0.6605 (tp30) REVERT: G 113 MET cc_start: 0.7083 (tpp) cc_final: 0.6848 (tpp) REVERT: G 116 PHE cc_start: 0.8130 (m-80) cc_final: 0.7796 (m-80) REVERT: G 118 ARG cc_start: 0.7629 (mtt-85) cc_final: 0.7353 (mtt-85) REVERT: G 123 ARG cc_start: 0.7816 (ttt90) cc_final: 0.7300 (mtp85) REVERT: G 128 LYS cc_start: 0.7188 (tppt) cc_final: 0.6931 (mppt) REVERT: G 167 THR cc_start: 0.8019 (m) cc_final: 0.7763 (p) REVERT: G 189 ASP cc_start: 0.7065 (m-30) cc_final: 0.6741 (m-30) REVERT: G 201 LYS cc_start: 0.8040 (mttt) cc_final: 0.7741 (mttt) REVERT: G 242 ASP cc_start: 0.7443 (m-30) cc_final: 0.7210 (m-30) REVERT: G 260 MET cc_start: 0.4506 (tmm) cc_final: 0.4254 (tmm) REVERT: G 264 MET cc_start: 0.5095 (mmm) cc_final: 0.4548 (mmm) REVERT: G 270 GLU cc_start: 0.6487 (mt-10) cc_final: 0.6155 (mt-10) REVERT: G 278 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6986 (mm-30) REVERT: G 280 ASN cc_start: 0.7914 (m-40) cc_final: 0.7487 (m-40) REVERT: G 282 VAL cc_start: 0.7964 (t) cc_final: 0.7690 (p) REVERT: G 303 GLU cc_start: 0.6551 (mp0) cc_final: 0.6312 (mp0) REVERT: G 314 TYR cc_start: 0.8213 (t80) cc_final: 0.7880 (t80) REVERT: G 322 SER cc_start: 0.8094 (p) cc_final: 0.7669 (m) REVERT: G 396 GLU cc_start: 0.6251 (mm-30) cc_final: 0.5744 (mm-30) REVERT: H 46 MET cc_start: 0.7822 (mmm) cc_final: 0.7330 (mmm) REVERT: H 61 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7061 (mm-30) REVERT: H 129 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7366 (t) REVERT: H 130 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7661 (ttp80) REVERT: H 139 GLU cc_start: 0.7537 (pt0) cc_final: 0.7170 (pt0) REVERT: H 178 MET cc_start: 0.7648 (mmm) cc_final: 0.7374 (tpp) REVERT: H 207 ARG cc_start: 0.8154 (ptp-170) cc_final: 0.7847 (ptp90) REVERT: H 241 THR cc_start: 0.7730 (m) cc_final: 0.7363 (t) REVERT: H 275 GLN cc_start: 0.6468 (mt0) cc_final: 0.6254 (mt0) REVERT: H 279 LYS cc_start: 0.7570 (tptt) cc_final: 0.7252 (tptt) REVERT: H 300 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6628 (mm-30) REVERT: H 305 ASP cc_start: 0.7403 (p0) cc_final: 0.7130 (p0) REVERT: H 314 ARG cc_start: 0.7034 (mmm160) cc_final: 0.6725 (tpt170) REVERT: H 352 ASP cc_start: 0.7011 (m-30) cc_final: 0.6665 (m-30) REVERT: H 365 LYS cc_start: 0.7762 (tttt) cc_final: 0.7539 (tttt) REVERT: H 376 GLU cc_start: 0.7250 (tt0) cc_final: 0.6891 (tt0) REVERT: H 379 ASP cc_start: 0.7711 (t0) cc_final: 0.7422 (m-30) REVERT: H 392 ARG cc_start: 0.7877 (ttt180) cc_final: 0.7606 (ttt180) REVERT: H 413 CYS cc_start: 0.7765 (t) cc_final: 0.7465 (p) REVERT: H 420 GLU cc_start: 0.6993 (tt0) cc_final: 0.6763 (tt0) REVERT: H 427 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7552 (mmtm) REVERT: H 443 MET cc_start: 0.6912 (ttp) cc_final: 0.6651 (ttm) REVERT: H 444 LYS cc_start: 0.7134 (ttpt) cc_final: 0.6813 (ttpt) REVERT: I 54 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7351 (mm-30) REVERT: I 61 MET cc_start: 0.7827 (mmt) cc_final: 0.7621 (mmt) REVERT: I 182 LYS cc_start: 0.7581 (mttm) cc_final: 0.7362 (mttm) REVERT: I 202 ARG cc_start: 0.7951 (ttt-90) cc_final: 0.7282 (ttt-90) REVERT: I 231 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7513 (mmmt) REVERT: I 247 ASN cc_start: 0.7460 (m-40) cc_final: 0.7145 (m-40) REVERT: I 260 MET cc_start: 0.5865 (mtt) cc_final: 0.5555 (mtt) REVERT: I 276 ARG cc_start: 0.7117 (mtt-85) cc_final: 0.6889 (mtt-85) REVERT: I 281 LYS cc_start: 0.7332 (mttt) cc_final: 0.7124 (mttt) REVERT: I 317 ARG cc_start: 0.6691 (ttt-90) cc_final: 0.6463 (ttt-90) REVERT: I 341 THR cc_start: 0.7562 (m) cc_final: 0.7166 (p) REVERT: I 376 LYS cc_start: 0.7684 (tptt) cc_final: 0.7353 (tppt) REVERT: I 396 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6941 (mt-10) REVERT: I 399 THR cc_start: 0.7912 (m) cc_final: 0.7371 (p) REVERT: I 404 ARG cc_start: 0.6904 (mtm-85) cc_final: 0.6571 (mtm-85) REVERT: I 418 LYS cc_start: 0.7760 (mtpt) cc_final: 0.7481 (mtpp) REVERT: I 427 LYS cc_start: 0.7632 (tttt) cc_final: 0.7387 (ttmm) REVERT: J 92 GLN cc_start: 0.7356 (mm110) cc_final: 0.7076 (mm110) REVERT: J 107 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7167 (mt-10) REVERT: J 274 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7298 (mt-10) REVERT: J 368 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7460 (ttmm) REVERT: J 377 GLU cc_start: 0.6745 (tp30) cc_final: 0.6344 (tp30) REVERT: J 384 GLU cc_start: 0.7325 (mm-30) cc_final: 0.6839 (mm-30) REVERT: J 404 GLN cc_start: 0.7666 (mt0) cc_final: 0.7447 (mt0) REVERT: J 427 LYS cc_start: 0.7911 (mmtp) cc_final: 0.7638 (mmtp) REVERT: J 436 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6896 (tm-30) REVERT: K 119 MET cc_start: 0.5852 (mtp) cc_final: 0.5553 (mtp) REVERT: K 140 LEU cc_start: 0.7551 (mt) cc_final: 0.7345 (mt) REVERT: K 153 MET cc_start: -0.0423 (tmm) cc_final: -0.1006 (tmm) REVERT: K 190 MET cc_start: -0.2489 (mtm) cc_final: -0.2889 (ptm) REVERT: K 283 MET cc_start: 0.3787 (mmm) cc_final: 0.3321 (mmm) REVERT: L 57 GLU cc_start: 0.7385 (tp30) cc_final: 0.6414 (tp30) REVERT: L 61 LYS cc_start: 0.8317 (mtmt) cc_final: 0.7436 (mtmt) REVERT: L 100 GLU cc_start: 0.7671 (tt0) cc_final: 0.7445 (tt0) REVERT: L 166 TYR cc_start: 0.8170 (t80) cc_final: 0.7693 (t80) REVERT: L 167 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7046 (mm-30) REVERT: L 253 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7945 (mp0) REVERT: L 259 GLU cc_start: 0.7316 (tp30) cc_final: 0.7054 (tp30) REVERT: L 312 ARG cc_start: 0.8795 (tpt90) cc_final: 0.8535 (tpt-90) REVERT: L 329 ILE cc_start: 0.8705 (tp) cc_final: 0.8497 (tp) REVERT: M 30 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7464 (mm-30) REVERT: M 31 ASP cc_start: 0.6576 (p0) cc_final: 0.6203 (p0) REVERT: M 67 THR cc_start: 0.8581 (m) cc_final: 0.8037 (p) REVERT: M 71 ASP cc_start: 0.6035 (p0) cc_final: 0.5788 (p0) REVERT: M 130 ARG cc_start: 0.7636 (ttm110) cc_final: 0.7276 (ttm170) REVERT: M 134 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7180 (mt-10) REVERT: M 138 GLU cc_start: 0.7541 (tt0) cc_final: 0.7223 (tt0) REVERT: M 189 GLN cc_start: 0.8154 (mt0) cc_final: 0.7944 (mt0) REVERT: M 200 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7528 (t0) REVERT: M 205 GLN cc_start: 0.7931 (mm110) cc_final: 0.7636 (mm110) REVERT: M 226 LYS cc_start: 0.8523 (pttt) cc_final: 0.7919 (pttt) REVERT: M 227 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7338 (mm-30) REVERT: M 238 LYS cc_start: 0.8434 (mmtt) cc_final: 0.8079 (mmtt) REVERT: M 252 ASN cc_start: 0.8287 (m-40) cc_final: 0.7924 (m110) REVERT: M 256 ASN cc_start: 0.8339 (m-40) cc_final: 0.7958 (m110) REVERT: M 260 GLN cc_start: 0.8112 (mt0) cc_final: 0.7730 (mt0) REVERT: M 276 GLU cc_start: 0.7358 (tp30) cc_final: 0.7046 (tp30) REVERT: M 300 GLU cc_start: 0.7471 (mp0) cc_final: 0.7257 (mp0) REVERT: M 301 ARG cc_start: 0.8095 (ptm-80) cc_final: 0.7805 (ptm-80) REVERT: M 303 LYS cc_start: 0.8553 (tttp) cc_final: 0.8188 (mtpp) REVERT: M 308 LEU cc_start: 0.8537 (mm) cc_final: 0.8280 (mt) REVERT: M 322 MET cc_start: 0.7254 (mtm) cc_final: 0.6904 (mtm) REVERT: M 341 ARG cc_start: 0.7971 (mtt180) cc_final: 0.7718 (mtt180) REVERT: M 347 SER cc_start: 0.7809 (t) cc_final: 0.7181 (p) REVERT: M 358 GLN cc_start: 0.7973 (mm-40) cc_final: 0.7670 (mm-40) REVERT: M 416 TYR cc_start: 0.8042 (t80) cc_final: 0.7493 (t80) REVERT: N 62 TYR cc_start: 0.8665 (p90) cc_final: 0.8173 (p90) REVERT: N 66 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7878 (mtmt) REVERT: N 91 LYS cc_start: 0.7727 (ptmm) cc_final: 0.7385 (ptmm) REVERT: N 96 LYS cc_start: 0.8245 (tttt) cc_final: 0.7907 (ttpp) REVERT: N 189 GLU cc_start: 0.8101 (mp0) cc_final: 0.7875 (mp0) REVERT: N 192 LYS cc_start: 0.7865 (mttt) cc_final: 0.7626 (mttt) REVERT: N 193 GLU cc_start: 0.7465 (tp30) cc_final: 0.7135 (tp30) REVERT: N 196 TYR cc_start: 0.7890 (m-80) cc_final: 0.7484 (m-10) REVERT: N 202 LEU cc_start: 0.8638 (mt) cc_final: 0.8312 (mt) REVERT: N 224 ARG cc_start: 0.8212 (mtt90) cc_final: 0.7954 (mtt90) REVERT: N 228 GLU cc_start: 0.8356 (tp30) cc_final: 0.7243 (tp30) REVERT: N 231 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7500 (mt-10) REVERT: N 232 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7674 (ttm170) REVERT: N 233 LEU cc_start: 0.7754 (mm) cc_final: 0.7357 (mm) outliers start: 71 outliers final: 40 residues processed: 1405 average time/residue: 0.2419 time to fit residues: 520.6278 Evaluate side-chains 1375 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 1328 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1392 SER Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 2099 ILE Chi-restraints excluded: chain A residue 2224 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 441 LYS Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 231 LYS Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 406 SER Chi-restraints excluded: chain J residue 132 LYS Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 155 SER Chi-restraints excluded: chain L residue 177 ARG Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 152 CYS Chi-restraints excluded: chain M residue 200 ASP Chi-restraints excluded: chain M residue 282 MET Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 163 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 180 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 444 optimal weight: 4.9990 chunk 283 optimal weight: 0.9990 chunk 501 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 488 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 420 optimal weight: 0.6980 chunk 320 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN G 115 ASN G 203 GLN H 121 GLN I 332 ASN I 385 ASN ** L 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 353 GLN L 354 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN M 354 ASN M 384 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.174311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141021 restraints weight = 66116.070| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.74 r_work: 0.3482 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41572 Z= 0.142 Angle : 0.549 9.177 56164 Z= 0.275 Chirality : 0.042 0.201 6364 Planarity : 0.004 0.064 7187 Dihedral : 6.728 150.936 5717 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.13 % Allowed : 11.15 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.89 (0.12), residues: 5082 helix: 1.79 (0.11), residues: 2310 sheet: 0.70 (0.18), residues: 811 loop : 1.06 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 194 TYR 0.017 0.001 TYR A1288 PHE 0.019 0.001 PHE N 183 TRP 0.014 0.001 TRP A1232 HIS 0.009 0.001 HIS M 143 Details of bonding type rmsd covalent geometry : bond 0.00311 (41572) covalent geometry : angle 0.54887 (56164) hydrogen bonds : bond 0.03994 ( 1947) hydrogen bonds : angle 4.37190 ( 5517) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1364 time to evaluate : 1.368 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: A 796 GLN cc_start: 0.7798 (tp-100) cc_final: 0.7349 (tp-100) REVERT: A 819 MET cc_start: 0.7846 (tmm) cc_final: 0.7416 (tmm) REVERT: A 838 LYS cc_start: 0.8333 (tttt) cc_final: 0.7827 (ttpp) REVERT: A 861 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7439 (mt-10) REVERT: A 862 GLU cc_start: 0.8473 (mm-30) cc_final: 0.7744 (mm-30) REVERT: A 863 GLN cc_start: 0.7658 (tt0) cc_final: 0.7190 (tp-100) REVERT: A 864 SER cc_start: 0.7610 (m) cc_final: 0.7358 (t) REVERT: A 865 ARG cc_start: 0.8028 (ttt180) cc_final: 0.7815 (ttt180) REVERT: A 867 ARG cc_start: 0.7888 (mtt180) cc_final: 0.7539 (mtt180) REVERT: A 889 GLU cc_start: 0.8768 (tt0) cc_final: 0.8540 (tm-30) REVERT: A 1192 HIS cc_start: 0.7235 (m170) cc_final: 0.6691 (m90) REVERT: A 1215 CYS cc_start: 0.7225 (t) cc_final: 0.6510 (p) REVERT: A 1242 GLN cc_start: 0.3310 (pt0) cc_final: 0.2056 (pt0) REVERT: A 1261 MET cc_start: 0.3124 (mmp) cc_final: 0.2700 (mmp) REVERT: A 1337 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7495 (mp0) REVERT: A 1362 VAL cc_start: 0.7742 (t) cc_final: 0.7428 (m) REVERT: A 1363 ARG cc_start: 0.8043 (ttt180) cc_final: 0.7545 (mmm-85) REVERT: A 1364 LEU cc_start: 0.8377 (mt) cc_final: 0.8016 (tt) REVERT: A 1390 TYR cc_start: 0.8076 (t80) cc_final: 0.7810 (t80) REVERT: A 1428 GLU cc_start: 0.6875 (tp30) cc_final: 0.6459 (tp30) REVERT: A 1433 LYS cc_start: 0.7775 (mttt) cc_final: 0.7329 (mtmt) REVERT: A 1442 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7190 (mt-10) REVERT: A 1472 LYS cc_start: 0.7727 (mmtp) cc_final: 0.7380 (mmtp) REVERT: A 1747 LYS cc_start: 0.8016 (tmtt) cc_final: 0.7460 (tmtt) REVERT: A 1751 ASP cc_start: 0.7870 (t70) cc_final: 0.7389 (m-30) REVERT: A 1758 GLU cc_start: 0.8045 (tt0) cc_final: 0.7713 (mt-10) REVERT: A 1762 SER cc_start: 0.7407 (t) cc_final: 0.7177 (p) REVERT: A 1769 ARG cc_start: 0.7710 (mtp-110) cc_final: 0.7170 (mtm180) REVERT: A 1773 ARG cc_start: 0.7372 (mmm160) cc_final: 0.6948 (mmm160) REVERT: A 1774 ILE cc_start: 0.8507 (tp) cc_final: 0.8249 (tp) REVERT: A 1859 ARG cc_start: 0.6994 (mtm110) cc_final: 0.6716 (mtm110) REVERT: A 1877 ARG cc_start: 0.6665 (tpm170) cc_final: 0.6381 (tpm170) REVERT: A 1897 SER cc_start: 0.7635 (t) cc_final: 0.7414 (t) REVERT: A 1909 LYS cc_start: 0.7695 (tttt) cc_final: 0.7368 (ttmm) REVERT: A 1911 LYS cc_start: 0.8197 (tttt) cc_final: 0.7965 (tppp) REVERT: A 1921 SER cc_start: 0.6765 (t) cc_final: 0.6301 (p) REVERT: A 1926 MET cc_start: 0.8018 (tpp) cc_final: 0.7673 (tpt) REVERT: A 1958 ARG cc_start: 0.7728 (mtt180) cc_final: 0.7348 (mtt180) REVERT: A 1974 HIS cc_start: 0.7802 (m-70) cc_final: 0.7596 (m-70) REVERT: A 1996 ASN cc_start: 0.7660 (t0) cc_final: 0.7459 (t0) REVERT: A 2000 ASP cc_start: 0.7935 (t70) cc_final: 0.7324 (t0) REVERT: A 2004 GLN cc_start: 0.7376 (mm-40) cc_final: 0.7087 (mm-40) REVERT: A 2206 GLU cc_start: 0.7282 (tt0) cc_final: 0.6618 (tm-30) REVERT: A 2260 ILE cc_start: 0.8292 (mt) cc_final: 0.8063 (mm) REVERT: A 2263 ASP cc_start: 0.8207 (t0) cc_final: 0.7821 (t0) REVERT: A 2265 VAL cc_start: 0.8192 (t) cc_final: 0.7828 (m) REVERT: A 2266 MET cc_start: 0.7218 (ttp) cc_final: 0.6980 (ttp) REVERT: A 2269 MET cc_start: 0.7119 (mmm) cc_final: 0.6842 (mmm) REVERT: B 277 TRP cc_start: 0.8166 (m100) cc_final: 0.7657 (m100) REVERT: B 294 VAL cc_start: 0.8901 (t) cc_final: 0.8682 (m) REVERT: B 318 ILE cc_start: 0.8179 (mt) cc_final: 0.7976 (mm) REVERT: C 469 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.7284 (mtm-85) REVERT: E 14 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7547 (mtp180) REVERT: E 90 LYS cc_start: 0.7712 (mmtp) cc_final: 0.7412 (mmtp) REVERT: E 101 VAL cc_start: 0.7823 (t) cc_final: 0.7529 (m) REVERT: E 104 THR cc_start: 0.7693 (t) cc_final: 0.7481 (p) REVERT: E 123 ARG cc_start: 0.7345 (mtp180) cc_final: 0.7074 (tpp80) REVERT: E 128 LYS cc_start: 0.7518 (mtpp) cc_final: 0.7261 (mtpp) REVERT: E 129 GLU cc_start: 0.6802 (pm20) cc_final: 0.6377 (pm20) REVERT: E 134 GLU cc_start: 0.7341 (tt0) cc_final: 0.6984 (tt0) REVERT: E 206 CYS cc_start: 0.8261 (t) cc_final: 0.7873 (t) REVERT: E 209 TYR cc_start: 0.7867 (m-80) cc_final: 0.7343 (m-80) REVERT: E 262 GLN cc_start: 0.6692 (mt0) cc_final: 0.6462 (mt0) REVERT: E 264 MET cc_start: 0.6484 (mmm) cc_final: 0.6092 (mmm) REVERT: E 267 LYS cc_start: 0.7010 (tttt) cc_final: 0.6722 (tmtt) REVERT: E 274 LYS cc_start: 0.6676 (tttm) cc_final: 0.6183 (tttm) REVERT: E 278 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: E 285 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7179 (ttmt) REVERT: E 317 ARG cc_start: 0.7179 (ttt-90) cc_final: 0.6907 (ttt180) REVERT: E 332 ASN cc_start: 0.7760 (p0) cc_final: 0.7504 (p0) REVERT: E 336 CYS cc_start: 0.6780 (p) cc_final: 0.6438 (p) REVERT: E 337 VAL cc_start: 0.7406 (t) cc_final: 0.7007 (m) REVERT: E 356 ASP cc_start: 0.6851 (t70) cc_final: 0.6538 (t0) REVERT: E 372 LYS cc_start: 0.7481 (mtpp) cc_final: 0.7250 (mttp) REVERT: E 388 GLU cc_start: 0.7564 (tt0) cc_final: 0.7306 (tt0) REVERT: E 393 HIS cc_start: 0.7537 (t-90) cc_final: 0.7220 (t70) REVERT: E 396 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6480 (tm-30) REVERT: E 418 LYS cc_start: 0.7886 (ttmm) cc_final: 0.7671 (ttmm) REVERT: F 20 GLU cc_start: 0.7153 (mp0) cc_final: 0.6740 (mp0) REVERT: F 22 ILE cc_start: 0.7997 (mt) cc_final: 0.7710 (mt) REVERT: F 65 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6833 (mm-30) REVERT: F 67 LYS cc_start: 0.8212 (mttt) cc_final: 0.7927 (mttt) REVERT: F 71 ARG cc_start: 0.7717 (mmm-85) cc_final: 0.7362 (mmm160) REVERT: F 74 LEU cc_start: 0.8195 (tp) cc_final: 0.7922 (tp) REVERT: F 88 MET cc_start: 0.7313 (mmp) cc_final: 0.7096 (mmt) REVERT: F 90 MET cc_start: 0.7681 (mtp) cc_final: 0.7375 (mtp) REVERT: F 115 LYS cc_start: 0.7653 (mtmm) cc_final: 0.7210 (mttp) REVERT: F 125 ARG cc_start: 0.7336 (mtm-85) cc_final: 0.7079 (ttm110) REVERT: F 136 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6970 (mm-30) REVERT: F 148 ASP cc_start: 0.7555 (t0) cc_final: 0.7162 (t70) REVERT: F 192 VAL cc_start: 0.8057 (t) cc_final: 0.7837 (p) REVERT: F 231 GLU cc_start: 0.7633 (mp0) cc_final: 0.7389 (mp0) REVERT: F 232 LEU cc_start: 0.8096 (mt) cc_final: 0.7697 (mp) REVERT: F 261 PHE cc_start: 0.7551 (m-80) cc_final: 0.7164 (m-80) REVERT: F 264 ASP cc_start: 0.7030 (t0) cc_final: 0.6437 (t0) REVERT: F 269 LYS cc_start: 0.7225 (mptt) cc_final: 0.6899 (mttt) REVERT: F 313 ASN cc_start: 0.7825 (m-40) cc_final: 0.7208 (m-40) REVERT: F 314 ARG cc_start: 0.7556 (tpt90) cc_final: 0.7102 (tpt90) REVERT: F 336 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7764 (mmm160) REVERT: F 349 ASP cc_start: 0.7228 (p0) cc_final: 0.7019 (p0) REVERT: F 411 LEU cc_start: 0.7584 (mt) cc_final: 0.7354 (mm) REVERT: F 414 ARG cc_start: 0.6939 (mtm-85) cc_final: 0.6687 (mtm-85) REVERT: F 415 LYS cc_start: 0.8022 (tptt) cc_final: 0.7797 (tptt) REVERT: F 420 GLU cc_start: 0.6806 (tt0) cc_final: 0.6378 (tt0) REVERT: F 427 LYS cc_start: 0.7654 (mmmt) cc_final: 0.7369 (mmmt) REVERT: G 17 SER cc_start: 0.7817 (p) cc_final: 0.7217 (t) REVERT: G 42 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7581 (mm-40) REVERT: G 54 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7012 (mm-30) REVERT: G 57 LYS cc_start: 0.7910 (mttt) cc_final: 0.7626 (mtmm) REVERT: G 61 MET cc_start: 0.7732 (mmm) cc_final: 0.7327 (mmm) REVERT: G 110 GLU cc_start: 0.7098 (tp30) cc_final: 0.6823 (tp30) REVERT: G 113 MET cc_start: 0.7048 (tpp) cc_final: 0.6783 (tpp) REVERT: G 116 PHE cc_start: 0.8123 (m-80) cc_final: 0.7801 (m-80) REVERT: G 123 ARG cc_start: 0.7848 (ttt90) cc_final: 0.7325 (mtp85) REVERT: G 128 LYS cc_start: 0.7493 (tppt) cc_final: 0.7198 (mppt) REVERT: G 167 THR cc_start: 0.8075 (m) cc_final: 0.7765 (p) REVERT: G 201 LYS cc_start: 0.8065 (mttt) cc_final: 0.7769 (mttt) REVERT: G 260 MET cc_start: 0.4614 (tmm) cc_final: 0.4340 (tmm) REVERT: G 264 MET cc_start: 0.5178 (mmm) cc_final: 0.4597 (mmm) REVERT: G 282 VAL cc_start: 0.7989 (t) cc_final: 0.7716 (p) REVERT: G 314 TYR cc_start: 0.8224 (t80) cc_final: 0.7869 (t80) REVERT: G 322 SER cc_start: 0.8070 (p) cc_final: 0.7701 (m) REVERT: G 396 GLU cc_start: 0.6269 (mm-30) cc_final: 0.5715 (mm-30) REVERT: G 431 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6677 (mt-10) REVERT: G 434 SER cc_start: 0.7346 (m) cc_final: 0.6764 (p) REVERT: H 61 GLU cc_start: 0.7288 (mm-30) cc_final: 0.7074 (mm-30) REVERT: H 129 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7408 (t) REVERT: H 130 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7683 (ttp80) REVERT: H 139 GLU cc_start: 0.7487 (pt0) cc_final: 0.7077 (pt0) REVERT: H 178 MET cc_start: 0.7636 (mmm) cc_final: 0.7354 (tpp) REVERT: H 182 LEU cc_start: 0.8553 (mt) cc_final: 0.8203 (mp) REVERT: H 207 ARG cc_start: 0.8131 (ptp-170) cc_final: 0.7788 (ptp90) REVERT: H 233 GLN cc_start: 0.7954 (tt0) cc_final: 0.7646 (tp40) REVERT: H 241 THR cc_start: 0.7761 (m) cc_final: 0.7420 (t) REVERT: H 267 GLU cc_start: 0.7136 (mt-10) cc_final: 0.6437 (mt-10) REVERT: H 279 LYS cc_start: 0.7701 (tptt) cc_final: 0.7389 (tptt) REVERT: H 300 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6596 (mm-30) REVERT: H 305 ASP cc_start: 0.7493 (p0) cc_final: 0.7255 (p0) REVERT: H 314 ARG cc_start: 0.7131 (mmm160) cc_final: 0.6817 (tpt170) REVERT: H 352 ASP cc_start: 0.7053 (m-30) cc_final: 0.6690 (m-30) REVERT: H 365 LYS cc_start: 0.7793 (tttt) cc_final: 0.7589 (tttt) REVERT: H 376 GLU cc_start: 0.7269 (tt0) cc_final: 0.6927 (tt0) REVERT: H 379 ASP cc_start: 0.7732 (t0) cc_final: 0.7438 (m-30) REVERT: H 392 ARG cc_start: 0.7853 (ttt180) cc_final: 0.7573 (ttt180) REVERT: H 413 CYS cc_start: 0.7747 (t) cc_final: 0.7385 (p) REVERT: H 420 GLU cc_start: 0.7044 (tt0) cc_final: 0.6806 (tt0) REVERT: H 427 LYS cc_start: 0.7787 (mmtm) cc_final: 0.7561 (mmtm) REVERT: H 436 GLU cc_start: 0.5496 (tm-30) cc_final: 0.5112 (tm-30) REVERT: H 441 GLN cc_start: 0.7649 (tt0) cc_final: 0.7413 (tt0) REVERT: H 443 MET cc_start: 0.6901 (ttp) cc_final: 0.6637 (ttm) REVERT: H 444 LYS cc_start: 0.7144 (ttpt) cc_final: 0.6805 (ttpt) REVERT: I 123 ARG cc_start: 0.7976 (mmm-85) cc_final: 0.7674 (mmm-85) REVERT: I 126 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6684 (tm-30) REVERT: I 134 GLU cc_start: 0.7045 (tt0) cc_final: 0.6505 (tm-30) REVERT: I 173 ASP cc_start: 0.7386 (t70) cc_final: 0.6969 (t0) REVERT: I 175 SER cc_start: 0.8710 (m) cc_final: 0.8429 (p) REVERT: I 189 ASP cc_start: 0.5787 (m-30) cc_final: 0.5260 (m-30) REVERT: I 202 ARG cc_start: 0.7915 (ttt-90) cc_final: 0.7520 (ttt-90) REVERT: I 231 LYS cc_start: 0.7633 (mmmm) cc_final: 0.7413 (mmmm) REVERT: I 237 ASP cc_start: 0.7280 (m-30) cc_final: 0.7045 (m-30) REVERT: I 247 ASN cc_start: 0.7415 (m-40) cc_final: 0.7079 (m-40) REVERT: I 260 MET cc_start: 0.5940 (mtt) cc_final: 0.5609 (mtt) REVERT: I 281 LYS cc_start: 0.7319 (mttt) cc_final: 0.7082 (mttt) REVERT: I 317 ARG cc_start: 0.6761 (ttt-90) cc_final: 0.6477 (ttt-90) REVERT: I 341 THR cc_start: 0.7687 (m) cc_final: 0.7388 (p) REVERT: I 356 ASP cc_start: 0.7142 (t0) cc_final: 0.6874 (t70) REVERT: I 362 ARG cc_start: 0.7717 (tmm-80) cc_final: 0.7492 (ttp-110) REVERT: I 376 LYS cc_start: 0.7667 (tptt) cc_final: 0.7332 (tppt) REVERT: I 389 GLU cc_start: 0.7632 (pt0) cc_final: 0.7325 (pt0) REVERT: I 396 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7039 (mt-10) REVERT: I 399 THR cc_start: 0.7838 (m) cc_final: 0.7393 (p) REVERT: I 418 LYS cc_start: 0.7765 (mtpt) cc_final: 0.7434 (mtpp) REVERT: I 427 LYS cc_start: 0.7611 (tttt) cc_final: 0.7338 (ttmm) REVERT: I 428 GLU cc_start: 0.7622 (mp0) cc_final: 0.7378 (pm20) REVERT: I 445 LYS cc_start: 0.7531 (mttp) cc_final: 0.7125 (tttp) REVERT: J 83 LYS cc_start: 0.7505 (mtmt) cc_final: 0.6026 (ptpt) REVERT: J 92 GLN cc_start: 0.7326 (mm110) cc_final: 0.7026 (mm110) REVERT: J 94 LEU cc_start: 0.7717 (tp) cc_final: 0.7430 (tp) REVERT: J 236 LYS cc_start: 0.8369 (mtpt) cc_final: 0.8106 (mtpt) REVERT: J 264 ASP cc_start: 0.6313 (t0) cc_final: 0.6034 (t0) REVERT: J 274 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7298 (mt-10) REVERT: J 282 GLU cc_start: 0.7370 (tp30) cc_final: 0.7030 (tp30) REVERT: J 368 LYS cc_start: 0.7856 (ttmt) cc_final: 0.7458 (ttmm) REVERT: J 377 GLU cc_start: 0.6736 (tp30) cc_final: 0.6310 (tp30) REVERT: J 384 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6831 (mm-30) REVERT: J 404 GLN cc_start: 0.7655 (mt0) cc_final: 0.7383 (mt0) REVERT: J 420 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6998 (tt0) REVERT: J 427 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7600 (mmtp) REVERT: J 436 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6819 (tm-30) REVERT: J 438 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7824 (mtp180) REVERT: K 119 MET cc_start: 0.5780 (mtp) cc_final: 0.5536 (mtp) REVERT: K 153 MET cc_start: -0.0423 (tmm) cc_final: -0.0996 (tmm) REVERT: K 190 MET cc_start: -0.2702 (mtm) cc_final: -0.2958 (ptm) REVERT: K 283 MET cc_start: 0.3782 (mmm) cc_final: 0.3289 (mmm) REVERT: L 57 GLU cc_start: 0.7460 (tp30) cc_final: 0.6576 (tp30) REVERT: L 61 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7380 (mtmt) REVERT: L 100 GLU cc_start: 0.7642 (tt0) cc_final: 0.7399 (tt0) REVERT: L 151 ILE cc_start: 0.8410 (tt) cc_final: 0.8138 (pt) REVERT: L 166 TYR cc_start: 0.8189 (t80) cc_final: 0.7642 (t80) REVERT: L 167 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7176 (mm-30) REVERT: L 300 SER cc_start: 0.8426 (p) cc_final: 0.8142 (m) REVERT: L 312 ARG cc_start: 0.8762 (tpt90) cc_final: 0.8537 (tpt-90) REVERT: L 373 LYS cc_start: 0.8085 (mttm) cc_final: 0.7645 (mttt) REVERT: M 30 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7545 (mm-30) REVERT: M 31 ASP cc_start: 0.6618 (p0) cc_final: 0.6264 (p0) REVERT: M 67 THR cc_start: 0.8625 (m) cc_final: 0.8078 (p) REVERT: M 130 ARG cc_start: 0.7710 (ttm110) cc_final: 0.7365 (ttm170) REVERT: M 134 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7163 (mt-10) REVERT: M 186 TYR cc_start: 0.7729 (m-80) cc_final: 0.7342 (m-80) REVERT: M 202 ILE cc_start: 0.8532 (mm) cc_final: 0.7826 (tp) REVERT: M 226 LYS cc_start: 0.8527 (pttt) cc_final: 0.7917 (pttt) REVERT: M 227 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7287 (mm-30) REVERT: M 238 LYS cc_start: 0.8450 (mmtt) cc_final: 0.8124 (mmtt) REVERT: M 252 ASN cc_start: 0.8244 (m-40) cc_final: 0.7903 (m110) REVERT: M 256 ASN cc_start: 0.8340 (m-40) cc_final: 0.8022 (m110) REVERT: M 260 GLN cc_start: 0.8088 (mt0) cc_final: 0.7856 (mt0) REVERT: M 294 ASN cc_start: 0.8183 (p0) cc_final: 0.7546 (p0) REVERT: M 301 ARG cc_start: 0.8153 (ptm-80) cc_final: 0.7753 (ptm-80) REVERT: M 303 LYS cc_start: 0.8531 (tttp) cc_final: 0.8157 (mtpp) REVERT: M 306 GLU cc_start: 0.8567 (tp30) cc_final: 0.8350 (tp30) REVERT: M 308 LEU cc_start: 0.8560 (mm) cc_final: 0.8256 (mt) REVERT: M 322 MET cc_start: 0.7279 (mtm) cc_final: 0.6893 (mtm) REVERT: M 347 SER cc_start: 0.7563 (t) cc_final: 0.6960 (p) REVERT: M 358 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7682 (mm-40) REVERT: M 384 ASN cc_start: 0.7922 (t0) cc_final: 0.7683 (t0) REVERT: M 416 TYR cc_start: 0.7869 (t80) cc_final: 0.7640 (t80) REVERT: N 55 ARG cc_start: 0.7921 (mtt180) cc_final: 0.7453 (mtt180) REVERT: N 57 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.8034 (t) REVERT: N 62 TYR cc_start: 0.8674 (p90) cc_final: 0.8220 (p90) REVERT: N 90 LYS cc_start: 0.8324 (mmtp) cc_final: 0.8103 (mmtt) REVERT: N 91 LYS cc_start: 0.7745 (ptmm) cc_final: 0.7400 (ptmm) REVERT: N 92 VAL cc_start: 0.8222 (m) cc_final: 0.7940 (p) REVERT: N 96 LYS cc_start: 0.8277 (tttt) cc_final: 0.7975 (ttpp) REVERT: N 190 ASP cc_start: 0.7267 (m-30) cc_final: 0.7017 (m-30) REVERT: N 192 LYS cc_start: 0.7871 (mttt) cc_final: 0.7619 (mttt) REVERT: N 193 GLU cc_start: 0.7465 (tp30) cc_final: 0.7119 (tp30) REVERT: N 196 TYR cc_start: 0.7889 (m-80) cc_final: 0.7505 (m-80) REVERT: N 202 LEU cc_start: 0.8666 (mt) cc_final: 0.8341 (mt) REVERT: N 224 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7897 (mtt90) REVERT: N 228 GLU cc_start: 0.8334 (tp30) cc_final: 0.7698 (tp30) REVERT: N 232 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7786 (ttm170) outliers start: 94 outliers final: 57 residues processed: 1391 average time/residue: 0.2495 time to fit residues: 530.8771 Evaluate side-chains 1388 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 1327 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2099 ILE Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 451 LEU Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 234 ILE Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 332 ASN Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 132 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 237 GLU Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 339 VAL Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 152 CYS Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 268 GLN Chi-restraints excluded: chain M residue 282 MET Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 188 VAL Chi-restraints excluded: chain N residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 313 optimal weight: 4.9990 chunk 339 optimal weight: 1.9990 chunk 379 optimal weight: 30.0000 chunk 291 optimal weight: 1.9990 chunk 287 optimal weight: 0.5980 chunk 340 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 307 optimal weight: 6.9990 chunk 204 optimal weight: 0.8980 chunk 251 optimal weight: 4.9990 chunk 445 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN G 115 ASN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 332 ASN I 385 ASN J 275 GLN ** L 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 353 GLN M 100 GLN M 118 HIS ** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 268 GLN M 354 ASN N 235 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.173083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140928 restraints weight = 65781.873| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.75 r_work: 0.3457 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 41572 Z= 0.193 Angle : 0.575 8.538 56164 Z= 0.289 Chirality : 0.043 0.239 6364 Planarity : 0.004 0.064 7187 Dihedral : 6.795 149.829 5717 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.55 % Allowed : 12.46 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.72 (0.12), residues: 5082 helix: 1.70 (0.11), residues: 2329 sheet: 0.52 (0.18), residues: 820 loop : 0.94 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1916 TYR 0.020 0.002 TYR A1288 PHE 0.023 0.002 PHE N 183 TRP 0.033 0.002 TRP A1155 HIS 0.009 0.001 HIS L 275 Details of bonding type rmsd covalent geometry : bond 0.00423 (41572) covalent geometry : angle 0.57520 (56164) hydrogen bonds : bond 0.04148 ( 1947) hydrogen bonds : angle 4.38105 ( 5517) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1485 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1372 time to evaluate : 1.363 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: A 796 GLN cc_start: 0.7744 (tp-100) cc_final: 0.7279 (tp-100) REVERT: A 816 LEU cc_start: 0.8265 (mt) cc_final: 0.7947 (mm) REVERT: A 838 LYS cc_start: 0.8403 (tttt) cc_final: 0.8035 (ttpp) REVERT: A 861 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7423 (mt-10) REVERT: A 862 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 863 GLN cc_start: 0.7711 (tt0) cc_final: 0.7406 (tp40) REVERT: A 864 SER cc_start: 0.7672 (m) cc_final: 0.7413 (t) REVERT: A 865 ARG cc_start: 0.8018 (ttt180) cc_final: 0.7774 (ttt180) REVERT: A 867 ARG cc_start: 0.7919 (mtt180) cc_final: 0.7599 (mtt180) REVERT: A 1192 HIS cc_start: 0.7529 (m170) cc_final: 0.7041 (m90) REVERT: A 1215 CYS cc_start: 0.7596 (t) cc_final: 0.6810 (p) REVERT: A 1242 GLN cc_start: 0.3352 (pt0) cc_final: 0.1994 (pt0) REVERT: A 1261 MET cc_start: 0.3166 (mmp) cc_final: 0.2717 (mmp) REVERT: A 1337 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7632 (mp0) REVERT: A 1363 ARG cc_start: 0.8013 (ttt180) cc_final: 0.7467 (mtp85) REVERT: A 1428 GLU cc_start: 0.6854 (tp30) cc_final: 0.6410 (tp30) REVERT: A 1433 LYS cc_start: 0.7827 (mttt) cc_final: 0.7443 (mtmt) REVERT: A 1442 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 1472 LYS cc_start: 0.7786 (mmtp) cc_final: 0.7478 (mmtp) REVERT: A 1758 GLU cc_start: 0.8025 (tt0) cc_final: 0.7692 (mt-10) REVERT: A 1762 SER cc_start: 0.7523 (t) cc_final: 0.7305 (p) REVERT: A 1769 ARG cc_start: 0.7719 (mtp-110) cc_final: 0.7138 (mtm180) REVERT: A 1770 ASP cc_start: 0.8033 (p0) cc_final: 0.7828 (p0) REVERT: A 1773 ARG cc_start: 0.7392 (mmm160) cc_final: 0.7187 (mmm160) REVERT: A 1774 ILE cc_start: 0.8543 (tp) cc_final: 0.8297 (tp) REVERT: A 1877 ARG cc_start: 0.6675 (tpm170) cc_final: 0.6355 (tpm170) REVERT: A 1897 SER cc_start: 0.7821 (t) cc_final: 0.7517 (p) REVERT: A 1901 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7248 (mm-30) REVERT: A 1909 LYS cc_start: 0.7774 (tttt) cc_final: 0.7444 (ttmm) REVERT: A 1911 LYS cc_start: 0.8186 (tttt) cc_final: 0.7970 (tppp) REVERT: A 1922 GLN cc_start: 0.6958 (pt0) cc_final: 0.6717 (mt0) REVERT: A 1953 ARG cc_start: 0.7620 (mtm180) cc_final: 0.7403 (mtm110) REVERT: A 1958 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7399 (mtt180) REVERT: A 1974 HIS cc_start: 0.7919 (m-70) cc_final: 0.7650 (m-70) REVERT: A 2000 ASP cc_start: 0.7938 (t70) cc_final: 0.7287 (t0) REVERT: A 2004 GLN cc_start: 0.7420 (mm-40) cc_final: 0.7132 (mm-40) REVERT: A 2206 GLU cc_start: 0.7279 (tt0) cc_final: 0.6655 (tm-30) REVERT: A 2260 ILE cc_start: 0.8343 (mt) cc_final: 0.8135 (mm) REVERT: A 2263 ASP cc_start: 0.8257 (t0) cc_final: 0.7883 (t0) REVERT: A 2265 VAL cc_start: 0.8205 (t) cc_final: 0.7891 (m) REVERT: A 2266 MET cc_start: 0.7280 (ttp) cc_final: 0.7071 (ttp) REVERT: B 277 TRP cc_start: 0.8226 (m100) cc_final: 0.7806 (m100) REVERT: B 294 VAL cc_start: 0.8990 (t) cc_final: 0.8743 (m) REVERT: B 318 ILE cc_start: 0.8224 (mt) cc_final: 0.8016 (mm) REVERT: E 14 ARG cc_start: 0.8018 (mtp180) cc_final: 0.7627 (mtp180) REVERT: E 90 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7460 (mmtp) REVERT: E 93 PHE cc_start: 0.8020 (t80) cc_final: 0.7551 (t80) REVERT: E 101 VAL cc_start: 0.7850 (t) cc_final: 0.7595 (m) REVERT: E 123 ARG cc_start: 0.7432 (mtp180) cc_final: 0.7078 (tpp80) REVERT: E 128 LYS cc_start: 0.7605 (mtpp) cc_final: 0.7220 (mtpp) REVERT: E 129 GLU cc_start: 0.6890 (pm20) cc_final: 0.6411 (pm20) REVERT: E 134 GLU cc_start: 0.7468 (tt0) cc_final: 0.7128 (tt0) REVERT: E 194 GLU cc_start: 0.7410 (tt0) cc_final: 0.7009 (tm-30) REVERT: E 209 TYR cc_start: 0.7858 (m-80) cc_final: 0.7402 (m-80) REVERT: E 258 SER cc_start: 0.7712 (m) cc_final: 0.7024 (p) REVERT: E 262 GLN cc_start: 0.6707 (mt0) cc_final: 0.6449 (mt0) REVERT: E 264 MET cc_start: 0.6529 (mmm) cc_final: 0.6169 (mmm) REVERT: E 265 LYS cc_start: 0.8126 (tttt) cc_final: 0.7775 (tttt) REVERT: E 274 LYS cc_start: 0.6694 (tttm) cc_final: 0.6360 (ttmm) REVERT: E 278 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6506 (mp0) REVERT: E 285 LYS cc_start: 0.7596 (OUTLIER) cc_final: 0.7218 (ttmt) REVERT: E 317 ARG cc_start: 0.7279 (ttt-90) cc_final: 0.6985 (ttt180) REVERT: E 332 ASN cc_start: 0.7781 (p0) cc_final: 0.7550 (p0) REVERT: E 336 CYS cc_start: 0.6662 (p) cc_final: 0.6331 (p) REVERT: E 337 VAL cc_start: 0.7397 (t) cc_final: 0.7005 (m) REVERT: E 356 ASP cc_start: 0.6946 (t70) cc_final: 0.6591 (t0) REVERT: E 372 LYS cc_start: 0.7430 (mtpp) cc_final: 0.7221 (mttp) REVERT: E 388 GLU cc_start: 0.7501 (tt0) cc_final: 0.7247 (tt0) REVERT: E 396 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6507 (tm-30) REVERT: E 418 LYS cc_start: 0.7936 (ttmm) cc_final: 0.7731 (ttmm) REVERT: F 20 GLU cc_start: 0.7213 (mp0) cc_final: 0.6793 (mp0) REVERT: F 65 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6843 (mm-30) REVERT: F 67 LYS cc_start: 0.8281 (mttt) cc_final: 0.7983 (mttt) REVERT: F 71 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7436 (mmm160) REVERT: F 125 ARG cc_start: 0.7323 (mtm-85) cc_final: 0.7080 (ttm110) REVERT: F 192 VAL cc_start: 0.8026 (t) cc_final: 0.7787 (p) REVERT: F 231 GLU cc_start: 0.7709 (mp0) cc_final: 0.7422 (mp0) REVERT: F 232 LEU cc_start: 0.8188 (mt) cc_final: 0.7725 (mp) REVERT: F 261 PHE cc_start: 0.7585 (m-80) cc_final: 0.7174 (m-80) REVERT: F 269 LYS cc_start: 0.7284 (mptt) cc_final: 0.6942 (mttt) REVERT: F 307 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: F 313 ASN cc_start: 0.7863 (m-40) cc_final: 0.7308 (m-40) REVERT: F 314 ARG cc_start: 0.7576 (tpt90) cc_final: 0.7122 (tpt90) REVERT: F 349 ASP cc_start: 0.7266 (p0) cc_final: 0.7003 (p0) REVERT: F 379 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6893 (m-30) REVERT: F 411 LEU cc_start: 0.7603 (mt) cc_final: 0.7363 (mm) REVERT: F 414 ARG cc_start: 0.7097 (mtm-85) cc_final: 0.6845 (mtm-85) REVERT: F 415 LYS cc_start: 0.8078 (tptt) cc_final: 0.7833 (tptt) REVERT: F 427 LYS cc_start: 0.7668 (mmmt) cc_final: 0.7187 (mmmt) REVERT: G 15 ILE cc_start: 0.8065 (mt) cc_final: 0.7758 (mm) REVERT: G 17 SER cc_start: 0.7833 (p) cc_final: 0.7398 (t) REVERT: G 54 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6951 (mm-30) REVERT: G 57 LYS cc_start: 0.7954 (mttt) cc_final: 0.7681 (mtmm) REVERT: G 61 MET cc_start: 0.7614 (mmm) cc_final: 0.7344 (mmp) REVERT: G 110 GLU cc_start: 0.7267 (tp30) cc_final: 0.6918 (tp30) REVERT: G 113 MET cc_start: 0.7001 (tpp) cc_final: 0.6735 (tpp) REVERT: G 123 ARG cc_start: 0.7827 (ttt90) cc_final: 0.7346 (mtp85) REVERT: G 128 LYS cc_start: 0.7826 (tppt) cc_final: 0.7378 (tppt) REVERT: G 152 LYS cc_start: 0.6623 (mtpt) cc_final: 0.6329 (mtpt) REVERT: G 167 THR cc_start: 0.8076 (m) cc_final: 0.7855 (p) REVERT: G 201 LYS cc_start: 0.8074 (mttt) cc_final: 0.7840 (mttt) REVERT: G 221 VAL cc_start: 0.8182 (p) cc_final: 0.7705 (m) REVERT: G 230 LYS cc_start: 0.7984 (mttt) cc_final: 0.7775 (mttm) REVERT: G 260 MET cc_start: 0.4713 (tmm) cc_final: 0.4370 (tmm) REVERT: G 264 MET cc_start: 0.5289 (mmm) cc_final: 0.4639 (mmm) REVERT: G 270 GLU cc_start: 0.6485 (mt-10) cc_final: 0.6261 (mt-10) REVERT: G 281 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7535 (mtpt) REVERT: G 282 VAL cc_start: 0.8004 (t) cc_final: 0.7722 (p) REVERT: G 285 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7534 (mtpt) REVERT: G 314 TYR cc_start: 0.8187 (t80) cc_final: 0.7843 (t80) REVERT: G 322 SER cc_start: 0.8048 (p) cc_final: 0.7686 (m) REVERT: G 396 GLU cc_start: 0.6324 (mm-30) cc_final: 0.5772 (mm-30) REVERT: G 431 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6680 (mt-10) REVERT: G 434 SER cc_start: 0.7388 (m) cc_final: 0.6828 (p) REVERT: H 61 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7105 (mm-30) REVERT: H 129 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7544 (t) REVERT: H 130 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7723 (ttp80) REVERT: H 139 GLU cc_start: 0.7539 (pt0) cc_final: 0.7132 (pt0) REVERT: H 178 MET cc_start: 0.7722 (mmm) cc_final: 0.7501 (tpp) REVERT: H 182 LEU cc_start: 0.8593 (mt) cc_final: 0.8253 (mp) REVERT: H 207 ARG cc_start: 0.8260 (ptp-170) cc_final: 0.8003 (ptp90) REVERT: H 233 GLN cc_start: 0.7919 (tt0) cc_final: 0.7647 (tp40) REVERT: H 241 THR cc_start: 0.7827 (m) cc_final: 0.7464 (t) REVERT: H 267 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6247 (mt-10) REVERT: H 275 GLN cc_start: 0.6533 (mt0) cc_final: 0.6274 (mt0) REVERT: H 279 LYS cc_start: 0.7725 (tptt) cc_final: 0.7413 (tptt) REVERT: H 300 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6661 (mm-30) REVERT: H 303 MET cc_start: 0.6778 (mmt) cc_final: 0.6512 (mmm) REVERT: H 305 ASP cc_start: 0.7502 (p0) cc_final: 0.7284 (p0) REVERT: H 352 ASP cc_start: 0.7066 (m-30) cc_final: 0.6718 (m-30) REVERT: H 365 LYS cc_start: 0.7869 (tttt) cc_final: 0.7661 (tttt) REVERT: H 376 GLU cc_start: 0.7272 (tt0) cc_final: 0.6960 (tt0) REVERT: H 379 ASP cc_start: 0.7750 (t0) cc_final: 0.7448 (m-30) REVERT: H 392 ARG cc_start: 0.7886 (ttt180) cc_final: 0.7605 (ttt180) REVERT: H 413 CYS cc_start: 0.7658 (t) cc_final: 0.7301 (p) REVERT: H 420 GLU cc_start: 0.7062 (tt0) cc_final: 0.6835 (tt0) REVERT: H 427 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7477 (mmtm) REVERT: H 436 GLU cc_start: 0.5597 (tm-30) cc_final: 0.5197 (tm-30) REVERT: H 441 GLN cc_start: 0.7760 (tt0) cc_final: 0.7481 (tt0) REVERT: H 443 MET cc_start: 0.6928 (ttp) cc_final: 0.6668 (ttm) REVERT: I 64 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6673 (mmt90) REVERT: I 125 LYS cc_start: 0.8331 (ttmt) cc_final: 0.8088 (ttpp) REVERT: I 126 GLU cc_start: 0.7030 (tm-30) cc_final: 0.6824 (tm-30) REVERT: I 134 GLU cc_start: 0.7009 (tt0) cc_final: 0.6808 (tt0) REVERT: I 173 ASP cc_start: 0.7488 (t70) cc_final: 0.7183 (t0) REVERT: I 175 SER cc_start: 0.8719 (m) cc_final: 0.8458 (p) REVERT: I 189 ASP cc_start: 0.5681 (m-30) cc_final: 0.5089 (m-30) REVERT: I 202 ARG cc_start: 0.7912 (ttt-90) cc_final: 0.7466 (ttt-90) REVERT: I 247 ASN cc_start: 0.7339 (m-40) cc_final: 0.7012 (m-40) REVERT: I 260 MET cc_start: 0.5881 (mtt) cc_final: 0.5551 (mtt) REVERT: I 281 LYS cc_start: 0.7364 (mttt) cc_final: 0.7096 (mttt) REVERT: I 312 PHE cc_start: 0.7653 (m-80) cc_final: 0.7227 (m-80) REVERT: I 317 ARG cc_start: 0.6748 (ttt-90) cc_final: 0.6528 (ttt-90) REVERT: I 320 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6319 (mp0) REVERT: I 335 ASN cc_start: 0.7834 (t0) cc_final: 0.7408 (t0) REVERT: I 341 THR cc_start: 0.7833 (OUTLIER) cc_final: 0.7570 (p) REVERT: I 356 ASP cc_start: 0.7186 (t0) cc_final: 0.6875 (t70) REVERT: I 389 GLU cc_start: 0.7690 (pt0) cc_final: 0.7362 (pt0) REVERT: I 396 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7032 (mt-10) REVERT: I 399 THR cc_start: 0.7844 (m) cc_final: 0.7428 (p) REVERT: I 404 ARG cc_start: 0.6865 (mtm-85) cc_final: 0.6603 (mtm-85) REVERT: I 418 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7463 (mtpp) REVERT: I 427 LYS cc_start: 0.7677 (tttt) cc_final: 0.7396 (ttmm) REVERT: I 428 GLU cc_start: 0.7686 (mp0) cc_final: 0.7449 (pm20) REVERT: I 445 LYS cc_start: 0.7535 (mttp) cc_final: 0.7154 (tttp) REVERT: J 40 ARG cc_start: 0.7307 (mtt-85) cc_final: 0.7059 (mtt90) REVERT: J 83 LYS cc_start: 0.7471 (mtmt) cc_final: 0.7153 (mtmt) REVERT: J 94 LEU cc_start: 0.7589 (tp) cc_final: 0.7318 (tp) REVERT: J 236 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8152 (mtpt) REVERT: J 264 ASP cc_start: 0.6393 (t0) cc_final: 0.6061 (t0) REVERT: J 274 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7293 (mt-10) REVERT: J 282 GLU cc_start: 0.7337 (tp30) cc_final: 0.7022 (tp30) REVERT: J 377 GLU cc_start: 0.6752 (tp30) cc_final: 0.6281 (tp30) REVERT: J 384 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6832 (mm-30) REVERT: J 404 GLN cc_start: 0.7644 (mt0) cc_final: 0.7417 (mt0) REVERT: J 427 LYS cc_start: 0.7827 (mmtp) cc_final: 0.7568 (mmtp) REVERT: J 436 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6900 (tm-30) REVERT: K 119 MET cc_start: 0.5661 (mtp) cc_final: 0.5429 (mtp) REVERT: K 153 MET cc_start: -0.0270 (tmm) cc_final: -0.0868 (tmm) REVERT: K 190 MET cc_start: -0.2800 (mtm) cc_final: -0.3035 (ptm) REVERT: K 283 MET cc_start: 0.3782 (mmm) cc_final: 0.3269 (mmm) REVERT: L 57 GLU cc_start: 0.7536 (tp30) cc_final: 0.6604 (tp30) REVERT: L 61 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7370 (mtmt) REVERT: L 62 ARG cc_start: 0.8146 (mtm180) cc_final: 0.7942 (mtp180) REVERT: L 100 GLU cc_start: 0.7643 (tt0) cc_final: 0.7384 (tt0) REVERT: L 107 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6832 (pt0) REVERT: L 166 TYR cc_start: 0.8219 (t80) cc_final: 0.7709 (t80) REVERT: L 167 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7282 (mm-30) REVERT: L 300 SER cc_start: 0.8446 (p) cc_final: 0.8210 (m) REVERT: L 312 ARG cc_start: 0.8811 (tpt90) cc_final: 0.8603 (tpt-90) REVERT: L 373 LYS cc_start: 0.8151 (mttm) cc_final: 0.7702 (mttt) REVERT: M 30 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7526 (mm-30) REVERT: M 31 ASP cc_start: 0.6667 (p0) cc_final: 0.6319 (p0) REVERT: M 67 THR cc_start: 0.8655 (m) cc_final: 0.8120 (p) REVERT: M 128 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7336 (p0) REVERT: M 130 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7550 (ttm170) REVERT: M 134 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7196 (mt-10) REVERT: M 189 GLN cc_start: 0.8287 (mt0) cc_final: 0.8035 (mp10) REVERT: M 202 ILE cc_start: 0.8533 (mm) cc_final: 0.8059 (tp) REVERT: M 226 LYS cc_start: 0.8522 (pttt) cc_final: 0.7908 (pttt) REVERT: M 227 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7360 (mm-30) REVERT: M 238 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8066 (mmtt) REVERT: M 252 ASN cc_start: 0.8227 (m-40) cc_final: 0.7883 (m110) REVERT: M 276 GLU cc_start: 0.7307 (tp30) cc_final: 0.6993 (tp30) REVERT: M 294 ASN cc_start: 0.8248 (p0) cc_final: 0.7620 (p0) REVERT: M 301 ARG cc_start: 0.8191 (ptm-80) cc_final: 0.7782 (ptm-80) REVERT: M 303 LYS cc_start: 0.8617 (tttp) cc_final: 0.8231 (mtpp) REVERT: M 306 GLU cc_start: 0.8621 (tp30) cc_final: 0.8388 (tp30) REVERT: M 308 LEU cc_start: 0.8596 (mm) cc_final: 0.8287 (mt) REVERT: M 322 MET cc_start: 0.7288 (mtm) cc_final: 0.6895 (mtm) REVERT: M 347 SER cc_start: 0.7615 (t) cc_final: 0.7114 (p) REVERT: M 358 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7718 (mm-40) REVERT: N 55 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7431 (mtt180) REVERT: N 57 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8072 (t) REVERT: N 62 TYR cc_start: 0.8717 (p90) cc_final: 0.8352 (p90) REVERT: N 90 LYS cc_start: 0.8328 (mmtp) cc_final: 0.8123 (mmtt) REVERT: N 91 LYS cc_start: 0.7773 (ptmm) cc_final: 0.7472 (ptmm) REVERT: N 96 LYS cc_start: 0.8291 (tttt) cc_final: 0.7957 (ttpp) REVERT: N 192 LYS cc_start: 0.7958 (mttt) cc_final: 0.7732 (mttt) REVERT: N 193 GLU cc_start: 0.7542 (tp30) cc_final: 0.7152 (tp30) REVERT: N 196 TYR cc_start: 0.7921 (m-80) cc_final: 0.7600 (m-10) REVERT: N 202 LEU cc_start: 0.8706 (mt) cc_final: 0.8382 (mt) REVERT: N 224 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7929 (mtt90) REVERT: N 228 GLU cc_start: 0.8261 (tp30) cc_final: 0.7535 (tp30) REVERT: N 232 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7826 (ttm170) outliers start: 113 outliers final: 70 residues processed: 1410 average time/residue: 0.2461 time to fit residues: 529.4948 Evaluate side-chains 1439 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1358 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 1367 ILE Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 2099 ILE Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 353 ASP Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 254 THR Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 382 MET Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 328 THR Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 109 THR Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 341 THR Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 132 LYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 177 ARG Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 128 ASN Chi-restraints excluded: chain M residue 152 CYS Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 268 GLN Chi-restraints excluded: chain M residue 282 MET Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 322 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 404 optimal weight: 40.0000 chunk 46 optimal weight: 0.8980 chunk 146 optimal weight: 0.0270 chunk 335 optimal weight: 0.9980 chunk 301 optimal weight: 0.5980 chunk 327 optimal weight: 0.9980 chunk 429 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 811 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2148 GLN E 280 ASN G 115 ASN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 HIS I 385 ASN J 275 GLN ** L 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 353 GLN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 GLN M 268 GLN M 384 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.173416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141732 restraints weight = 65795.409| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.71 r_work: 0.3477 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41572 Z= 0.134 Angle : 0.545 8.537 56164 Z= 0.271 Chirality : 0.041 0.209 6364 Planarity : 0.004 0.062 7187 Dihedral : 6.630 147.971 5717 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.46 % Allowed : 13.70 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.74 (0.12), residues: 5082 helix: 1.76 (0.11), residues: 2332 sheet: 0.52 (0.18), residues: 810 loop : 0.89 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 130 TYR 0.021 0.001 TYR M 293 PHE 0.018 0.001 PHE N 183 TRP 0.022 0.001 TRP A1232 HIS 0.010 0.001 HIS M 143 Details of bonding type rmsd covalent geometry : bond 0.00297 (41572) covalent geometry : angle 0.54520 (56164) hydrogen bonds : bond 0.03758 ( 1947) hydrogen bonds : angle 4.25976 ( 5517) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1366 time to evaluate : 1.198 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: A 796 GLN cc_start: 0.7706 (tp-100) cc_final: 0.7233 (tp-100) REVERT: A 816 LEU cc_start: 0.8238 (mt) cc_final: 0.7925 (mm) REVERT: A 838 LYS cc_start: 0.8358 (tttt) cc_final: 0.7888 (ttpp) REVERT: A 861 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 862 GLU cc_start: 0.8469 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 863 GLN cc_start: 0.7655 (tt0) cc_final: 0.7348 (tp40) REVERT: A 864 SER cc_start: 0.7629 (m) cc_final: 0.7347 (t) REVERT: A 865 ARG cc_start: 0.7964 (ttt180) cc_final: 0.7761 (ttt180) REVERT: A 867 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7328 (mmt180) REVERT: A 1192 HIS cc_start: 0.7546 (m170) cc_final: 0.7051 (m90) REVERT: A 1215 CYS cc_start: 0.7748 (t) cc_final: 0.6234 (p) REVERT: A 1242 GLN cc_start: 0.3178 (pt0) cc_final: 0.1504 (mt0) REVERT: A 1261 MET cc_start: 0.3075 (mmp) cc_final: 0.2640 (mmp) REVERT: A 1337 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7512 (mp0) REVERT: A 1362 VAL cc_start: 0.7686 (t) cc_final: 0.7391 (m) REVERT: A 1363 ARG cc_start: 0.7941 (ttt180) cc_final: 0.7472 (mmm-85) REVERT: A 1406 LYS cc_start: 0.7197 (mttt) cc_final: 0.6856 (mttp) REVERT: A 1428 GLU cc_start: 0.6817 (tp30) cc_final: 0.6554 (tp30) REVERT: A 1433 LYS cc_start: 0.7787 (mttt) cc_final: 0.7423 (mtmt) REVERT: A 1442 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7156 (mt-10) REVERT: A 1758 GLU cc_start: 0.8012 (tt0) cc_final: 0.7685 (mt-10) REVERT: A 1762 SER cc_start: 0.7496 (t) cc_final: 0.7270 (p) REVERT: A 1769 ARG cc_start: 0.7666 (mtp-110) cc_final: 0.7132 (mtm180) REVERT: A 1774 ILE cc_start: 0.8549 (tp) cc_final: 0.8080 (mt) REVERT: A 1877 ARG cc_start: 0.6666 (tpm170) cc_final: 0.6390 (tpm170) REVERT: A 1897 SER cc_start: 0.7797 (t) cc_final: 0.7469 (p) REVERT: A 1901 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7236 (mm-30) REVERT: A 1909 LYS cc_start: 0.7734 (tttt) cc_final: 0.7385 (ttmm) REVERT: A 1911 LYS cc_start: 0.8146 (tttt) cc_final: 0.7928 (tppp) REVERT: A 1921 SER cc_start: 0.7066 (t) cc_final: 0.6797 (p) REVERT: A 1953 ARG cc_start: 0.7597 (mtm180) cc_final: 0.7354 (mtm110) REVERT: A 1958 ARG cc_start: 0.7706 (mtt180) cc_final: 0.7340 (mtt180) REVERT: A 1974 HIS cc_start: 0.7891 (m-70) cc_final: 0.7622 (m-70) REVERT: A 1982 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7053 (tt) REVERT: A 1986 ASP cc_start: 0.7000 (p0) cc_final: 0.6596 (p0) REVERT: A 2000 ASP cc_start: 0.7967 (t70) cc_final: 0.7224 (t0) REVERT: A 2004 GLN cc_start: 0.7397 (mm-40) cc_final: 0.7190 (mm-40) REVERT: A 2052 MET cc_start: 0.6466 (mmm) cc_final: 0.6074 (tmm) REVERT: A 2206 GLU cc_start: 0.7239 (tt0) cc_final: 0.6617 (tm-30) REVERT: A 2213 LEU cc_start: 0.8530 (mt) cc_final: 0.8306 (mp) REVERT: A 2260 ILE cc_start: 0.8337 (mt) cc_final: 0.8123 (mm) REVERT: A 2263 ASP cc_start: 0.8176 (t0) cc_final: 0.7872 (t0) REVERT: A 2265 VAL cc_start: 0.8205 (t) cc_final: 0.7878 (m) REVERT: A 2269 MET cc_start: 0.6944 (mmm) cc_final: 0.6591 (mpp) REVERT: B 267 THR cc_start: 0.8100 (m) cc_final: 0.7746 (p) REVERT: B 277 TRP cc_start: 0.8193 (m100) cc_final: 0.7842 (m100) REVERT: B 294 VAL cc_start: 0.8946 (t) cc_final: 0.8710 (m) REVERT: B 318 ILE cc_start: 0.8219 (mt) cc_final: 0.8011 (mm) REVERT: E 14 ARG cc_start: 0.8024 (mtp180) cc_final: 0.7583 (mtp180) REVERT: E 90 LYS cc_start: 0.7659 (mmtp) cc_final: 0.7365 (mmtp) REVERT: E 101 VAL cc_start: 0.7849 (t) cc_final: 0.7581 (m) REVERT: E 123 ARG cc_start: 0.7383 (mtp180) cc_final: 0.7019 (tpp80) REVERT: E 129 GLU cc_start: 0.6802 (pm20) cc_final: 0.6336 (pm20) REVERT: E 134 GLU cc_start: 0.7482 (tt0) cc_final: 0.6983 (tt0) REVERT: E 194 GLU cc_start: 0.7368 (tt0) cc_final: 0.7028 (tm-30) REVERT: E 209 TYR cc_start: 0.7854 (m-80) cc_final: 0.7352 (m-80) REVERT: E 258 SER cc_start: 0.7685 (m) cc_final: 0.7085 (p) REVERT: E 262 GLN cc_start: 0.6682 (mt0) cc_final: 0.6467 (mt0) REVERT: E 264 MET cc_start: 0.6471 (mmm) cc_final: 0.6120 (mmm) REVERT: E 265 LYS cc_start: 0.8178 (tttt) cc_final: 0.7846 (tttt) REVERT: E 274 LYS cc_start: 0.6622 (tttm) cc_final: 0.6286 (tttm) REVERT: E 278 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: E 285 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7231 (ttmt) REVERT: E 304 VAL cc_start: 0.7822 (m) cc_final: 0.7487 (p) REVERT: E 317 ARG cc_start: 0.7255 (ttt-90) cc_final: 0.6971 (ttt180) REVERT: E 333 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7585 (mmt90) REVERT: E 336 CYS cc_start: 0.6769 (p) cc_final: 0.6467 (p) REVERT: E 337 VAL cc_start: 0.7439 (t) cc_final: 0.7019 (m) REVERT: E 356 ASP cc_start: 0.6885 (t70) cc_final: 0.6540 (t0) REVERT: E 372 LYS cc_start: 0.7525 (mtpp) cc_final: 0.7317 (mttp) REVERT: E 388 GLU cc_start: 0.7388 (tt0) cc_final: 0.7125 (tt0) REVERT: E 396 GLU cc_start: 0.6907 (tm-30) cc_final: 0.6502 (tm-30) REVERT: F 20 GLU cc_start: 0.7221 (mp0) cc_final: 0.6771 (mp0) REVERT: F 65 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6806 (mm-30) REVERT: F 67 LYS cc_start: 0.8258 (mttt) cc_final: 0.7994 (mttt) REVERT: F 71 ARG cc_start: 0.7783 (mmm-85) cc_final: 0.7477 (mmm160) REVERT: F 115 LYS cc_start: 0.7673 (mttp) cc_final: 0.7316 (mttp) REVERT: F 125 ARG cc_start: 0.7305 (mtm-85) cc_final: 0.7058 (ttm110) REVERT: F 231 GLU cc_start: 0.7666 (mp0) cc_final: 0.7419 (mp0) REVERT: F 232 LEU cc_start: 0.8134 (mt) cc_final: 0.7694 (mp) REVERT: F 261 PHE cc_start: 0.7535 (m-80) cc_final: 0.7124 (m-80) REVERT: F 269 LYS cc_start: 0.7214 (mptt) cc_final: 0.6877 (mttt) REVERT: F 307 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: F 313 ASN cc_start: 0.7896 (m-40) cc_final: 0.7352 (m-40) REVERT: F 314 ARG cc_start: 0.7607 (tpt90) cc_final: 0.7138 (tpt90) REVERT: F 336 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7851 (mmm160) REVERT: F 349 ASP cc_start: 0.7302 (p0) cc_final: 0.7036 (p0) REVERT: F 415 LYS cc_start: 0.8081 (tptt) cc_final: 0.7828 (tptt) REVERT: F 427 LYS cc_start: 0.7637 (mmmt) cc_final: 0.7167 (mmmt) REVERT: G 17 SER cc_start: 0.7882 (p) cc_final: 0.7463 (t) REVERT: G 54 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6917 (mm-30) REVERT: G 57 LYS cc_start: 0.7958 (mttt) cc_final: 0.7683 (mtmm) REVERT: G 60 LYS cc_start: 0.7529 (mtpp) cc_final: 0.7277 (ttpp) REVERT: G 61 MET cc_start: 0.7656 (mmm) cc_final: 0.7215 (mmp) REVERT: G 110 GLU cc_start: 0.7299 (tp30) cc_final: 0.6948 (tp30) REVERT: G 123 ARG cc_start: 0.7744 (ttt90) cc_final: 0.7292 (mtp85) REVERT: G 128 LYS cc_start: 0.7848 (tppt) cc_final: 0.7404 (tppt) REVERT: G 139 THR cc_start: 0.7929 (p) cc_final: 0.7717 (t) REVERT: G 152 LYS cc_start: 0.6639 (mtpt) cc_final: 0.6315 (mtpt) REVERT: G 156 HIS cc_start: 0.8147 (m-70) cc_final: 0.7928 (m90) REVERT: G 167 THR cc_start: 0.8048 (m) cc_final: 0.7828 (p) REVERT: G 209 TYR cc_start: 0.8353 (m-80) cc_final: 0.7904 (m-80) REVERT: G 260 MET cc_start: 0.4582 (tmm) cc_final: 0.4303 (tmm) REVERT: G 264 MET cc_start: 0.5231 (mmm) cc_final: 0.4663 (mmm) REVERT: G 281 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7554 (mtpt) REVERT: G 282 VAL cc_start: 0.8024 (t) cc_final: 0.7734 (p) REVERT: G 285 LYS cc_start: 0.7714 (mtpt) cc_final: 0.7492 (mtpt) REVERT: G 314 TYR cc_start: 0.8214 (t80) cc_final: 0.7835 (t80) REVERT: G 322 SER cc_start: 0.8033 (p) cc_final: 0.7717 (m) REVERT: G 378 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7569 (mmm-85) REVERT: G 396 GLU cc_start: 0.6306 (mm-30) cc_final: 0.5730 (mm-30) REVERT: G 431 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6627 (mt-10) REVERT: G 434 SER cc_start: 0.7357 (m) cc_final: 0.6786 (p) REVERT: H 61 GLU cc_start: 0.7259 (mm-30) cc_final: 0.7045 (mm-30) REVERT: H 129 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7521 (t) REVERT: H 132 LYS cc_start: 0.8716 (ptpp) cc_final: 0.8462 (ptpp) REVERT: H 139 GLU cc_start: 0.7543 (pt0) cc_final: 0.7142 (pt0) REVERT: H 178 MET cc_start: 0.7695 (mmm) cc_final: 0.7473 (tpp) REVERT: H 182 LEU cc_start: 0.8571 (mt) cc_final: 0.8228 (mp) REVERT: H 207 ARG cc_start: 0.8149 (ptp-170) cc_final: 0.7878 (ptp90) REVERT: H 233 GLN cc_start: 0.7891 (tt0) cc_final: 0.7580 (tp40) REVERT: H 241 THR cc_start: 0.7797 (m) cc_final: 0.7378 (t) REVERT: H 272 VAL cc_start: 0.7667 (t) cc_final: 0.7443 (p) REVERT: H 275 GLN cc_start: 0.6483 (mt0) cc_final: 0.6237 (mt0) REVERT: H 279 LYS cc_start: 0.7731 (tptt) cc_final: 0.7437 (tptt) REVERT: H 300 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6657 (mm-30) REVERT: H 305 ASP cc_start: 0.7508 (p0) cc_final: 0.7282 (p0) REVERT: H 352 ASP cc_start: 0.7068 (m-30) cc_final: 0.6723 (m-30) REVERT: H 365 LYS cc_start: 0.7827 (tttt) cc_final: 0.7602 (tttt) REVERT: H 379 ASP cc_start: 0.7769 (t0) cc_final: 0.7448 (m-30) REVERT: H 392 ARG cc_start: 0.7841 (ttt180) cc_final: 0.7565 (ttt180) REVERT: H 413 CYS cc_start: 0.7762 (t) cc_final: 0.7449 (p) REVERT: H 420 GLU cc_start: 0.7089 (tt0) cc_final: 0.6871 (tt0) REVERT: H 427 LYS cc_start: 0.7739 (mmtm) cc_final: 0.7459 (mmtm) REVERT: H 436 GLU cc_start: 0.5521 (tm-30) cc_final: 0.5117 (tm-30) REVERT: H 441 GLN cc_start: 0.7683 (tt0) cc_final: 0.7398 (tt0) REVERT: H 443 MET cc_start: 0.6901 (ttp) cc_final: 0.6640 (ttm) REVERT: I 64 ARG cc_start: 0.6919 (OUTLIER) cc_final: 0.6669 (mmt90) REVERT: I 125 LYS cc_start: 0.8394 (ttmt) cc_final: 0.8138 (ttpp) REVERT: I 126 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6952 (tm-30) REVERT: I 173 ASP cc_start: 0.7431 (t70) cc_final: 0.7154 (t0) REVERT: I 175 SER cc_start: 0.8746 (m) cc_final: 0.8518 (p) REVERT: I 189 ASP cc_start: 0.5555 (m-30) cc_final: 0.4995 (m-30) REVERT: I 202 ARG cc_start: 0.7717 (ttt-90) cc_final: 0.7350 (ttt-90) REVERT: I 260 MET cc_start: 0.5875 (mtt) cc_final: 0.5541 (mtt) REVERT: I 281 LYS cc_start: 0.7357 (mttt) cc_final: 0.7137 (mttt) REVERT: I 310 GLU cc_start: 0.7228 (mt-10) cc_final: 0.7023 (mt-10) REVERT: I 312 PHE cc_start: 0.7677 (m-80) cc_final: 0.7272 (m-80) REVERT: I 317 ARG cc_start: 0.6739 (ttt-90) cc_final: 0.6455 (ttt-90) REVERT: I 335 ASN cc_start: 0.7787 (t0) cc_final: 0.7346 (t0) REVERT: I 356 ASP cc_start: 0.7197 (t0) cc_final: 0.6871 (t70) REVERT: I 362 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7461 (ttp-110) REVERT: I 376 LYS cc_start: 0.7689 (tptt) cc_final: 0.7329 (tppt) REVERT: I 389 GLU cc_start: 0.7634 (pt0) cc_final: 0.7340 (pt0) REVERT: I 396 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7041 (mt-10) REVERT: I 399 THR cc_start: 0.7865 (m) cc_final: 0.7471 (p) REVERT: I 418 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7448 (mtpp) REVERT: I 427 LYS cc_start: 0.7679 (tttt) cc_final: 0.7456 (ttmm) REVERT: I 428 GLU cc_start: 0.7661 (mp0) cc_final: 0.7447 (pm20) REVERT: I 431 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6853 (mm-30) REVERT: I 445 LYS cc_start: 0.7536 (mttp) cc_final: 0.7141 (tttp) REVERT: J 40 ARG cc_start: 0.7298 (mtt-85) cc_final: 0.7067 (mtt90) REVERT: J 59 VAL cc_start: 0.7610 (t) cc_final: 0.7384 (m) REVERT: J 83 LYS cc_start: 0.7513 (mtmt) cc_final: 0.7181 (mtmt) REVERT: J 94 LEU cc_start: 0.7585 (tp) cc_final: 0.7326 (tp) REVERT: J 236 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8080 (mtpt) REVERT: J 264 ASP cc_start: 0.6297 (t0) cc_final: 0.5976 (t0) REVERT: J 274 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7273 (mt-10) REVERT: J 341 GLN cc_start: 0.7254 (mt0) cc_final: 0.7007 (mt0) REVERT: J 377 GLU cc_start: 0.6698 (tp30) cc_final: 0.6223 (tp30) REVERT: J 384 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6863 (mm-30) REVERT: J 404 GLN cc_start: 0.7644 (mt0) cc_final: 0.7405 (mt0) REVERT: J 420 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7053 (tt0) REVERT: J 427 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7608 (mmtp) REVERT: J 436 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6878 (tm-30) REVERT: K 119 MET cc_start: 0.5658 (mtp) cc_final: 0.5439 (mtp) REVERT: K 153 MET cc_start: -0.0382 (tmm) cc_final: -0.1009 (tmm) REVERT: K 283 MET cc_start: 0.3798 (mmm) cc_final: 0.3277 (mmm) REVERT: L 57 GLU cc_start: 0.7508 (tp30) cc_final: 0.6589 (tp30) REVERT: L 61 LYS cc_start: 0.8377 (mtmt) cc_final: 0.7400 (mtmt) REVERT: L 100 GLU cc_start: 0.7524 (tt0) cc_final: 0.7306 (tt0) REVERT: L 107 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6785 (pt0) REVERT: L 166 TYR cc_start: 0.8159 (t80) cc_final: 0.7641 (t80) REVERT: L 167 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7218 (mm-30) REVERT: L 259 GLU cc_start: 0.7653 (tp30) cc_final: 0.7301 (tp30) REVERT: L 300 SER cc_start: 0.8482 (p) cc_final: 0.8199 (m) REVERT: L 312 ARG cc_start: 0.8815 (tpt90) cc_final: 0.8441 (tpt-90) REVERT: M 30 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7496 (mm-30) REVERT: M 31 ASP cc_start: 0.6631 (p0) cc_final: 0.6287 (p0) REVERT: M 67 THR cc_start: 0.8576 (m) cc_final: 0.8060 (p) REVERT: M 128 ASN cc_start: 0.7710 (t0) cc_final: 0.7271 (p0) REVERT: M 130 ARG cc_start: 0.7661 (ttm110) cc_final: 0.7324 (ttm170) REVERT: M 134 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7111 (mt-10) REVERT: M 186 TYR cc_start: 0.7730 (m-80) cc_final: 0.7317 (m-80) REVERT: M 189 GLN cc_start: 0.8291 (mt0) cc_final: 0.7895 (mp10) REVERT: M 226 LYS cc_start: 0.8505 (pttt) cc_final: 0.7776 (ptpt) REVERT: M 227 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7329 (mm-30) REVERT: M 238 LYS cc_start: 0.8448 (mmtt) cc_final: 0.8064 (mmtt) REVERT: M 252 ASN cc_start: 0.8173 (m-40) cc_final: 0.7872 (m110) REVERT: M 253 TYR cc_start: 0.8020 (t80) cc_final: 0.7775 (t80) REVERT: M 276 GLU cc_start: 0.7279 (tp30) cc_final: 0.6974 (tp30) REVERT: M 287 TYR cc_start: 0.8120 (t80) cc_final: 0.7790 (t80) REVERT: M 294 ASN cc_start: 0.8204 (p0) cc_final: 0.7593 (p0) REVERT: M 301 ARG cc_start: 0.8196 (ptm-80) cc_final: 0.7845 (ptm-80) REVERT: M 303 LYS cc_start: 0.8690 (tttp) cc_final: 0.8306 (mtpp) REVERT: M 306 GLU cc_start: 0.8624 (tp30) cc_final: 0.8382 (tp30) REVERT: M 308 LEU cc_start: 0.8564 (mm) cc_final: 0.8338 (mt) REVERT: M 322 MET cc_start: 0.7257 (mtm) cc_final: 0.6866 (mtm) REVERT: M 347 SER cc_start: 0.7553 (t) cc_final: 0.7024 (p) REVERT: M 358 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7609 (mm-40) REVERT: N 55 ARG cc_start: 0.7857 (mtt180) cc_final: 0.7387 (mtt180) REVERT: N 57 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8107 (t) REVERT: N 62 TYR cc_start: 0.8719 (p90) cc_final: 0.8335 (p90) REVERT: N 91 LYS cc_start: 0.7776 (ptmm) cc_final: 0.7471 (ptmm) REVERT: N 142 GLU cc_start: 0.7616 (mt-10) cc_final: 0.6842 (mt-10) REVERT: N 186 ARG cc_start: 0.7771 (tpp-160) cc_final: 0.7346 (mtp85) REVERT: N 193 GLU cc_start: 0.7439 (tp30) cc_final: 0.7092 (tp30) REVERT: N 194 ARG cc_start: 0.7887 (tpt90) cc_final: 0.7495 (tpt-90) REVERT: N 196 TYR cc_start: 0.7876 (m-80) cc_final: 0.7570 (m-10) REVERT: N 202 LEU cc_start: 0.8704 (mt) cc_final: 0.8370 (mt) REVERT: N 224 ARG cc_start: 0.8158 (mtt90) cc_final: 0.7901 (mtt90) REVERT: N 228 GLU cc_start: 0.8198 (tp30) cc_final: 0.7844 (tp30) REVERT: N 232 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7853 (ttm170) REVERT: N 255 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6474 (mm-30) outliers start: 109 outliers final: 75 residues processed: 1405 average time/residue: 0.2492 time to fit residues: 535.7258 Evaluate side-chains 1424 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1341 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1845 LEU Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2099 ILE Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain A residue 2224 THR Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain E residue 345 THR Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain J residue 132 LYS Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 340 TYR Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 132 MET Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 339 VAL Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 152 CYS Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 211 GLN Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 268 GLN Chi-restraints excluded: chain M residue 282 MET Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain M residue 356 LEU Chi-restraints excluded: chain M residue 378 LEU Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 131 LYS Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 122 optimal weight: 10.0000 chunk 164 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 359 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 356 optimal weight: 1.9990 chunk 139 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 372 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 811 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN E 332 ASN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 275 GLN ** L 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 353 GLN M 100 GLN M 268 GLN M 384 ASN ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 235 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.173222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.140694 restraints weight = 66029.001| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.64 r_work: 0.3467 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 41572 Z= 0.142 Angle : 0.549 9.033 56164 Z= 0.273 Chirality : 0.042 0.183 6364 Planarity : 0.004 0.062 7187 Dihedral : 6.585 146.112 5717 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.78 % Allowed : 14.20 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.72 (0.12), residues: 5082 helix: 1.78 (0.11), residues: 2330 sheet: 0.47 (0.18), residues: 812 loop : 0.84 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 184 TYR 0.022 0.001 TYR M 293 PHE 0.013 0.001 PHE A1933 TRP 0.027 0.001 TRP A1232 HIS 0.009 0.001 HIS L 275 Details of bonding type rmsd covalent geometry : bond 0.00316 (41572) covalent geometry : angle 0.54886 (56164) hydrogen bonds : bond 0.03751 ( 1947) hydrogen bonds : angle 4.23202 ( 5517) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1469 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 1346 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7734 (mtp180) REVERT: A 796 GLN cc_start: 0.7707 (tp-100) cc_final: 0.7226 (tp-100) REVERT: A 816 LEU cc_start: 0.8223 (mt) cc_final: 0.7918 (mm) REVERT: A 838 LYS cc_start: 0.8369 (tttt) cc_final: 0.7926 (ttpp) REVERT: A 861 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7567 (mt-10) REVERT: A 862 GLU cc_start: 0.8528 (mm-30) cc_final: 0.7764 (mm-30) REVERT: A 863 GLN cc_start: 0.7701 (tt0) cc_final: 0.7352 (tp40) REVERT: A 864 SER cc_start: 0.7637 (m) cc_final: 0.7358 (t) REVERT: A 865 ARG cc_start: 0.7928 (ttt180) cc_final: 0.7720 (ttt180) REVERT: A 867 ARG cc_start: 0.7879 (mtt180) cc_final: 0.7388 (mmt180) REVERT: A 1192 HIS cc_start: 0.7467 (m170) cc_final: 0.7079 (m90) REVERT: A 1215 CYS cc_start: 0.7588 (t) cc_final: 0.6332 (p) REVERT: A 1242 GLN cc_start: 0.2511 (pt0) cc_final: 0.2192 (mm110) REVERT: A 1261 MET cc_start: 0.3053 (mmp) cc_final: 0.2623 (mmp) REVERT: A 1337 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7555 (mp0) REVERT: A 1362 VAL cc_start: 0.7807 (t) cc_final: 0.7554 (m) REVERT: A 1363 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7444 (mtp85) REVERT: A 1390 TYR cc_start: 0.8021 (t80) cc_final: 0.7740 (t80) REVERT: A 1406 LYS cc_start: 0.7220 (mttt) cc_final: 0.6908 (mttm) REVERT: A 1428 GLU cc_start: 0.6818 (tp30) cc_final: 0.6554 (tp30) REVERT: A 1433 LYS cc_start: 0.7782 (mttt) cc_final: 0.7424 (mtmt) REVERT: A 1442 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7128 (mt-10) REVERT: A 1758 GLU cc_start: 0.8046 (tt0) cc_final: 0.7721 (mt-10) REVERT: A 1769 ARG cc_start: 0.7714 (mtp-110) cc_final: 0.7430 (mtm180) REVERT: A 1774 ILE cc_start: 0.8573 (tp) cc_final: 0.8080 (mt) REVERT: A 1877 ARG cc_start: 0.6580 (tpm170) cc_final: 0.6292 (tpm170) REVERT: A 1897 SER cc_start: 0.7842 (t) cc_final: 0.7464 (p) REVERT: A 1901 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7203 (mm-30) REVERT: A 1909 LYS cc_start: 0.7734 (tttt) cc_final: 0.7400 (ttmm) REVERT: A 1911 LYS cc_start: 0.8138 (tttt) cc_final: 0.7897 (tppp) REVERT: A 1917 VAL cc_start: 0.8176 (p) cc_final: 0.7913 (m) REVERT: A 1921 SER cc_start: 0.6980 (t) cc_final: 0.6614 (p) REVERT: A 1958 ARG cc_start: 0.7636 (mtt180) cc_final: 0.7269 (mtt180) REVERT: A 1971 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7791 (pt) REVERT: A 1974 HIS cc_start: 0.7808 (m-70) cc_final: 0.7588 (m-70) REVERT: A 1982 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7073 (tt) REVERT: A 1986 ASP cc_start: 0.7003 (p0) cc_final: 0.6587 (p0) REVERT: A 2000 ASP cc_start: 0.7981 (t70) cc_final: 0.7216 (t0) REVERT: A 2004 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7210 (mm-40) REVERT: A 2017 HIS cc_start: 0.6496 (m90) cc_final: 0.6272 (m90) REVERT: A 2052 MET cc_start: 0.6420 (mmm) cc_final: 0.6030 (tmm) REVERT: A 2206 GLU cc_start: 0.7227 (tt0) cc_final: 0.6632 (tm-30) REVERT: A 2207 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7386 (ttt180) REVERT: A 2213 LEU cc_start: 0.8508 (mt) cc_final: 0.8298 (mp) REVERT: B 267 THR cc_start: 0.8092 (m) cc_final: 0.7724 (p) REVERT: B 277 TRP cc_start: 0.8213 (m100) cc_final: 0.8008 (m100) REVERT: B 294 VAL cc_start: 0.8904 (t) cc_final: 0.8674 (m) REVERT: C 407 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7946 (mmtt) REVERT: C 469 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7355 (mtm-85) REVERT: E 14 ARG cc_start: 0.8041 (mtp180) cc_final: 0.7723 (mtp180) REVERT: E 90 LYS cc_start: 0.7682 (mmtp) cc_final: 0.7390 (mmtp) REVERT: E 101 VAL cc_start: 0.7862 (t) cc_final: 0.7582 (m) REVERT: E 123 ARG cc_start: 0.7443 (mtp180) cc_final: 0.7060 (tpp80) REVERT: E 127 THR cc_start: 0.7765 (p) cc_final: 0.7517 (p) REVERT: E 129 GLU cc_start: 0.6855 (pm20) cc_final: 0.6445 (pm20) REVERT: E 134 GLU cc_start: 0.7371 (tt0) cc_final: 0.6906 (tt0) REVERT: E 209 TYR cc_start: 0.7809 (m-80) cc_final: 0.7142 (m-80) REVERT: E 255 ASP cc_start: 0.7159 (t0) cc_final: 0.6872 (t70) REVERT: E 258 SER cc_start: 0.7712 (m) cc_final: 0.7060 (p) REVERT: E 262 GLN cc_start: 0.6591 (mt0) cc_final: 0.6363 (mt0) REVERT: E 264 MET cc_start: 0.6430 (mmm) cc_final: 0.6100 (mmm) REVERT: E 265 LYS cc_start: 0.8166 (tttt) cc_final: 0.7798 (tttt) REVERT: E 274 LYS cc_start: 0.6620 (tttm) cc_final: 0.6160 (tttm) REVERT: E 278 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: E 285 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7225 (ttmt) REVERT: E 304 VAL cc_start: 0.7829 (m) cc_final: 0.7494 (p) REVERT: E 317 ARG cc_start: 0.7256 (ttt-90) cc_final: 0.6982 (ttt180) REVERT: E 332 ASN cc_start: 0.7616 (p0) cc_final: 0.7408 (p0) REVERT: E 333 ARG cc_start: 0.7779 (mmt180) cc_final: 0.7480 (mmt-90) REVERT: E 336 CYS cc_start: 0.6783 (p) cc_final: 0.6442 (p) REVERT: E 337 VAL cc_start: 0.7391 (t) cc_final: 0.6980 (m) REVERT: E 356 ASP cc_start: 0.6885 (t70) cc_final: 0.6523 (t0) REVERT: E 388 GLU cc_start: 0.7415 (tt0) cc_final: 0.7147 (tt0) REVERT: E 396 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6576 (tm-30) REVERT: F 20 GLU cc_start: 0.7207 (mp0) cc_final: 0.6770 (mp0) REVERT: F 65 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6830 (mm-30) REVERT: F 67 LYS cc_start: 0.8223 (mttt) cc_final: 0.7961 (mttt) REVERT: F 71 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7458 (mmm160) REVERT: F 90 MET cc_start: 0.7619 (mtp) cc_final: 0.7399 (mtp) REVERT: F 125 ARG cc_start: 0.7338 (mtm-85) cc_final: 0.7086 (ttm110) REVERT: F 231 GLU cc_start: 0.7677 (mp0) cc_final: 0.7427 (mp0) REVERT: F 232 LEU cc_start: 0.8132 (mt) cc_final: 0.7714 (mp) REVERT: F 269 LYS cc_start: 0.7235 (mptt) cc_final: 0.6922 (mttt) REVERT: F 307 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: F 313 ASN cc_start: 0.7894 (m-40) cc_final: 0.7386 (m-40) REVERT: F 314 ARG cc_start: 0.7600 (tpt90) cc_final: 0.7147 (tpt90) REVERT: F 415 LYS cc_start: 0.8051 (tptt) cc_final: 0.7814 (tptt) REVERT: F 427 LYS cc_start: 0.7643 (mmmt) cc_final: 0.7179 (mmmt) REVERT: G 17 SER cc_start: 0.7883 (p) cc_final: 0.7527 (t) REVERT: G 54 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6908 (mm-30) REVERT: G 57 LYS cc_start: 0.7936 (mttt) cc_final: 0.7669 (mtmm) REVERT: G 60 LYS cc_start: 0.7504 (mtpp) cc_final: 0.7256 (ttpp) REVERT: G 61 MET cc_start: 0.7720 (mmm) cc_final: 0.7259 (mmp) REVERT: G 110 GLU cc_start: 0.7343 (tp30) cc_final: 0.6948 (tp30) REVERT: G 123 ARG cc_start: 0.7782 (ttt90) cc_final: 0.7325 (mtp85) REVERT: G 137 GLU cc_start: 0.8003 (pm20) cc_final: 0.7629 (pm20) REVERT: G 139 THR cc_start: 0.7922 (p) cc_final: 0.7696 (t) REVERT: G 152 LYS cc_start: 0.6646 (mtpt) cc_final: 0.6326 (mtpt) REVERT: G 167 THR cc_start: 0.8041 (m) cc_final: 0.7840 (p) REVERT: G 209 TYR cc_start: 0.8351 (m-80) cc_final: 0.7953 (m-80) REVERT: G 230 LYS cc_start: 0.8065 (mttm) cc_final: 0.7643 (mttm) REVERT: G 260 MET cc_start: 0.4626 (tmm) cc_final: 0.4358 (tmm) REVERT: G 264 MET cc_start: 0.5232 (mmm) cc_final: 0.4744 (mmm) REVERT: G 270 GLU cc_start: 0.6446 (mt-10) cc_final: 0.6226 (mt-10) REVERT: G 281 LYS cc_start: 0.7912 (mtpt) cc_final: 0.7544 (mtpt) REVERT: G 282 VAL cc_start: 0.8011 (t) cc_final: 0.7726 (p) REVERT: G 285 LYS cc_start: 0.7783 (mtpt) cc_final: 0.7548 (mtpt) REVERT: G 314 TYR cc_start: 0.8237 (t80) cc_final: 0.7848 (t80) REVERT: G 322 SER cc_start: 0.8028 (p) cc_final: 0.7710 (m) REVERT: G 396 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5686 (mm-30) REVERT: G 431 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6570 (mt-10) REVERT: G 434 SER cc_start: 0.7310 (m) cc_final: 0.6745 (p) REVERT: H 20 GLU cc_start: 0.6680 (mp0) cc_final: 0.6430 (mp0) REVERT: H 38 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6639 (mm-30) REVERT: H 61 GLU cc_start: 0.7237 (mm-30) cc_final: 0.7020 (mm-30) REVERT: H 112 GLU cc_start: 0.6865 (tp30) cc_final: 0.6528 (tp30) REVERT: H 129 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.7582 (t) REVERT: H 139 GLU cc_start: 0.7477 (pt0) cc_final: 0.7078 (pt0) REVERT: H 168 MET cc_start: 0.7544 (mtp) cc_final: 0.7333 (mtp) REVERT: H 178 MET cc_start: 0.7666 (mmm) cc_final: 0.7440 (tpp) REVERT: H 182 LEU cc_start: 0.8586 (mt) cc_final: 0.8236 (mp) REVERT: H 207 ARG cc_start: 0.8196 (ptp-170) cc_final: 0.7923 (ptp90) REVERT: H 241 THR cc_start: 0.7744 (m) cc_final: 0.7291 (t) REVERT: H 279 LYS cc_start: 0.7732 (tptt) cc_final: 0.7424 (tptt) REVERT: H 300 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6665 (mm-30) REVERT: H 352 ASP cc_start: 0.7096 (m-30) cc_final: 0.6757 (m-30) REVERT: H 379 ASP cc_start: 0.7745 (t0) cc_final: 0.7384 (m-30) REVERT: H 392 ARG cc_start: 0.7810 (ttt180) cc_final: 0.7530 (ttt180) REVERT: H 413 CYS cc_start: 0.7691 (t) cc_final: 0.7411 (p) REVERT: H 420 GLU cc_start: 0.7041 (tt0) cc_final: 0.6733 (tt0) REVERT: H 422 GLN cc_start: 0.7257 (mm110) cc_final: 0.7041 (mm-40) REVERT: H 427 LYS cc_start: 0.7793 (mmtm) cc_final: 0.7530 (mmtm) REVERT: H 436 GLU cc_start: 0.5552 (tm-30) cc_final: 0.5148 (tm-30) REVERT: H 441 GLN cc_start: 0.7728 (tt0) cc_final: 0.7435 (tt0) REVERT: H 443 MET cc_start: 0.6881 (ttp) cc_final: 0.6633 (ttm) REVERT: I 61 MET cc_start: 0.7875 (mmt) cc_final: 0.7225 (mmt) REVERT: I 64 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6308 (mmt90) REVERT: I 125 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8180 (ttpp) REVERT: I 126 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6927 (tm-30) REVERT: I 173 ASP cc_start: 0.7400 (t70) cc_final: 0.6950 (t70) REVERT: I 175 SER cc_start: 0.8746 (m) cc_final: 0.8325 (p) REVERT: I 189 ASP cc_start: 0.5776 (m-30) cc_final: 0.5111 (m-30) REVERT: I 202 ARG cc_start: 0.7802 (ttt-90) cc_final: 0.7296 (ttt-90) REVERT: I 260 MET cc_start: 0.6077 (mtt) cc_final: 0.5770 (mtt) REVERT: I 281 LYS cc_start: 0.7272 (mttt) cc_final: 0.7063 (mttt) REVERT: I 312 PHE cc_start: 0.7667 (m-80) cc_final: 0.7302 (m-80) REVERT: I 317 ARG cc_start: 0.6667 (ttt-90) cc_final: 0.6435 (ttt-90) REVERT: I 320 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: I 335 ASN cc_start: 0.7775 (t0) cc_final: 0.7356 (t0) REVERT: I 356 ASP cc_start: 0.7163 (t0) cc_final: 0.6809 (t70) REVERT: I 362 ARG cc_start: 0.7782 (ttp80) cc_final: 0.7510 (ttp-110) REVERT: I 389 GLU cc_start: 0.7680 (pt0) cc_final: 0.7373 (pt0) REVERT: I 396 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7039 (mt-10) REVERT: I 399 THR cc_start: 0.7889 (m) cc_final: 0.7473 (p) REVERT: I 408 GLN cc_start: 0.7661 (mt0) cc_final: 0.7419 (mt0) REVERT: I 418 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7469 (mtpp) REVERT: I 427 LYS cc_start: 0.7710 (tttt) cc_final: 0.7423 (ttpp) REVERT: I 428 GLU cc_start: 0.7670 (mp0) cc_final: 0.7450 (pm20) REVERT: I 431 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6761 (mm-30) REVERT: I 445 LYS cc_start: 0.7571 (mttp) cc_final: 0.7170 (tttp) REVERT: J 26 SER cc_start: 0.8052 (m) cc_final: 0.7595 (t) REVERT: J 59 VAL cc_start: 0.7608 (t) cc_final: 0.7364 (m) REVERT: J 94 LEU cc_start: 0.7577 (tp) cc_final: 0.7347 (tp) REVERT: J 236 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8170 (mtpt) REVERT: J 264 ASP cc_start: 0.6332 (t0) cc_final: 0.6001 (t0) REVERT: J 274 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7329 (mt-10) REVERT: J 336 ARG cc_start: 0.7152 (mtm180) cc_final: 0.6826 (mtm180) REVERT: J 341 GLN cc_start: 0.7208 (mt0) cc_final: 0.6983 (mt0) REVERT: J 377 GLU cc_start: 0.6711 (tp30) cc_final: 0.6257 (tp30) REVERT: J 384 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6863 (mm-30) REVERT: J 404 GLN cc_start: 0.7654 (mt0) cc_final: 0.7394 (mt0) REVERT: J 420 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7079 (tt0) REVERT: J 427 LYS cc_start: 0.7910 (mmtp) cc_final: 0.7680 (mmtp) REVERT: J 436 GLU cc_start: 0.7086 (tm-30) cc_final: 0.6825 (tm-30) REVERT: K 153 MET cc_start: -0.0733 (tmm) cc_final: -0.1319 (tmm) REVERT: K 283 MET cc_start: 0.3712 (mmm) cc_final: 0.3207 (mmm) REVERT: L 34 ILE cc_start: 0.8735 (mt) cc_final: 0.8435 (mt) REVERT: L 57 GLU cc_start: 0.7486 (tp30) cc_final: 0.6647 (tp30) REVERT: L 61 LYS cc_start: 0.8443 (mtmt) cc_final: 0.7535 (mtmt) REVERT: L 62 ARG cc_start: 0.7919 (mtm180) cc_final: 0.7679 (mtp180) REVERT: L 100 GLU cc_start: 0.7613 (tt0) cc_final: 0.7384 (tt0) REVERT: L 107 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6711 (pt0) REVERT: L 166 TYR cc_start: 0.8172 (t80) cc_final: 0.7614 (t80) REVERT: L 167 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7207 (mm-30) REVERT: L 253 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8146 (mm-30) REVERT: L 259 GLU cc_start: 0.7647 (tp30) cc_final: 0.7310 (tp30) REVERT: L 300 SER cc_start: 0.8449 (p) cc_final: 0.8140 (m) REVERT: L 312 ARG cc_start: 0.8831 (tpt90) cc_final: 0.8468 (tpt-90) REVERT: L 326 LYS cc_start: 0.8189 (tttp) cc_final: 0.7887 (tttp) REVERT: M 30 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7517 (mm-30) REVERT: M 31 ASP cc_start: 0.6613 (p0) cc_final: 0.6295 (p0) REVERT: M 67 THR cc_start: 0.8537 (m) cc_final: 0.8016 (p) REVERT: M 128 ASN cc_start: 0.7699 (t0) cc_final: 0.7323 (p0) REVERT: M 130 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7441 (ttm170) REVERT: M 134 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7136 (mt-10) REVERT: M 186 TYR cc_start: 0.7714 (m-80) cc_final: 0.7458 (m-80) REVERT: M 189 GLN cc_start: 0.8249 (mt0) cc_final: 0.7907 (mp10) REVERT: M 226 LYS cc_start: 0.8489 (pttt) cc_final: 0.7769 (ptpt) REVERT: M 227 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7345 (mm-30) REVERT: M 238 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8093 (mmtt) REVERT: M 252 ASN cc_start: 0.8213 (m-40) cc_final: 0.7886 (m110) REVERT: M 253 TYR cc_start: 0.8068 (t80) cc_final: 0.7845 (t80) REVERT: M 276 GLU cc_start: 0.7350 (tp30) cc_final: 0.7047 (tp30) REVERT: M 287 TYR cc_start: 0.8130 (t80) cc_final: 0.7831 (t80) REVERT: M 294 ASN cc_start: 0.8237 (p0) cc_final: 0.7667 (p0) REVERT: M 301 ARG cc_start: 0.8174 (ptm-80) cc_final: 0.7880 (ptm-80) REVERT: M 303 LYS cc_start: 0.8667 (tttp) cc_final: 0.8338 (mtpp) REVERT: M 322 MET cc_start: 0.7230 (mtm) cc_final: 0.6856 (mtm) REVERT: M 347 SER cc_start: 0.7597 (t) cc_final: 0.7139 (p) REVERT: M 358 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7589 (mm-40) REVERT: M 409 MET cc_start: 0.8010 (mmm) cc_final: 0.7620 (mtm) REVERT: N 55 ARG cc_start: 0.7804 (mtt180) cc_final: 0.7334 (mtt180) REVERT: N 62 TYR cc_start: 0.8708 (p90) cc_final: 0.8407 (p90) REVERT: N 91 LYS cc_start: 0.7779 (ptmm) cc_final: 0.7500 (ptmm) REVERT: N 193 GLU cc_start: 0.7313 (tp30) cc_final: 0.6978 (tp30) REVERT: N 194 ARG cc_start: 0.7745 (tpt90) cc_final: 0.7175 (tpt-90) REVERT: N 196 TYR cc_start: 0.7804 (m-80) cc_final: 0.7534 (m-10) REVERT: N 202 LEU cc_start: 0.8688 (mt) cc_final: 0.8380 (mt) REVERT: N 224 ARG cc_start: 0.8093 (mtt90) cc_final: 0.7824 (mtt90) REVERT: N 228 GLU cc_start: 0.8149 (tp30) cc_final: 0.7815 (tp30) REVERT: N 232 ARG cc_start: 0.8097 (mtp85) cc_final: 0.7896 (ttm170) REVERT: N 255 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6783 (mm-30) outliers start: 123 outliers final: 79 residues processed: 1389 average time/residue: 0.2434 time to fit residues: 517.3257 Evaluate side-chains 1414 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 1325 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 1971 LEU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2099 ILE Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain A residue 2224 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 212 GLU Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 194 GLU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 132 LYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 368 LYS Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 339 VAL Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 152 CYS Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 268 GLN Chi-restraints excluded: chain M residue 282 MET Chi-restraints excluded: chain M residue 293 TYR Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain M residue 356 LEU Chi-restraints excluded: chain M residue 378 LEU Chi-restraints excluded: chain N residue 131 LYS Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 188 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 75 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 352 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 296 optimal weight: 0.9990 chunk 494 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 225 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 203 GLN E 280 ASN E 392 ASN ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN ** L 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN M 354 ASN M 384 ASN N 235 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.171444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138117 restraints weight = 66127.697| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.69 r_work: 0.3442 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 41572 Z= 0.162 Angle : 0.564 8.780 56164 Z= 0.281 Chirality : 0.042 0.233 6364 Planarity : 0.004 0.061 7187 Dihedral : 6.618 148.170 5717 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.62 % Allowed : 14.94 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.65 (0.12), residues: 5082 helix: 1.75 (0.11), residues: 2325 sheet: 0.43 (0.18), residues: 821 loop : 0.79 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 184 TYR 0.016 0.001 TYR I 314 PHE 0.014 0.001 PHE A1933 TRP 0.031 0.001 TRP A1232 HIS 0.009 0.001 HIS L 275 Details of bonding type rmsd covalent geometry : bond 0.00359 (41572) covalent geometry : angle 0.56351 (56164) hydrogen bonds : bond 0.03830 ( 1947) hydrogen bonds : angle 4.24158 ( 5517) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1450 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1334 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 789 ARG cc_start: 0.8009 (mtp180) cc_final: 0.7743 (mtp180) REVERT: A 796 GLN cc_start: 0.7629 (tp-100) cc_final: 0.7148 (tp-100) REVERT: A 816 LEU cc_start: 0.8253 (mt) cc_final: 0.7959 (mm) REVERT: A 838 LYS cc_start: 0.8355 (tttt) cc_final: 0.7950 (ttpp) REVERT: A 850 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7398 (tp30) REVERT: A 861 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7580 (mt-10) REVERT: A 862 GLU cc_start: 0.8631 (mm-30) cc_final: 0.7866 (mm-30) REVERT: A 863 GLN cc_start: 0.7709 (tt0) cc_final: 0.7328 (tp40) REVERT: A 864 SER cc_start: 0.7619 (m) cc_final: 0.7320 (t) REVERT: A 867 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7388 (mmt180) REVERT: A 1099 LEU cc_start: 0.6961 (tp) cc_final: 0.6648 (tp) REVERT: A 1192 HIS cc_start: 0.7423 (m170) cc_final: 0.7095 (m90) REVERT: A 1215 CYS cc_start: 0.7607 (t) cc_final: 0.6397 (p) REVERT: A 1242 GLN cc_start: 0.2615 (pt0) cc_final: 0.2214 (mm-40) REVERT: A 1261 MET cc_start: 0.3042 (mmp) cc_final: 0.2611 (mmp) REVERT: A 1337 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7595 (mp0) REVERT: A 1362 VAL cc_start: 0.7825 (t) cc_final: 0.7573 (m) REVERT: A 1363 ARG cc_start: 0.7889 (ttt180) cc_final: 0.7425 (mtp85) REVERT: A 1364 LEU cc_start: 0.8409 (tp) cc_final: 0.7987 (tt) REVERT: A 1388 LEU cc_start: 0.8302 (mt) cc_final: 0.8099 (mt) REVERT: A 1390 TYR cc_start: 0.8016 (t80) cc_final: 0.7737 (t80) REVERT: A 1406 LYS cc_start: 0.7218 (mttt) cc_final: 0.6897 (mttm) REVERT: A 1428 GLU cc_start: 0.6837 (tp30) cc_final: 0.6590 (tp30) REVERT: A 1433 LYS cc_start: 0.7819 (mttt) cc_final: 0.7476 (mtmt) REVERT: A 1442 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7137 (mt-10) REVERT: A 1758 GLU cc_start: 0.8056 (tt0) cc_final: 0.7731 (mt-10) REVERT: A 1769 ARG cc_start: 0.7669 (mtp-110) cc_final: 0.7444 (mtm180) REVERT: A 1774 ILE cc_start: 0.8670 (tp) cc_final: 0.8132 (mt) REVERT: A 1872 TYR cc_start: 0.6298 (m-80) cc_final: 0.5970 (m-80) REVERT: A 1877 ARG cc_start: 0.6649 (tpm170) cc_final: 0.6349 (tpm170) REVERT: A 1897 SER cc_start: 0.7867 (t) cc_final: 0.7492 (p) REVERT: A 1901 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7308 (mm-30) REVERT: A 1909 LYS cc_start: 0.7724 (tttt) cc_final: 0.7394 (ttmm) REVERT: A 1911 LYS cc_start: 0.8138 (tttt) cc_final: 0.7899 (tppp) REVERT: A 1917 VAL cc_start: 0.8173 (p) cc_final: 0.7903 (m) REVERT: A 1921 SER cc_start: 0.7074 (t) cc_final: 0.6759 (p) REVERT: A 1958 ARG cc_start: 0.7606 (mtt180) cc_final: 0.7237 (mtt180) REVERT: A 1974 HIS cc_start: 0.7933 (m-70) cc_final: 0.7593 (m170) REVERT: A 1982 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7160 (tt) REVERT: A 1986 ASP cc_start: 0.6942 (p0) cc_final: 0.6561 (p0) REVERT: A 2000 ASP cc_start: 0.8029 (t70) cc_final: 0.7218 (t0) REVERT: A 2004 GLN cc_start: 0.7428 (mm-40) cc_final: 0.7189 (mm-40) REVERT: A 2052 MET cc_start: 0.6473 (mmm) cc_final: 0.6072 (tmm) REVERT: A 2206 GLU cc_start: 0.7285 (tt0) cc_final: 0.6690 (tm-30) REVERT: A 2207 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7383 (ttt180) REVERT: B 267 THR cc_start: 0.8114 (m) cc_final: 0.7776 (p) REVERT: B 277 TRP cc_start: 0.8301 (m100) cc_final: 0.8038 (m100) REVERT: B 294 VAL cc_start: 0.8903 (t) cc_final: 0.8681 (m) REVERT: C 407 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8083 (mptt) REVERT: C 469 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7328 (mtm-85) REVERT: E 14 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7744 (mtp180) REVERT: E 90 LYS cc_start: 0.7694 (mmtp) cc_final: 0.7400 (mmtp) REVERT: E 101 VAL cc_start: 0.7861 (t) cc_final: 0.7599 (m) REVERT: E 123 ARG cc_start: 0.7444 (mtp180) cc_final: 0.7054 (tpp80) REVERT: E 127 THR cc_start: 0.7738 (p) cc_final: 0.7524 (p) REVERT: E 129 GLU cc_start: 0.6891 (pm20) cc_final: 0.6394 (pm20) REVERT: E 134 GLU cc_start: 0.7382 (tt0) cc_final: 0.6854 (tt0) REVERT: E 168 LYS cc_start: 0.8058 (mptt) cc_final: 0.7662 (mptt) REVERT: E 209 TYR cc_start: 0.7863 (m-80) cc_final: 0.7176 (m-80) REVERT: E 255 ASP cc_start: 0.7279 (t0) cc_final: 0.6956 (t70) REVERT: E 258 SER cc_start: 0.7684 (m) cc_final: 0.7036 (p) REVERT: E 262 GLN cc_start: 0.6626 (mt0) cc_final: 0.6393 (mt0) REVERT: E 264 MET cc_start: 0.6412 (mmm) cc_final: 0.6082 (mmm) REVERT: E 265 LYS cc_start: 0.8194 (tttt) cc_final: 0.7814 (tttt) REVERT: E 274 LYS cc_start: 0.6702 (tttm) cc_final: 0.6212 (tttm) REVERT: E 278 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: E 285 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7221 (ttmt) REVERT: E 304 VAL cc_start: 0.7826 (m) cc_final: 0.7503 (p) REVERT: E 317 ARG cc_start: 0.7357 (ttt-90) cc_final: 0.7060 (ttt180) REVERT: E 333 ARG cc_start: 0.7774 (mmt180) cc_final: 0.7489 (mmt90) REVERT: E 336 CYS cc_start: 0.6769 (p) cc_final: 0.6411 (p) REVERT: E 337 VAL cc_start: 0.7370 (t) cc_final: 0.6939 (m) REVERT: E 356 ASP cc_start: 0.6950 (t70) cc_final: 0.6568 (t0) REVERT: E 388 GLU cc_start: 0.7396 (tt0) cc_final: 0.7183 (tt0) REVERT: E 396 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6549 (tm-30) REVERT: F 20 GLU cc_start: 0.7251 (mp0) cc_final: 0.6803 (mp0) REVERT: F 65 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6808 (mm-30) REVERT: F 67 LYS cc_start: 0.8275 (mttt) cc_final: 0.8010 (mttt) REVERT: F 125 ARG cc_start: 0.7391 (mtm-85) cc_final: 0.7129 (ttm110) REVERT: F 231 GLU cc_start: 0.7744 (mp0) cc_final: 0.7488 (mp0) REVERT: F 232 LEU cc_start: 0.8151 (mt) cc_final: 0.7718 (mp) REVERT: F 269 LYS cc_start: 0.7221 (mptt) cc_final: 0.6912 (mttt) REVERT: F 307 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6812 (mp0) REVERT: F 314 ARG cc_start: 0.7613 (tpt90) cc_final: 0.7392 (tpt90) REVERT: F 336 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7823 (mmm160) REVERT: F 365 LYS cc_start: 0.8193 (mmtm) cc_final: 0.7991 (mmtm) REVERT: F 400 ARG cc_start: 0.7377 (mtm-85) cc_final: 0.6952 (ttm-80) REVERT: F 415 LYS cc_start: 0.8036 (tptt) cc_final: 0.7801 (tptt) REVERT: F 427 LYS cc_start: 0.7619 (mmmt) cc_final: 0.7169 (mmmt) REVERT: F 428 ARG cc_start: 0.7152 (tpt170) cc_final: 0.6805 (tpt170) REVERT: G 15 ILE cc_start: 0.8084 (mt) cc_final: 0.7794 (mm) REVERT: G 17 SER cc_start: 0.7971 (p) cc_final: 0.7541 (t) REVERT: G 54 GLU cc_start: 0.7297 (mm-30) cc_final: 0.6933 (mm-30) REVERT: G 57 LYS cc_start: 0.7907 (mttt) cc_final: 0.7620 (mtmm) REVERT: G 60 LYS cc_start: 0.7496 (mtpp) cc_final: 0.7258 (ttpp) REVERT: G 61 MET cc_start: 0.7696 (mmm) cc_final: 0.7425 (mmm) REVERT: G 96 MET cc_start: 0.7189 (ttt) cc_final: 0.6895 (ttt) REVERT: G 110 GLU cc_start: 0.7404 (tp30) cc_final: 0.6990 (tp30) REVERT: G 123 ARG cc_start: 0.7771 (ttt90) cc_final: 0.7305 (mtp85) REVERT: G 137 GLU cc_start: 0.8056 (pm20) cc_final: 0.7610 (pm20) REVERT: G 139 THR cc_start: 0.8038 (p) cc_final: 0.7811 (t) REVERT: G 152 LYS cc_start: 0.6727 (mtpt) cc_final: 0.6432 (mtpt) REVERT: G 167 THR cc_start: 0.8063 (m) cc_final: 0.7845 (p) REVERT: G 181 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7261 (mm-40) REVERT: G 209 TYR cc_start: 0.8343 (m-80) cc_final: 0.7991 (m-80) REVERT: G 260 MET cc_start: 0.4589 (tmm) cc_final: 0.4325 (tmm) REVERT: G 264 MET cc_start: 0.5218 (mmm) cc_final: 0.4725 (mmm) REVERT: G 281 LYS cc_start: 0.7904 (mtpt) cc_final: 0.7539 (mtpt) REVERT: G 282 VAL cc_start: 0.7972 (t) cc_final: 0.7689 (p) REVERT: G 285 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7531 (mtpt) REVERT: G 314 TYR cc_start: 0.8238 (t80) cc_final: 0.7873 (t80) REVERT: G 322 SER cc_start: 0.8031 (p) cc_final: 0.7728 (m) REVERT: G 371 MET cc_start: 0.7509 (mtp) cc_final: 0.6929 (mtt) REVERT: G 396 GLU cc_start: 0.6340 (mm-30) cc_final: 0.5722 (mm-30) REVERT: G 431 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6601 (mt-10) REVERT: G 434 SER cc_start: 0.7311 (m) cc_final: 0.6747 (p) REVERT: H 20 GLU cc_start: 0.6735 (mp0) cc_final: 0.6510 (mp0) REVERT: H 38 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6680 (mm-30) REVERT: H 61 GLU cc_start: 0.7239 (mm-30) cc_final: 0.7020 (mm-30) REVERT: H 112 GLU cc_start: 0.6952 (tp30) cc_final: 0.6570 (tp30) REVERT: H 129 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7578 (t) REVERT: H 132 LYS cc_start: 0.8707 (ptpp) cc_final: 0.8468 (ptpp) REVERT: H 139 GLU cc_start: 0.7524 (pt0) cc_final: 0.7128 (pt0) REVERT: H 178 MET cc_start: 0.7695 (mmm) cc_final: 0.7471 (tpp) REVERT: H 207 ARG cc_start: 0.8222 (ptp-170) cc_final: 0.7927 (ptp90) REVERT: H 225 VAL cc_start: 0.8813 (p) cc_final: 0.8592 (m) REVERT: H 241 THR cc_start: 0.7739 (m) cc_final: 0.7310 (t) REVERT: H 271 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6552 (mt-10) REVERT: H 279 LYS cc_start: 0.7724 (tptt) cc_final: 0.7429 (tptt) REVERT: H 300 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6603 (mm-30) REVERT: H 334 ARG cc_start: 0.7370 (ttt180) cc_final: 0.7103 (ttt180) REVERT: H 352 ASP cc_start: 0.7053 (m-30) cc_final: 0.6722 (m-30) REVERT: H 379 ASP cc_start: 0.7739 (t0) cc_final: 0.7411 (m-30) REVERT: H 392 ARG cc_start: 0.7761 (ttt180) cc_final: 0.7478 (ttt180) REVERT: H 413 CYS cc_start: 0.7717 (t) cc_final: 0.7425 (p) REVERT: H 420 GLU cc_start: 0.7017 (tt0) cc_final: 0.6776 (tt0) REVERT: H 427 LYS cc_start: 0.7792 (mmtm) cc_final: 0.7533 (mmtm) REVERT: H 436 GLU cc_start: 0.5586 (tm-30) cc_final: 0.5193 (tm-30) REVERT: H 441 GLN cc_start: 0.7648 (tt0) cc_final: 0.7351 (tt0) REVERT: H 443 MET cc_start: 0.6892 (ttp) cc_final: 0.6634 (ttm) REVERT: I 60 LYS cc_start: 0.7906 (mtmt) cc_final: 0.7691 (mmmt) REVERT: I 61 MET cc_start: 0.7891 (mmt) cc_final: 0.7225 (mmt) REVERT: I 64 ARG cc_start: 0.7017 (OUTLIER) cc_final: 0.6348 (mmt90) REVERT: I 125 LYS cc_start: 0.8464 (ttmt) cc_final: 0.8231 (ttpp) REVERT: I 173 ASP cc_start: 0.7393 (t70) cc_final: 0.6956 (t70) REVERT: I 175 SER cc_start: 0.8743 (m) cc_final: 0.8307 (p) REVERT: I 189 ASP cc_start: 0.5868 (m-30) cc_final: 0.4987 (m-30) REVERT: I 202 ARG cc_start: 0.7774 (ttt-90) cc_final: 0.7404 (ttt-90) REVERT: I 242 ASP cc_start: 0.7414 (m-30) cc_final: 0.7159 (m-30) REVERT: I 260 MET cc_start: 0.6078 (mtt) cc_final: 0.5786 (mtt) REVERT: I 280 ASN cc_start: 0.7480 (m-40) cc_final: 0.6942 (m-40) REVERT: I 281 LYS cc_start: 0.7315 (mttt) cc_final: 0.7097 (mttt) REVERT: I 312 PHE cc_start: 0.7643 (m-80) cc_final: 0.7287 (m-80) REVERT: I 317 ARG cc_start: 0.6728 (ttt-90) cc_final: 0.6481 (ttt-90) REVERT: I 320 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6322 (mp0) REVERT: I 335 ASN cc_start: 0.7756 (t0) cc_final: 0.7335 (t0) REVERT: I 356 ASP cc_start: 0.7146 (t0) cc_final: 0.6782 (t70) REVERT: I 376 LYS cc_start: 0.7622 (tptt) cc_final: 0.7300 (tppt) REVERT: I 389 GLU cc_start: 0.7683 (pt0) cc_final: 0.7367 (pt0) REVERT: I 396 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7131 (mt-10) REVERT: I 399 THR cc_start: 0.7834 (m) cc_final: 0.7455 (p) REVERT: I 418 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7465 (mtpp) REVERT: I 427 LYS cc_start: 0.7756 (tttt) cc_final: 0.7420 (ttpp) REVERT: I 428 GLU cc_start: 0.7696 (mp0) cc_final: 0.7428 (pm20) REVERT: I 431 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6904 (mm-30) REVERT: I 445 LYS cc_start: 0.7517 (mttp) cc_final: 0.7124 (tttp) REVERT: J 26 SER cc_start: 0.8039 (m) cc_final: 0.7590 (t) REVERT: J 50 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7723 (mm) REVERT: J 59 VAL cc_start: 0.7569 (t) cc_final: 0.7329 (m) REVERT: J 83 LYS cc_start: 0.7532 (mtmt) cc_final: 0.7152 (mtmt) REVERT: J 94 LEU cc_start: 0.7589 (tp) cc_final: 0.7356 (tp) REVERT: J 236 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8148 (mtpt) REVERT: J 264 ASP cc_start: 0.6329 (t0) cc_final: 0.6010 (t0) REVERT: J 274 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7282 (mt-10) REVERT: J 377 GLU cc_start: 0.6761 (tp30) cc_final: 0.6320 (tp30) REVERT: J 384 GLU cc_start: 0.7252 (mm-30) cc_final: 0.6878 (mm-30) REVERT: J 404 GLN cc_start: 0.7685 (mt0) cc_final: 0.7453 (mt0) REVERT: J 420 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7148 (tt0) REVERT: J 427 LYS cc_start: 0.7916 (mmtp) cc_final: 0.7688 (mmtp) REVERT: J 436 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6858 (tm-30) REVERT: K 153 MET cc_start: -0.0749 (tmm) cc_final: -0.1299 (tmm) REVERT: K 283 MET cc_start: 0.3652 (mmm) cc_final: 0.3158 (mmm) REVERT: L 11 ASP cc_start: 0.8277 (t0) cc_final: 0.8048 (t70) REVERT: L 34 ILE cc_start: 0.8721 (mt) cc_final: 0.8418 (mt) REVERT: L 57 GLU cc_start: 0.7560 (tp30) cc_final: 0.6674 (tp30) REVERT: L 61 LYS cc_start: 0.8507 (mtmt) cc_final: 0.7678 (mtmt) REVERT: L 62 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7663 (mtp180) REVERT: L 100 GLU cc_start: 0.7681 (tt0) cc_final: 0.7462 (tt0) REVERT: L 107 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6729 (pt0) REVERT: L 166 TYR cc_start: 0.8156 (t80) cc_final: 0.7598 (t80) REVERT: L 167 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7241 (mm-30) REVERT: L 259 GLU cc_start: 0.7651 (tp30) cc_final: 0.7298 (tp30) REVERT: L 300 SER cc_start: 0.8525 (p) cc_final: 0.8283 (m) REVERT: L 312 ARG cc_start: 0.8848 (tpt90) cc_final: 0.8428 (tpt-90) REVERT: L 326 LYS cc_start: 0.8239 (tttp) cc_final: 0.7904 (tttp) REVERT: M 30 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7563 (mm-30) REVERT: M 31 ASP cc_start: 0.6597 (p0) cc_final: 0.6264 (p0) REVERT: M 67 THR cc_start: 0.8512 (m) cc_final: 0.8010 (p) REVERT: M 128 ASN cc_start: 0.7757 (t0) cc_final: 0.7388 (p0) REVERT: M 130 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7306 (ttm170) REVERT: M 134 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7105 (mt-10) REVERT: M 186 TYR cc_start: 0.7766 (m-80) cc_final: 0.7424 (m-80) REVERT: M 189 GLN cc_start: 0.8309 (mt0) cc_final: 0.7960 (mp10) REVERT: M 205 GLN cc_start: 0.7933 (mm110) cc_final: 0.7636 (mm110) REVERT: M 226 LYS cc_start: 0.8534 (pttt) cc_final: 0.7832 (ptpt) REVERT: M 227 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7391 (mm-30) REVERT: M 238 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8118 (mmtt) REVERT: M 252 ASN cc_start: 0.8211 (m-40) cc_final: 0.7886 (m110) REVERT: M 276 GLU cc_start: 0.7344 (tp30) cc_final: 0.7036 (tp30) REVERT: M 287 TYR cc_start: 0.8121 (t80) cc_final: 0.7820 (t80) REVERT: M 294 ASN cc_start: 0.8255 (p0) cc_final: 0.7675 (p0) REVERT: M 301 ARG cc_start: 0.8175 (ptm-80) cc_final: 0.7866 (ptm-80) REVERT: M 303 LYS cc_start: 0.8673 (tttp) cc_final: 0.8343 (mtpp) REVERT: M 322 MET cc_start: 0.7313 (mtm) cc_final: 0.6938 (mtm) REVERT: M 347 SER cc_start: 0.7644 (t) cc_final: 0.7180 (p) REVERT: M 358 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7575 (mm-40) REVERT: M 376 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6628 (ttm) REVERT: N 55 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7333 (mtt180) REVERT: N 62 TYR cc_start: 0.8714 (p90) cc_final: 0.8434 (p90) REVERT: N 91 LYS cc_start: 0.7822 (ptmm) cc_final: 0.7549 (ptmm) REVERT: N 128 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7638 (ttm110) REVERT: N 149 ASP cc_start: 0.6718 (t0) cc_final: 0.6505 (t70) REVERT: N 193 GLU cc_start: 0.7333 (tp30) cc_final: 0.6957 (tp30) REVERT: N 196 TYR cc_start: 0.7801 (m-80) cc_final: 0.7524 (m-10) REVERT: N 202 LEU cc_start: 0.8705 (mt) cc_final: 0.8409 (mt) REVERT: N 224 ARG cc_start: 0.8127 (mtt90) cc_final: 0.7848 (mtt90) REVERT: N 228 GLU cc_start: 0.8130 (tp30) cc_final: 0.7808 (tp30) REVERT: N 232 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7882 (ttm170) REVERT: N 255 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6773 (mm-30) outliers start: 116 outliers final: 85 residues processed: 1376 average time/residue: 0.2461 time to fit residues: 517.8729 Evaluate side-chains 1413 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1318 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 841 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2099 ILE Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain A residue 2224 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 360 THR Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 132 LYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 340 TYR Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 368 LYS Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 177 ARG Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 ILE Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 339 VAL Chi-restraints excluded: chain L residue 350 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 152 CYS Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 211 GLN Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 282 MET Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain M residue 356 LEU Chi-restraints excluded: chain M residue 376 MET Chi-restraints excluded: chain M residue 378 LEU Chi-restraints excluded: chain N residue 131 LYS Chi-restraints excluded: chain N residue 188 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 290 optimal weight: 2.9990 chunk 375 optimal weight: 0.0980 chunk 199 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 chunk 423 optimal weight: 0.9990 chunk 358 optimal weight: 0.5980 chunk 30 optimal weight: 0.0980 chunk 26 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2017 HIS E 280 ASN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 GLN I 34 GLN I 408 GLN ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN J 255 GLN ** L 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 384 ASN N 235 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.172238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139122 restraints weight = 66128.201| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.75 r_work: 0.3466 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41572 Z= 0.118 Angle : 0.556 13.051 56164 Z= 0.275 Chirality : 0.041 0.220 6364 Planarity : 0.004 0.061 7187 Dihedral : 6.471 147.455 5717 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.19 % Allowed : 15.78 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.75 (0.12), residues: 5082 helix: 1.83 (0.11), residues: 2328 sheet: 0.46 (0.18), residues: 817 loop : 0.83 (0.15), residues: 1937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG J 40 TYR 0.030 0.001 TYR C 413 PHE 0.020 0.001 PHE A1990 TRP 0.033 0.001 TRP A1232 HIS 0.023 0.001 HIS A1290 Details of bonding type rmsd covalent geometry : bond 0.00263 (41572) covalent geometry : angle 0.55648 (56164) hydrogen bonds : bond 0.03533 ( 1947) hydrogen bonds : angle 4.16299 ( 5517) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 1317 time to evaluate : 1.364 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: A 787 GLU cc_start: 0.6944 (tt0) cc_final: 0.6506 (tp30) REVERT: A 796 GLN cc_start: 0.7637 (tp-100) cc_final: 0.7152 (tp-100) REVERT: A 816 LEU cc_start: 0.8237 (mt) cc_final: 0.7965 (mm) REVERT: A 838 LYS cc_start: 0.8323 (tttt) cc_final: 0.7916 (ttpp) REVERT: A 861 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7509 (mt-10) REVERT: A 862 GLU cc_start: 0.8617 (mm-30) cc_final: 0.7780 (mm-30) REVERT: A 863 GLN cc_start: 0.7720 (tt0) cc_final: 0.7327 (tp40) REVERT: A 864 SER cc_start: 0.7594 (m) cc_final: 0.7301 (t) REVERT: A 867 ARG cc_start: 0.7875 (mtt180) cc_final: 0.7403 (mmt180) REVERT: A 1099 LEU cc_start: 0.7037 (tp) cc_final: 0.6783 (tp) REVERT: A 1192 HIS cc_start: 0.7343 (m170) cc_final: 0.7008 (m90) REVERT: A 1215 CYS cc_start: 0.7457 (t) cc_final: 0.6769 (t) REVERT: A 1227 MET cc_start: 0.7548 (tpp) cc_final: 0.7134 (tpp) REVERT: A 1242 GLN cc_start: 0.2355 (pt0) cc_final: 0.2142 (mm-40) REVERT: A 1261 MET cc_start: 0.2988 (mmp) cc_final: 0.2577 (mmp) REVERT: A 1337 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7516 (mp0) REVERT: A 1362 VAL cc_start: 0.7815 (t) cc_final: 0.7571 (m) REVERT: A 1363 ARG cc_start: 0.7955 (ttt180) cc_final: 0.7484 (mtp85) REVERT: A 1364 LEU cc_start: 0.8394 (tp) cc_final: 0.7981 (tt) REVERT: A 1390 TYR cc_start: 0.8026 (t80) cc_final: 0.7749 (t80) REVERT: A 1406 LYS cc_start: 0.7301 (mttt) cc_final: 0.7021 (mttm) REVERT: A 1428 GLU cc_start: 0.6842 (tp30) cc_final: 0.6589 (tp30) REVERT: A 1433 LYS cc_start: 0.7802 (mttt) cc_final: 0.7418 (mtmt) REVERT: A 1442 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7133 (mt-10) REVERT: A 1758 GLU cc_start: 0.7995 (tt0) cc_final: 0.7692 (mt-10) REVERT: A 1769 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7400 (mtm180) REVERT: A 1872 TYR cc_start: 0.6231 (m-80) cc_final: 0.5917 (m-80) REVERT: A 1877 ARG cc_start: 0.6602 (tpm170) cc_final: 0.6342 (tpm170) REVERT: A 1897 SER cc_start: 0.7741 (t) cc_final: 0.7351 (p) REVERT: A 1901 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 1909 LYS cc_start: 0.7697 (tttt) cc_final: 0.7364 (ttmm) REVERT: A 1911 LYS cc_start: 0.8098 (tttt) cc_final: 0.7872 (tppp) REVERT: A 1916 ARG cc_start: 0.7605 (mtp85) cc_final: 0.7251 (mtp180) REVERT: A 1917 VAL cc_start: 0.8167 (p) cc_final: 0.7875 (m) REVERT: A 1921 SER cc_start: 0.7020 (t) cc_final: 0.6652 (p) REVERT: A 1958 ARG cc_start: 0.7644 (mtt180) cc_final: 0.7272 (mtt180) REVERT: A 1974 HIS cc_start: 0.7858 (m-70) cc_final: 0.7495 (m170) REVERT: A 1982 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7145 (tt) REVERT: A 1986 ASP cc_start: 0.6941 (p0) cc_final: 0.6566 (p0) REVERT: A 2000 ASP cc_start: 0.7984 (t70) cc_final: 0.7164 (t0) REVERT: A 2004 GLN cc_start: 0.7420 (mm-40) cc_final: 0.7212 (mm-40) REVERT: A 2052 MET cc_start: 0.6448 (mmm) cc_final: 0.6044 (tmm) REVERT: A 2058 ARG cc_start: 0.6825 (tpp-160) cc_final: 0.6244 (tpp-160) REVERT: A 2206 GLU cc_start: 0.7279 (tt0) cc_final: 0.6666 (tm-30) REVERT: A 2207 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7304 (ttt180) REVERT: B 267 THR cc_start: 0.8116 (m) cc_final: 0.7778 (p) REVERT: B 277 TRP cc_start: 0.8273 (m100) cc_final: 0.7996 (m100) REVERT: B 294 VAL cc_start: 0.8874 (t) cc_final: 0.8652 (m) REVERT: B 297 ARG cc_start: 0.7923 (mtp180) cc_final: 0.7682 (mtp180) REVERT: C 407 LYS cc_start: 0.8288 (mmtt) cc_final: 0.8056 (mptt) REVERT: E 14 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7685 (mtp180) REVERT: E 60 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7562 (mtpt) REVERT: E 90 LYS cc_start: 0.7667 (mmtp) cc_final: 0.7344 (mmtp) REVERT: E 101 VAL cc_start: 0.7870 (t) cc_final: 0.7578 (m) REVERT: E 123 ARG cc_start: 0.7449 (mtp180) cc_final: 0.7042 (tpp80) REVERT: E 127 THR cc_start: 0.7699 (p) cc_final: 0.7466 (p) REVERT: E 129 GLU cc_start: 0.6891 (pm20) cc_final: 0.6376 (pm20) REVERT: E 168 LYS cc_start: 0.8015 (mptt) cc_final: 0.7663 (mptt) REVERT: E 258 SER cc_start: 0.7689 (m) cc_final: 0.7034 (p) REVERT: E 262 GLN cc_start: 0.6566 (mt0) cc_final: 0.6339 (mt0) REVERT: E 264 MET cc_start: 0.6394 (mmm) cc_final: 0.6048 (mmm) REVERT: E 265 LYS cc_start: 0.8194 (tttt) cc_final: 0.7803 (tttt) REVERT: E 274 LYS cc_start: 0.6621 (tttm) cc_final: 0.6117 (tttm) REVERT: E 278 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: E 285 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7180 (ttmt) REVERT: E 304 VAL cc_start: 0.7761 (m) cc_final: 0.7454 (p) REVERT: E 317 ARG cc_start: 0.7297 (ttt-90) cc_final: 0.7001 (ttt180) REVERT: E 336 CYS cc_start: 0.6803 (p) cc_final: 0.6461 (p) REVERT: E 337 VAL cc_start: 0.7335 (t) cc_final: 0.6904 (m) REVERT: E 356 ASP cc_start: 0.6923 (t70) cc_final: 0.6542 (t0) REVERT: E 369 GLN cc_start: 0.7218 (mp10) cc_final: 0.6988 (mp10) REVERT: E 388 GLU cc_start: 0.7451 (tt0) cc_final: 0.7200 (tt0) REVERT: E 396 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6573 (tm-30) REVERT: E 426 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6293 (mp0) REVERT: E 441 LYS cc_start: 0.7525 (mtmm) cc_final: 0.7323 (mttm) REVERT: F 20 GLU cc_start: 0.7242 (mp0) cc_final: 0.6795 (mp0) REVERT: F 65 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6830 (mm-30) REVERT: F 67 LYS cc_start: 0.8259 (mttt) cc_final: 0.7989 (mttt) REVERT: F 78 GLN cc_start: 0.7960 (mt0) cc_final: 0.7734 (mp10) REVERT: F 125 ARG cc_start: 0.7364 (mtm-85) cc_final: 0.7112 (ttm110) REVERT: F 231 GLU cc_start: 0.7684 (mp0) cc_final: 0.7425 (mp0) REVERT: F 232 LEU cc_start: 0.8136 (mt) cc_final: 0.7708 (mp) REVERT: F 269 LYS cc_start: 0.7194 (mptt) cc_final: 0.6884 (mttt) REVERT: F 307 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6806 (mp0) REVERT: F 314 ARG cc_start: 0.7616 (tpt90) cc_final: 0.7322 (tpt90) REVERT: F 336 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7837 (mmm160) REVERT: F 400 ARG cc_start: 0.7324 (mtm-85) cc_final: 0.6889 (ttm-80) REVERT: F 415 LYS cc_start: 0.8036 (tptt) cc_final: 0.7796 (tptt) REVERT: F 427 LYS cc_start: 0.7595 (mmmt) cc_final: 0.7148 (mmmt) REVERT: G 17 SER cc_start: 0.7873 (p) cc_final: 0.7557 (t) REVERT: G 54 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6992 (mm-30) REVERT: G 57 LYS cc_start: 0.7881 (mttt) cc_final: 0.7600 (mtmm) REVERT: G 60 LYS cc_start: 0.7487 (mtpp) cc_final: 0.7249 (ttpp) REVERT: G 61 MET cc_start: 0.7698 (mmm) cc_final: 0.7172 (mmm) REVERT: G 110 GLU cc_start: 0.7393 (tp30) cc_final: 0.6963 (tp30) REVERT: G 123 ARG cc_start: 0.7766 (ttt90) cc_final: 0.7255 (mtp85) REVERT: G 132 GLU cc_start: 0.7825 (pt0) cc_final: 0.7467 (pm20) REVERT: G 137 GLU cc_start: 0.8052 (pm20) cc_final: 0.7598 (pm20) REVERT: G 139 THR cc_start: 0.7997 (p) cc_final: 0.7733 (t) REVERT: G 152 LYS cc_start: 0.6702 (mtpt) cc_final: 0.6397 (mtpt) REVERT: G 167 THR cc_start: 0.8031 (m) cc_final: 0.7822 (p) REVERT: G 181 GLN cc_start: 0.7674 (mm-40) cc_final: 0.7274 (mm-40) REVERT: G 209 TYR cc_start: 0.8344 (m-80) cc_final: 0.8009 (m-80) REVERT: G 230 LYS cc_start: 0.7981 (mttt) cc_final: 0.7526 (mttm) REVERT: G 260 MET cc_start: 0.4573 (tmm) cc_final: 0.4076 (tmm) REVERT: G 264 MET cc_start: 0.5234 (mmm) cc_final: 0.4741 (mmm) REVERT: G 281 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7529 (mtpt) REVERT: G 282 VAL cc_start: 0.7975 (t) cc_final: 0.7690 (p) REVERT: G 285 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7503 (mtpt) REVERT: G 314 TYR cc_start: 0.8209 (t80) cc_final: 0.7832 (t80) REVERT: G 322 SER cc_start: 0.8037 (p) cc_final: 0.7724 (m) REVERT: G 371 MET cc_start: 0.7498 (mtp) cc_final: 0.6904 (mtt) REVERT: G 396 GLU cc_start: 0.6290 (mm-30) cc_final: 0.5677 (mm-30) REVERT: G 431 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6521 (mt-10) REVERT: G 434 SER cc_start: 0.7352 (m) cc_final: 0.6772 (p) REVERT: H 20 GLU cc_start: 0.6771 (mp0) cc_final: 0.6567 (mp0) REVERT: H 38 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6626 (mm-30) REVERT: H 61 GLU cc_start: 0.7230 (mm-30) cc_final: 0.7014 (mm-30) REVERT: H 112 GLU cc_start: 0.6928 (tp30) cc_final: 0.6530 (tp30) REVERT: H 124 ARG cc_start: 0.7611 (mtt-85) cc_final: 0.7039 (mtp85) REVERT: H 129 VAL cc_start: 0.7786 (OUTLIER) cc_final: 0.7484 (t) REVERT: H 132 LYS cc_start: 0.8693 (ptpp) cc_final: 0.8441 (ptpp) REVERT: H 139 GLU cc_start: 0.7453 (pt0) cc_final: 0.7051 (pt0) REVERT: H 207 ARG cc_start: 0.8180 (ptp-170) cc_final: 0.7897 (ptp90) REVERT: H 218 MET cc_start: 0.7308 (mmm) cc_final: 0.7059 (mmm) REVERT: H 241 THR cc_start: 0.7644 (m) cc_final: 0.7216 (t) REVERT: H 279 LYS cc_start: 0.7725 (tptt) cc_final: 0.7421 (tptt) REVERT: H 300 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6588 (mm-30) REVERT: H 334 ARG cc_start: 0.7427 (ttt180) cc_final: 0.7148 (ttt180) REVERT: H 352 ASP cc_start: 0.7051 (m-30) cc_final: 0.6721 (m-30) REVERT: H 379 ASP cc_start: 0.7736 (t0) cc_final: 0.7391 (m-30) REVERT: H 392 ARG cc_start: 0.7751 (ttt180) cc_final: 0.7467 (ttt180) REVERT: H 413 CYS cc_start: 0.7678 (t) cc_final: 0.7428 (p) REVERT: H 420 GLU cc_start: 0.7051 (tt0) cc_final: 0.6765 (tt0) REVERT: H 422 GLN cc_start: 0.7471 (mm-40) cc_final: 0.7172 (mm110) REVERT: H 427 LYS cc_start: 0.7725 (mmtm) cc_final: 0.7460 (mmtm) REVERT: H 436 GLU cc_start: 0.5556 (tm-30) cc_final: 0.5273 (tm-30) REVERT: H 441 GLN cc_start: 0.7625 (tt0) cc_final: 0.7336 (tt0) REVERT: H 443 MET cc_start: 0.6888 (ttp) cc_final: 0.6615 (ttm) REVERT: I 60 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7653 (mmmt) REVERT: I 61 MET cc_start: 0.7903 (mmt) cc_final: 0.7319 (mmt) REVERT: I 64 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.6174 (mmt90) REVERT: I 125 LYS cc_start: 0.8420 (ttmt) cc_final: 0.8175 (ttpp) REVERT: I 126 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6861 (tm-30) REVERT: I 173 ASP cc_start: 0.7370 (t70) cc_final: 0.6915 (t70) REVERT: I 175 SER cc_start: 0.8756 (m) cc_final: 0.8324 (p) REVERT: I 189 ASP cc_start: 0.5659 (m-30) cc_final: 0.4954 (m-30) REVERT: I 202 ARG cc_start: 0.7777 (ttt-90) cc_final: 0.7372 (ttt-90) REVERT: I 242 ASP cc_start: 0.7363 (m-30) cc_final: 0.7159 (m-30) REVERT: I 260 MET cc_start: 0.6095 (mtt) cc_final: 0.5801 (mtt) REVERT: I 280 ASN cc_start: 0.7491 (m-40) cc_final: 0.6934 (m-40) REVERT: I 281 LYS cc_start: 0.7329 (mttt) cc_final: 0.7106 (mttt) REVERT: I 312 PHE cc_start: 0.7628 (m-80) cc_final: 0.7272 (m-80) REVERT: I 317 ARG cc_start: 0.6681 (ttt-90) cc_final: 0.6458 (ttt-90) REVERT: I 320 GLU cc_start: 0.6928 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: I 335 ASN cc_start: 0.7733 (t0) cc_final: 0.7330 (t0) REVERT: I 356 ASP cc_start: 0.7156 (t0) cc_final: 0.6803 (t70) REVERT: I 376 LYS cc_start: 0.7614 (tptt) cc_final: 0.7276 (tppt) REVERT: I 389 GLU cc_start: 0.7591 (pt0) cc_final: 0.7279 (pt0) REVERT: I 393 HIS cc_start: 0.7928 (t70) cc_final: 0.6903 (t70) REVERT: I 396 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6999 (mt-10) REVERT: I 399 THR cc_start: 0.7819 (m) cc_final: 0.7422 (p) REVERT: I 418 LYS cc_start: 0.7794 (mtpt) cc_final: 0.7471 (mtpp) REVERT: I 427 LYS cc_start: 0.7725 (tttt) cc_final: 0.7418 (ttpp) REVERT: I 428 GLU cc_start: 0.7665 (mp0) cc_final: 0.7438 (pm20) REVERT: I 445 LYS cc_start: 0.7542 (mttp) cc_final: 0.7160 (tttp) REVERT: J 26 SER cc_start: 0.8026 (m) cc_final: 0.7579 (t) REVERT: J 40 ARG cc_start: 0.7322 (mtt90) cc_final: 0.7102 (mtt90) REVERT: J 50 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7711 (mm) REVERT: J 59 VAL cc_start: 0.7545 (t) cc_final: 0.7295 (m) REVERT: J 94 LEU cc_start: 0.7574 (tp) cc_final: 0.7343 (tp) REVERT: J 236 LYS cc_start: 0.8384 (mtpt) cc_final: 0.8162 (mtpt) REVERT: J 264 ASP cc_start: 0.6379 (t0) cc_final: 0.6032 (t0) REVERT: J 274 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7233 (mt-10) REVERT: J 336 ARG cc_start: 0.7106 (mtm180) cc_final: 0.6757 (mtm180) REVERT: J 377 GLU cc_start: 0.6721 (tp30) cc_final: 0.6278 (tp30) REVERT: J 384 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6876 (mm-30) REVERT: J 404 GLN cc_start: 0.7660 (mt0) cc_final: 0.7417 (mt0) REVERT: J 420 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7143 (tt0) REVERT: J 427 LYS cc_start: 0.7898 (mmtp) cc_final: 0.7664 (mmtp) REVERT: J 436 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6844 (tm-30) REVERT: K 153 MET cc_start: -0.0687 (tmm) cc_final: -0.1217 (tmm) REVERT: K 283 MET cc_start: 0.3592 (mmm) cc_final: 0.3110 (mmm) REVERT: L 11 ASP cc_start: 0.8253 (t0) cc_final: 0.8026 (t70) REVERT: L 34 ILE cc_start: 0.8692 (mt) cc_final: 0.8371 (mt) REVERT: L 57 GLU cc_start: 0.7509 (tp30) cc_final: 0.6617 (tp30) REVERT: L 61 LYS cc_start: 0.8507 (mtmt) cc_final: 0.7650 (mtmt) REVERT: L 100 GLU cc_start: 0.7671 (tt0) cc_final: 0.7450 (tt0) REVERT: L 107 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6716 (pt0) REVERT: L 166 TYR cc_start: 0.8196 (t80) cc_final: 0.7664 (t80) REVERT: L 167 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7232 (mm-30) REVERT: L 253 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7928 (mm-30) REVERT: L 259 GLU cc_start: 0.7625 (tp30) cc_final: 0.7307 (tp30) REVERT: L 300 SER cc_start: 0.8449 (p) cc_final: 0.8190 (m) REVERT: L 312 ARG cc_start: 0.8840 (tpt90) cc_final: 0.8412 (tpt-90) REVERT: L 326 LYS cc_start: 0.8259 (tttp) cc_final: 0.7920 (tttp) REVERT: M 30 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7528 (mm-30) REVERT: M 31 ASP cc_start: 0.6543 (p0) cc_final: 0.6198 (p0) REVERT: M 67 THR cc_start: 0.8507 (m) cc_final: 0.8014 (p) REVERT: M 128 ASN cc_start: 0.7737 (t0) cc_final: 0.7372 (p0) REVERT: M 130 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7370 (ttm170) REVERT: M 134 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7096 (mt-10) REVERT: M 186 TYR cc_start: 0.7735 (m-80) cc_final: 0.7261 (m-80) REVERT: M 189 GLN cc_start: 0.8257 (mt0) cc_final: 0.7808 (mp10) REVERT: M 194 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7734 (mtpt) REVERT: M 226 LYS cc_start: 0.8514 (pttt) cc_final: 0.7803 (ptpt) REVERT: M 227 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7424 (mm-30) REVERT: M 238 LYS cc_start: 0.8421 (mmtt) cc_final: 0.8073 (mmtt) REVERT: M 252 ASN cc_start: 0.8209 (m-40) cc_final: 0.7899 (m110) REVERT: M 276 GLU cc_start: 0.7359 (tp30) cc_final: 0.7015 (tp30) REVERT: M 287 TYR cc_start: 0.8101 (t80) cc_final: 0.7823 (t80) REVERT: M 294 ASN cc_start: 0.8268 (p0) cc_final: 0.7724 (p0) REVERT: M 301 ARG cc_start: 0.8176 (ptm-80) cc_final: 0.7827 (ptm-80) REVERT: M 303 LYS cc_start: 0.8675 (tttp) cc_final: 0.8372 (mtpp) REVERT: M 308 LEU cc_start: 0.8432 (mm) cc_final: 0.8163 (mt) REVERT: M 322 MET cc_start: 0.7274 (mtm) cc_final: 0.6922 (mtm) REVERT: M 347 SER cc_start: 0.7616 (t) cc_final: 0.7170 (p) REVERT: M 358 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7547 (mm-40) REVERT: M 376 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6570 (ttm) REVERT: N 55 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7291 (mtt180) REVERT: N 62 TYR cc_start: 0.8701 (p90) cc_final: 0.8439 (p90) REVERT: N 91 LYS cc_start: 0.7805 (ptmm) cc_final: 0.7538 (ptmm) REVERT: N 128 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7640 (ttm110) REVERT: N 193 GLU cc_start: 0.7300 (tp30) cc_final: 0.6931 (tp30) REVERT: N 196 TYR cc_start: 0.7791 (m-80) cc_final: 0.7504 (m-10) REVERT: N 202 LEU cc_start: 0.8695 (mt) cc_final: 0.8390 (mt) REVERT: N 228 GLU cc_start: 0.8100 (tp30) cc_final: 0.7764 (tp30) REVERT: N 232 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7909 (ttm170) REVERT: N 255 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6803 (mm-30) outliers start: 97 outliers final: 72 residues processed: 1351 average time/residue: 0.2564 time to fit residues: 528.8178 Evaluate side-chains 1396 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1312 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2099 ILE Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain A residue 2224 THR Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 403 LEU Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 433 ILE Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 132 LYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 340 TYR Chi-restraints excluded: chain J residue 342 SER Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 368 LYS Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain L residue 329 ILE Chi-restraints excluded: chain L residue 339 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 211 GLN Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 282 MET Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain M residue 376 MET Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain N residue 131 LYS Chi-restraints excluded: chain N residue 188 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 215 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 441 optimal weight: 0.7980 chunk 418 optimal weight: 1.9990 chunk 453 optimal weight: 0.9980 chunk 464 optimal weight: 1.9990 chunk 315 optimal weight: 0.0470 chunk 443 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 413 optimal weight: 2.9990 chunk 427 optimal weight: 1.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 280 ASN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN ** L 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 384 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.171497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138001 restraints weight = 66203.001| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.69 r_work: 0.3430 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 41572 Z= 0.161 Angle : 0.579 11.380 56164 Z= 0.288 Chirality : 0.042 0.212 6364 Planarity : 0.004 0.059 7187 Dihedral : 6.573 148.953 5717 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.03 % Allowed : 16.05 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.64 (0.12), residues: 5082 helix: 1.75 (0.11), residues: 2328 sheet: 0.44 (0.18), residues: 799 loop : 0.74 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 184 TYR 0.042 0.001 TYR I 314 PHE 0.014 0.001 PHE A1933 TRP 0.039 0.001 TRP A1232 HIS 0.010 0.001 HIS L 275 Details of bonding type rmsd covalent geometry : bond 0.00360 (41572) covalent geometry : angle 0.57909 (56164) hydrogen bonds : bond 0.03818 ( 1947) hydrogen bonds : angle 4.22343 ( 5517) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 1316 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 787 GLU cc_start: 0.7052 (tt0) cc_final: 0.6583 (tp30) REVERT: A 796 GLN cc_start: 0.7648 (tp-100) cc_final: 0.7159 (tp-100) REVERT: A 816 LEU cc_start: 0.8257 (mt) cc_final: 0.7980 (mm) REVERT: A 838 LYS cc_start: 0.8331 (tttt) cc_final: 0.7919 (ttpp) REVERT: A 861 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7582 (mt-10) REVERT: A 862 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7795 (mm-30) REVERT: A 863 GLN cc_start: 0.7698 (tt0) cc_final: 0.7328 (tp40) REVERT: A 864 SER cc_start: 0.7637 (m) cc_final: 0.7341 (t) REVERT: A 867 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7423 (mmt180) REVERT: A 1093 ASP cc_start: 0.7933 (m-30) cc_final: 0.7675 (t70) REVERT: A 1099 LEU cc_start: 0.7124 (tp) cc_final: 0.6849 (tp) REVERT: A 1192 HIS cc_start: 0.7433 (m170) cc_final: 0.7102 (m90) REVERT: A 1215 CYS cc_start: 0.7583 (t) cc_final: 0.6213 (p) REVERT: A 1227 MET cc_start: 0.7736 (tpp) cc_final: 0.7303 (tpp) REVERT: A 1242 GLN cc_start: 0.2794 (pt0) cc_final: 0.2371 (mm-40) REVERT: A 1261 MET cc_start: 0.3004 (mmp) cc_final: 0.2601 (mmp) REVERT: A 1337 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7492 (mp0) REVERT: A 1362 VAL cc_start: 0.7825 (t) cc_final: 0.7565 (m) REVERT: A 1363 ARG cc_start: 0.8045 (ttt180) cc_final: 0.7565 (mtp85) REVERT: A 1364 LEU cc_start: 0.8402 (tp) cc_final: 0.7958 (tt) REVERT: A 1390 TYR cc_start: 0.8020 (t80) cc_final: 0.7737 (t80) REVERT: A 1403 ASP cc_start: 0.6988 (p0) cc_final: 0.6170 (p0) REVERT: A 1406 LYS cc_start: 0.7321 (mttt) cc_final: 0.7090 (mttm) REVERT: A 1428 GLU cc_start: 0.6850 (tp30) cc_final: 0.6465 (tp30) REVERT: A 1433 LYS cc_start: 0.7832 (mttt) cc_final: 0.7438 (mtmt) REVERT: A 1442 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7197 (mt-10) REVERT: A 1758 GLU cc_start: 0.8039 (tt0) cc_final: 0.7728 (mt-10) REVERT: A 1769 ARG cc_start: 0.7661 (mtp-110) cc_final: 0.7430 (mtm180) REVERT: A 1774 ILE cc_start: 0.8672 (tp) cc_final: 0.8138 (mt) REVERT: A 1872 TYR cc_start: 0.6365 (m-80) cc_final: 0.6013 (m-80) REVERT: A 1877 ARG cc_start: 0.6649 (tpm170) cc_final: 0.6350 (tpm170) REVERT: A 1896 ASP cc_start: 0.7815 (m-30) cc_final: 0.7180 (m-30) REVERT: A 1897 SER cc_start: 0.7800 (t) cc_final: 0.7405 (p) REVERT: A 1901 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7315 (mm-30) REVERT: A 1909 LYS cc_start: 0.7711 (tttt) cc_final: 0.7382 (ttmm) REVERT: A 1911 LYS cc_start: 0.8112 (tttt) cc_final: 0.7858 (tppp) REVERT: A 1917 VAL cc_start: 0.8160 (p) cc_final: 0.7859 (m) REVERT: A 1921 SER cc_start: 0.7171 (t) cc_final: 0.6873 (p) REVERT: A 1958 ARG cc_start: 0.7723 (mtt180) cc_final: 0.7353 (mtt180) REVERT: A 1974 HIS cc_start: 0.7912 (m-70) cc_final: 0.7560 (m170) REVERT: A 1982 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7219 (tt) REVERT: A 1986 ASP cc_start: 0.6950 (p0) cc_final: 0.6617 (p0) REVERT: A 2000 ASP cc_start: 0.8028 (t70) cc_final: 0.7151 (t0) REVERT: A 2004 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7170 (mm-40) REVERT: A 2052 MET cc_start: 0.6457 (mmm) cc_final: 0.6062 (tmm) REVERT: A 2058 ARG cc_start: 0.6822 (tpp-160) cc_final: 0.6476 (tpp-160) REVERT: A 2206 GLU cc_start: 0.7300 (tt0) cc_final: 0.6699 (tm-30) REVERT: A 2207 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7325 (ttt180) REVERT: B 267 THR cc_start: 0.8096 (m) cc_final: 0.7732 (p) REVERT: B 277 TRP cc_start: 0.8278 (m100) cc_final: 0.8060 (m100) REVERT: B 294 VAL cc_start: 0.8910 (t) cc_final: 0.8663 (m) REVERT: B 297 ARG cc_start: 0.7936 (mtp180) cc_final: 0.7702 (mtp180) REVERT: C 407 LYS cc_start: 0.8316 (mmtt) cc_final: 0.8057 (mptt) REVERT: C 469 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7145 (mtm-85) REVERT: E 14 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7694 (mtp180) REVERT: E 57 LYS cc_start: 0.8123 (mttp) cc_final: 0.7885 (mttp) REVERT: E 60 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7593 (mtpt) REVERT: E 90 LYS cc_start: 0.7560 (mmtp) cc_final: 0.7251 (mmtp) REVERT: E 101 VAL cc_start: 0.7856 (t) cc_final: 0.7589 (m) REVERT: E 123 ARG cc_start: 0.7447 (mtp180) cc_final: 0.7040 (tpp80) REVERT: E 127 THR cc_start: 0.7722 (p) cc_final: 0.7482 (p) REVERT: E 129 GLU cc_start: 0.6860 (pm20) cc_final: 0.6323 (pm20) REVERT: E 134 GLU cc_start: 0.7427 (tt0) cc_final: 0.7094 (tt0) REVERT: E 168 LYS cc_start: 0.8045 (mptt) cc_final: 0.7709 (mptt) REVERT: E 258 SER cc_start: 0.7677 (m) cc_final: 0.7003 (p) REVERT: E 262 GLN cc_start: 0.6608 (mt0) cc_final: 0.6381 (mt0) REVERT: E 264 MET cc_start: 0.6381 (mmm) cc_final: 0.6045 (mmm) REVERT: E 265 LYS cc_start: 0.8198 (tttt) cc_final: 0.7807 (tttt) REVERT: E 267 LYS cc_start: 0.6970 (tttt) cc_final: 0.6689 (tmtt) REVERT: E 274 LYS cc_start: 0.6706 (tttm) cc_final: 0.6208 (tttm) REVERT: E 278 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: E 285 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7219 (ttmt) REVERT: E 304 VAL cc_start: 0.7772 (m) cc_final: 0.7459 (p) REVERT: E 317 ARG cc_start: 0.7366 (ttt-90) cc_final: 0.7067 (ttt180) REVERT: E 336 CYS cc_start: 0.6776 (p) cc_final: 0.6423 (p) REVERT: E 337 VAL cc_start: 0.7324 (t) cc_final: 0.6898 (m) REVERT: E 356 ASP cc_start: 0.7069 (t70) cc_final: 0.6632 (t0) REVERT: E 369 GLN cc_start: 0.7241 (mp10) cc_final: 0.6990 (mp10) REVERT: E 388 GLU cc_start: 0.7432 (tt0) cc_final: 0.7184 (tt0) REVERT: E 396 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6578 (tm-30) REVERT: E 426 GLU cc_start: 0.6941 (mm-30) cc_final: 0.6140 (mp0) REVERT: E 441 LYS cc_start: 0.7512 (mtmm) cc_final: 0.7309 (mttm) REVERT: F 20 GLU cc_start: 0.7273 (mp0) cc_final: 0.6826 (mp0) REVERT: F 65 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6800 (mm-30) REVERT: F 67 LYS cc_start: 0.8278 (mttt) cc_final: 0.7997 (mttt) REVERT: F 71 ARG cc_start: 0.7815 (mmm-85) cc_final: 0.7449 (mmm160) REVERT: F 78 GLN cc_start: 0.7895 (mt0) cc_final: 0.7691 (mp10) REVERT: F 125 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.7137 (ttm110) REVERT: F 231 GLU cc_start: 0.7738 (mp0) cc_final: 0.7478 (mp0) REVERT: F 232 LEU cc_start: 0.8155 (mt) cc_final: 0.7724 (mp) REVERT: F 269 LYS cc_start: 0.7220 (mptt) cc_final: 0.6913 (mttt) REVERT: F 307 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6805 (mp0) REVERT: F 314 ARG cc_start: 0.7611 (tpt90) cc_final: 0.7236 (tpt90) REVERT: F 336 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7831 (mmm160) REVERT: F 365 LYS cc_start: 0.8176 (mmtm) cc_final: 0.7972 (mmtm) REVERT: F 415 LYS cc_start: 0.8038 (tptt) cc_final: 0.7800 (tptt) REVERT: F 427 LYS cc_start: 0.7615 (mmmt) cc_final: 0.7157 (mmmt) REVERT: F 428 ARG cc_start: 0.7156 (tpt170) cc_final: 0.6800 (tpt170) REVERT: G 17 SER cc_start: 0.7901 (p) cc_final: 0.7572 (t) REVERT: G 54 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6986 (mm-30) REVERT: G 57 LYS cc_start: 0.7873 (mttt) cc_final: 0.7598 (mtmm) REVERT: G 60 LYS cc_start: 0.7477 (mtpp) cc_final: 0.7256 (ttpp) REVERT: G 61 MET cc_start: 0.7681 (mmm) cc_final: 0.7131 (mmm) REVERT: G 110 GLU cc_start: 0.7409 (tp30) cc_final: 0.6992 (tp30) REVERT: G 123 ARG cc_start: 0.7804 (ttt90) cc_final: 0.7296 (mtp85) REVERT: G 128 LYS cc_start: 0.8045 (tppt) cc_final: 0.7532 (tppt) REVERT: G 132 GLU cc_start: 0.7823 (pt0) cc_final: 0.7472 (pm20) REVERT: G 137 GLU cc_start: 0.8090 (pm20) cc_final: 0.7632 (pm20) REVERT: G 139 THR cc_start: 0.8046 (p) cc_final: 0.7842 (t) REVERT: G 140 PRO cc_start: 0.8570 (Cg_endo) cc_final: 0.8126 (Cg_exo) REVERT: G 152 LYS cc_start: 0.6730 (mtpt) cc_final: 0.6435 (mtpt) REVERT: G 167 THR cc_start: 0.8079 (m) cc_final: 0.7853 (p) REVERT: G 181 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7346 (mm-40) REVERT: G 209 TYR cc_start: 0.8374 (m-80) cc_final: 0.8019 (m-80) REVERT: G 230 LYS cc_start: 0.7978 (mttt) cc_final: 0.7561 (mttm) REVERT: G 260 MET cc_start: 0.4606 (tmm) cc_final: 0.4135 (tmm) REVERT: G 264 MET cc_start: 0.5241 (mmm) cc_final: 0.4723 (mmm) REVERT: G 281 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7528 (mtpt) REVERT: G 282 VAL cc_start: 0.7942 (t) cc_final: 0.7659 (p) REVERT: G 285 LYS cc_start: 0.7734 (mtpt) cc_final: 0.7500 (mtpt) REVERT: G 314 TYR cc_start: 0.8229 (t80) cc_final: 0.7857 (t80) REVERT: G 322 SER cc_start: 0.8021 (p) cc_final: 0.7720 (m) REVERT: G 371 MET cc_start: 0.7504 (mtp) cc_final: 0.6935 (mtt) REVERT: G 396 GLU cc_start: 0.6329 (mm-30) cc_final: 0.5707 (mm-30) REVERT: G 431 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6570 (mt-10) REVERT: G 434 SER cc_start: 0.7323 (m) cc_final: 0.6746 (p) REVERT: H 38 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6700 (mm-30) REVERT: H 61 GLU cc_start: 0.7236 (mm-30) cc_final: 0.7022 (mm-30) REVERT: H 112 GLU cc_start: 0.6961 (tp30) cc_final: 0.6576 (tp30) REVERT: H 124 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.7049 (mtp85) REVERT: H 129 VAL cc_start: 0.7841 (OUTLIER) cc_final: 0.7572 (t) REVERT: H 132 LYS cc_start: 0.8729 (ptpp) cc_final: 0.8484 (ptpp) REVERT: H 139 GLU cc_start: 0.7508 (pt0) cc_final: 0.7137 (pt0) REVERT: H 207 ARG cc_start: 0.8191 (ptp-170) cc_final: 0.7883 (ptp90) REVERT: H 218 MET cc_start: 0.7269 (mmm) cc_final: 0.7005 (mmm) REVERT: H 241 THR cc_start: 0.7731 (m) cc_final: 0.7300 (t) REVERT: H 279 LYS cc_start: 0.7717 (tptt) cc_final: 0.7409 (tptt) REVERT: H 300 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6614 (mm-30) REVERT: H 334 ARG cc_start: 0.7408 (ttt180) cc_final: 0.7093 (ttt180) REVERT: H 352 ASP cc_start: 0.7039 (m-30) cc_final: 0.6706 (m-30) REVERT: H 379 ASP cc_start: 0.7741 (t0) cc_final: 0.7402 (m-30) REVERT: H 392 ARG cc_start: 0.7846 (ttt180) cc_final: 0.7565 (ttt180) REVERT: H 413 CYS cc_start: 0.7684 (t) cc_final: 0.7412 (p) REVERT: H 420 GLU cc_start: 0.7067 (tt0) cc_final: 0.6784 (tt0) REVERT: H 422 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7261 (mm110) REVERT: H 427 LYS cc_start: 0.7651 (mmtm) cc_final: 0.7402 (mmtm) REVERT: H 436 GLU cc_start: 0.5561 (tm-30) cc_final: 0.5168 (tm-30) REVERT: H 441 GLN cc_start: 0.7577 (tt0) cc_final: 0.7286 (tt0) REVERT: H 443 MET cc_start: 0.6857 (ttp) cc_final: 0.6593 (ttm) REVERT: I 31 LEU cc_start: 0.7863 (mt) cc_final: 0.7493 (mm) REVERT: I 60 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7651 (mmmt) REVERT: I 61 MET cc_start: 0.7927 (mmt) cc_final: 0.7332 (mmt) REVERT: I 64 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.6211 (mmt90) REVERT: I 125 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8277 (ttpp) REVERT: I 173 ASP cc_start: 0.7456 (t70) cc_final: 0.6992 (t70) REVERT: I 175 SER cc_start: 0.8746 (m) cc_final: 0.8302 (p) REVERT: I 189 ASP cc_start: 0.5832 (m-30) cc_final: 0.5158 (m-30) REVERT: I 202 ARG cc_start: 0.7713 (ttt-90) cc_final: 0.7295 (ttt-90) REVERT: I 260 MET cc_start: 0.6032 (mtt) cc_final: 0.5745 (mtt) REVERT: I 280 ASN cc_start: 0.7504 (m-40) cc_final: 0.6976 (m-40) REVERT: I 281 LYS cc_start: 0.7300 (mttt) cc_final: 0.7091 (mttt) REVERT: I 312 PHE cc_start: 0.7640 (m-80) cc_final: 0.7197 (m-80) REVERT: I 317 ARG cc_start: 0.6706 (ttt-90) cc_final: 0.6473 (ttt-90) REVERT: I 320 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: I 335 ASN cc_start: 0.7737 (t0) cc_final: 0.7330 (t0) REVERT: I 356 ASP cc_start: 0.7137 (t0) cc_final: 0.6764 (t70) REVERT: I 376 LYS cc_start: 0.7628 (tptt) cc_final: 0.7287 (tppt) REVERT: I 389 GLU cc_start: 0.7652 (pt0) cc_final: 0.7335 (pt0) REVERT: I 393 HIS cc_start: 0.7861 (t70) cc_final: 0.7522 (t-90) REVERT: I 396 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7068 (mt-10) REVERT: I 399 THR cc_start: 0.7848 (m) cc_final: 0.7435 (p) REVERT: I 418 LYS cc_start: 0.7724 (mtpt) cc_final: 0.7392 (mtpp) REVERT: I 427 LYS cc_start: 0.7702 (tttt) cc_final: 0.7415 (ttpp) REVERT: I 428 GLU cc_start: 0.7708 (mp0) cc_final: 0.7453 (pm20) REVERT: I 431 GLU cc_start: 0.7382 (mm-30) cc_final: 0.7003 (mm-30) REVERT: I 445 LYS cc_start: 0.7551 (mttp) cc_final: 0.7228 (ttpp) REVERT: J 26 SER cc_start: 0.8021 (m) cc_final: 0.7575 (t) REVERT: J 40 ARG cc_start: 0.7369 (mtt90) cc_final: 0.7155 (mtt90) REVERT: J 50 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7699 (mm) REVERT: J 59 VAL cc_start: 0.7550 (t) cc_final: 0.7308 (m) REVERT: J 94 LEU cc_start: 0.7563 (tp) cc_final: 0.7343 (tp) REVERT: J 236 LYS cc_start: 0.8379 (mtpt) cc_final: 0.8133 (mtpt) REVERT: J 264 ASP cc_start: 0.6404 (t0) cc_final: 0.6090 (t0) REVERT: J 274 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7314 (mt-10) REVERT: J 336 ARG cc_start: 0.7083 (mtm180) cc_final: 0.6772 (mtm180) REVERT: J 377 GLU cc_start: 0.6730 (tp30) cc_final: 0.6285 (tp30) REVERT: J 384 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6915 (mm-30) REVERT: J 404 GLN cc_start: 0.7681 (mt0) cc_final: 0.7432 (mt0) REVERT: J 420 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7118 (tt0) REVERT: J 427 LYS cc_start: 0.7873 (mmtp) cc_final: 0.7638 (mmtp) REVERT: J 436 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6846 (tm-30) REVERT: K 153 MET cc_start: -0.0562 (tmm) cc_final: -0.1114 (tmm) REVERT: K 283 MET cc_start: 0.3773 (mmm) cc_final: 0.3232 (mmm) REVERT: L 11 ASP cc_start: 0.8254 (t0) cc_final: 0.8018 (t70) REVERT: L 34 ILE cc_start: 0.8689 (mt) cc_final: 0.8369 (mt) REVERT: L 57 GLU cc_start: 0.7547 (tp30) cc_final: 0.6622 (tp30) REVERT: L 61 LYS cc_start: 0.8566 (mtmt) cc_final: 0.7685 (mtmt) REVERT: L 100 GLU cc_start: 0.7658 (tt0) cc_final: 0.7430 (tt0) REVERT: L 107 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6705 (pt0) REVERT: L 132 MET cc_start: 0.8246 (tmm) cc_final: 0.7892 (tmm) REVERT: L 167 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7243 (mm-30) REVERT: L 259 GLU cc_start: 0.7647 (tp30) cc_final: 0.7371 (tp30) REVERT: L 300 SER cc_start: 0.8471 (p) cc_final: 0.8189 (m) REVERT: L 312 ARG cc_start: 0.8823 (tpt90) cc_final: 0.8374 (tpt-90) REVERT: L 326 LYS cc_start: 0.8293 (tttp) cc_final: 0.7944 (tttp) REVERT: M 30 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7554 (mm-30) REVERT: M 31 ASP cc_start: 0.6613 (p0) cc_final: 0.6300 (p0) REVERT: M 67 THR cc_start: 0.8508 (m) cc_final: 0.8006 (p) REVERT: M 128 ASN cc_start: 0.7776 (t0) cc_final: 0.7431 (p0) REVERT: M 130 ARG cc_start: 0.7593 (ttm110) cc_final: 0.7286 (ttm170) REVERT: M 134 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7081 (mt-10) REVERT: M 189 GLN cc_start: 0.8304 (mt0) cc_final: 0.7923 (mp10) REVERT: M 205 GLN cc_start: 0.7940 (mm110) cc_final: 0.7645 (mm110) REVERT: M 226 LYS cc_start: 0.8533 (pttt) cc_final: 0.7806 (ptpt) REVERT: M 227 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7373 (mm-30) REVERT: M 238 LYS cc_start: 0.8468 (mmtt) cc_final: 0.8098 (mmtt) REVERT: M 252 ASN cc_start: 0.8250 (m-40) cc_final: 0.7915 (m110) REVERT: M 276 GLU cc_start: 0.7335 (tp30) cc_final: 0.6985 (tp30) REVERT: M 294 ASN cc_start: 0.8259 (p0) cc_final: 0.7670 (p0) REVERT: M 301 ARG cc_start: 0.8174 (ptm-80) cc_final: 0.7826 (ptm-80) REVERT: M 303 LYS cc_start: 0.8651 (tttp) cc_final: 0.8335 (mtpp) REVERT: M 308 LEU cc_start: 0.8489 (mm) cc_final: 0.8194 (mt) REVERT: M 322 MET cc_start: 0.7317 (mtm) cc_final: 0.6981 (mtm) REVERT: M 347 SER cc_start: 0.7591 (t) cc_final: 0.7163 (p) REVERT: M 358 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7536 (mm-40) REVERT: M 376 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6648 (ttm) REVERT: N 55 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7519 (mtt180) REVERT: N 62 TYR cc_start: 0.8688 (p90) cc_final: 0.8400 (p90) REVERT: N 91 LYS cc_start: 0.7801 (ptmm) cc_final: 0.7523 (ptmm) REVERT: N 128 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7703 (ttm110) REVERT: N 193 GLU cc_start: 0.7368 (tp30) cc_final: 0.6986 (tp30) REVERT: N 196 TYR cc_start: 0.7825 (m-80) cc_final: 0.7542 (m-10) REVERT: N 202 LEU cc_start: 0.8734 (mt) cc_final: 0.8426 (mt) REVERT: N 228 GLU cc_start: 0.8189 (tp30) cc_final: 0.7837 (tp30) REVERT: N 232 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7825 (ttm170) REVERT: N 255 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6853 (mm-30) outliers start: 90 outliers final: 74 residues processed: 1349 average time/residue: 0.2465 time to fit residues: 510.3042 Evaluate side-chains 1390 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1306 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2099 ILE Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain A residue 2224 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain G residue 59 LYS Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 207 ASP Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain H residue 346 ILE Chi-restraints excluded: chain H residue 391 THR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 269 THR Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 132 LYS Chi-restraints excluded: chain J residue 168 MET Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 368 LYS Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 274 ILE Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain L residue 339 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 282 MET Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain M residue 376 MET Chi-restraints excluded: chain M residue 378 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain N residue 131 LYS Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 388 optimal weight: 20.0000 chunk 155 optimal weight: 0.1980 chunk 471 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 198 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 334 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2004 GLN C 416 HIS E 280 ASN F 404 GLN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 HIS I 385 ASN I 408 GLN ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN J 369 GLN ** L 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN M 384 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.171955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.138947 restraints weight = 65786.574| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.65 r_work: 0.3461 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 41572 Z= 0.135 Angle : 0.581 11.091 56164 Z= 0.288 Chirality : 0.042 0.213 6364 Planarity : 0.004 0.058 7187 Dihedral : 6.497 149.680 5717 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.92 % Allowed : 16.35 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % 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: 1.66 (0.12), residues: 5082 helix: 1.80 (0.11), residues: 2323 sheet: 0.42 (0.18), residues: 803 loop : 0.73 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 830 TYR 0.042 0.001 TYR I 314 PHE 0.021 0.001 PHE L 255 TRP 0.031 0.001 TRP A1232 HIS 0.011 0.001 HIS G 305 Details of bonding type rmsd covalent geometry : bond 0.00305 (41572) covalent geometry : angle 0.58109 (56164) hydrogen bonds : bond 0.03640 ( 1947) hydrogen bonds : angle 4.18893 ( 5517) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10164 Ramachandran restraints generated. 5082 Oldfield, 0 Emsley, 5082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1308 time to evaluate : 1.496 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: A 787 GLU cc_start: 0.7049 (tt0) cc_final: 0.6569 (tp30) REVERT: A 796 GLN cc_start: 0.7629 (tp-100) cc_final: 0.7132 (tp-100) REVERT: A 838 LYS cc_start: 0.8317 (tttt) cc_final: 0.7965 (tttm) REVERT: A 842 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.7231 (mmm-85) REVERT: A 861 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7443 (mt-10) REVERT: A 862 GLU cc_start: 0.8537 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 863 GLN cc_start: 0.7654 (tt0) cc_final: 0.7351 (tp40) REVERT: A 864 SER cc_start: 0.7658 (m) cc_final: 0.7360 (t) REVERT: A 867 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7393 (mmt180) REVERT: A 1099 LEU cc_start: 0.7104 (tp) cc_final: 0.6844 (tp) REVERT: A 1192 HIS cc_start: 0.7423 (m170) cc_final: 0.7069 (m90) REVERT: A 1215 CYS cc_start: 0.7578 (t) cc_final: 0.6761 (t) REVERT: A 1242 GLN cc_start: 0.2700 (pt0) cc_final: 0.2306 (mm-40) REVERT: A 1261 MET cc_start: 0.2939 (mmp) cc_final: 0.2559 (mmp) REVERT: A 1337 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7436 (mp0) REVERT: A 1362 VAL cc_start: 0.7865 (t) cc_final: 0.7619 (m) REVERT: A 1363 ARG cc_start: 0.7991 (ttt180) cc_final: 0.7530 (mtp85) REVERT: A 1364 LEU cc_start: 0.8397 (tp) cc_final: 0.7962 (tt) REVERT: A 1390 TYR cc_start: 0.8015 (t80) cc_final: 0.7737 (t80) REVERT: A 1406 LYS cc_start: 0.7356 (mttt) cc_final: 0.7038 (mttm) REVERT: A 1428 GLU cc_start: 0.6847 (tp30) cc_final: 0.6450 (tp30) REVERT: A 1433 LYS cc_start: 0.7813 (mttt) cc_final: 0.7430 (mtmt) REVERT: A 1442 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 1478 VAL cc_start: 0.8616 (m) cc_final: 0.8381 (t) REVERT: A 1758 GLU cc_start: 0.7955 (tt0) cc_final: 0.7654 (mt-10) REVERT: A 1774 ILE cc_start: 0.8650 (tp) cc_final: 0.8308 (tp) REVERT: A 1872 TYR cc_start: 0.6342 (m-80) cc_final: 0.5982 (m-80) REVERT: A 1877 ARG cc_start: 0.6560 (tpm170) cc_final: 0.6276 (tpm170) REVERT: A 1897 SER cc_start: 0.7772 (t) cc_final: 0.7366 (p) REVERT: A 1901 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7291 (mm-30) REVERT: A 1909 LYS cc_start: 0.7706 (tttt) cc_final: 0.7375 (ttmm) REVERT: A 1911 LYS cc_start: 0.8079 (tttt) cc_final: 0.7819 (tppp) REVERT: A 1917 VAL cc_start: 0.8147 (p) cc_final: 0.7841 (m) REVERT: A 1921 SER cc_start: 0.7130 (t) cc_final: 0.6849 (p) REVERT: A 1958 ARG cc_start: 0.7775 (mtt180) cc_final: 0.7400 (mtt180) REVERT: A 1974 HIS cc_start: 0.7890 (m-70) cc_final: 0.7542 (m170) REVERT: A 1982 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7213 (tt) REVERT: A 1986 ASP cc_start: 0.6951 (p0) cc_final: 0.6623 (p0) REVERT: A 2000 ASP cc_start: 0.8015 (t70) cc_final: 0.7199 (t0) REVERT: A 2004 GLN cc_start: 0.7367 (mm110) cc_final: 0.7131 (mm-40) REVERT: A 2023 SER cc_start: 0.7396 (m) cc_final: 0.6707 (p) REVERT: A 2052 MET cc_start: 0.6518 (mmm) cc_final: 0.6118 (tmm) REVERT: A 2206 GLU cc_start: 0.7315 (tt0) cc_final: 0.6701 (tm-30) REVERT: A 2207 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7249 (ttt180) REVERT: B 267 THR cc_start: 0.8089 (m) cc_final: 0.7726 (p) REVERT: B 277 TRP cc_start: 0.8273 (m100) cc_final: 0.8061 (m100) REVERT: B 294 VAL cc_start: 0.8899 (t) cc_final: 0.8661 (m) REVERT: B 297 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7659 (mtp180) REVERT: C 407 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8077 (mptt) REVERT: C 469 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7202 (mtm-85) REVERT: E 14 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7703 (mtp180) REVERT: E 60 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7579 (mtpt) REVERT: E 90 LYS cc_start: 0.7546 (mmtp) cc_final: 0.7231 (mmtp) REVERT: E 101 VAL cc_start: 0.7852 (t) cc_final: 0.7573 (m) REVERT: E 123 ARG cc_start: 0.7455 (mtp180) cc_final: 0.7045 (tpp80) REVERT: E 127 THR cc_start: 0.7731 (p) cc_final: 0.7460 (p) REVERT: E 129 GLU cc_start: 0.6848 (pm20) cc_final: 0.6320 (pm20) REVERT: E 134 GLU cc_start: 0.7407 (tt0) cc_final: 0.7176 (tt0) REVERT: E 168 LYS cc_start: 0.8030 (mptt) cc_final: 0.7687 (mptt) REVERT: E 258 SER cc_start: 0.7644 (m) cc_final: 0.7018 (p) REVERT: E 262 GLN cc_start: 0.6537 (mt0) cc_final: 0.6301 (mt0) REVERT: E 264 MET cc_start: 0.6369 (mmm) cc_final: 0.6033 (mmm) REVERT: E 265 LYS cc_start: 0.8190 (tttt) cc_final: 0.7796 (tttt) REVERT: E 268 LYS cc_start: 0.8099 (mttt) cc_final: 0.7887 (mttp) REVERT: E 274 LYS cc_start: 0.6673 (tttm) cc_final: 0.6160 (tttm) REVERT: E 278 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: E 304 VAL cc_start: 0.7758 (m) cc_final: 0.7471 (p) REVERT: E 317 ARG cc_start: 0.7288 (ttt-90) cc_final: 0.6995 (ttt180) REVERT: E 336 CYS cc_start: 0.6812 (p) cc_final: 0.6465 (p) REVERT: E 337 VAL cc_start: 0.7338 (t) cc_final: 0.6906 (m) REVERT: E 356 ASP cc_start: 0.7051 (t70) cc_final: 0.6608 (t0) REVERT: E 369 GLN cc_start: 0.7244 (mp10) cc_final: 0.6993 (mp10) REVERT: E 388 GLU cc_start: 0.7485 (tt0) cc_final: 0.7243 (tt0) REVERT: E 396 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6554 (tm-30) REVERT: E 405 TYR cc_start: 0.7961 (t80) cc_final: 0.7757 (t80) REVERT: E 426 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6169 (mp0) REVERT: E 441 LYS cc_start: 0.7482 (mtmm) cc_final: 0.7280 (mttm) REVERT: F 20 GLU cc_start: 0.7256 (mp0) cc_final: 0.6801 (mp0) REVERT: F 65 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6849 (mm-30) REVERT: F 67 LYS cc_start: 0.8300 (mttt) cc_final: 0.8013 (mttt) REVERT: F 71 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7455 (mmm160) REVERT: F 90 MET cc_start: 0.7568 (mtp) cc_final: 0.7365 (mtp) REVERT: F 125 ARG cc_start: 0.7365 (mtm-85) cc_final: 0.7093 (ttm110) REVERT: F 231 GLU cc_start: 0.7688 (mp0) cc_final: 0.7431 (mp0) REVERT: F 232 LEU cc_start: 0.8137 (mt) cc_final: 0.7708 (mp) REVERT: F 269 LYS cc_start: 0.7200 (mptt) cc_final: 0.6885 (mttt) REVERT: F 307 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6819 (mp0) REVERT: F 314 ARG cc_start: 0.7563 (tpt90) cc_final: 0.7203 (tpt90) REVERT: F 336 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7840 (mmm160) REVERT: F 415 LYS cc_start: 0.8048 (tptt) cc_final: 0.7806 (tptt) REVERT: F 427 LYS cc_start: 0.7607 (mmmt) cc_final: 0.7148 (mmmt) REVERT: G 17 SER cc_start: 0.7837 (p) cc_final: 0.7568 (t) REVERT: G 54 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6971 (mm-30) REVERT: G 57 LYS cc_start: 0.7857 (mttt) cc_final: 0.7577 (mtmm) REVERT: G 60 LYS cc_start: 0.7463 (mtpp) cc_final: 0.7254 (ttpp) REVERT: G 61 MET cc_start: 0.7688 (mmm) cc_final: 0.7156 (mmm) REVERT: G 110 GLU cc_start: 0.7413 (tp30) cc_final: 0.6946 (tp30) REVERT: G 123 ARG cc_start: 0.7711 (ttt90) cc_final: 0.7220 (mtp85) REVERT: G 128 LYS cc_start: 0.8082 (tppt) cc_final: 0.7616 (tppt) REVERT: G 132 GLU cc_start: 0.7814 (pt0) cc_final: 0.7446 (pm20) REVERT: G 137 GLU cc_start: 0.8075 (pm20) cc_final: 0.7630 (pm20) REVERT: G 139 THR cc_start: 0.8029 (p) cc_final: 0.7826 (t) REVERT: G 140 PRO cc_start: 0.8562 (Cg_endo) cc_final: 0.8139 (Cg_exo) REVERT: G 152 LYS cc_start: 0.6699 (mtpt) cc_final: 0.6409 (mtpt) REVERT: G 167 THR cc_start: 0.8069 (m) cc_final: 0.7843 (p) REVERT: G 181 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7345 (mm-40) REVERT: G 209 TYR cc_start: 0.8374 (m-80) cc_final: 0.8138 (m-80) REVERT: G 230 LYS cc_start: 0.7997 (mttt) cc_final: 0.7578 (mttm) REVERT: G 260 MET cc_start: 0.4695 (tmm) cc_final: 0.4180 (tmm) REVERT: G 264 MET cc_start: 0.5232 (mmm) cc_final: 0.4677 (mmm) REVERT: G 281 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7497 (mtpt) REVERT: G 282 VAL cc_start: 0.7958 (t) cc_final: 0.7670 (p) REVERT: G 285 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7490 (mtpt) REVERT: G 314 TYR cc_start: 0.8196 (t80) cc_final: 0.7813 (t80) REVERT: G 322 SER cc_start: 0.8021 (p) cc_final: 0.7713 (m) REVERT: G 371 MET cc_start: 0.7494 (mtp) cc_final: 0.6925 (mtt) REVERT: G 396 GLU cc_start: 0.6312 (mm-30) cc_final: 0.5687 (mm-30) REVERT: G 431 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6512 (mt-10) REVERT: G 434 SER cc_start: 0.7318 (m) cc_final: 0.6739 (p) REVERT: H 19 ILE cc_start: 0.7724 (tp) cc_final: 0.7488 (tt) REVERT: H 38 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6668 (mm-30) REVERT: H 61 GLU cc_start: 0.7239 (mm-30) cc_final: 0.7025 (mm-30) REVERT: H 112 GLU cc_start: 0.6954 (tp30) cc_final: 0.6548 (tp30) REVERT: H 124 ARG cc_start: 0.7632 (mtt-85) cc_final: 0.7045 (mtp85) REVERT: H 129 VAL cc_start: 0.7832 (OUTLIER) cc_final: 0.7549 (t) REVERT: H 132 LYS cc_start: 0.8705 (ptpp) cc_final: 0.8447 (ptpp) REVERT: H 139 GLU cc_start: 0.7477 (pt0) cc_final: 0.7141 (pt0) REVERT: H 207 ARG cc_start: 0.8160 (ptp-170) cc_final: 0.7876 (ptp90) REVERT: H 218 MET cc_start: 0.7244 (mmm) cc_final: 0.7036 (mmm) REVERT: H 241 THR cc_start: 0.7716 (m) cc_final: 0.7278 (t) REVERT: H 279 LYS cc_start: 0.7687 (tptt) cc_final: 0.7375 (tptt) REVERT: H 300 GLU cc_start: 0.6962 (mm-30) cc_final: 0.6564 (mm-30) REVERT: H 303 MET cc_start: 0.6941 (mmt) cc_final: 0.6527 (mmm) REVERT: H 334 ARG cc_start: 0.7450 (ttt180) cc_final: 0.7144 (ttt180) REVERT: H 352 ASP cc_start: 0.7049 (m-30) cc_final: 0.6723 (m-30) REVERT: H 365 LYS cc_start: 0.7819 (tttt) cc_final: 0.7463 (tptt) REVERT: H 379 ASP cc_start: 0.7737 (t0) cc_final: 0.7393 (m-30) REVERT: H 392 ARG cc_start: 0.7879 (ttt180) cc_final: 0.7597 (ttt180) REVERT: H 413 CYS cc_start: 0.7664 (t) cc_final: 0.7407 (p) REVERT: H 420 GLU cc_start: 0.7068 (tt0) cc_final: 0.6798 (tt0) REVERT: H 422 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7274 (mm110) REVERT: H 427 LYS cc_start: 0.7643 (mmtm) cc_final: 0.7387 (mmtm) REVERT: H 436 GLU cc_start: 0.5555 (tm-30) cc_final: 0.5261 (tm-30) REVERT: H 441 GLN cc_start: 0.7570 (tt0) cc_final: 0.7274 (tt0) REVERT: H 443 MET cc_start: 0.6864 (ttp) cc_final: 0.6593 (ttm) REVERT: I 31 LEU cc_start: 0.7863 (mt) cc_final: 0.7487 (mm) REVERT: I 60 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7647 (mmmt) REVERT: I 61 MET cc_start: 0.7903 (mmt) cc_final: 0.7302 (mmt) REVERT: I 64 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6106 (mmt90) REVERT: I 125 LYS cc_start: 0.8492 (ttmt) cc_final: 0.8276 (ttpp) REVERT: I 126 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6815 (tm-30) REVERT: I 169 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7836 (mm110) REVERT: I 173 ASP cc_start: 0.7450 (t70) cc_final: 0.7014 (t70) REVERT: I 175 SER cc_start: 0.8740 (m) cc_final: 0.8308 (p) REVERT: I 189 ASP cc_start: 0.6100 (m-30) cc_final: 0.5370 (m-30) REVERT: I 202 ARG cc_start: 0.7741 (ttt-90) cc_final: 0.7299 (ttt-90) REVERT: I 260 MET cc_start: 0.6046 (mtt) cc_final: 0.5741 (mtt) REVERT: I 280 ASN cc_start: 0.7470 (m-40) cc_final: 0.7032 (m-40) REVERT: I 281 LYS cc_start: 0.7313 (mttt) cc_final: 0.7079 (mttt) REVERT: I 312 PHE cc_start: 0.7640 (m-80) cc_final: 0.7283 (m-80) REVERT: I 317 ARG cc_start: 0.6670 (ttt-90) cc_final: 0.6456 (ttt-90) REVERT: I 320 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6285 (mp0) REVERT: I 335 ASN cc_start: 0.7729 (t0) cc_final: 0.7325 (t0) REVERT: I 356 ASP cc_start: 0.7135 (t0) cc_final: 0.6766 (t70) REVERT: I 376 LYS cc_start: 0.7624 (tptt) cc_final: 0.7281 (tppt) REVERT: I 389 GLU cc_start: 0.7600 (pt0) cc_final: 0.7274 (pt0) REVERT: I 396 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7017 (mt-10) REVERT: I 399 THR cc_start: 0.7837 (m) cc_final: 0.7448 (p) REVERT: I 418 LYS cc_start: 0.7752 (mtpt) cc_final: 0.7415 (mtpp) REVERT: I 427 LYS cc_start: 0.7694 (tttt) cc_final: 0.7392 (ttpp) REVERT: I 428 GLU cc_start: 0.7674 (mp0) cc_final: 0.7437 (pm20) REVERT: I 445 LYS cc_start: 0.7557 (mttp) cc_final: 0.7229 (ttpp) REVERT: J 26 SER cc_start: 0.7996 (m) cc_final: 0.7564 (t) REVERT: J 40 ARG cc_start: 0.7348 (mtt90) cc_final: 0.7131 (mtt90) REVERT: J 50 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7684 (mm) REVERT: J 59 VAL cc_start: 0.7536 (t) cc_final: 0.7282 (m) REVERT: J 94 LEU cc_start: 0.7566 (tp) cc_final: 0.7333 (tp) REVERT: J 236 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8173 (mtpt) REVERT: J 264 ASP cc_start: 0.6389 (t0) cc_final: 0.6045 (t0) REVERT: J 274 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7218 (mt-10) REVERT: J 336 ARG cc_start: 0.7070 (mtm180) cc_final: 0.6762 (mtm180) REVERT: J 377 GLU cc_start: 0.6687 (tp30) cc_final: 0.6255 (tp30) REVERT: J 384 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6941 (mm-30) REVERT: J 404 GLN cc_start: 0.7660 (mt0) cc_final: 0.7397 (mt0) REVERT: J 420 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7120 (tt0) REVERT: J 427 LYS cc_start: 0.7884 (mmtp) cc_final: 0.7653 (mmtp) REVERT: J 436 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6835 (tm-30) REVERT: K 153 MET cc_start: -0.0369 (tmm) cc_final: -0.0952 (tmm) REVERT: K 283 MET cc_start: 0.3842 (mmm) cc_final: 0.3274 (mmm) REVERT: L 11 ASP cc_start: 0.8226 (t0) cc_final: 0.7999 (t70) REVERT: L 34 ILE cc_start: 0.8672 (mt) cc_final: 0.8360 (mt) REVERT: L 57 GLU cc_start: 0.7522 (tp30) cc_final: 0.6678 (tp30) REVERT: L 61 LYS cc_start: 0.8543 (mtmt) cc_final: 0.7654 (mtmt) REVERT: L 100 GLU cc_start: 0.7610 (tt0) cc_final: 0.7382 (tt0) REVERT: L 107 GLU cc_start: 0.6920 (OUTLIER) cc_final: 0.6715 (pt0) REVERT: L 132 MET cc_start: 0.8209 (tmm) cc_final: 0.7771 (tmm) REVERT: L 167 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7233 (mm-30) REVERT: L 259 GLU cc_start: 0.7561 (tp30) cc_final: 0.7274 (tp30) REVERT: L 300 SER cc_start: 0.8446 (p) cc_final: 0.8171 (m) REVERT: L 312 ARG cc_start: 0.8825 (tpt90) cc_final: 0.8351 (tpt-90) REVERT: L 326 LYS cc_start: 0.8271 (tttp) cc_final: 0.7926 (tttp) REVERT: M 30 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7599 (mm-30) REVERT: M 31 ASP cc_start: 0.6583 (p0) cc_final: 0.6238 (p0) REVERT: M 128 ASN cc_start: 0.7781 (t0) cc_final: 0.7431 (p0) REVERT: M 130 ARG cc_start: 0.7650 (ttm110) cc_final: 0.7341 (ttm170) REVERT: M 134 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7109 (mt-10) REVERT: M 186 TYR cc_start: 0.7746 (m-80) cc_final: 0.7305 (m-80) REVERT: M 189 GLN cc_start: 0.8272 (mt0) cc_final: 0.7860 (mp10) REVERT: M 205 GLN cc_start: 0.7934 (mm110) cc_final: 0.7674 (mm110) REVERT: M 226 LYS cc_start: 0.8534 (pttt) cc_final: 0.7805 (ptpt) REVERT: M 227 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7421 (mm-30) REVERT: M 238 LYS cc_start: 0.8465 (mmtt) cc_final: 0.8088 (mmtt) REVERT: M 252 ASN cc_start: 0.8244 (m-40) cc_final: 0.7914 (m110) REVERT: M 276 GLU cc_start: 0.7351 (tp30) cc_final: 0.6997 (tp30) REVERT: M 287 TYR cc_start: 0.8093 (t80) cc_final: 0.7795 (t80) REVERT: M 294 ASN cc_start: 0.8264 (p0) cc_final: 0.7708 (p0) REVERT: M 301 ARG cc_start: 0.8163 (ptm-80) cc_final: 0.7773 (ptm-80) REVERT: M 303 LYS cc_start: 0.8678 (tttp) cc_final: 0.8355 (mtpp) REVERT: M 308 LEU cc_start: 0.8489 (mm) cc_final: 0.8224 (mt) REVERT: M 322 MET cc_start: 0.7324 (mtm) cc_final: 0.6981 (mtm) REVERT: M 347 SER cc_start: 0.7611 (t) cc_final: 0.7165 (p) REVERT: N 55 ARG cc_start: 0.7983 (mtt180) cc_final: 0.7441 (mtt180) REVERT: N 62 TYR cc_start: 0.8658 (p90) cc_final: 0.8380 (p90) REVERT: N 91 LYS cc_start: 0.7788 (ptmm) cc_final: 0.7516 (ptmm) REVERT: N 128 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7675 (ttm110) REVERT: N 193 GLU cc_start: 0.7400 (tp30) cc_final: 0.7007 (tp30) REVERT: N 196 TYR cc_start: 0.7856 (m-80) cc_final: 0.7559 (m-10) REVERT: N 202 LEU cc_start: 0.8721 (mt) cc_final: 0.8404 (mt) REVERT: N 228 GLU cc_start: 0.8177 (tp30) cc_final: 0.7840 (tp30) REVERT: N 232 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7873 (ttm170) REVERT: N 255 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6890 (mm-30) outliers start: 85 outliers final: 70 residues processed: 1340 average time/residue: 0.2524 time to fit residues: 517.4562 Evaluate side-chains 1377 residues out of total 4423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 1299 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1955 GLU Chi-restraints excluded: chain A residue 1982 LEU Chi-restraints excluded: chain A residue 2099 ILE Chi-restraints excluded: chain A residue 2193 VAL Chi-restraints excluded: chain A residue 2207 ARG Chi-restraints excluded: chain A residue 2224 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 307 ASP Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 289 GLN Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 284 ARG Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 336 CYS Chi-restraints excluded: chain G residue 346 SER Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain H residue 167 GLU Chi-restraints excluded: chain H residue 195 ILE Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 295 VAL Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 235 ILE Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain I residue 320 GLU Chi-restraints excluded: chain I residue 415 LEU Chi-restraints excluded: chain I residue 435 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 132 LYS Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain J residue 295 VAL Chi-restraints excluded: chain J residue 358 SER Chi-restraints excluded: chain J residue 368 LYS Chi-restraints excluded: chain J residue 390 LEU Chi-restraints excluded: chain K residue 269 MET Chi-restraints excluded: chain L residue 18 LYS Chi-restraints excluded: chain L residue 80 ASP Chi-restraints excluded: chain L residue 107 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 227 MET Chi-restraints excluded: chain L residue 315 LYS Chi-restraints excluded: chain L residue 339 VAL Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 100 GLN Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 247 THR Chi-restraints excluded: chain M residue 282 MET Chi-restraints excluded: chain M residue 321 THR Chi-restraints excluded: chain M residue 323 LEU Chi-restraints excluded: chain M residue 378 LEU Chi-restraints excluded: chain M residue 385 THR Chi-restraints excluded: chain N residue 131 LYS Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 188 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 464 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 336 optimal weight: 3.9990 chunk 332 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 201 optimal weight: 0.9980 chunk 309 optimal weight: 0.0980 chunk 198 optimal weight: 0.0670 chunk 279 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** G 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 385 ASN ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN J 255 GLN ** L 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 100 GLN M 384 ASN ** M 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.171989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138503 restraints weight = 66479.579| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.75 r_work: 0.3453 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 41572 Z= 0.153 Angle : 0.666 59.193 56164 Z= 0.357 Chirality : 0.042 0.200 6364 Planarity : 0.004 0.057 7187 Dihedral : 6.497 149.688 5717 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.88 % Allowed : 16.80 % Favored : 81.32 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.46 % 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: 1.65 (0.12), residues: 5082 helix: 1.78 (0.11), residues: 2324 sheet: 0.42 (0.18), residues: 803 loop : 0.73 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 164 TYR 0.037 0.001 TYR I 314 PHE 0.020 0.001 PHE L 255 TRP 0.028 0.001 TRP A1232 HIS 0.014 0.001 HIS A1290 Details of bonding type rmsd covalent geometry : bond 0.00337 (41572) covalent geometry : angle 0.66625 (56164) hydrogen bonds : bond 0.03659 ( 1947) hydrogen bonds : angle 4.19225 ( 5517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12192.11 seconds wall clock time: 208 minutes 11.21 seconds (12491.21 seconds total)