Starting phenix.real_space_refine on Mon Aug 25 13:39:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ca9_45383/08_2025/9ca9_45383.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ca9_45383/08_2025/9ca9_45383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ca9_45383/08_2025/9ca9_45383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ca9_45383/08_2025/9ca9_45383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ca9_45383/08_2025/9ca9_45383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ca9_45383/08_2025/9ca9_45383.map" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 15 5.49 5 Mg 4 5.21 5 S 148 5.16 5 C 17956 2.51 5 N 4985 2.21 5 O 5479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28589 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3492 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 36, 'TRANS': 393} Chain breaks: 2 Chain: "B" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 692 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 9, 'TRANS': 75} Chain breaks: 1 Chain: "C" Number of atoms: 3226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3226 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 378} Chain: "D" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 831 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 8, 'TRANS': 96} Chain breaks: 1 Chain: "E" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3344 Classifications: {'peptide': 433} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 416} Chain breaks: 1 Chain: "F" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3395 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 11, 'TRANS': 426} Chain: "G" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3430 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 427} Chain: "H" Number of atoms: 3361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3361 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 10, 'TRANS': 421} Chain breaks: 1 Chain: "I" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3365 Classifications: {'peptide': 436} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 419} Chain breaks: 1 Chain: "J" Number of atoms: 3254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3254 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 10, 'TRANS': 407} Chain breaks: 2 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8044 SG CYS D 128 33.309 61.805 68.237 1.00102.18 S ATOM 8063 SG CYS D 131 33.800 60.043 64.887 1.00 99.34 S ATOM 8203 SG CYS D 149 30.183 60.933 65.989 1.00122.52 S ATOM 7966 SG CYS D 117 38.640 70.150 62.857 1.00 83.75 S ATOM 7984 SG CYS D 120 39.464 73.542 61.408 1.00 80.70 S ATOM 8101 SG CYS D 136 39.513 73.119 65.110 1.00 89.43 S ATOM 8132 SG CYS D 140 36.186 73.010 63.333 1.00 91.88 S Time building chain proxies: 5.62, per 1000 atoms: 0.20 Number of scatterers: 28589 At special positions: 0 Unit cell: (141.45, 141.45, 184.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 148 16.00 P 15 15.00 Mg 4 11.99 O 5479 8.00 N 4985 7.00 C 17956 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: 2.12 Conformation dependent library (CDL) restraints added in 964.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" NE2 HIS D 144 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 131 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 128 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 149 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 120 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 117 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 140 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 136 " Number of angles added : 9 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6740 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 32 sheets defined 47.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 862 through 877 removed outlier: 4.150A pdb=" N THR A 877 " --> pdb=" O MET A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 903 Processing helix chain 'A' and resid 904 through 907 Processing helix chain 'A' and resid 928 through 932 Processing helix chain 'A' and resid 936 through 940 Processing helix chain 'A' and resid 942 through 947 removed outlier: 3.836A pdb=" N ARG A 945 " --> pdb=" O ASP A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 952 Processing helix chain 'A' and resid 956 through 962 Processing helix chain 'A' and resid 962 through 968 removed outlier: 3.869A pdb=" N ARG A 966 " --> pdb=" O THR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'A' and resid 1886 through 1911 Processing helix chain 'A' and resid 1919 through 1927 Processing helix chain 'A' and resid 1945 through 1950 Processing helix chain 'A' and resid 1952 through 1958 Processing helix chain 'A' and resid 1961 through 1969 Processing helix chain 'A' and resid 1969 through 1977 removed outlier: 3.501A pdb=" N ILE A1977 " --> pdb=" O ILE A1973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2015 Processing helix chain 'A' and resid 2016 through 2020 removed outlier: 3.615A pdb=" N ARG A2019 " --> pdb=" O PRO A2016 " (cutoff:3.500A) Proline residue: A2020 - end of helix No H-bonds generated for 'chain 'A' and resid 2016 through 2020' Processing helix chain 'A' and resid 2021 through 2030 Processing helix chain 'A' and resid 2035 through 2041 removed outlier: 4.249A pdb=" N GLN A2039 " --> pdb=" O LEU A2035 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2059 Processing helix chain 'A' and resid 2068 through 2083 Processing helix chain 'A' and resid 2094 through 2108 removed outlier: 3.680A pdb=" N GLN A2099 " --> pdb=" O VAL A2095 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A2100 " --> pdb=" O GLU A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2141 through 2154 removed outlier: 3.823A pdb=" N ASP A2145 " --> pdb=" O ASN A2141 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS A2152 " --> pdb=" O ALA A2148 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2180 removed outlier: 4.071A pdb=" N ASN A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 312 through 331 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 67 through 80 removed outlier: 3.757A pdb=" N GLN C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 166 through 170 removed outlier: 3.561A pdb=" N ILE C 170 " --> pdb=" O LYS C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 215 through 225 removed outlier: 3.530A pdb=" N LEU C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.632A pdb=" N VAL C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 4.565A pdb=" N LEU C 281 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 293 through 305 removed outlier: 3.611A pdb=" N LEU C 305 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 315 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 328 through 341 Processing helix chain 'C' and resid 357 through 369 removed outlier: 3.513A pdb=" N ASN C 369 " --> pdb=" O LEU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 376 removed outlier: 3.672A pdb=" N MET C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 394 removed outlier: 4.212A pdb=" N GLU C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N SER C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU C 391 " --> pdb=" O HIS C 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 35 Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 137 through 148 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.691A 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: 3.620A pdb=" N VAL E 101 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 3.708A 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 183 Processing helix chain 'E' and resid 208 through 210 No H-bonds generated for 'chain 'E' and resid 208 through 210' Processing helix chain 'E' and resid 240 through 249 Processing helix chain 'E' and resid 255 through 265 removed outlier: 3.556A pdb=" N MET E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 289 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 308 through 321 removed outlier: 3.816A 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 removed outlier: 3.542A pdb=" N LYS E 400 " --> pdb=" O GLU E 396 " (cutoff:3.500A) 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 450 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 Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 175 through 186 Processing helix chain 'F' and resid 244 through 253 removed outlier: 4.011A pdb=" N ARG F 253 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 263 removed outlier: 4.173A 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 301 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.647A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 378 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.551A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.827A 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 'G' and resid 42 through 59 removed outlier: 3.671A 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 Processing helix chain 'G' and resid 107 through 119 Processing helix chain 'G' and resid 175 through 183 removed outlier: 4.202A 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 255 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 321 removed outlier: 3.548A pdb=" N HIS G 316 " --> pdb=" O PHE G 312 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG G 317 " --> pdb=" O THR G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 356 Processing helix chain 'G' and resid 367 through 382 Processing helix chain 'G' and resid 387 through 400 Processing helix chain 'G' and resid 402 through 409 removed outlier: 3.602A pdb=" N SER G 406 " --> pdb=" O THR G 402 " (cutoff:3.500A) Processing helix chain 'G' and resid 409 through 421 Processing helix chain 'G' and resid 426 through 437 Processing helix chain 'G' and resid 439 through 450 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 Processing helix chain 'H' and resid 114 through 126 removed outlier: 3.502A pdb=" N SER H 126 " --> pdb=" O ALA H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 210 through 214 removed outlier: 4.023A pdb=" N ASP H 214 " --> pdb=" O ARG H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 251 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 301 through 304 Processing helix chain 'H' and resid 305 through 316 removed outlier: 3.764A 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: 3.786A 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 58 Processing helix chain 'I' and resid 75 through 88 Processing helix chain 'I' and resid 99 through 102 removed outlier: 3.828A 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 120 Processing helix chain 'I' and resid 175 through 183 removed outlier: 4.021A 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 263 removed outlier: 3.664A pdb=" N LEU I 263 " --> pdb=" O MET I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 290 Processing helix chain 'I' and resid 303 through 307 Processing helix chain 'I' and resid 308 through 320 removed outlier: 3.595A pdb=" N ARG I 317 " --> pdb=" O THR I 313 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU I 320 " --> pdb=" O HIS I 316 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 356 Processing helix chain 'I' and resid 367 through 382 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 421 Processing helix chain 'I' and resid 426 through 437 Processing helix chain 'I' and resid 439 through 450 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 removed outlier: 3.565A pdb=" N SER J 126 " --> pdb=" O ALA J 122 " (cutoff:3.500A) 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 286 Processing helix chain 'J' and resid 301 through 304 Processing helix chain 'J' and resid 305 through 316 removed outlier: 3.680A 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: 4.024A pdb=" N THR J 407 " --> pdb=" O ILE J 403 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA J 408 " --> pdb=" O GLN J 404 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 433 Processing helix chain 'J' and resid 435 through 446 Processing sheet with id=AA1, first strand: chain 'A' and resid 852 through 859 removed outlier: 6.043A pdb=" N LEU A2063 " --> pdb=" O VAL A2134 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A2062 " --> pdb=" O PHE A2114 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N LEU A2116 " --> pdb=" O VAL A2062 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE A2064 " --> pdb=" O LEU A2116 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A2117 " --> pdb=" O LEU A2089 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 916 through 917 removed outlier: 5.903A pdb=" N PHE A 916 " --> pdb=" O GLU A1984 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 922 through 924 Processing sheet with id=AA4, first strand: chain 'B' and resid 211 through 219 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 261 through 268 current: chain 'F' and resid 158 through 164 removed outlier: 4.190A pdb=" N GLY F 159 " --> pdb=" O LEU F 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 169 through 174 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 152 through 163 removed outlier: 3.789A pdb=" N GLY G 166 " --> pdb=" O THR G 163 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 166 through 172 current: chain 'G' and resid 200 through 206 removed outlier: 5.343A pdb=" N VAL G 221 " --> pdb=" O GLN G 203 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ARG G 205 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 301 through 303 removed outlier: 3.797A pdb=" N ILE B 308 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 23 through 26 removed outlier: 6.667A pdb=" N THR C 2 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE C 94 " --> pdb=" O THR C 2 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU C 4 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N THR C 96 " --> pdb=" O LEU C 4 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU C 6 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR C 91 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU C 123 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 93 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL C 125 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE C 95 " --> pdb=" O VAL C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA9, first strand: chain 'C' and resid 171 through 173 removed outlier: 6.409A pdb=" N ILE C 146 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N THR C 320 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VAL C 148 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE C 317 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.532A pdb=" N PHE C 248 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AB3, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.596A pdb=" N LEU E 299 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N ALA E 330 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL E 301 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N SER E 331 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU E 68 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA E 65 " --> pdb=" O MET E 359 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE E 361 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU E 67 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 121 through 141 removed outlier: 5.757A pdb=" N VAL E 135 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS E 162 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU E 137 " --> pdb=" O GLY E 160 " (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: 5.493A pdb=" N VAL E 221 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG E 205 " --> pdb=" O VAL E 221 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AB6, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB7, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.614A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY F 77 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR F 359 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA F 76 " --> pdb=" O THR F 359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 332 through 334 Processing sheet with id=AB9, first strand: chain 'G' and resid 35 through 36 Processing sheet with id=AC1, first strand: chain 'G' and resid 93 through 97 removed outlier: 6.251A pdb=" N CYS G 94 " --> pdb=" O PHE G 300 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP G 302 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N MET G 96 " --> pdb=" O ASP G 302 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU G 299 " --> pdb=" O ILE G 328 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ALA G 330 " --> pdb=" O LEU G 299 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL G 301 " --> pdb=" O ALA G 330 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL G 66 " --> pdb=" O PHE G 329 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N SER G 331 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU G 68 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA G 65 " --> pdb=" O MET G 359 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ILE G 361 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU G 67 " --> pdb=" O ILE G 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 336 through 337 Processing sheet with id=AC3, first strand: chain 'H' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'H' and resid 100 through 104 removed outlier: 6.854A pdb=" N ALA H 72 " --> pdb=" O LEU H 355 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL H 357 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU H 74 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR H 359 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA H 76 " --> pdb=" O THR H 359 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 127 through 148 removed outlier: 6.809A pdb=" N THR H 162 " --> pdb=" O VAL H 143 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE H 145 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS H 160 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ILE H 147 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL H 158 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.933A 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=AC6, first strand: chain 'H' and resid 333 through 334 Processing sheet with id=AC7, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AC8, first strand: chain 'I' and resid 93 through 97 removed outlier: 6.401A pdb=" N VAL I 66 " --> pdb=" O PHE I 329 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N SER I 331 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU I 68 " --> pdb=" O SER I 331 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA I 65 " --> pdb=" O MET I 359 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE I 361 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU I 67 " --> pdb=" O ILE I 361 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 121 through 141 removed outlier: 6.024A pdb=" N GLY I 160 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU I 138 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE I 158 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N HIS I 156 " --> pdb=" O PRO I 140 " (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: 5.229A pdb=" N VAL I 221 " --> pdb=" O GLN I 203 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ARG I 205 " --> pdb=" O VAL I 221 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 336 through 337 Processing sheet with id=AD2, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AD3, first strand: chain 'J' and resid 100 through 104 removed outlier: 6.443A pdb=" N THR J 101 " --> pdb=" O PHE J 297 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASP J 299 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE J 103 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU J 296 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ALA J 327 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE J 298 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY J 77 " --> pdb=" O THR J 328 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ALA J 72 " --> pdb=" O LEU J 355 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL J 357 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU J 74 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR J 359 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ALA J 76 " --> pdb=" O THR J 359 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 127 through 148 removed outlier: 6.694A pdb=" N THR J 162 " --> pdb=" O VAL J 143 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE J 145 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS J 160 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ILE J 147 " --> pdb=" O VAL J 158 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL J 158 " --> pdb=" O ILE J 147 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY J 159 " --> pdb=" O LEU J 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 169 through 174 current: chain 'J' and resid 201 through 207 Processing sheet with id=AD5, first strand: chain 'J' and resid 333 through 334 1224 hydrogen bonds defined for protein. 3483 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: 4.27 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 9728 1.37 - 1.51: 7973 1.51 - 1.66: 11104 1.66 - 1.80: 163 1.80 - 1.95: 77 Bond restraints: 29045 Sorted by residual: bond pdb=" C4 ADP J 501 " pdb=" C5 ADP J 501 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.84e+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 1.79e+00 bond pdb=" C4 ADP I 501 " pdb=" C5 ADP I 501 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.79e+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 1.73e+00 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 29040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 38615 1.49 - 2.98: 494 2.98 - 4.47: 80 4.47 - 5.97: 39 5.97 - 7.46: 8 Bond angle restraints: 39236 Sorted by residual: angle pdb=" O1B ADP H 501 " pdb=" PB ADP H 501 " pdb=" O3B ADP H 501 " ideal model delta sigma weight residual 119.90 112.44 7.46 3.00e+00 1.11e-01 6.18e+00 angle pdb=" C1' ADP J 501 " pdb=" C2' ADP J 501 " pdb=" C3' ADP J 501 " ideal model delta sigma weight residual 111.00 104.23 6.77 3.00e+00 1.11e-01 5.09e+00 angle pdb=" C1' ADP F 501 " pdb=" C2' ADP F 501 " pdb=" C3' ADP F 501 " ideal model delta sigma weight residual 111.00 104.56 6.44 3.00e+00 1.11e-01 4.61e+00 angle pdb=" C1' ADP E 501 " pdb=" C2' ADP E 501 " pdb=" C3' ADP E 501 " ideal model delta sigma weight residual 111.00 104.88 6.12 3.00e+00 1.11e-01 4.16e+00 angle pdb=" C1' ADP I 501 " pdb=" C2' ADP I 501 " pdb=" C3' ADP I 501 " ideal model delta sigma weight residual 111.00 104.97 6.03 3.00e+00 1.11e-01 4.04e+00 ... (remaining 39231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 17427 32.59 - 65.18: 381 65.18 - 97.78: 59 97.78 - 130.37: 3 130.37 - 162.96: 1 Dihedral angle restraints: 17871 sinusoidal: 7432 harmonic: 10439 Sorted by residual: dihedral pdb=" C5' ADP H 501 " pdb=" O5' ADP H 501 " pdb=" PA ADP H 501 " pdb=" O2A ADP H 501 " ideal model delta sinusoidal sigma weight residual 300.00 169.94 130.07 1 2.00e+01 2.50e-03 3.94e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 -178.98 118.99 1 2.00e+01 2.50e-03 3.56e+01 dihedral pdb=" O2A ADP E 501 " pdb=" O3A ADP E 501 " pdb=" PA ADP E 501 " pdb=" PB ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 54.52 -114.52 1 2.00e+01 2.50e-03 3.40e+01 ... (remaining 17868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 3181 0.038 - 0.075: 900 0.075 - 0.113: 361 0.113 - 0.151: 56 0.151 - 0.189: 1 Chirality restraints: 4499 Sorted by residual: chirality pdb=" CA ILE J 346 " pdb=" N ILE J 346 " pdb=" C ILE J 346 " pdb=" CB ILE J 346 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CA ILE H 346 " pdb=" N ILE H 346 " pdb=" C ILE H 346 " pdb=" CB ILE H 346 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ILE I 350 " pdb=" N ILE I 350 " pdb=" C ILE I 350 " pdb=" CB ILE I 350 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 4496 not shown) Planarity restraints: 5042 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 99 " 0.006 2.00e-02 2.50e+03 3.41e-02 2.33e+01 pdb=" CG TYR C 99 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR C 99 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR C 99 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C 99 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR C 99 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 99 " -0.047 2.00e-02 2.50e+03 pdb=" OH TYR C 99 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 382 " 0.015 2.00e-02 2.50e+03 2.98e-02 8.88e+00 pdb=" C TYR C 382 " -0.052 2.00e-02 2.50e+03 pdb=" O TYR C 382 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU C 383 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 162 " -0.161 9.50e-02 1.11e+02 7.28e-02 4.54e+00 pdb=" NE ARG C 162 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 162 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C 162 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG C 162 " 0.001 2.00e-02 2.50e+03 ... (remaining 5039 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 107 2.48 - 3.08: 19571 3.08 - 3.69: 43183 3.69 - 4.29: 65787 4.29 - 4.90: 109064 Nonbonded interactions: 237712 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 1.873 2.170 nonbonded pdb=" OG1 THR F 84 " pdb="MG MG F 502 " model vdw 1.941 2.170 nonbonded pdb=" O2B ADP H 501 " pdb="MG MG H 502 " model vdw 2.007 2.170 nonbonded pdb=" O2B ADP J 501 " pdb="MG MG J 502 " model vdw 2.009 2.170 nonbonded pdb=" O2B AGS C 401 " pdb="MG MG C 402 " model vdw 2.060 2.170 ... (remaining 237707 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' selection = (chain 'G' and (resid 13 through 142 or resid 154 through 501)) selection = (chain 'I' and (resid 13 through 142 or resid 154 through 501)) } ncs_group { reference = (chain 'F' and (resid 16 through 149 or resid 157 through 209 or resid 224 throu \ gh 502)) selection = (chain 'H' and (resid 16 through 149 or resid 157 through 209 or resid 224 throu \ gh 502)) selection = (chain 'J' and (resid 16 through 453 or resid 501 through 502)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 24.530 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 0.048 29053 Z= 0.133 Angle : 0.484 7.457 39245 Z= 0.242 Chirality : 0.042 0.189 4499 Planarity : 0.004 0.073 5042 Dihedral : 14.199 162.961 11131 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.14), residues: 3580 helix: 1.45 (0.13), residues: 1582 sheet: 0.88 (0.20), residues: 660 loop : 0.47 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 162 TYR 0.052 0.002 TYR C 99 PHE 0.022 0.001 PHE C 154 TRP 0.012 0.001 TRP H 283 HIS 0.006 0.001 HIS G 316 Details of bonding type rmsd covalent geometry : bond 0.00277 (29045) covalent geometry : angle 0.48283 (39236) hydrogen bonds : bond 0.15193 ( 1224) hydrogen bonds : angle 5.26128 ( 3483) metal coordination : bond 0.01604 ( 8) metal coordination : angle 2.16428 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1291 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 873 MET cc_start: 0.5696 (mmm) cc_final: 0.5433 (mmm) REVERT: A 933 THR cc_start: 0.8435 (m) cc_final: 0.8125 (t) REVERT: A 939 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7489 (mm-40) REVERT: A 971 ARG cc_start: 0.7537 (mtt90) cc_final: 0.7320 (mtp85) REVERT: A 973 VAL cc_start: 0.8549 (t) cc_final: 0.8308 (p) REVERT: A 975 LEU cc_start: 0.8417 (mt) cc_final: 0.8140 (mt) REVERT: A 1887 ASP cc_start: 0.7282 (t0) cc_final: 0.6807 (t0) REVERT: A 1902 GLU cc_start: 0.8336 (tp30) cc_final: 0.7602 (tp30) REVERT: A 1906 GLN cc_start: 0.8148 (mm110) cc_final: 0.7826 (mm110) REVERT: A 1926 CYS cc_start: 0.8759 (m) cc_final: 0.8457 (m) REVERT: A 1934 SER cc_start: 0.8648 (m) cc_final: 0.8330 (p) REVERT: A 1943 PRO cc_start: 0.8004 (Cg_exo) cc_final: 0.7645 (Cg_endo) REVERT: A 1951 TYR cc_start: 0.8450 (m-80) cc_final: 0.7988 (m-80) REVERT: A 1965 ARG cc_start: 0.8315 (mmt180) cc_final: 0.7987 (mmm-85) REVERT: A 2014 LEU cc_start: 0.8707 (mt) cc_final: 0.8483 (mm) REVERT: A 2017 ARG cc_start: 0.8243 (mtt-85) cc_final: 0.7788 (mtp85) REVERT: A 2019 ARG cc_start: 0.8428 (mtt180) cc_final: 0.8009 (mtt180) REVERT: A 2032 PHE cc_start: 0.8242 (m-80) cc_final: 0.7631 (m-80) REVERT: A 2054 GLN cc_start: 0.8017 (mt0) cc_final: 0.7668 (mt0) REVERT: A 2071 MET cc_start: 0.6604 (tpp) cc_final: 0.5700 (tpp) REVERT: C 8 ASN cc_start: 0.7105 (t0) cc_final: 0.6437 (t0) REVERT: C 23 SER cc_start: 0.8007 (m) cc_final: 0.7757 (t) REVERT: C 60 PHE cc_start: 0.7651 (m-80) cc_final: 0.7052 (m-80) REVERT: C 90 ASP cc_start: 0.6563 (t0) cc_final: 0.6296 (t0) REVERT: C 92 ASN cc_start: 0.7630 (m-40) cc_final: 0.7344 (m110) REVERT: C 98 PRO cc_start: 0.8665 (Cg_exo) cc_final: 0.8425 (Cg_endo) REVERT: C 103 THR cc_start: 0.8533 (m) cc_final: 0.8259 (t) REVERT: C 138 ASP cc_start: 0.7680 (m-30) cc_final: 0.7347 (m-30) REVERT: C 142 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7508 (mm-30) REVERT: C 149 ASP cc_start: 0.8055 (t0) cc_final: 0.7788 (t0) REVERT: C 168 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7802 (mm-30) REVERT: C 187 ILE cc_start: 0.8203 (mt) cc_final: 0.7936 (pt) REVERT: C 204 GLN cc_start: 0.8308 (tp40) cc_final: 0.8085 (tp-100) REVERT: C 237 VAL cc_start: 0.9000 (t) cc_final: 0.8468 (m) REVERT: C 255 MET cc_start: 0.6329 (ttm) cc_final: 0.5808 (tpp) REVERT: C 267 ILE cc_start: 0.8630 (mt) cc_final: 0.8298 (pt) REVERT: C 279 GLU cc_start: 0.8019 (tp30) cc_final: 0.7640 (tp30) REVERT: C 286 ASP cc_start: 0.7730 (m-30) cc_final: 0.7474 (m-30) REVERT: C 307 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7182 (mm-30) REVERT: C 310 GLN cc_start: 0.8443 (mt0) cc_final: 0.8234 (mt0) REVERT: C 316 ASN cc_start: 0.8211 (m-40) cc_final: 0.7900 (m-40) REVERT: C 364 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7417 (ptmm) REVERT: C 366 ILE cc_start: 0.8639 (tt) cc_final: 0.8250 (tp) REVERT: D 24 ARG cc_start: 0.7579 (mtt-85) cc_final: 0.6977 (mtt-85) REVERT: D 82 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7501 (mtmm) REVERT: D 93 LEU cc_start: 0.8318 (tp) cc_final: 0.8040 (tp) REVERT: E 22 LYS cc_start: 0.8357 (mmtp) cc_final: 0.8073 (mmmm) REVERT: E 34 GLN cc_start: 0.7774 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 40 VAL cc_start: 0.8258 (t) cc_final: 0.7522 (p) REVERT: E 42 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8031 (mm-40) REVERT: E 43 GLU cc_start: 0.7923 (mp0) cc_final: 0.7264 (mp0) REVERT: E 60 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8169 (mtpp) REVERT: E 64 ARG cc_start: 0.8211 (mmt90) cc_final: 0.7950 (tpp-160) REVERT: E 86 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7987 (mm-30) REVERT: E 90 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8246 (ttmt) REVERT: E 99 SER cc_start: 0.8820 (m) cc_final: 0.8371 (t) REVERT: E 110 GLU cc_start: 0.8378 (tp30) cc_final: 0.8126 (tp30) REVERT: E 114 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7753 (mt-10) REVERT: E 115 ASN cc_start: 0.8097 (m-40) cc_final: 0.7757 (m-40) REVERT: E 129 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7423 (mt-10) REVERT: E 168 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7579 (ttmt) REVERT: E 193 ILE cc_start: 0.7800 (mt) cc_final: 0.7575 (mp) REVERT: E 200 VAL cc_start: 0.8374 (t) cc_final: 0.8041 (p) REVERT: E 201 LYS cc_start: 0.7797 (tptm) cc_final: 0.7126 (tptm) REVERT: E 259 MET cc_start: 0.8382 (tpt) cc_final: 0.8116 (mmm) REVERT: E 267 LYS cc_start: 0.7980 (mttp) cc_final: 0.7545 (mttp) REVERT: E 268 LYS cc_start: 0.8272 (mttt) cc_final: 0.8047 (mtmm) REVERT: E 276 ARG cc_start: 0.8169 (mtt90) cc_final: 0.7846 (mtt-85) REVERT: E 278 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7651 (mm-30) REVERT: E 285 LYS cc_start: 0.8388 (ttmm) cc_final: 0.8017 (ttmm) REVERT: E 295 VAL cc_start: 0.8602 (t) cc_final: 0.8317 (m) REVERT: E 302 ASP cc_start: 0.7530 (t0) cc_final: 0.7235 (t0) REVERT: E 314 TYR cc_start: 0.8539 (t80) cc_final: 0.7972 (t80) REVERT: E 339 ARG cc_start: 0.8378 (mtp85) cc_final: 0.8160 (mmm160) REVERT: E 343 ASP cc_start: 0.7165 (t0) cc_final: 0.6771 (t70) REVERT: E 354 LEU cc_start: 0.8287 (tp) cc_final: 0.8054 (tp) REVERT: E 371 MET cc_start: 0.8565 (mtt) cc_final: 0.8217 (mtp) REVERT: E 372 LYS cc_start: 0.8615 (mtpt) cc_final: 0.8355 (ttmm) REVERT: E 376 LYS cc_start: 0.8472 (tptt) cc_final: 0.8200 (tptt) REVERT: E 392 ASN cc_start: 0.8230 (m-40) cc_final: 0.7785 (m-40) REVERT: E 396 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7750 (mt-10) REVERT: E 414 ASN cc_start: 0.8343 (t0) cc_final: 0.7876 (t0) REVERT: E 415 LEU cc_start: 0.8423 (mt) cc_final: 0.8129 (mt) REVERT: E 416 LEU cc_start: 0.8648 (mt) cc_final: 0.8259 (mm) REVERT: E 427 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8426 (ttpp) REVERT: E 435 GLU cc_start: 0.7992 (tt0) cc_final: 0.7749 (tt0) REVERT: E 446 ILE cc_start: 0.8097 (mt) cc_final: 0.7876 (mm) REVERT: E 455 MET cc_start: 0.6946 (mmm) cc_final: 0.6654 (mmm) REVERT: F 19 ILE cc_start: 0.8248 (tt) cc_final: 0.8006 (tp) REVERT: F 44 GLN cc_start: 0.8548 (mt0) cc_final: 0.8197 (mt0) REVERT: F 67 LYS cc_start: 0.8450 (tttp) cc_final: 0.8249 (tttp) REVERT: F 92 GLN cc_start: 0.8378 (mm110) cc_final: 0.8113 (mm-40) REVERT: F 107 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7751 (mt-10) REVERT: F 112 GLU cc_start: 0.7374 (tp30) cc_final: 0.7020 (tp30) REVERT: F 131 ILE cc_start: 0.8463 (mt) cc_final: 0.8125 (mt) REVERT: F 138 ILE cc_start: 0.8702 (mt) cc_final: 0.8465 (mm) REVERT: F 160 LYS cc_start: 0.7853 (ttpt) cc_final: 0.7563 (ttpt) REVERT: F 162 THR cc_start: 0.8097 (m) cc_final: 0.7426 (p) REVERT: F 170 THR cc_start: 0.8644 (m) cc_final: 0.8346 (t) REVERT: F 176 THR cc_start: 0.8102 (m) cc_final: 0.7637 (p) REVERT: F 179 ILE cc_start: 0.8645 (mm) cc_final: 0.8259 (mm) REVERT: F 180 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7622 (mm-30) REVERT: F 186 LYS cc_start: 0.8315 (mtpp) cc_final: 0.7998 (mtpp) REVERT: F 188 GLN cc_start: 0.7516 (mt0) cc_final: 0.7179 (mt0) REVERT: F 192 VAL cc_start: 0.8521 (t) cc_final: 0.8258 (p) REVERT: F 194 THR cc_start: 0.8241 (m) cc_final: 0.8015 (t) REVERT: F 196 ASP cc_start: 0.7688 (t0) cc_final: 0.7321 (t0) REVERT: F 201 LYS cc_start: 0.8091 (tttp) cc_final: 0.7647 (tttp) REVERT: F 202 ILE cc_start: 0.8564 (mt) cc_final: 0.8348 (mp) REVERT: F 236 LYS cc_start: 0.7241 (mmtp) cc_final: 0.6939 (mmtp) REVERT: F 238 VAL cc_start: 0.8411 (t) cc_final: 0.8209 (p) REVERT: F 253 ARG cc_start: 0.7800 (ptp90) cc_final: 0.7464 (ptp90) REVERT: F 262 SER cc_start: 0.8545 (p) cc_final: 0.8140 (t) REVERT: F 264 ASP cc_start: 0.7956 (t0) cc_final: 0.7672 (t0) REVERT: F 269 LYS cc_start: 0.8522 (mmtp) cc_final: 0.8141 (mmtp) REVERT: F 271 GLU cc_start: 0.7819 (mp0) cc_final: 0.7612 (mp0) REVERT: F 274 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7541 (mm-30) REVERT: F 280 VAL cc_start: 0.8666 (t) cc_final: 0.8409 (m) REVERT: F 285 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7817 (mt-10) REVERT: F 291 ILE cc_start: 0.8728 (mt) cc_final: 0.8515 (mt) REVERT: F 300 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7371 (mm-30) REVERT: F 307 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7858 (mt-10) REVERT: F 314 ARG cc_start: 0.7716 (mmt180) cc_final: 0.7429 (mmt180) REVERT: F 317 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7486 (mt-10) REVERT: F 376 GLU cc_start: 0.8175 (tt0) cc_final: 0.7846 (tt0) REVERT: F 420 GLU cc_start: 0.8007 (tt0) cc_final: 0.7548 (tt0) REVERT: F 422 GLN cc_start: 0.8119 (mm-40) cc_final: 0.7665 (mm110) REVERT: F 431 SER cc_start: 0.8638 (m) cc_final: 0.8293 (p) REVERT: F 444 LYS cc_start: 0.8679 (mmtp) cc_final: 0.8336 (mmtp) REVERT: F 445 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7578 (mm-30) REVERT: F 446 TYR cc_start: 0.7595 (m-80) cc_final: 0.7279 (m-80) REVERT: F 447 GLN cc_start: 0.7709 (tp40) cc_final: 0.7071 (tp40) REVERT: G 27 ASP cc_start: 0.8037 (t70) cc_final: 0.7782 (t70) REVERT: G 33 LYS cc_start: 0.7642 (mtmt) cc_final: 0.7354 (mtmm) REVERT: G 54 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7861 (mm-30) REVERT: G 60 LYS cc_start: 0.8503 (ptmt) cc_final: 0.8041 (ttpp) REVERT: G 61 MET cc_start: 0.8382 (mmt) cc_final: 0.8083 (mpp) REVERT: G 77 THR cc_start: 0.8074 (m) cc_final: 0.7652 (p) REVERT: G 90 LYS cc_start: 0.8775 (tptm) cc_final: 0.8392 (tptm) REVERT: G 107 LYS cc_start: 0.8661 (pttt) cc_final: 0.8451 (pttt) REVERT: G 108 LYS cc_start: 0.8290 (mtmt) cc_final: 0.7990 (mtmt) REVERT: G 110 GLU cc_start: 0.8252 (tp30) cc_final: 0.7973 (tp30) REVERT: G 113 MET cc_start: 0.8285 (tpt) cc_final: 0.7772 (tpt) REVERT: G 125 LYS cc_start: 0.8474 (mtmt) cc_final: 0.7843 (mtpp) REVERT: G 128 LYS cc_start: 0.8591 (tttt) cc_final: 0.8056 (ttmm) REVERT: G 129 GLU cc_start: 0.7855 (tt0) cc_final: 0.7398 (tt0) REVERT: G 131 TYR cc_start: 0.8089 (m-80) cc_final: 0.7837 (m-80) REVERT: G 134 GLU cc_start: 0.8187 (tt0) cc_final: 0.7916 (tm-30) REVERT: G 137 GLU cc_start: 0.7735 (tt0) cc_final: 0.7182 (tt0) REVERT: G 158 ILE cc_start: 0.8458 (mt) cc_final: 0.8182 (mt) REVERT: G 159 ILE cc_start: 0.8337 (mt) cc_final: 0.7944 (tp) REVERT: G 168 LYS cc_start: 0.8331 (tttm) cc_final: 0.8032 (tttm) REVERT: G 169 GLN cc_start: 0.8378 (mt0) cc_final: 0.7300 (mt0) REVERT: G 171 LYS cc_start: 0.8552 (mtpt) cc_final: 0.8345 (mttm) REVERT: G 176 ILE cc_start: 0.8707 (mt) cc_final: 0.8437 (tp) REVERT: G 178 GLU cc_start: 0.8366 (tt0) cc_final: 0.7965 (tt0) REVERT: G 183 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7783 (mm-30) REVERT: G 201 LYS cc_start: 0.7824 (mmtm) cc_final: 0.7465 (mmtm) REVERT: G 203 GLN cc_start: 0.8507 (pt0) cc_final: 0.8167 (tt0) REVERT: G 225 LYS cc_start: 0.7651 (mmpt) cc_final: 0.7410 (mmpt) REVERT: G 231 LYS cc_start: 0.8691 (ptmt) cc_final: 0.8342 (ptmt) REVERT: G 233 GLU cc_start: 0.8133 (tt0) cc_final: 0.7896 (tt0) REVERT: G 244 ASP cc_start: 0.7831 (m-30) cc_final: 0.7497 (m-30) REVERT: G 258 SER cc_start: 0.8083 (m) cc_final: 0.7708 (t) REVERT: G 259 MET cc_start: 0.8297 (mmt) cc_final: 0.7901 (mmt) REVERT: G 260 MET cc_start: 0.8101 (mmt) cc_final: 0.7394 (mmt) REVERT: G 265 LYS cc_start: 0.8061 (ttpt) cc_final: 0.7837 (ttpt) REVERT: G 267 LYS cc_start: 0.7954 (tttp) cc_final: 0.7653 (tttp) REVERT: G 270 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7662 (mt-10) REVERT: G 274 LYS cc_start: 0.8571 (tttp) cc_final: 0.7791 (tttp) REVERT: G 278 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7573 (mt-10) REVERT: G 295 VAL cc_start: 0.8596 (t) cc_final: 0.8244 (p) REVERT: G 303 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7614 (mm-30) REVERT: G 306 MET cc_start: 0.8539 (mmp) cc_final: 0.8075 (mmp) REVERT: G 311 CYS cc_start: 0.8270 (m) cc_final: 0.7806 (m) REVERT: G 322 SER cc_start: 0.8687 (p) cc_final: 0.8422 (p) REVERT: G 326 ILE cc_start: 0.8768 (mt) cc_final: 0.8475 (mm) REVERT: G 327 VAL cc_start: 0.8806 (t) cc_final: 0.8494 (m) REVERT: G 339 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8121 (mmm-85) REVERT: G 364 MET cc_start: 0.8211 (mtm) cc_final: 0.7968 (mtp) REVERT: G 371 MET cc_start: 0.8008 (mtm) cc_final: 0.7761 (mtp) REVERT: G 372 LYS cc_start: 0.8131 (ttmt) cc_final: 0.7925 (mtmt) REVERT: G 376 LYS cc_start: 0.8471 (tptp) cc_final: 0.8216 (tttm) REVERT: G 388 GLU cc_start: 0.7597 (tp30) cc_final: 0.7285 (tp30) REVERT: G 389 GLU cc_start: 0.8050 (pt0) cc_final: 0.7830 (pt0) REVERT: G 391 LEU cc_start: 0.8648 (tp) cc_final: 0.8298 (tt) REVERT: G 392 ASN cc_start: 0.8489 (m-40) cc_final: 0.8007 (m-40) REVERT: G 396 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7787 (mt-10) REVERT: G 404 ARG cc_start: 0.7154 (mtt90) cc_final: 0.6923 (mtt180) REVERT: G 439 ASP cc_start: 0.8094 (p0) cc_final: 0.7844 (p0) REVERT: G 446 ILE cc_start: 0.8274 (mt) cc_final: 0.8066 (mm) REVERT: H 18 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7809 (mmm-85) REVERT: H 22 ILE cc_start: 0.8765 (mt) cc_final: 0.8540 (mm) REVERT: H 38 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7856 (mm-30) REVERT: H 41 GLN cc_start: 0.8257 (tp40) cc_final: 0.7447 (tm-30) REVERT: H 88 MET cc_start: 0.8145 (mmp) cc_final: 0.7826 (mmm) REVERT: H 107 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7977 (mt-10) REVERT: H 126 SER cc_start: 0.8665 (m) cc_final: 0.8031 (t) REVERT: H 130 ARG cc_start: 0.8132 (ttp80) cc_final: 0.7875 (ttp-110) REVERT: H 132 LYS cc_start: 0.8315 (ttmm) cc_final: 0.8093 (ttmm) REVERT: H 146 GLN cc_start: 0.7807 (pt0) cc_final: 0.7595 (pt0) REVERT: H 160 LYS cc_start: 0.8132 (mttt) cc_final: 0.7463 (mttt) REVERT: H 162 THR cc_start: 0.8473 (m) cc_final: 0.7781 (p) REVERT: H 164 LYS cc_start: 0.8378 (pttt) cc_final: 0.8042 (ptmm) REVERT: H 167 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7372 (mt-10) REVERT: H 169 GLU cc_start: 0.7367 (tt0) cc_final: 0.6960 (tt0) REVERT: H 177 LYS cc_start: 0.8575 (ptpt) cc_final: 0.8123 (ptpt) REVERT: H 180 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7508 (tm-30) REVERT: H 182 LEU cc_start: 0.8753 (mt) cc_final: 0.8531 (mt) REVERT: H 187 VAL cc_start: 0.8522 (t) cc_final: 0.8281 (p) REVERT: H 204 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8248 (mtpt) REVERT: H 205 LEU cc_start: 0.8578 (mt) cc_final: 0.8271 (mt) REVERT: H 209 PHE cc_start: 0.8706 (t80) cc_final: 0.8169 (t80) REVERT: H 211 ARG cc_start: 0.8371 (ttt180) cc_final: 0.8152 (ttt180) REVERT: H 218 MET cc_start: 0.7751 (mtp) cc_final: 0.7548 (mtp) REVERT: H 231 GLU cc_start: 0.7556 (tt0) cc_final: 0.7299 (tt0) REVERT: H 233 GLN cc_start: 0.8046 (mt0) cc_final: 0.7632 (mt0) REVERT: H 238 VAL cc_start: 0.8637 (t) cc_final: 0.8331 (m) REVERT: H 246 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7957 (mt-10) REVERT: H 251 ASN cc_start: 0.8743 (m-40) cc_final: 0.8374 (m110) REVERT: H 260 LEU cc_start: 0.8479 (mt) cc_final: 0.8162 (mt) REVERT: H 269 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8267 (mtmt) REVERT: H 271 GLU cc_start: 0.8012 (mp0) cc_final: 0.7572 (mp0) REVERT: H 274 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7781 (mt-10) REVERT: H 279 LYS cc_start: 0.8539 (tppt) cc_final: 0.8244 (tppp) REVERT: H 282 GLU cc_start: 0.8337 (tt0) cc_final: 0.7778 (tt0) REVERT: H 286 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7422 (mt-10) REVERT: H 295 VAL cc_start: 0.8215 (t) cc_final: 0.8005 (t) REVERT: H 303 MET cc_start: 0.8520 (mmp) cc_final: 0.8079 (mmm) REVERT: H 313 ASN cc_start: 0.8352 (m-40) cc_final: 0.7921 (m-40) REVERT: H 324 LEU cc_start: 0.8436 (tp) cc_final: 0.8077 (tp) REVERT: H 326 MET cc_start: 0.7784 (mtm) cc_final: 0.7528 (mtm) REVERT: H 332 ILE cc_start: 0.8124 (mt) cc_final: 0.7844 (mt) REVERT: H 353 ARG cc_start: 0.7780 (mtt90) cc_final: 0.7341 (mtt-85) REVERT: H 365 LYS cc_start: 0.8223 (ttpt) cc_final: 0.7960 (ttpt) REVERT: H 376 GLU cc_start: 0.8255 (tp30) cc_final: 0.8026 (tp30) REVERT: H 384 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7648 (mm-30) REVERT: H 392 ARG cc_start: 0.7913 (ttm-80) cc_final: 0.7625 (ttp-110) REVERT: H 427 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7975 (mmtp) REVERT: I 17 SER cc_start: 0.8053 (m) cc_final: 0.7689 (p) REVERT: I 31 LEU cc_start: 0.7907 (mt) cc_final: 0.7581 (mm) REVERT: I 34 GLN cc_start: 0.7567 (tm-30) cc_final: 0.7245 (tm-30) REVERT: I 74 THR cc_start: 0.8216 (p) cc_final: 0.7951 (p) REVERT: I 86 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7954 (mm-30) REVERT: I 89 SER cc_start: 0.8739 (m) cc_final: 0.8475 (t) REVERT: I 105 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7621 (mt-10) REVERT: I 125 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8300 (ttpp) REVERT: I 137 GLU cc_start: 0.7898 (tt0) cc_final: 0.7623 (tt0) REVERT: I 139 THR cc_start: 0.8344 (m) cc_final: 0.7786 (p) REVERT: I 158 ILE cc_start: 0.8504 (mm) cc_final: 0.8142 (mt) REVERT: I 159 ILE cc_start: 0.8588 (tt) cc_final: 0.8263 (mt) REVERT: I 169 GLN cc_start: 0.8198 (mm110) cc_final: 0.7866 (mm-40) REVERT: I 173 ASP cc_start: 0.7938 (t70) cc_final: 0.7564 (t0) REVERT: I 177 PHE cc_start: 0.8901 (t80) cc_final: 0.8438 (t80) REVERT: I 181 GLN cc_start: 0.7990 (mt0) cc_final: 0.7744 (mt0) REVERT: I 186 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7536 (mm-30) REVERT: I 194 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7457 (mm-30) REVERT: I 196 ASN cc_start: 0.8538 (p0) cc_final: 0.8241 (p0) REVERT: I 201 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7548 (ttmm) REVERT: I 209 TYR cc_start: 0.8375 (m-80) cc_final: 0.7925 (m-80) REVERT: I 214 ASP cc_start: 0.7875 (m-30) cc_final: 0.7568 (m-30) REVERT: I 219 GLU cc_start: 0.8007 (tp30) cc_final: 0.7679 (tp30) REVERT: I 221 VAL cc_start: 0.8896 (t) cc_final: 0.8573 (p) REVERT: I 230 LYS cc_start: 0.8424 (mttp) cc_final: 0.7966 (mttp) REVERT: I 233 GLU cc_start: 0.7989 (tt0) cc_final: 0.7766 (tm-30) REVERT: I 236 GLN cc_start: 0.7966 (tt0) cc_final: 0.7757 (tt0) REVERT: I 242 ASP cc_start: 0.7988 (m-30) cc_final: 0.7769 (m-30) REVERT: I 247 ASN cc_start: 0.8115 (m-40) cc_final: 0.7807 (m-40) REVERT: I 259 MET cc_start: 0.8692 (mtp) cc_final: 0.8288 (mtm) REVERT: I 268 LYS cc_start: 0.8388 (mtmt) cc_final: 0.7884 (mtmm) REVERT: I 280 ASN cc_start: 0.8208 (m-40) cc_final: 0.7909 (m-40) REVERT: I 284 ASN cc_start: 0.8535 (m-40) cc_final: 0.8332 (m-40) REVERT: I 294 LEU cc_start: 0.8660 (tp) cc_final: 0.8411 (tp) REVERT: I 295 VAL cc_start: 0.8542 (t) cc_final: 0.8318 (m) REVERT: I 316 HIS cc_start: 0.7957 (m170) cc_final: 0.7623 (m170) REVERT: I 352 LEU cc_start: 0.8505 (mt) cc_final: 0.8269 (mm) REVERT: I 362 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8123 (ptm160) REVERT: I 371 MET cc_start: 0.8124 (mtt) cc_final: 0.7858 (mtp) REVERT: I 372 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8134 (mtmm) REVERT: I 376 LYS cc_start: 0.8351 (tptp) cc_final: 0.8151 (tptm) REVERT: I 392 ASN cc_start: 0.8197 (m-40) cc_final: 0.7718 (m110) REVERT: I 396 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7859 (mt-10) REVERT: I 408 GLN cc_start: 0.8200 (mt0) cc_final: 0.7948 (mt0) REVERT: I 427 LYS cc_start: 0.8710 (tttt) cc_final: 0.8310 (tttp) REVERT: I 432 GLU cc_start: 0.7696 (tt0) cc_final: 0.7317 (tp30) REVERT: I 441 LYS cc_start: 0.8047 (mttm) cc_final: 0.7824 (mttm) REVERT: J 38 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7393 (mm-30) REVERT: J 71 ARG cc_start: 0.7699 (tpp80) cc_final: 0.7408 (mmt90) REVERT: J 90 MET cc_start: 0.8125 (mtm) cc_final: 0.7833 (mtp) REVERT: J 134 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7363 (mt-10) REVERT: J 135 THR cc_start: 0.8185 (t) cc_final: 0.7908 (m) REVERT: J 136 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7712 (mt-10) REVERT: J 139 GLU cc_start: 0.6958 (tt0) cc_final: 0.6611 (tt0) REVERT: J 160 LYS cc_start: 0.7515 (mmtm) cc_final: 0.7258 (mmtm) REVERT: J 161 LEU cc_start: 0.8604 (tp) cc_final: 0.8309 (tt) REVERT: J 164 LYS cc_start: 0.8128 (pttt) cc_final: 0.7708 (pttt) REVERT: J 167 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7639 (mt-10) REVERT: J 178 MET cc_start: 0.8224 (tpp) cc_final: 0.7352 (tpp) REVERT: J 182 LEU cc_start: 0.8914 (mt) cc_final: 0.8584 (mt) REVERT: J 183 THR cc_start: 0.8449 (m) cc_final: 0.8061 (p) REVERT: J 185 ASP cc_start: 0.7424 (t0) cc_final: 0.7158 (t0) REVERT: J 186 LYS cc_start: 0.7801 (tttt) cc_final: 0.7470 (tttt) REVERT: J 234 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7974 (ttpt) REVERT: J 235 ARG cc_start: 0.8068 (mtp180) cc_final: 0.7405 (ttm-80) REVERT: J 241 THR cc_start: 0.8319 (m) cc_final: 0.8101 (t) REVERT: J 251 ASN cc_start: 0.8394 (m-40) cc_final: 0.8188 (m-40) REVERT: J 269 LYS cc_start: 0.8482 (mmtp) cc_final: 0.8262 (mmtp) REVERT: J 279 LYS cc_start: 0.8561 (tppt) cc_final: 0.8181 (tttp) REVERT: J 282 GLU cc_start: 0.8036 (tt0) cc_final: 0.7820 (tt0) REVERT: J 290 GLU cc_start: 0.8115 (tt0) cc_final: 0.7904 (tt0) REVERT: J 334 ARG cc_start: 0.7814 (ttp80) cc_final: 0.7594 (ttt-90) REVERT: J 342 SER cc_start: 0.8528 (m) cc_final: 0.8308 (p) REVERT: J 348 ILE cc_start: 0.8593 (tp) cc_final: 0.8149 (tp) REVERT: J 352 ASP cc_start: 0.7851 (m-30) cc_final: 0.7497 (m-30) REVERT: J 364 GLU cc_start: 0.7971 (tt0) cc_final: 0.7733 (tt0) REVERT: J 377 GLU cc_start: 0.8175 (tp30) cc_final: 0.7797 (tp30) REVERT: J 379 ASP cc_start: 0.8066 (m-30) cc_final: 0.7823 (m-30) REVERT: J 391 THR cc_start: 0.8099 (m) cc_final: 0.7721 (p) REVERT: J 404 GLN cc_start: 0.7972 (mt0) cc_final: 0.7569 (mt0) REVERT: J 413 CYS cc_start: 0.8527 (t) cc_final: 0.8283 (t) REVERT: J 415 LYS cc_start: 0.8417 (tptt) cc_final: 0.8036 (tppp) REVERT: J 430 TYR cc_start: 0.8204 (t80) cc_final: 0.7766 (t80) REVERT: J 436 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6820 (tm-30) REVERT: J 441 GLN cc_start: 0.7576 (mt0) cc_final: 0.7124 (mt0) REVERT: J 445 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7519 (mt-10) outliers start: 0 outliers final: 0 residues processed: 1291 average time/residue: 0.2083 time to fit residues: 395.5826 Evaluate side-chains 1167 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1167 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.0020 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.5980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2003 GLN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN C 387 HIS E 229 HIS E 316 HIS F 41 GLN ** G 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 380 GLN G 408 GLN I 373 GLN I 380 GLN I 393 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.109384 restraints weight = 48832.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112738 restraints weight = 20255.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114832 restraints weight = 10751.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116169 restraints weight = 6900.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117046 restraints weight = 5161.340| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29053 Z= 0.147 Angle : 0.562 16.711 39245 Z= 0.277 Chirality : 0.043 0.156 4499 Planarity : 0.004 0.058 5042 Dihedral : 7.264 148.477 4020 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.61 % Allowed : 8.91 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.14), residues: 3580 helix: 1.68 (0.13), residues: 1590 sheet: 0.91 (0.20), residues: 652 loop : 0.58 (0.17), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 123 TYR 0.017 0.001 TYR C 152 PHE 0.025 0.001 PHE C 248 TRP 0.007 0.001 TRP H 283 HIS 0.007 0.001 HIS G 316 Details of bonding type rmsd covalent geometry : bond 0.00311 (29045) covalent geometry : angle 0.56057 (39236) hydrogen bonds : bond 0.04091 ( 1224) hydrogen bonds : angle 4.25557 ( 3483) metal coordination : bond 0.00992 ( 8) metal coordination : angle 2.39041 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1216 time to evaluate : 1.032 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 873 MET cc_start: 0.5636 (mmm) cc_final: 0.5037 (mmm) REVERT: A 933 THR cc_start: 0.8288 (m) cc_final: 0.8024 (t) REVERT: A 939 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7088 (mm-40) REVERT: A 940 ARG cc_start: 0.7362 (ptt-90) cc_final: 0.7148 (ptp90) REVERT: A 955 VAL cc_start: 0.8639 (t) cc_final: 0.8186 (p) REVERT: A 957 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7661 (mtp85) REVERT: A 961 ASP cc_start: 0.7270 (m-30) cc_final: 0.6928 (m-30) REVERT: A 973 VAL cc_start: 0.8488 (t) cc_final: 0.8161 (p) REVERT: A 975 LEU cc_start: 0.8444 (mt) cc_final: 0.8165 (mt) REVERT: A 1887 ASP cc_start: 0.6626 (t0) cc_final: 0.6141 (t0) REVERT: A 1900 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7842 (ttp-110) REVERT: A 1902 GLU cc_start: 0.7861 (tp30) cc_final: 0.6657 (tp30) REVERT: A 1906 GLN cc_start: 0.7610 (mm110) cc_final: 0.7244 (mm110) REVERT: A 1920 THR cc_start: 0.8396 (t) cc_final: 0.8148 (p) REVERT: A 1926 CYS cc_start: 0.8412 (m) cc_final: 0.8042 (m) REVERT: A 1934 SER cc_start: 0.8399 (m) cc_final: 0.7988 (p) REVERT: A 1943 PRO cc_start: 0.7818 (Cg_exo) cc_final: 0.7465 (Cg_endo) REVERT: A 1951 TYR cc_start: 0.8149 (m-80) cc_final: 0.7602 (m-80) REVERT: A 1969 LEU cc_start: 0.7887 (mt) cc_final: 0.7586 (mt) REVERT: A 1973 ILE cc_start: 0.8837 (mt) cc_final: 0.8189 (mm) REVERT: A 1977 ILE cc_start: 0.8705 (mt) cc_final: 0.8368 (mt) REVERT: A 2001 PRO cc_start: 0.8548 (Cg_exo) cc_final: 0.8302 (Cg_endo) REVERT: A 2008 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7045 (tt0) REVERT: A 2014 LEU cc_start: 0.8522 (mt) cc_final: 0.8201 (mm) REVERT: A 2017 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.7715 (mtt-85) REVERT: A 2019 ARG cc_start: 0.7934 (mtt180) cc_final: 0.7471 (mtt180) REVERT: A 2032 PHE cc_start: 0.8327 (m-80) cc_final: 0.7922 (m-80) REVERT: A 2054 GLN cc_start: 0.8033 (mt0) cc_final: 0.7553 (mt0) REVERT: A 2068 MET cc_start: 0.5857 (mtt) cc_final: 0.5614 (mtt) REVERT: A 2071 MET cc_start: 0.6290 (tpp) cc_final: 0.5734 (tpp) REVERT: C 8 ASN cc_start: 0.7333 (t0) cc_final: 0.6793 (t0) REVERT: C 55 PHE cc_start: 0.7976 (t80) cc_final: 0.7681 (t80) REVERT: C 60 PHE cc_start: 0.7289 (m-80) cc_final: 0.6916 (m-80) REVERT: C 85 GLN cc_start: 0.8356 (mp10) cc_final: 0.8141 (pm20) REVERT: C 90 ASP cc_start: 0.5644 (t0) cc_final: 0.5367 (t0) REVERT: C 97 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7080 (mt-10) REVERT: C 103 THR cc_start: 0.8323 (m) cc_final: 0.8023 (t) REVERT: C 134 ARG cc_start: 0.8024 (ttt-90) cc_final: 0.7337 (ttt90) REVERT: C 138 ASP cc_start: 0.6947 (m-30) cc_final: 0.6706 (m-30) REVERT: C 149 ASP cc_start: 0.7755 (t0) cc_final: 0.7485 (t0) REVERT: C 167 LYS cc_start: 0.8493 (mttt) cc_final: 0.8273 (mttt) REVERT: C 187 ILE cc_start: 0.8182 (mt) cc_final: 0.7610 (tp) REVERT: C 204 GLN cc_start: 0.7994 (tp40) cc_final: 0.7719 (tp-100) REVERT: C 208 ASP cc_start: 0.7115 (m-30) cc_final: 0.6841 (m-30) REVERT: C 218 ARG cc_start: 0.7008 (ttp80) cc_final: 0.6750 (ttp80) REVERT: C 228 GLU cc_start: 0.7145 (pm20) cc_final: 0.6707 (pm20) REVERT: C 230 ASN cc_start: 0.7935 (t0) cc_final: 0.7251 (t0) REVERT: C 237 VAL cc_start: 0.8896 (t) cc_final: 0.8612 (m) REVERT: C 267 ILE cc_start: 0.8543 (mt) cc_final: 0.8332 (pt) REVERT: C 286 ASP cc_start: 0.7268 (m-30) cc_final: 0.7042 (m-30) REVERT: C 310 GLN cc_start: 0.7821 (mt0) cc_final: 0.7612 (mt0) REVERT: C 316 ASN cc_start: 0.7804 (m-40) cc_final: 0.7580 (m-40) REVERT: C 326 PHE cc_start: 0.8628 (m-80) cc_final: 0.8396 (m-80) REVERT: C 366 ILE cc_start: 0.8568 (tt) cc_final: 0.8349 (tp) REVERT: D 82 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7359 (mtmm) REVERT: D 93 LEU cc_start: 0.8442 (tp) cc_final: 0.8217 (tp) REVERT: E 34 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7460 (tm-30) REVERT: E 40 VAL cc_start: 0.8158 (t) cc_final: 0.7424 (p) REVERT: E 43 GLU cc_start: 0.7438 (mp0) cc_final: 0.6895 (mt-10) REVERT: E 60 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7832 (mtpp) REVERT: E 99 SER cc_start: 0.8657 (m) cc_final: 0.8242 (t) REVERT: E 108 LYS cc_start: 0.8046 (mtmm) cc_final: 0.7647 (mtpt) REVERT: E 110 GLU cc_start: 0.7854 (tp30) cc_final: 0.7221 (tp30) REVERT: E 113 MET cc_start: 0.7249 (tpt) cc_final: 0.6899 (tpt) REVERT: E 114 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7099 (mt-10) REVERT: E 115 ASN cc_start: 0.7824 (m-40) cc_final: 0.7308 (m-40) REVERT: E 118 ARG cc_start: 0.7189 (mtp85) cc_final: 0.6947 (ttp80) REVERT: E 168 LYS cc_start: 0.8076 (ttmt) cc_final: 0.7594 (ttmt) REVERT: E 200 VAL cc_start: 0.8225 (t) cc_final: 0.7920 (p) REVERT: E 201 LYS cc_start: 0.7801 (tptm) cc_final: 0.7097 (tptm) REVERT: E 257 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8180 (mm) REVERT: E 259 MET cc_start: 0.7747 (tpt) cc_final: 0.7416 (tmm) REVERT: E 267 LYS cc_start: 0.7782 (mttp) cc_final: 0.7481 (mttp) REVERT: E 268 LYS cc_start: 0.8136 (mttt) cc_final: 0.7915 (mtmm) REVERT: E 278 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6845 (mm-30) REVERT: E 285 LYS cc_start: 0.7877 (ttmm) cc_final: 0.7508 (ttmm) REVERT: E 295 VAL cc_start: 0.8430 (t) cc_final: 0.8136 (m) REVERT: E 302 ASP cc_start: 0.6611 (t0) cc_final: 0.6338 (t0) REVERT: E 308 ASP cc_start: 0.7311 (p0) cc_final: 0.7055 (p0) REVERT: E 314 TYR cc_start: 0.8296 (t80) cc_final: 0.6769 (t80) REVERT: E 317 ARG cc_start: 0.7635 (ttp80) cc_final: 0.7389 (ttt-90) REVERT: E 343 ASP cc_start: 0.6482 (t0) cc_final: 0.6146 (t70) REVERT: E 354 LEU cc_start: 0.8204 (tp) cc_final: 0.7941 (tp) REVERT: E 356 ASP cc_start: 0.7748 (t0) cc_final: 0.7441 (t0) REVERT: E 371 MET cc_start: 0.8227 (mtt) cc_final: 0.7959 (mtt) REVERT: E 372 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8022 (ttmm) REVERT: E 376 LYS cc_start: 0.8191 (tptt) cc_final: 0.7848 (tptt) REVERT: E 396 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7040 (mt-10) REVERT: E 414 ASN cc_start: 0.8210 (t0) cc_final: 0.7781 (t0) REVERT: E 415 LEU cc_start: 0.8411 (mt) cc_final: 0.8156 (mt) REVERT: E 416 LEU cc_start: 0.8541 (mt) cc_final: 0.8121 (mm) REVERT: E 427 LYS cc_start: 0.8510 (ttpp) cc_final: 0.8138 (ttpp) REVERT: E 432 GLU cc_start: 0.7308 (tt0) cc_final: 0.6862 (tt0) REVERT: E 435 GLU cc_start: 0.7223 (tt0) cc_final: 0.6956 (tt0) REVERT: E 446 ILE cc_start: 0.8099 (mt) cc_final: 0.7889 (mm) REVERT: E 455 MET cc_start: 0.6336 (mmm) cc_final: 0.6029 (mmm) REVERT: F 19 ILE cc_start: 0.8258 (tt) cc_final: 0.8041 (tp) REVERT: F 44 GLN cc_start: 0.8311 (mt0) cc_final: 0.7990 (mt0) REVERT: F 107 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7374 (mt-10) REVERT: F 112 GLU cc_start: 0.6738 (tp30) cc_final: 0.6398 (tp30) REVERT: F 138 ILE cc_start: 0.8534 (mt) cc_final: 0.8261 (mm) REVERT: F 160 LYS cc_start: 0.7603 (ttpt) cc_final: 0.7306 (ttpt) REVERT: F 162 THR cc_start: 0.8077 (m) cc_final: 0.7390 (p) REVERT: F 170 THR cc_start: 0.8387 (m) cc_final: 0.7943 (t) REVERT: F 176 THR cc_start: 0.8000 (m) cc_final: 0.7480 (p) REVERT: F 179 ILE cc_start: 0.8634 (mm) cc_final: 0.8295 (mt) REVERT: F 180 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7244 (mm-30) REVERT: F 186 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7937 (mtpp) REVERT: F 192 VAL cc_start: 0.8516 (t) cc_final: 0.8242 (p) REVERT: F 194 THR cc_start: 0.8170 (m) cc_final: 0.7957 (t) REVERT: F 196 ASP cc_start: 0.7478 (t0) cc_final: 0.6825 (p0) REVERT: F 201 LYS cc_start: 0.8143 (tttp) cc_final: 0.7454 (tttp) REVERT: F 236 LYS cc_start: 0.7085 (mmtp) cc_final: 0.6774 (mmtp) REVERT: F 253 ARG cc_start: 0.7249 (ptp90) cc_final: 0.6843 (ptp90) REVERT: F 262 SER cc_start: 0.8190 (p) cc_final: 0.7840 (t) REVERT: F 264 ASP cc_start: 0.7622 (t0) cc_final: 0.7274 (t0) REVERT: F 269 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7662 (mmtp) REVERT: F 274 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6735 (mm-30) REVERT: F 285 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7180 (mt-10) REVERT: F 299 ASP cc_start: 0.7560 (t0) cc_final: 0.7135 (t0) REVERT: F 300 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6730 (mm-30) REVERT: F 314 ARG cc_start: 0.7374 (mmt180) cc_final: 0.6645 (mmt180) REVERT: F 317 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6578 (mt-10) REVERT: F 342 SER cc_start: 0.8746 (t) cc_final: 0.8387 (t) REVERT: F 353 ARG cc_start: 0.7499 (mtt-85) cc_final: 0.6177 (mtt-85) REVERT: F 376 GLU cc_start: 0.7489 (tt0) cc_final: 0.7235 (tt0) REVERT: F 412 VAL cc_start: 0.8294 (t) cc_final: 0.7881 (m) REVERT: F 425 ASP cc_start: 0.7907 (m-30) cc_final: 0.7658 (m-30) REVERT: F 431 SER cc_start: 0.8483 (m) cc_final: 0.8105 (p) REVERT: F 436 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7156 (tm-30) REVERT: F 444 LYS cc_start: 0.8473 (mmtp) cc_final: 0.8130 (mmtp) REVERT: F 445 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6840 (mm-30) REVERT: F 447 GLN cc_start: 0.7259 (tp40) cc_final: 0.6658 (tp40) REVERT: G 33 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7497 (mtmm) REVERT: G 59 LYS cc_start: 0.8809 (mtpt) cc_final: 0.8601 (mtpt) REVERT: G 76 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7570 (mtmm) REVERT: G 77 THR cc_start: 0.7950 (m) cc_final: 0.7524 (p) REVERT: G 81 LEU cc_start: 0.8306 (mt) cc_final: 0.7942 (mt) REVERT: G 86 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7335 (mm-30) REVERT: G 90 LYS cc_start: 0.8380 (tptm) cc_final: 0.7987 (tptm) REVERT: G 110 GLU cc_start: 0.7761 (tp30) cc_final: 0.7496 (tp30) REVERT: G 113 MET cc_start: 0.7585 (tpt) cc_final: 0.6981 (tpt) REVERT: G 125 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7754 (mtpp) REVERT: G 128 LYS cc_start: 0.8500 (tttt) cc_final: 0.8104 (ttmm) REVERT: G 129 GLU cc_start: 0.7195 (tt0) cc_final: 0.6709 (tt0) REVERT: G 131 TYR cc_start: 0.7885 (m-80) cc_final: 0.7148 (m-80) REVERT: G 134 GLU cc_start: 0.7590 (tt0) cc_final: 0.7372 (tm-30) REVERT: G 137 GLU cc_start: 0.7202 (tt0) cc_final: 0.6715 (tt0) REVERT: G 158 ILE cc_start: 0.8449 (mt) cc_final: 0.8122 (mt) REVERT: G 159 ILE cc_start: 0.8141 (mt) cc_final: 0.7910 (tp) REVERT: G 169 GLN cc_start: 0.8060 (mt0) cc_final: 0.7142 (mt0) REVERT: G 171 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8204 (mttm) REVERT: G 178 GLU cc_start: 0.8047 (tt0) cc_final: 0.7580 (tt0) REVERT: G 183 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7421 (mm-30) REVERT: G 192 TYR cc_start: 0.7463 (p90) cc_final: 0.6845 (p90) REVERT: G 201 LYS cc_start: 0.7677 (mmtm) cc_final: 0.7369 (mmtm) REVERT: G 203 GLN cc_start: 0.8166 (pt0) cc_final: 0.7805 (tt0) REVERT: G 229 HIS cc_start: 0.7918 (t-90) cc_final: 0.7554 (t70) REVERT: G 230 LYS cc_start: 0.8296 (mttp) cc_final: 0.8072 (mttp) REVERT: G 231 LYS cc_start: 0.8414 (ptmt) cc_final: 0.7984 (ptmt) REVERT: G 233 GLU cc_start: 0.7474 (tt0) cc_final: 0.7255 (tt0) REVERT: G 244 ASP cc_start: 0.7320 (m-30) cc_final: 0.6937 (m-30) REVERT: G 258 SER cc_start: 0.7999 (m) cc_final: 0.7301 (t) REVERT: G 262 GLN cc_start: 0.7718 (mm-40) cc_final: 0.7265 (mp10) REVERT: G 265 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7422 (ttpt) REVERT: G 273 ASP cc_start: 0.7414 (m-30) cc_final: 0.7163 (m-30) REVERT: G 274 LYS cc_start: 0.8328 (tttp) cc_final: 0.7430 (tttp) REVERT: G 275 LEU cc_start: 0.8485 (tp) cc_final: 0.7963 (tp) REVERT: G 278 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6841 (mt-10) REVERT: G 295 VAL cc_start: 0.8577 (t) cc_final: 0.8110 (p) REVERT: G 303 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7043 (mm-30) REVERT: G 306 MET cc_start: 0.8332 (mmp) cc_final: 0.8008 (mmp) REVERT: G 308 ASP cc_start: 0.7972 (p0) cc_final: 0.7236 (p0) REVERT: G 311 CYS cc_start: 0.7857 (m) cc_final: 0.7444 (m) REVERT: G 326 ILE cc_start: 0.8656 (mt) cc_final: 0.8383 (mm) REVERT: G 327 VAL cc_start: 0.8808 (t) cc_final: 0.8477 (m) REVERT: G 339 ARG cc_start: 0.7963 (mtp85) cc_final: 0.7758 (mtp-110) REVERT: G 354 LEU cc_start: 0.8136 (tp) cc_final: 0.7795 (tp) REVERT: G 356 ASP cc_start: 0.7710 (t0) cc_final: 0.7359 (t0) REVERT: G 364 MET cc_start: 0.7270 (mtm) cc_final: 0.7043 (mtp) REVERT: G 372 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7459 (mtpp) REVERT: G 388 GLU cc_start: 0.7034 (tp30) cc_final: 0.6700 (tp30) REVERT: G 389 GLU cc_start: 0.7308 (pt0) cc_final: 0.7047 (pt0) REVERT: G 392 ASN cc_start: 0.8404 (m-40) cc_final: 0.7681 (m-40) REVERT: G 396 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6985 (mt-10) REVERT: G 439 ASP cc_start: 0.7535 (p0) cc_final: 0.7316 (p0) REVERT: H 22 ILE cc_start: 0.8668 (mt) cc_final: 0.8464 (mm) REVERT: H 41 GLN cc_start: 0.7937 (tp40) cc_final: 0.7106 (tm-30) REVERT: H 88 MET cc_start: 0.7597 (mmp) cc_final: 0.7230 (mmm) REVERT: H 107 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7263 (mt-10) REVERT: H 117 GLU cc_start: 0.7362 (tp30) cc_final: 0.6983 (tp30) REVERT: H 125 ARG cc_start: 0.8062 (mtm-85) cc_final: 0.7858 (ttm170) REVERT: H 126 SER cc_start: 0.8438 (m) cc_final: 0.7661 (t) REVERT: H 130 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7450 (ttp-110) REVERT: H 132 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7750 (ttmm) REVERT: H 141 GLU cc_start: 0.6945 (tt0) cc_final: 0.6707 (tt0) REVERT: H 146 GLN cc_start: 0.7379 (pt0) cc_final: 0.7163 (pt0) REVERT: H 164 LYS cc_start: 0.8348 (pttt) cc_final: 0.8010 (ptmm) REVERT: H 167 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6978 (mt-10) REVERT: H 168 MET cc_start: 0.6811 (mtp) cc_final: 0.6589 (mtp) REVERT: H 172 TYR cc_start: 0.8199 (m-80) cc_final: 0.7701 (m-80) REVERT: H 177 LYS cc_start: 0.8142 (ptpt) cc_final: 0.7569 (ptpt) REVERT: H 204 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7909 (mtpt) REVERT: H 209 PHE cc_start: 0.8499 (t80) cc_final: 0.8122 (t80) REVERT: H 211 ARG cc_start: 0.7675 (ttt180) cc_final: 0.7450 (ttt180) REVERT: H 216 ASP cc_start: 0.7988 (m-30) cc_final: 0.7635 (m-30) REVERT: H 218 MET cc_start: 0.7451 (mtp) cc_final: 0.7172 (mtp) REVERT: H 232 LEU cc_start: 0.8056 (mt) cc_final: 0.7805 (mt) REVERT: H 234 LYS cc_start: 0.8492 (mttp) cc_final: 0.8192 (mttt) REVERT: H 236 LYS cc_start: 0.7630 (ttmt) cc_final: 0.7130 (ptmt) REVERT: H 238 VAL cc_start: 0.8706 (t) cc_final: 0.8296 (m) REVERT: H 246 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7586 (mt-10) REVERT: H 249 VAL cc_start: 0.8536 (t) cc_final: 0.8106 (p) REVERT: H 251 ASN cc_start: 0.8384 (m-40) cc_final: 0.7998 (m110) REVERT: H 260 LEU cc_start: 0.8324 (mt) cc_final: 0.8114 (mt) REVERT: H 269 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7656 (mtmt) REVERT: H 271 GLU cc_start: 0.7310 (mp0) cc_final: 0.6970 (mp0) REVERT: H 276 ILE cc_start: 0.8409 (mt) cc_final: 0.8190 (mm) REVERT: H 279 LYS cc_start: 0.8280 (tppt) cc_final: 0.7871 (tppp) REVERT: H 282 GLU cc_start: 0.7614 (tt0) cc_final: 0.6864 (tt0) REVERT: H 286 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6788 (mt-10) REVERT: H 292 ILE cc_start: 0.8165 (mt) cc_final: 0.7914 (mt) REVERT: H 295 VAL cc_start: 0.8030 (t) cc_final: 0.7809 (t) REVERT: H 303 MET cc_start: 0.8050 (mmp) cc_final: 0.7626 (mmm) REVERT: H 313 ASN cc_start: 0.8095 (m-40) cc_final: 0.7738 (m-40) REVERT: H 324 LEU cc_start: 0.8315 (tp) cc_final: 0.8002 (tp) REVERT: H 332 ILE cc_start: 0.8008 (mt) cc_final: 0.7783 (mt) REVERT: H 342 SER cc_start: 0.8502 (m) cc_final: 0.8158 (t) REVERT: H 353 ARG cc_start: 0.7448 (mtt90) cc_final: 0.7081 (mtt-85) REVERT: H 379 ASP cc_start: 0.7485 (m-30) cc_final: 0.7236 (m-30) REVERT: H 384 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7147 (mm-30) REVERT: H 427 LYS cc_start: 0.8040 (mmtp) cc_final: 0.7708 (mmtp) REVERT: I 17 SER cc_start: 0.7981 (m) cc_final: 0.7714 (p) REVERT: I 22 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8139 (mmmt) REVERT: I 31 LEU cc_start: 0.8151 (mt) cc_final: 0.7832 (mm) REVERT: I 34 GLN cc_start: 0.7435 (tm-30) cc_final: 0.7180 (tm-30) REVERT: I 59 LYS cc_start: 0.8456 (mttt) cc_final: 0.8145 (mtpt) REVERT: I 74 THR cc_start: 0.8067 (p) cc_final: 0.7788 (p) REVERT: I 86 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7288 (mm-30) REVERT: I 105 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7043 (mt-10) REVERT: I 110 GLU cc_start: 0.7423 (tp30) cc_final: 0.7201 (tp30) REVERT: I 114 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7110 (mt-10) REVERT: I 125 LYS cc_start: 0.8315 (ttpp) cc_final: 0.7948 (ttpp) REVERT: I 129 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7286 (mt-10) REVERT: I 139 THR cc_start: 0.8177 (m) cc_final: 0.7706 (p) REVERT: I 158 ILE cc_start: 0.8450 (mm) cc_final: 0.8195 (mt) REVERT: I 171 LYS cc_start: 0.8025 (tttp) cc_final: 0.7785 (tttp) REVERT: I 177 PHE cc_start: 0.8803 (t80) cc_final: 0.8319 (t80) REVERT: I 181 GLN cc_start: 0.7415 (mt0) cc_final: 0.7081 (mt0) REVERT: I 196 ASN cc_start: 0.8127 (p0) cc_final: 0.7852 (p0) REVERT: I 201 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7388 (ttmm) REVERT: I 209 TYR cc_start: 0.7723 (m-80) cc_final: 0.7282 (m-80) REVERT: I 219 GLU cc_start: 0.7321 (tp30) cc_final: 0.6973 (tp30) REVERT: I 221 VAL cc_start: 0.8677 (t) cc_final: 0.8474 (p) REVERT: I 230 LYS cc_start: 0.8086 (mttp) cc_final: 0.7826 (mttp) REVERT: I 242 ASP cc_start: 0.7674 (m-30) cc_final: 0.7379 (m-30) REVERT: I 247 ASN cc_start: 0.8188 (m-40) cc_final: 0.7922 (m110) REVERT: I 274 LYS cc_start: 0.8481 (tttm) cc_final: 0.8219 (tttp) REVERT: I 278 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7409 (mm-30) REVERT: I 294 LEU cc_start: 0.8487 (tp) cc_final: 0.8116 (tp) REVERT: I 295 VAL cc_start: 0.8360 (t) cc_final: 0.8135 (m) REVERT: I 352 LEU cc_start: 0.8341 (mt) cc_final: 0.8106 (mm) REVERT: I 362 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7618 (ptm160) REVERT: I 370 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6917 (mt-10) REVERT: I 408 GLN cc_start: 0.7722 (mt0) cc_final: 0.7461 (mt0) REVERT: I 427 LYS cc_start: 0.8408 (tttt) cc_final: 0.8130 (tttm) REVERT: I 443 SER cc_start: 0.8574 (t) cc_final: 0.8187 (m) REVERT: J 90 MET cc_start: 0.7717 (mtm) cc_final: 0.7420 (mtp) REVERT: J 115 LYS cc_start: 0.8229 (mtmm) cc_final: 0.8020 (mtmm) REVERT: J 117 GLU cc_start: 0.7817 (tp30) cc_final: 0.7163 (mm-30) REVERT: J 131 ILE cc_start: 0.8543 (mt) cc_final: 0.8286 (mt) REVERT: J 134 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6628 (mt-10) REVERT: J 135 THR cc_start: 0.8165 (t) cc_final: 0.7879 (m) REVERT: J 136 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6980 (mt-10) REVERT: J 139 GLU cc_start: 0.6346 (tt0) cc_final: 0.6112 (tt0) REVERT: J 164 LYS cc_start: 0.7823 (pttt) cc_final: 0.7512 (pttt) REVERT: J 167 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6780 (mt-10) REVERT: J 178 MET cc_start: 0.7780 (tpp) cc_final: 0.7128 (tpp) REVERT: J 183 THR cc_start: 0.8253 (m) cc_final: 0.7916 (p) REVERT: J 234 LYS cc_start: 0.8300 (mtpt) cc_final: 0.8064 (ttpt) REVERT: J 235 ARG cc_start: 0.7441 (mtp180) cc_final: 0.7045 (ttm-80) REVERT: J 241 THR cc_start: 0.8165 (m) cc_final: 0.7851 (t) REVERT: J 242 VAL cc_start: 0.8183 (t) cc_final: 0.7780 (p) REVERT: J 251 ASN cc_start: 0.8207 (m-40) cc_final: 0.7828 (m-40) REVERT: J 260 LEU cc_start: 0.8561 (mt) cc_final: 0.8307 (mt) REVERT: J 267 GLU cc_start: 0.6818 (mt-10) cc_final: 0.5959 (mt-10) REVERT: J 279 LYS cc_start: 0.8348 (tppt) cc_final: 0.8019 (tptp) REVERT: J 282 GLU cc_start: 0.7411 (tt0) cc_final: 0.7203 (tt0) REVERT: J 334 ARG cc_start: 0.7359 (ttp80) cc_final: 0.7145 (ttt-90) REVERT: J 342 SER cc_start: 0.8462 (m) cc_final: 0.8101 (p) REVERT: J 364 GLU cc_start: 0.7194 (tt0) cc_final: 0.6909 (tt0) REVERT: J 377 GLU cc_start: 0.7663 (tp30) cc_final: 0.7408 (tp30) REVERT: J 379 ASP cc_start: 0.7659 (m-30) cc_final: 0.7369 (m-30) REVERT: J 384 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6688 (mm-30) REVERT: J 391 THR cc_start: 0.7823 (m) cc_final: 0.7529 (p) REVERT: J 404 GLN cc_start: 0.7518 (mt0) cc_final: 0.7216 (mt0) REVERT: J 413 CYS cc_start: 0.7677 (t) cc_final: 0.7448 (t) REVERT: J 415 LYS cc_start: 0.8425 (tptt) cc_final: 0.8156 (tppp) REVERT: J 422 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7344 (mm-40) REVERT: J 430 TYR cc_start: 0.7950 (t80) cc_final: 0.7492 (t80) REVERT: J 436 GLU cc_start: 0.6671 (tm-30) cc_final: 0.6302 (tm-30) REVERT: J 441 GLN cc_start: 0.7024 (mt0) cc_final: 0.6434 (mt0) REVERT: J 445 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6999 (mt-10) outliers start: 50 outliers final: 31 residues processed: 1236 average time/residue: 0.1989 time to fit residues: 365.4787 Evaluate side-chains 1200 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1168 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 399 THR Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 194 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 254 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 226 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 2 optimal weight: 50.0000 chunk 235 optimal weight: 2.9990 chunk 240 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 84 optimal weight: 0.9980 chunk 350 optimal weight: 0.9990 chunk 316 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 29 GLN C 92 ASN C 174 ASN E 284 ASN ** E 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 241 HIS ** G 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 229 HIS J 245 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109356 restraints weight = 48636.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112607 restraints weight = 20053.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114711 restraints weight = 10639.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115808 restraints weight = 6836.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.116704 restraints weight = 5250.573| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29053 Z= 0.164 Angle : 0.549 13.950 39245 Z= 0.273 Chirality : 0.043 0.196 4499 Planarity : 0.004 0.045 5042 Dihedral : 7.214 144.047 4020 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.12 % Allowed : 12.83 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.14), residues: 3580 helix: 1.72 (0.13), residues: 1591 sheet: 0.72 (0.20), residues: 648 loop : 0.61 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 123 TYR 0.016 0.001 TYR C 11 PHE 0.025 0.001 PHE C 248 TRP 0.006 0.001 TRP C 360 HIS 0.008 0.001 HIS G 316 Details of bonding type rmsd covalent geometry : bond 0.00353 (29045) covalent geometry : angle 0.54830 (39236) hydrogen bonds : bond 0.03910 ( 1224) hydrogen bonds : angle 4.14366 ( 3483) metal coordination : bond 0.01516 ( 8) metal coordination : angle 2.34117 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 1190 time to evaluate : 0.900 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 873 MET cc_start: 0.5714 (mmm) cc_final: 0.5139 (mmm) REVERT: A 933 THR cc_start: 0.8344 (m) cc_final: 0.8058 (t) REVERT: A 939 GLN cc_start: 0.7656 (mm-40) cc_final: 0.7153 (mm-40) REVERT: A 957 ARG cc_start: 0.8205 (mtp85) cc_final: 0.7753 (mtp85) REVERT: A 961 ASP cc_start: 0.7342 (m-30) cc_final: 0.6990 (m-30) REVERT: A 973 VAL cc_start: 0.8520 (t) cc_final: 0.8250 (p) REVERT: A 975 LEU cc_start: 0.8441 (mt) cc_final: 0.8214 (mt) REVERT: A 1902 GLU cc_start: 0.7617 (tp30) cc_final: 0.7266 (tp30) REVERT: A 1906 GLN cc_start: 0.7582 (mm110) cc_final: 0.7293 (mm110) REVERT: A 1920 THR cc_start: 0.8461 (t) cc_final: 0.8170 (p) REVERT: A 1926 CYS cc_start: 0.8440 (m) cc_final: 0.8112 (m) REVERT: A 1934 SER cc_start: 0.8457 (m) cc_final: 0.8043 (p) REVERT: A 1943 PRO cc_start: 0.7829 (Cg_exo) cc_final: 0.7489 (Cg_endo) REVERT: A 1951 TYR cc_start: 0.8158 (m-80) cc_final: 0.7627 (m-80) REVERT: A 1957 ARG cc_start: 0.7835 (mtp180) cc_final: 0.7532 (mtm-85) REVERT: A 1960 LEU cc_start: 0.7116 (mp) cc_final: 0.6823 (mt) REVERT: A 2001 PRO cc_start: 0.8515 (Cg_exo) cc_final: 0.8260 (Cg_endo) REVERT: A 2008 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7057 (tt0) REVERT: A 2009 GLN cc_start: 0.7596 (tt0) cc_final: 0.7257 (tt0) REVERT: A 2014 LEU cc_start: 0.8475 (mt) cc_final: 0.8200 (mm) REVERT: A 2017 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7684 (mtt-85) REVERT: A 2019 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7477 (mtt180) REVERT: A 2032 PHE cc_start: 0.8296 (m-80) cc_final: 0.7944 (m-80) REVERT: A 2068 MET cc_start: 0.5836 (mtt) cc_final: 0.5608 (mtt) REVERT: A 2071 MET cc_start: 0.6342 (tpp) cc_final: 0.5858 (tpp) REVERT: C 8 ASN cc_start: 0.7500 (t0) cc_final: 0.7055 (t0) REVERT: C 55 PHE cc_start: 0.8031 (t80) cc_final: 0.7769 (t80) REVERT: C 60 PHE cc_start: 0.7332 (m-80) cc_final: 0.7043 (m-80) REVERT: C 97 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7092 (mt-10) REVERT: C 103 THR cc_start: 0.8301 (m) cc_final: 0.8015 (t) REVERT: C 133 HIS cc_start: 0.7928 (t-170) cc_final: 0.7510 (t-90) REVERT: C 137 ARG cc_start: 0.7411 (tpp80) cc_final: 0.7078 (tpp80) REVERT: C 138 ASP cc_start: 0.6931 (m-30) cc_final: 0.6689 (m-30) REVERT: C 149 ASP cc_start: 0.7770 (t0) cc_final: 0.7524 (t0) REVERT: C 187 ILE cc_start: 0.8215 (mt) cc_final: 0.7909 (tp) REVERT: C 204 GLN cc_start: 0.7890 (tp40) cc_final: 0.7479 (tp-100) REVERT: C 208 ASP cc_start: 0.7182 (m-30) cc_final: 0.6677 (m-30) REVERT: C 224 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8081 (ttmt) REVERT: C 230 ASN cc_start: 0.8100 (t0) cc_final: 0.7417 (t0) REVERT: C 234 ILE cc_start: 0.8211 (tp) cc_final: 0.7963 (tp) REVERT: C 237 VAL cc_start: 0.8884 (t) cc_final: 0.8601 (m) REVERT: C 255 MET cc_start: 0.6563 (tpp) cc_final: 0.6291 (tpt) REVERT: C 256 VAL cc_start: 0.8542 (t) cc_final: 0.8099 (p) REVERT: C 286 ASP cc_start: 0.7257 (m-30) cc_final: 0.7040 (m-30) REVERT: C 316 ASN cc_start: 0.7906 (m-40) cc_final: 0.7550 (m-40) REVERT: C 326 PHE cc_start: 0.8611 (m-80) cc_final: 0.8384 (m-80) REVERT: C 360 TRP cc_start: 0.8229 (t60) cc_final: 0.8009 (t60) REVERT: C 364 LYS cc_start: 0.8051 (ptmt) cc_final: 0.7200 (ttmt) REVERT: D 82 LYS cc_start: 0.7710 (mtmm) cc_final: 0.7468 (mtmm) REVERT: D 93 LEU cc_start: 0.8418 (tp) cc_final: 0.8170 (tp) REVERT: D 134 ARG cc_start: 0.7594 (mmt180) cc_final: 0.7387 (mmt180) REVERT: E 34 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7526 (tm-30) REVERT: E 40 VAL cc_start: 0.8086 (t) cc_final: 0.7524 (p) REVERT: E 43 GLU cc_start: 0.7454 (mp0) cc_final: 0.6906 (mt-10) REVERT: E 60 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7814 (mtpp) REVERT: E 99 SER cc_start: 0.8659 (m) cc_final: 0.8372 (p) REVERT: E 108 LYS cc_start: 0.8126 (mtmm) cc_final: 0.7688 (mtpt) REVERT: E 110 GLU cc_start: 0.7870 (tp30) cc_final: 0.7658 (tp30) REVERT: E 113 MET cc_start: 0.7238 (tpt) cc_final: 0.6903 (tpt) REVERT: E 128 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7845 (mmtt) REVERT: E 168 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7619 (ttmt) REVERT: E 200 VAL cc_start: 0.8215 (t) cc_final: 0.7964 (p) REVERT: E 201 LYS cc_start: 0.7856 (tptm) cc_final: 0.7159 (tptm) REVERT: E 205 ARG cc_start: 0.7066 (tpt-90) cc_final: 0.6764 (mmm160) REVERT: E 209 TYR cc_start: 0.7874 (m-80) cc_final: 0.6493 (m-80) REVERT: E 216 GLU cc_start: 0.6706 (tp30) cc_final: 0.6473 (tp30) REVERT: E 259 MET cc_start: 0.7712 (tpt) cc_final: 0.7387 (tmm) REVERT: E 267 LYS cc_start: 0.7829 (mttp) cc_final: 0.7495 (mttp) REVERT: E 268 LYS cc_start: 0.8258 (mttt) cc_final: 0.7993 (mtmm) REVERT: E 270 GLU cc_start: 0.7701 (mp0) cc_final: 0.7357 (mt-10) REVERT: E 278 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6855 (mm-30) REVERT: E 285 LYS cc_start: 0.7874 (ttmm) cc_final: 0.7464 (ttmm) REVERT: E 295 VAL cc_start: 0.8474 (t) cc_final: 0.8144 (m) REVERT: E 302 ASP cc_start: 0.6654 (t0) cc_final: 0.6331 (t0) REVERT: E 308 ASP cc_start: 0.7277 (p0) cc_final: 0.7021 (p0) REVERT: E 314 TYR cc_start: 0.8318 (t80) cc_final: 0.6914 (t80) REVERT: E 343 ASP cc_start: 0.6498 (t0) cc_final: 0.6158 (t70) REVERT: E 354 LEU cc_start: 0.8231 (tp) cc_final: 0.7970 (tp) REVERT: E 356 ASP cc_start: 0.7716 (t0) cc_final: 0.7476 (t0) REVERT: E 371 MET cc_start: 0.8224 (mtt) cc_final: 0.7964 (mtt) REVERT: E 372 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7924 (ttmm) REVERT: E 376 LYS cc_start: 0.8202 (tptt) cc_final: 0.7881 (tptt) REVERT: E 388 GLU cc_start: 0.7345 (tp30) cc_final: 0.6950 (tp30) REVERT: E 392 ASN cc_start: 0.7742 (m-40) cc_final: 0.6896 (m-40) REVERT: E 396 GLU cc_start: 0.7341 (mt-10) cc_final: 0.7016 (mt-10) REVERT: E 414 ASN cc_start: 0.8210 (t0) cc_final: 0.7807 (t0) REVERT: E 415 LEU cc_start: 0.8459 (mt) cc_final: 0.8150 (mt) REVERT: E 416 LEU cc_start: 0.8512 (mt) cc_final: 0.8122 (mm) REVERT: E 422 LYS cc_start: 0.7548 (mmtp) cc_final: 0.7242 (mmtp) REVERT: E 427 LYS cc_start: 0.8507 (ttpp) cc_final: 0.8215 (ttpp) REVERT: E 432 GLU cc_start: 0.7327 (tt0) cc_final: 0.6927 (tt0) REVERT: E 435 GLU cc_start: 0.7242 (tt0) cc_final: 0.6971 (tt0) REVERT: E 446 ILE cc_start: 0.8120 (mt) cc_final: 0.7905 (mm) REVERT: E 455 MET cc_start: 0.6311 (mmm) cc_final: 0.5987 (mmm) REVERT: F 41 GLN cc_start: 0.8619 (tp40) cc_final: 0.8419 (tp-100) REVERT: F 61 GLU cc_start: 0.7880 (tp30) cc_final: 0.7671 (mm-30) REVERT: F 92 GLN cc_start: 0.8022 (mm110) cc_final: 0.7741 (mm-40) REVERT: F 107 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7377 (mt-10) REVERT: F 112 GLU cc_start: 0.6845 (tp30) cc_final: 0.6341 (tp30) REVERT: F 124 ARG cc_start: 0.8238 (mtp-110) cc_final: 0.7973 (mtt-85) REVERT: F 138 ILE cc_start: 0.8516 (mt) cc_final: 0.8224 (mm) REVERT: F 160 LYS cc_start: 0.7601 (ttpt) cc_final: 0.7291 (ttpt) REVERT: F 162 THR cc_start: 0.8079 (m) cc_final: 0.7329 (p) REVERT: F 179 ILE cc_start: 0.8651 (mm) cc_final: 0.8283 (mt) REVERT: F 180 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7239 (mm-30) REVERT: F 186 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7878 (mtpp) REVERT: F 188 GLN cc_start: 0.7404 (mt0) cc_final: 0.7198 (mt0) REVERT: F 192 VAL cc_start: 0.8483 (t) cc_final: 0.8194 (p) REVERT: F 194 THR cc_start: 0.8183 (m) cc_final: 0.7951 (t) REVERT: F 196 ASP cc_start: 0.7501 (t0) cc_final: 0.7102 (t0) REVERT: F 201 LYS cc_start: 0.8196 (tttp) cc_final: 0.7808 (tttp) REVERT: F 233 GLN cc_start: 0.7970 (tt0) cc_final: 0.7675 (tt0) REVERT: F 236 LYS cc_start: 0.7083 (mmtp) cc_final: 0.6804 (mmtp) REVERT: F 248 ASP cc_start: 0.7204 (m-30) cc_final: 0.6995 (m-30) REVERT: F 261 PHE cc_start: 0.8157 (m-80) cc_final: 0.7920 (m-80) REVERT: F 262 SER cc_start: 0.8216 (p) cc_final: 0.7829 (t) REVERT: F 264 ASP cc_start: 0.7595 (t0) cc_final: 0.7215 (t0) REVERT: F 269 LYS cc_start: 0.8004 (mmtp) cc_final: 0.7666 (mmtp) REVERT: F 274 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6717 (mm-30) REVERT: F 285 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7181 (mt-10) REVERT: F 299 ASP cc_start: 0.7587 (t0) cc_final: 0.7277 (t0) REVERT: F 300 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6758 (mm-30) REVERT: F 314 ARG cc_start: 0.7399 (mmt180) cc_final: 0.6833 (mmt180) REVERT: F 317 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6787 (mt-10) REVERT: F 329 ASN cc_start: 0.8238 (p0) cc_final: 0.7830 (p0) REVERT: F 342 SER cc_start: 0.8777 (t) cc_final: 0.8456 (t) REVERT: F 376 GLU cc_start: 0.7496 (tt0) cc_final: 0.7244 (tt0) REVERT: F 431 SER cc_start: 0.8429 (m) cc_final: 0.8067 (p) REVERT: F 444 LYS cc_start: 0.8454 (mmtp) cc_final: 0.8134 (mmtp) REVERT: F 445 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6863 (mm-30) REVERT: F 447 GLN cc_start: 0.7391 (tp40) cc_final: 0.6744 (tp40) REVERT: G 33 LYS cc_start: 0.7739 (mtmt) cc_final: 0.7425 (mtmm) REVERT: G 76 LYS cc_start: 0.7931 (mtmm) cc_final: 0.7508 (mtmm) REVERT: G 77 THR cc_start: 0.7939 (m) cc_final: 0.7461 (p) REVERT: G 81 LEU cc_start: 0.8325 (mt) cc_final: 0.7926 (mt) REVERT: G 90 LYS cc_start: 0.8375 (tptm) cc_final: 0.7977 (tptm) REVERT: G 108 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7374 (mtmt) REVERT: G 110 GLU cc_start: 0.7866 (tp30) cc_final: 0.7542 (tp30) REVERT: G 113 MET cc_start: 0.7585 (tpt) cc_final: 0.7037 (tpt) REVERT: G 125 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7856 (mtpp) REVERT: G 126 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6979 (mt-10) REVERT: G 128 LYS cc_start: 0.8516 (tttt) cc_final: 0.8143 (ttmm) REVERT: G 129 GLU cc_start: 0.7217 (tt0) cc_final: 0.6741 (tt0) REVERT: G 131 TYR cc_start: 0.7874 (m-80) cc_final: 0.7175 (m-80) REVERT: G 137 GLU cc_start: 0.7162 (tt0) cc_final: 0.6735 (tt0) REVERT: G 158 ILE cc_start: 0.8454 (mt) cc_final: 0.8092 (mt) REVERT: G 168 LYS cc_start: 0.7898 (mmtm) cc_final: 0.7641 (mmtm) REVERT: G 169 GLN cc_start: 0.7961 (mt0) cc_final: 0.7317 (mt0) REVERT: G 171 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8108 (mttm) REVERT: G 176 ILE cc_start: 0.8773 (tp) cc_final: 0.8554 (tp) REVERT: G 178 GLU cc_start: 0.7976 (tt0) cc_final: 0.7490 (tt0) REVERT: G 183 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7440 (mm-30) REVERT: G 192 TYR cc_start: 0.7481 (p90) cc_final: 0.6891 (p90) REVERT: G 201 LYS cc_start: 0.7710 (mmtm) cc_final: 0.7478 (mmtm) REVERT: G 203 GLN cc_start: 0.8190 (pt0) cc_final: 0.7850 (tt0) REVERT: G 216 GLU cc_start: 0.7138 (tp30) cc_final: 0.6931 (tp30) REVERT: G 229 HIS cc_start: 0.7942 (t-90) cc_final: 0.7637 (t70) REVERT: G 230 LYS cc_start: 0.8368 (mttp) cc_final: 0.8055 (mttp) REVERT: G 231 LYS cc_start: 0.8387 (ptmt) cc_final: 0.7987 (ptmt) REVERT: G 233 GLU cc_start: 0.7502 (tt0) cc_final: 0.7258 (tt0) REVERT: G 244 ASP cc_start: 0.7347 (m-30) cc_final: 0.6988 (m-30) REVERT: G 258 SER cc_start: 0.7989 (m) cc_final: 0.7634 (t) REVERT: G 265 LYS cc_start: 0.7782 (ttpt) cc_final: 0.7558 (ttpt) REVERT: G 273 ASP cc_start: 0.7414 (m-30) cc_final: 0.7152 (m-30) REVERT: G 274 LYS cc_start: 0.8307 (tttp) cc_final: 0.7481 (tttp) REVERT: G 278 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6902 (mt-10) REVERT: G 280 ASN cc_start: 0.7974 (m-40) cc_final: 0.7488 (m110) REVERT: G 295 VAL cc_start: 0.8632 (t) cc_final: 0.8213 (p) REVERT: G 303 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7052 (mm-30) REVERT: G 308 ASP cc_start: 0.7865 (p0) cc_final: 0.7034 (p0) REVERT: G 311 CYS cc_start: 0.7880 (m) cc_final: 0.7440 (m) REVERT: G 326 ILE cc_start: 0.8653 (mt) cc_final: 0.8368 (mm) REVERT: G 327 VAL cc_start: 0.8831 (t) cc_final: 0.8481 (m) REVERT: G 354 LEU cc_start: 0.8171 (tp) cc_final: 0.7801 (tp) REVERT: G 356 ASP cc_start: 0.7725 (t0) cc_final: 0.7395 (t0) REVERT: G 388 GLU cc_start: 0.7035 (tp30) cc_final: 0.6708 (tp30) REVERT: G 389 GLU cc_start: 0.7310 (pt0) cc_final: 0.7075 (pt0) REVERT: G 392 ASN cc_start: 0.8450 (m-40) cc_final: 0.7660 (m-40) REVERT: G 396 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6996 (mt-10) REVERT: G 404 ARG cc_start: 0.6999 (mtt90) cc_final: 0.6614 (mtt180) REVERT: G 439 ASP cc_start: 0.7488 (p0) cc_final: 0.7252 (p0) REVERT: H 22 ILE cc_start: 0.8688 (mt) cc_final: 0.8487 (mm) REVERT: H 41 GLN cc_start: 0.7990 (tp40) cc_final: 0.7146 (tm-30) REVERT: H 94 LEU cc_start: 0.8258 (tp) cc_final: 0.7917 (tt) REVERT: H 125 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7868 (mtm180) REVERT: H 126 SER cc_start: 0.8478 (m) cc_final: 0.7655 (t) REVERT: H 130 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7399 (ttp-110) REVERT: H 141 GLU cc_start: 0.6969 (tt0) cc_final: 0.6710 (tt0) REVERT: H 146 GLN cc_start: 0.7409 (pt0) cc_final: 0.7183 (pt0) REVERT: H 160 LYS cc_start: 0.7948 (mttt) cc_final: 0.7319 (mttt) REVERT: H 164 LYS cc_start: 0.8392 (pttt) cc_final: 0.8045 (ptmm) REVERT: H 167 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6867 (mt-10) REVERT: H 168 MET cc_start: 0.6790 (mtp) cc_final: 0.6574 (mtp) REVERT: H 172 TYR cc_start: 0.8218 (m-80) cc_final: 0.7824 (m-80) REVERT: H 177 LYS cc_start: 0.7999 (ptpt) cc_final: 0.7619 (ptpt) REVERT: H 204 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7931 (mtpt) REVERT: H 209 PHE cc_start: 0.8476 (t80) cc_final: 0.8128 (t80) REVERT: H 211 ARG cc_start: 0.7675 (ttt180) cc_final: 0.7456 (ttt180) REVERT: H 218 MET cc_start: 0.7472 (mtp) cc_final: 0.7170 (mtp) REVERT: H 232 LEU cc_start: 0.8241 (mt) cc_final: 0.7951 (mt) REVERT: H 234 LYS cc_start: 0.8503 (mttp) cc_final: 0.7922 (mttp) REVERT: H 236 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7191 (ptmt) REVERT: H 238 VAL cc_start: 0.8732 (t) cc_final: 0.8299 (m) REVERT: H 249 VAL cc_start: 0.8534 (t) cc_final: 0.8096 (p) REVERT: H 251 ASN cc_start: 0.8485 (m-40) cc_final: 0.8176 (m110) REVERT: H 255 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7317 (tp40) REVERT: H 260 LEU cc_start: 0.8349 (mt) cc_final: 0.8084 (mt) REVERT: H 269 LYS cc_start: 0.7928 (mtmt) cc_final: 0.7627 (mtmt) REVERT: H 271 GLU cc_start: 0.7307 (mp0) cc_final: 0.7030 (mp0) REVERT: H 279 LYS cc_start: 0.8301 (tppt) cc_final: 0.7964 (tppp) REVERT: H 282 GLU cc_start: 0.7552 (tt0) cc_final: 0.6889 (tt0) REVERT: H 285 GLU cc_start: 0.7232 (mt-10) cc_final: 0.7004 (mm-30) REVERT: H 286 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6783 (mt-10) REVERT: H 292 ILE cc_start: 0.8180 (mt) cc_final: 0.7888 (mt) REVERT: H 295 VAL cc_start: 0.8036 (t) cc_final: 0.7818 (t) REVERT: H 303 MET cc_start: 0.8053 (mmp) cc_final: 0.7641 (mmm) REVERT: H 313 ASN cc_start: 0.8132 (m-40) cc_final: 0.7794 (m-40) REVERT: H 324 LEU cc_start: 0.8388 (tp) cc_final: 0.8099 (tp) REVERT: H 332 ILE cc_start: 0.8034 (mt) cc_final: 0.7780 (mt) REVERT: H 342 SER cc_start: 0.8489 (m) cc_final: 0.8146 (t) REVERT: H 369 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7780 (mm-40) REVERT: H 379 ASP cc_start: 0.7469 (m-30) cc_final: 0.7230 (m-30) REVERT: H 443 MET cc_start: 0.7864 (ttm) cc_final: 0.7597 (ttp) REVERT: I 17 SER cc_start: 0.8010 (m) cc_final: 0.7729 (p) REVERT: I 22 LYS cc_start: 0.8349 (mmtt) cc_final: 0.8141 (mmmt) REVERT: I 31 LEU cc_start: 0.8170 (mt) cc_final: 0.7846 (mm) REVERT: I 34 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7238 (tm-30) REVERT: I 43 GLU cc_start: 0.7353 (mp0) cc_final: 0.6866 (mt-10) REVERT: I 59 LYS cc_start: 0.8452 (mttt) cc_final: 0.8161 (mtpt) REVERT: I 74 THR cc_start: 0.8099 (p) cc_final: 0.7868 (p) REVERT: I 86 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7337 (mm-30) REVERT: I 105 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6381 (mt-10) REVERT: I 110 GLU cc_start: 0.7425 (tp30) cc_final: 0.7187 (tp30) REVERT: I 114 GLU cc_start: 0.7425 (mt-10) cc_final: 0.7165 (mt-10) REVERT: I 129 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7273 (mt-10) REVERT: I 132 GLU cc_start: 0.6921 (tt0) cc_final: 0.6470 (tt0) REVERT: I 139 THR cc_start: 0.8152 (m) cc_final: 0.7551 (p) REVERT: I 158 ILE cc_start: 0.8474 (mm) cc_final: 0.8182 (mt) REVERT: I 163 THR cc_start: 0.8460 (p) cc_final: 0.8252 (t) REVERT: I 177 PHE cc_start: 0.8801 (t80) cc_final: 0.8254 (t80) REVERT: I 181 GLN cc_start: 0.7434 (mt0) cc_final: 0.7080 (mt0) REVERT: I 196 ASN cc_start: 0.8101 (p0) cc_final: 0.7881 (p0) REVERT: I 201 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7476 (ttmm) REVERT: I 219 GLU cc_start: 0.7329 (tp30) cc_final: 0.7002 (tp30) REVERT: I 221 VAL cc_start: 0.8662 (t) cc_final: 0.8322 (m) REVERT: I 230 LYS cc_start: 0.8033 (mttp) cc_final: 0.7487 (mttp) REVERT: I 242 ASP cc_start: 0.7737 (m-30) cc_final: 0.7424 (m-30) REVERT: I 258 SER cc_start: 0.8873 (m) cc_final: 0.8640 (p) REVERT: I 268 LYS cc_start: 0.8167 (mtmt) cc_final: 0.7118 (mtmm) REVERT: I 274 LYS cc_start: 0.8496 (tttm) cc_final: 0.8256 (tttp) REVERT: I 278 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7377 (mm-30) REVERT: I 294 LEU cc_start: 0.8550 (tp) cc_final: 0.8175 (tp) REVERT: I 295 VAL cc_start: 0.8415 (t) cc_final: 0.8187 (m) REVERT: I 352 LEU cc_start: 0.8310 (mt) cc_final: 0.8091 (mm) REVERT: I 370 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6901 (mt-10) REVERT: I 408 GLN cc_start: 0.7747 (mt0) cc_final: 0.7468 (mt0) REVERT: I 427 LYS cc_start: 0.8408 (tttt) cc_final: 0.8171 (tttm) REVERT: I 443 SER cc_start: 0.8560 (t) cc_final: 0.8172 (m) REVERT: J 38 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6571 (mm-30) REVERT: J 90 MET cc_start: 0.7726 (mtm) cc_final: 0.7462 (mtp) REVERT: J 115 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7996 (mtmm) REVERT: J 117 GLU cc_start: 0.7790 (tp30) cc_final: 0.7226 (mm-30) REVERT: J 131 ILE cc_start: 0.8510 (mt) cc_final: 0.8244 (mt) REVERT: J 134 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6662 (mt-10) REVERT: J 135 THR cc_start: 0.8130 (t) cc_final: 0.7815 (m) REVERT: J 136 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6954 (mt-10) REVERT: J 139 GLU cc_start: 0.6319 (tt0) cc_final: 0.6080 (tt0) REVERT: J 141 GLU cc_start: 0.6899 (mp0) cc_final: 0.6274 (mp0) REVERT: J 164 LYS cc_start: 0.7916 (pttt) cc_final: 0.7126 (pttt) REVERT: J 167 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6837 (mt-10) REVERT: J 178 MET cc_start: 0.7764 (tpp) cc_final: 0.7168 (tpp) REVERT: J 183 THR cc_start: 0.8255 (m) cc_final: 0.7898 (p) REVERT: J 194 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8070 (p) REVERT: J 196 ASP cc_start: 0.6796 (t0) cc_final: 0.6504 (t0) REVERT: J 234 LYS cc_start: 0.8272 (mtpt) cc_final: 0.8030 (ttpt) REVERT: J 235 ARG cc_start: 0.7439 (mtp180) cc_final: 0.7061 (ttm-80) REVERT: J 241 THR cc_start: 0.8204 (m) cc_final: 0.7888 (t) REVERT: J 242 VAL cc_start: 0.8187 (t) cc_final: 0.7809 (p) REVERT: J 251 ASN cc_start: 0.8198 (m-40) cc_final: 0.7844 (m-40) REVERT: J 260 LEU cc_start: 0.8561 (mt) cc_final: 0.8349 (mt) REVERT: J 264 ASP cc_start: 0.7321 (m-30) cc_final: 0.7045 (t0) REVERT: J 267 GLU cc_start: 0.6832 (mt-10) cc_final: 0.5639 (mt-10) REVERT: J 279 LYS cc_start: 0.8339 (tppt) cc_final: 0.8074 (tptp) REVERT: J 364 GLU cc_start: 0.7149 (tt0) cc_final: 0.6931 (tt0) REVERT: J 377 GLU cc_start: 0.7709 (tp30) cc_final: 0.7386 (tp30) REVERT: J 379 ASP cc_start: 0.7706 (m-30) cc_final: 0.7381 (m-30) REVERT: J 384 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6719 (mm-30) REVERT: J 391 THR cc_start: 0.7888 (m) cc_final: 0.7494 (p) REVERT: J 404 GLN cc_start: 0.7559 (mt0) cc_final: 0.7172 (mt0) REVERT: J 405 LEU cc_start: 0.8480 (mt) cc_final: 0.8265 (mt) REVERT: J 413 CYS cc_start: 0.7738 (t) cc_final: 0.7410 (t) REVERT: J 415 LYS cc_start: 0.8439 (tptt) cc_final: 0.8204 (tppp) REVERT: J 430 TYR cc_start: 0.8037 (t80) cc_final: 0.7584 (t80) REVERT: J 436 GLU cc_start: 0.6721 (tm-30) cc_final: 0.6330 (tm-30) REVERT: J 441 GLN cc_start: 0.7040 (mt0) cc_final: 0.6657 (mt0) REVERT: J 445 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7162 (mt-10) outliers start: 66 outliers final: 45 residues processed: 1211 average time/residue: 0.1995 time to fit residues: 357.8427 Evaluate side-chains 1187 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 1140 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1984 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 138 ILE Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 381 GLU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 376 LYS Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 179 ILE Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 383 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 356 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 215 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 285 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2007 GLN ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 HIS E 316 HIS F 245 HIS G 316 HIS I 115 ASN I 247 ASN I 280 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.131275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.108626 restraints weight = 48508.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111880 restraints weight = 20198.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113862 restraints weight = 10785.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.115205 restraints weight = 6979.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115873 restraints weight = 5289.849| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29053 Z= 0.161 Angle : 0.550 13.978 39245 Z= 0.273 Chirality : 0.043 0.187 4499 Planarity : 0.004 0.045 5042 Dihedral : 7.186 143.844 4020 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.54 % Allowed : 14.12 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.14), residues: 3580 helix: 1.72 (0.13), residues: 1590 sheet: 0.61 (0.20), residues: 639 loop : 0.59 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 332 TYR 0.016 0.001 TYR C 11 PHE 0.027 0.001 PHE C 248 TRP 0.005 0.001 TRP B 277 HIS 0.007 0.001 HIS G 316 Details of bonding type rmsd covalent geometry : bond 0.00348 (29045) covalent geometry : angle 0.54888 (39236) hydrogen bonds : bond 0.03706 ( 1224) hydrogen bonds : angle 4.06985 ( 3483) metal coordination : bond 0.01616 ( 8) metal coordination : angle 2.57155 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1144 time to evaluate : 1.164 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 873 MET cc_start: 0.5816 (mmm) cc_final: 0.5239 (mmm) REVERT: A 933 THR cc_start: 0.8300 (m) cc_final: 0.8049 (t) REVERT: A 939 GLN cc_start: 0.7654 (mm-40) cc_final: 0.7142 (mm-40) REVERT: A 973 VAL cc_start: 0.8493 (t) cc_final: 0.8246 (p) REVERT: A 975 LEU cc_start: 0.8475 (mt) cc_final: 0.8234 (mt) REVERT: A 1893 ARG cc_start: 0.7541 (mmm-85) cc_final: 0.7330 (mmt90) REVERT: A 1902 GLU cc_start: 0.7598 (tp30) cc_final: 0.7389 (tp30) REVERT: A 1906 GLN cc_start: 0.7586 (mm110) cc_final: 0.7286 (mm110) REVERT: A 1926 CYS cc_start: 0.8387 (m) cc_final: 0.8069 (m) REVERT: A 1934 SER cc_start: 0.8468 (m) cc_final: 0.8055 (p) REVERT: A 1943 PRO cc_start: 0.7751 (Cg_exo) cc_final: 0.7395 (Cg_endo) REVERT: A 1951 TYR cc_start: 0.8187 (m-80) cc_final: 0.7646 (m-80) REVERT: A 1957 ARG cc_start: 0.7809 (mtp180) cc_final: 0.7576 (mtm110) REVERT: A 1973 ILE cc_start: 0.8880 (mt) cc_final: 0.8646 (mm) REVERT: A 2001 PRO cc_start: 0.8490 (Cg_exo) cc_final: 0.8242 (Cg_endo) REVERT: A 2002 ARG cc_start: 0.7593 (mtm180) cc_final: 0.7259 (mtm-85) REVERT: A 2008 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7109 (tt0) REVERT: A 2014 LEU cc_start: 0.8466 (mt) cc_final: 0.8168 (mm) REVERT: A 2019 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7467 (mtt180) REVERT: A 2023 ARG cc_start: 0.7236 (mmm160) cc_final: 0.6483 (tpt90) REVERT: A 2032 PHE cc_start: 0.8259 (m-80) cc_final: 0.7903 (m-80) REVERT: A 2068 MET cc_start: 0.5827 (mtt) cc_final: 0.5585 (mtt) REVERT: A 2071 MET cc_start: 0.6416 (tpp) cc_final: 0.5926 (tpp) REVERT: C 8 ASN cc_start: 0.7631 (t0) cc_final: 0.7207 (t0) REVERT: C 33 LYS cc_start: 0.7076 (mtmm) cc_final: 0.6783 (mtmm) REVERT: C 55 PHE cc_start: 0.8031 (t80) cc_final: 0.7765 (t80) REVERT: C 60 PHE cc_start: 0.7374 (m-80) cc_final: 0.7158 (m-80) REVERT: C 103 THR cc_start: 0.8308 (m) cc_final: 0.8036 (t) REVERT: C 137 ARG cc_start: 0.7363 (tpp80) cc_final: 0.7053 (tpp80) REVERT: C 138 ASP cc_start: 0.6925 (m-30) cc_final: 0.6668 (m-30) REVERT: C 149 ASP cc_start: 0.7817 (t0) cc_final: 0.7524 (t0) REVERT: C 187 ILE cc_start: 0.8229 (mt) cc_final: 0.7900 (tp) REVERT: C 204 GLN cc_start: 0.7949 (tp40) cc_final: 0.7397 (tp-100) REVERT: C 208 ASP cc_start: 0.7102 (m-30) cc_final: 0.6844 (m-30) REVERT: C 218 ARG cc_start: 0.7126 (ttp80) cc_final: 0.6860 (ttp80) REVERT: C 224 LYS cc_start: 0.8440 (mtpp) cc_final: 0.8116 (ttmt) REVERT: C 230 ASN cc_start: 0.8118 (t0) cc_final: 0.7520 (t0) REVERT: C 235 ASP cc_start: 0.6659 (m-30) cc_final: 0.6345 (m-30) REVERT: C 237 VAL cc_start: 0.8816 (t) cc_final: 0.8534 (m) REVERT: C 256 VAL cc_start: 0.8516 (t) cc_final: 0.8043 (p) REVERT: C 286 ASP cc_start: 0.7266 (m-30) cc_final: 0.7054 (m-30) REVERT: C 315 LYS cc_start: 0.7882 (mtpt) cc_final: 0.7577 (ttpt) REVERT: C 316 ASN cc_start: 0.7879 (m-40) cc_final: 0.7574 (m-40) REVERT: C 326 PHE cc_start: 0.8614 (m-80) cc_final: 0.8341 (m-80) REVERT: C 341 THR cc_start: 0.8539 (t) cc_final: 0.8248 (m) REVERT: C 364 LYS cc_start: 0.7958 (ptmt) cc_final: 0.7277 (ttmt) REVERT: D 82 LYS cc_start: 0.7782 (mtmm) cc_final: 0.7512 (mtmm) REVERT: D 93 LEU cc_start: 0.8424 (tp) cc_final: 0.8193 (tp) REVERT: E 34 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7592 (tm-30) REVERT: E 40 VAL cc_start: 0.8190 (t) cc_final: 0.7577 (p) REVERT: E 47 GLU cc_start: 0.6947 (mt-10) cc_final: 0.6660 (mt-10) REVERT: E 60 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7832 (mtpp) REVERT: E 99 SER cc_start: 0.8665 (m) cc_final: 0.8338 (p) REVERT: E 105 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7162 (mt-10) REVERT: E 108 LYS cc_start: 0.8151 (mtmm) cc_final: 0.7609 (mtpt) REVERT: E 113 MET cc_start: 0.7287 (tpt) cc_final: 0.6934 (tpt) REVERT: E 168 LYS cc_start: 0.8105 (ttmt) cc_final: 0.7596 (ttmt) REVERT: E 200 VAL cc_start: 0.8234 (t) cc_final: 0.8006 (p) REVERT: E 201 LYS cc_start: 0.7862 (tptm) cc_final: 0.7249 (tptm) REVERT: E 205 ARG cc_start: 0.7049 (tpt-90) cc_final: 0.6838 (tpt-90) REVERT: E 209 TYR cc_start: 0.7907 (m-80) cc_final: 0.7082 (m-80) REVERT: E 216 GLU cc_start: 0.6851 (tp30) cc_final: 0.6580 (mm-30) REVERT: E 259 MET cc_start: 0.7755 (tpt) cc_final: 0.7503 (tmm) REVERT: E 267 LYS cc_start: 0.7835 (mttp) cc_final: 0.7561 (mttp) REVERT: E 268 LYS cc_start: 0.8254 (mttt) cc_final: 0.8010 (mtmm) REVERT: E 278 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6877 (mm-30) REVERT: E 284 ASN cc_start: 0.8802 (t0) cc_final: 0.8383 (t0) REVERT: E 285 LYS cc_start: 0.7865 (ttmm) cc_final: 0.7454 (ttmm) REVERT: E 295 VAL cc_start: 0.8376 (t) cc_final: 0.8068 (m) REVERT: E 302 ASP cc_start: 0.6659 (t0) cc_final: 0.6231 (t0) REVERT: E 314 TYR cc_start: 0.8326 (t80) cc_final: 0.6928 (t80) REVERT: E 343 ASP cc_start: 0.6510 (t0) cc_final: 0.6188 (t70) REVERT: E 354 LEU cc_start: 0.8247 (tp) cc_final: 0.7969 (tp) REVERT: E 356 ASP cc_start: 0.7715 (t0) cc_final: 0.7437 (t0) REVERT: E 371 MET cc_start: 0.8232 (mtt) cc_final: 0.7987 (mtt) REVERT: E 372 LYS cc_start: 0.8409 (mtpt) cc_final: 0.7960 (ttmm) REVERT: E 376 LYS cc_start: 0.8205 (tptt) cc_final: 0.7886 (tptt) REVERT: E 388 GLU cc_start: 0.7393 (tp30) cc_final: 0.6923 (tp30) REVERT: E 392 ASN cc_start: 0.7696 (m-40) cc_final: 0.6520 (m-40) REVERT: E 396 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7041 (mt-10) REVERT: E 414 ASN cc_start: 0.8215 (t0) cc_final: 0.7825 (t0) REVERT: E 415 LEU cc_start: 0.8431 (mt) cc_final: 0.8139 (mt) REVERT: E 416 LEU cc_start: 0.8486 (mt) cc_final: 0.8127 (mm) REVERT: E 422 LYS cc_start: 0.7589 (mmtp) cc_final: 0.7239 (mmtp) REVERT: E 426 GLU cc_start: 0.6994 (mp0) cc_final: 0.6457 (mp0) REVERT: E 427 LYS cc_start: 0.8467 (ttpp) cc_final: 0.8201 (ttpp) REVERT: E 432 GLU cc_start: 0.7332 (tt0) cc_final: 0.6979 (tt0) REVERT: E 446 ILE cc_start: 0.8132 (mt) cc_final: 0.7855 (mm) REVERT: E 455 MET cc_start: 0.6249 (mmm) cc_final: 0.5976 (mmm) REVERT: F 41 GLN cc_start: 0.8657 (tp40) cc_final: 0.8414 (tp-100) REVERT: F 107 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7361 (mt-10) REVERT: F 112 GLU cc_start: 0.6871 (tp30) cc_final: 0.6441 (tp30) REVERT: F 138 ILE cc_start: 0.8488 (mt) cc_final: 0.8047 (mm) REVERT: F 160 LYS cc_start: 0.7577 (ttpt) cc_final: 0.7271 (ttpt) REVERT: F 162 THR cc_start: 0.8064 (m) cc_final: 0.7347 (p) REVERT: F 179 ILE cc_start: 0.8619 (mm) cc_final: 0.8252 (mt) REVERT: F 180 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7203 (mm-30) REVERT: F 186 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7886 (mtpp) REVERT: F 188 GLN cc_start: 0.7502 (mt0) cc_final: 0.7238 (mt0) REVERT: F 192 VAL cc_start: 0.8493 (t) cc_final: 0.8194 (p) REVERT: F 194 THR cc_start: 0.8090 (m) cc_final: 0.7869 (t) REVERT: F 196 ASP cc_start: 0.7500 (t0) cc_final: 0.7125 (t0) REVERT: F 201 LYS cc_start: 0.8179 (tttp) cc_final: 0.7742 (tttp) REVERT: F 236 LYS cc_start: 0.7066 (mmtp) cc_final: 0.6801 (mmtp) REVERT: F 262 SER cc_start: 0.8248 (p) cc_final: 0.7813 (t) REVERT: F 264 ASP cc_start: 0.7594 (t0) cc_final: 0.7184 (t0) REVERT: F 269 LYS cc_start: 0.7988 (mmtp) cc_final: 0.7657 (mmtp) REVERT: F 274 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6698 (mm-30) REVERT: F 285 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7191 (mt-10) REVERT: F 299 ASP cc_start: 0.7619 (t0) cc_final: 0.7239 (t0) REVERT: F 300 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6720 (mm-30) REVERT: F 314 ARG cc_start: 0.7495 (mmt180) cc_final: 0.6891 (mpt180) REVERT: F 317 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6843 (mt-10) REVERT: F 329 ASN cc_start: 0.8263 (p0) cc_final: 0.7863 (p0) REVERT: F 353 ARG cc_start: 0.7836 (mtt90) cc_final: 0.7270 (ttp-110) REVERT: F 376 GLU cc_start: 0.7503 (tt0) cc_final: 0.7242 (tt0) REVERT: F 379 ASP cc_start: 0.7512 (t0) cc_final: 0.7285 (t0) REVERT: F 431 SER cc_start: 0.8421 (m) cc_final: 0.8085 (p) REVERT: F 444 LYS cc_start: 0.8451 (mmtp) cc_final: 0.8098 (mmtp) REVERT: F 445 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6996 (mm-30) REVERT: G 33 LYS cc_start: 0.7745 (mtmt) cc_final: 0.7543 (mtpp) REVERT: G 43 GLU cc_start: 0.7488 (mp0) cc_final: 0.6944 (pm20) REVERT: G 77 THR cc_start: 0.7960 (m) cc_final: 0.7612 (p) REVERT: G 90 LYS cc_start: 0.8359 (tptm) cc_final: 0.7961 (tptm) REVERT: G 108 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7439 (mtmt) REVERT: G 110 GLU cc_start: 0.7871 (tp30) cc_final: 0.7639 (tp30) REVERT: G 113 MET cc_start: 0.7619 (tpt) cc_final: 0.7008 (tpt) REVERT: G 128 LYS cc_start: 0.8556 (tttt) cc_final: 0.7976 (tttp) REVERT: G 129 GLU cc_start: 0.7223 (tt0) cc_final: 0.6779 (tt0) REVERT: G 131 TYR cc_start: 0.7861 (m-80) cc_final: 0.7197 (m-80) REVERT: G 137 GLU cc_start: 0.7150 (tt0) cc_final: 0.6854 (tt0) REVERT: G 158 ILE cc_start: 0.8471 (mt) cc_final: 0.8084 (mt) REVERT: G 169 GLN cc_start: 0.7968 (mt0) cc_final: 0.7373 (mt0) REVERT: G 171 LYS cc_start: 0.8545 (mtpt) cc_final: 0.7957 (mttm) REVERT: G 176 ILE cc_start: 0.8791 (tp) cc_final: 0.8538 (tp) REVERT: G 178 GLU cc_start: 0.8052 (tt0) cc_final: 0.7181 (tp30) REVERT: G 183 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7448 (mm-30) REVERT: G 192 TYR cc_start: 0.7527 (p90) cc_final: 0.6916 (p90) REVERT: G 201 LYS cc_start: 0.7729 (mmtm) cc_final: 0.7508 (mmtm) REVERT: G 203 GLN cc_start: 0.8178 (pt0) cc_final: 0.7869 (tt0) REVERT: G 216 GLU cc_start: 0.7066 (tp30) cc_final: 0.6529 (tp30) REVERT: G 227 ASP cc_start: 0.7395 (t0) cc_final: 0.7149 (t0) REVERT: G 229 HIS cc_start: 0.8060 (t-90) cc_final: 0.7630 (t70) REVERT: G 231 LYS cc_start: 0.8376 (ptmt) cc_final: 0.7940 (ptmt) REVERT: G 233 GLU cc_start: 0.7502 (tt0) cc_final: 0.7196 (tt0) REVERT: G 244 ASP cc_start: 0.7344 (m-30) cc_final: 0.6969 (m-30) REVERT: G 258 SER cc_start: 0.7973 (m) cc_final: 0.7699 (t) REVERT: G 260 MET cc_start: 0.7040 (mmt) cc_final: 0.6589 (mmt) REVERT: G 265 LYS cc_start: 0.7778 (ttpt) cc_final: 0.7337 (ttpp) REVERT: G 273 ASP cc_start: 0.7417 (m-30) cc_final: 0.7142 (m-30) REVERT: G 278 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6853 (mt-10) REVERT: G 280 ASN cc_start: 0.7872 (m-40) cc_final: 0.7480 (m110) REVERT: G 295 VAL cc_start: 0.8620 (t) cc_final: 0.8265 (p) REVERT: G 303 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7075 (mm-30) REVERT: G 311 CYS cc_start: 0.7906 (m) cc_final: 0.7447 (m) REVERT: G 326 ILE cc_start: 0.8655 (mt) cc_final: 0.8351 (mm) REVERT: G 327 VAL cc_start: 0.8838 (t) cc_final: 0.8474 (m) REVERT: G 354 LEU cc_start: 0.8142 (tp) cc_final: 0.7866 (tp) REVERT: G 356 ASP cc_start: 0.7725 (t0) cc_final: 0.7408 (t0) REVERT: G 388 GLU cc_start: 0.7032 (tp30) cc_final: 0.6651 (tp30) REVERT: G 389 GLU cc_start: 0.7303 (pt0) cc_final: 0.7084 (pt0) REVERT: G 392 ASN cc_start: 0.8417 (m-40) cc_final: 0.7648 (m-40) REVERT: G 396 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7012 (mt-10) REVERT: G 404 ARG cc_start: 0.6995 (mtt90) cc_final: 0.6717 (mtt180) REVERT: G 431 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7377 (mt-10) REVERT: G 439 ASP cc_start: 0.7462 (p0) cc_final: 0.7231 (p0) REVERT: G 445 LYS cc_start: 0.8197 (mttm) cc_final: 0.7690 (mtpp) REVERT: H 22 ILE cc_start: 0.8692 (mt) cc_final: 0.8453 (mm) REVERT: H 41 GLN cc_start: 0.8028 (tp40) cc_final: 0.7205 (tm-30) REVERT: H 94 LEU cc_start: 0.8245 (tp) cc_final: 0.7917 (tt) REVERT: H 126 SER cc_start: 0.8492 (m) cc_final: 0.7676 (t) REVERT: H 130 ARG cc_start: 0.7843 (ttp80) cc_final: 0.7380 (ttp-110) REVERT: H 135 THR cc_start: 0.7484 (OUTLIER) cc_final: 0.7261 (p) REVERT: H 141 GLU cc_start: 0.6970 (tt0) cc_final: 0.6749 (tt0) REVERT: H 146 GLN cc_start: 0.7439 (pt0) cc_final: 0.7208 (pt0) REVERT: H 160 LYS cc_start: 0.7996 (mttt) cc_final: 0.7351 (mttt) REVERT: H 164 LYS cc_start: 0.8387 (pttt) cc_final: 0.8006 (ptmm) REVERT: H 167 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6934 (mt-10) REVERT: H 168 MET cc_start: 0.6799 (mtp) cc_final: 0.6575 (mtp) REVERT: H 172 TYR cc_start: 0.8237 (m-80) cc_final: 0.7828 (m-80) REVERT: H 177 LYS cc_start: 0.8145 (ptpt) cc_final: 0.7718 (ptpt) REVERT: H 202 ILE cc_start: 0.8348 (mt) cc_final: 0.8058 (mm) REVERT: H 209 PHE cc_start: 0.8474 (t80) cc_final: 0.8104 (t80) REVERT: H 211 ARG cc_start: 0.7694 (ttt180) cc_final: 0.7428 (ttt180) REVERT: H 218 MET cc_start: 0.7500 (mtp) cc_final: 0.7233 (mtp) REVERT: H 223 LYS cc_start: 0.8654 (pttm) cc_final: 0.8445 (pttm) REVERT: H 232 LEU cc_start: 0.8180 (mt) cc_final: 0.7957 (mt) REVERT: H 234 LYS cc_start: 0.8348 (mttp) cc_final: 0.8112 (mttp) REVERT: H 238 VAL cc_start: 0.8676 (t) cc_final: 0.8303 (m) REVERT: H 249 VAL cc_start: 0.8517 (t) cc_final: 0.8021 (p) REVERT: H 251 ASN cc_start: 0.8494 (m-40) cc_final: 0.8192 (m110) REVERT: H 255 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7363 (tp40) REVERT: H 260 LEU cc_start: 0.8361 (mt) cc_final: 0.8058 (mt) REVERT: H 269 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7598 (mtmt) REVERT: H 271 GLU cc_start: 0.7313 (mp0) cc_final: 0.7073 (mp0) REVERT: H 279 LYS cc_start: 0.8326 (tppt) cc_final: 0.7870 (tppp) REVERT: H 282 GLU cc_start: 0.7573 (tt0) cc_final: 0.6788 (tt0) REVERT: H 286 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6603 (mt-10) REVERT: H 292 ILE cc_start: 0.8177 (mt) cc_final: 0.7881 (mt) REVERT: H 295 VAL cc_start: 0.8051 (t) cc_final: 0.7827 (t) REVERT: H 303 MET cc_start: 0.8032 (mmp) cc_final: 0.7778 (mmm) REVERT: H 313 ASN cc_start: 0.8148 (m-40) cc_final: 0.7801 (m-40) REVERT: H 324 LEU cc_start: 0.8389 (tp) cc_final: 0.8100 (tp) REVERT: H 332 ILE cc_start: 0.7981 (mt) cc_final: 0.7724 (mt) REVERT: H 342 SER cc_start: 0.8463 (m) cc_final: 0.8120 (t) REVERT: H 369 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7784 (mm-40) REVERT: H 379 ASP cc_start: 0.7446 (m-30) cc_final: 0.7209 (m-30) REVERT: I 17 SER cc_start: 0.8021 (m) cc_final: 0.7723 (p) REVERT: I 31 LEU cc_start: 0.8176 (mt) cc_final: 0.7873 (mm) REVERT: I 34 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7242 (tm-30) REVERT: I 43 GLU cc_start: 0.7436 (mp0) cc_final: 0.6818 (mt-10) REVERT: I 74 THR cc_start: 0.8121 (p) cc_final: 0.7909 (p) REVERT: I 86 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7380 (mm-30) REVERT: I 105 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6411 (mt-10) REVERT: I 114 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7061 (mt-10) REVERT: I 125 LYS cc_start: 0.8309 (ttpp) cc_final: 0.7944 (ttpp) REVERT: I 137 GLU cc_start: 0.7053 (tt0) cc_final: 0.6677 (tt0) REVERT: I 139 THR cc_start: 0.8077 (m) cc_final: 0.7351 (p) REVERT: I 154 ILE cc_start: 0.7999 (mp) cc_final: 0.7700 (mm) REVERT: I 158 ILE cc_start: 0.8444 (mm) cc_final: 0.8195 (mt) REVERT: I 177 PHE cc_start: 0.8799 (t80) cc_final: 0.8280 (t80) REVERT: I 181 GLN cc_start: 0.7435 (mt0) cc_final: 0.7087 (mt0) REVERT: I 196 ASN cc_start: 0.8122 (p0) cc_final: 0.7898 (p0) REVERT: I 201 LYS cc_start: 0.7984 (ttmt) cc_final: 0.7460 (ttmm) REVERT: I 221 VAL cc_start: 0.8661 (t) cc_final: 0.8298 (m) REVERT: I 230 LYS cc_start: 0.8016 (mttp) cc_final: 0.7552 (mttp) REVERT: I 242 ASP cc_start: 0.7746 (m-30) cc_final: 0.7430 (m-30) REVERT: I 258 SER cc_start: 0.8857 (m) cc_final: 0.8652 (p) REVERT: I 259 MET cc_start: 0.7556 (mtm) cc_final: 0.7244 (ptp) REVERT: I 268 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7205 (mtmm) REVERT: I 295 VAL cc_start: 0.8444 (t) cc_final: 0.8237 (m) REVERT: I 303 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6681 (mm-30) REVERT: I 352 LEU cc_start: 0.8273 (mt) cc_final: 0.8053 (mm) REVERT: I 370 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6908 (mt-10) REVERT: I 408 GLN cc_start: 0.7736 (mt0) cc_final: 0.7468 (mt0) REVERT: I 427 LYS cc_start: 0.8435 (tttt) cc_final: 0.8163 (ttmm) REVERT: I 443 SER cc_start: 0.8557 (t) cc_final: 0.8160 (m) REVERT: J 18 ARG cc_start: 0.7657 (mtp85) cc_final: 0.7399 (mtp85) REVERT: J 38 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6563 (mm-30) REVERT: J 90 MET cc_start: 0.7730 (mtm) cc_final: 0.7459 (mtp) REVERT: J 117 GLU cc_start: 0.7796 (tp30) cc_final: 0.7173 (mm-30) REVERT: J 131 ILE cc_start: 0.8490 (mt) cc_final: 0.8220 (mt) REVERT: J 134 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6710 (mt-10) REVERT: J 135 THR cc_start: 0.8129 (t) cc_final: 0.7823 (m) REVERT: J 136 GLU cc_start: 0.7414 (mt-10) cc_final: 0.6980 (mt-10) REVERT: J 164 LYS cc_start: 0.7888 (pttt) cc_final: 0.7569 (pttt) REVERT: J 167 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6830 (mt-10) REVERT: J 178 MET cc_start: 0.7783 (tpp) cc_final: 0.7182 (tpp) REVERT: J 194 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8106 (p) REVERT: J 196 ASP cc_start: 0.6776 (t0) cc_final: 0.6505 (t0) REVERT: J 234 LYS cc_start: 0.8270 (mtpt) cc_final: 0.8035 (ttpt) REVERT: J 235 ARG cc_start: 0.7460 (mtp180) cc_final: 0.7244 (ttm-80) REVERT: J 241 THR cc_start: 0.8202 (m) cc_final: 0.7910 (t) REVERT: J 242 VAL cc_start: 0.8190 (t) cc_final: 0.7824 (p) REVERT: J 251 ASN cc_start: 0.8186 (m-40) cc_final: 0.7847 (m-40) REVERT: J 264 ASP cc_start: 0.7335 (m-30) cc_final: 0.7056 (t0) REVERT: J 267 GLU cc_start: 0.6904 (mt-10) cc_final: 0.5846 (mt-10) REVERT: J 273 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7234 (mtt180) REVERT: J 279 LYS cc_start: 0.8281 (tppt) cc_final: 0.8068 (tptp) REVERT: J 364 GLU cc_start: 0.7157 (tt0) cc_final: 0.6923 (tt0) REVERT: J 377 GLU cc_start: 0.7700 (tp30) cc_final: 0.7379 (tp30) REVERT: J 378 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7137 (tt0) REVERT: J 379 ASP cc_start: 0.7695 (m-30) cc_final: 0.7377 (m-30) REVERT: J 384 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6739 (mm-30) REVERT: J 391 THR cc_start: 0.7896 (m) cc_final: 0.7492 (p) REVERT: J 404 GLN cc_start: 0.7538 (mt0) cc_final: 0.7213 (mt0) REVERT: J 405 LEU cc_start: 0.8497 (mt) cc_final: 0.8269 (mt) REVERT: J 413 CYS cc_start: 0.7715 (t) cc_final: 0.7407 (t) REVERT: J 415 LYS cc_start: 0.8469 (tptt) cc_final: 0.8223 (tppp) REVERT: J 430 TYR cc_start: 0.8080 (t80) cc_final: 0.7567 (t80) REVERT: J 436 GLU cc_start: 0.6746 (tm-30) cc_final: 0.6338 (tm-30) REVERT: J 441 GLN cc_start: 0.7052 (mt0) cc_final: 0.6658 (mt0) REVERT: J 445 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7160 (mt-10) outliers start: 79 outliers final: 60 residues processed: 1175 average time/residue: 0.2128 time to fit residues: 370.3565 Evaluate side-chains 1197 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1133 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1984 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 134 GLU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 262 GLN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 381 GLU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 414 ARG Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 162 LYS Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 376 LYS Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain J residue 60 LEU Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 443 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 124 optimal weight: 1.9990 chunk 333 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 56 optimal weight: 0.4980 chunk 182 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 324 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN G 289 GLN I 115 ASN I 280 ASN I 305 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.129863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107176 restraints weight = 48657.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.110535 restraints weight = 21094.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.112253 restraints weight = 11349.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113876 restraints weight = 7509.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114386 restraints weight = 5440.824| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29053 Z= 0.245 Angle : 0.599 14.276 39245 Z= 0.300 Chirality : 0.045 0.201 4499 Planarity : 0.004 0.047 5042 Dihedral : 7.361 147.526 4020 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.99 % Allowed : 14.98 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.36 (0.14), residues: 3580 helix: 1.54 (0.13), residues: 1592 sheet: 0.50 (0.20), residues: 638 loop : 0.50 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 64 TYR 0.021 0.002 TYR I 192 PHE 0.030 0.002 PHE C 248 TRP 0.011 0.001 TRP H 283 HIS 0.008 0.001 HIS A1956 Details of bonding type rmsd covalent geometry : bond 0.00518 (29045) covalent geometry : angle 0.59684 (39236) hydrogen bonds : bond 0.04262 ( 1224) hydrogen bonds : angle 4.20883 ( 3483) metal coordination : bond 0.02361 ( 8) metal coordination : angle 3.02607 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 1162 time to evaluate : 1.080 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 873 MET cc_start: 0.5842 (mmm) cc_final: 0.5305 (mmm) REVERT: A 916 PHE cc_start: 0.8388 (t80) cc_final: 0.8124 (t80) REVERT: A 933 THR cc_start: 0.8296 (m) cc_final: 0.8014 (t) REVERT: A 939 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7176 (mm-40) REVERT: A 940 ARG cc_start: 0.7394 (ptt-90) cc_final: 0.7101 (ptt90) REVERT: A 957 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7673 (mtp85) REVERT: A 973 VAL cc_start: 0.8488 (t) cc_final: 0.8244 (p) REVERT: A 975 LEU cc_start: 0.8480 (mt) cc_final: 0.8265 (mt) REVERT: A 1893 ARG cc_start: 0.7520 (mmm-85) cc_final: 0.7281 (mmt90) REVERT: A 1900 ARG cc_start: 0.8176 (ttp-110) cc_final: 0.7747 (ttp-110) REVERT: A 1902 GLU cc_start: 0.7615 (tp30) cc_final: 0.7258 (tp30) REVERT: A 1903 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7427 (ttm-80) REVERT: A 1906 GLN cc_start: 0.7618 (mm110) cc_final: 0.7302 (mm110) REVERT: A 1926 CYS cc_start: 0.8428 (m) cc_final: 0.8085 (m) REVERT: A 1934 SER cc_start: 0.8472 (m) cc_final: 0.8057 (p) REVERT: A 1943 PRO cc_start: 0.7861 (Cg_exo) cc_final: 0.7512 (Cg_endo) REVERT: A 1951 TYR cc_start: 0.8229 (m-80) cc_final: 0.7681 (m-80) REVERT: A 1957 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7513 (mtm-85) REVERT: A 1973 ILE cc_start: 0.8829 (mt) cc_final: 0.8579 (mm) REVERT: A 1978 PHE cc_start: 0.7989 (p90) cc_final: 0.7736 (p90) REVERT: A 2001 PRO cc_start: 0.8483 (Cg_exo) cc_final: 0.8242 (Cg_endo) REVERT: A 2008 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7111 (tt0) REVERT: A 2014 LEU cc_start: 0.8509 (mt) cc_final: 0.8212 (mm) REVERT: A 2017 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7713 (mtt-85) REVERT: A 2019 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7520 (mtt180) REVERT: A 2023 ARG cc_start: 0.7255 (mmm160) cc_final: 0.6751 (mmm160) REVERT: A 2032 PHE cc_start: 0.8298 (m-80) cc_final: 0.8015 (m-80) REVERT: A 2068 MET cc_start: 0.5867 (mtt) cc_final: 0.5655 (mtt) REVERT: A 2071 MET cc_start: 0.6460 (tpp) cc_final: 0.5978 (tpp) REVERT: A 2098 ARG cc_start: 0.7350 (mtt-85) cc_final: 0.7141 (mpp80) REVERT: C 8 ASN cc_start: 0.7879 (t0) cc_final: 0.7481 (t0) REVERT: C 33 LYS cc_start: 0.7188 (mtmm) cc_final: 0.6858 (mtmm) REVERT: C 55 PHE cc_start: 0.8093 (t80) cc_final: 0.7828 (t80) REVERT: C 73 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: C 103 THR cc_start: 0.8286 (m) cc_final: 0.8029 (t) REVERT: C 137 ARG cc_start: 0.7381 (tpp80) cc_final: 0.7028 (tpp80) REVERT: C 138 ASP cc_start: 0.6942 (m-30) cc_final: 0.6677 (m-30) REVERT: C 149 ASP cc_start: 0.7890 (t0) cc_final: 0.7594 (t0) REVERT: C 160 TYR cc_start: 0.7968 (m-80) cc_final: 0.7767 (m-80) REVERT: C 187 ILE cc_start: 0.8233 (mt) cc_final: 0.7938 (tp) REVERT: C 204 GLN cc_start: 0.7950 (tp40) cc_final: 0.7350 (tp-100) REVERT: C 208 ASP cc_start: 0.7392 (m-30) cc_final: 0.6774 (m-30) REVERT: C 218 ARG cc_start: 0.7168 (ttp80) cc_final: 0.6861 (ttp80) REVERT: C 224 LYS cc_start: 0.8492 (mtpp) cc_final: 0.8241 (ttmt) REVERT: C 230 ASN cc_start: 0.8229 (t0) cc_final: 0.7630 (t0) REVERT: C 235 ASP cc_start: 0.6647 (m-30) cc_final: 0.6437 (m-30) REVERT: C 237 VAL cc_start: 0.8848 (t) cc_final: 0.8598 (m) REVERT: C 256 VAL cc_start: 0.8554 (t) cc_final: 0.8066 (p) REVERT: C 286 ASP cc_start: 0.7359 (m-30) cc_final: 0.7121 (m-30) REVERT: C 315 LYS cc_start: 0.7842 (mtpt) cc_final: 0.7378 (ttpt) REVERT: C 326 PHE cc_start: 0.8677 (m-80) cc_final: 0.8417 (m-80) REVERT: C 341 THR cc_start: 0.8602 (t) cc_final: 0.8177 (p) REVERT: C 346 ASP cc_start: 0.7720 (m-30) cc_final: 0.7296 (m-30) REVERT: C 364 LYS cc_start: 0.8074 (ptmt) cc_final: 0.7753 (ttpp) REVERT: D 82 LYS cc_start: 0.7882 (mtmm) cc_final: 0.7555 (mtmm) REVERT: D 93 LEU cc_start: 0.8444 (tp) cc_final: 0.8222 (tp) REVERT: E 34 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7684 (tm-30) REVERT: E 40 VAL cc_start: 0.8221 (t) cc_final: 0.7624 (p) REVERT: E 47 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6673 (mt-10) REVERT: E 60 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7811 (mtpp) REVERT: E 99 SER cc_start: 0.8695 (m) cc_final: 0.8382 (p) REVERT: E 105 GLU cc_start: 0.7464 (mt-10) cc_final: 0.6802 (mt-10) REVERT: E 113 MET cc_start: 0.7310 (tpt) cc_final: 0.7013 (tpt) REVERT: E 168 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7616 (ttmt) REVERT: E 200 VAL cc_start: 0.8291 (t) cc_final: 0.8060 (p) REVERT: E 201 LYS cc_start: 0.7932 (tptm) cc_final: 0.7289 (tptm) REVERT: E 209 TYR cc_start: 0.7944 (m-80) cc_final: 0.7206 (m-80) REVERT: E 259 MET cc_start: 0.7730 (tpt) cc_final: 0.7489 (tmm) REVERT: E 267 LYS cc_start: 0.7842 (mttp) cc_final: 0.7552 (mttp) REVERT: E 268 LYS cc_start: 0.8277 (mttt) cc_final: 0.7914 (mtmm) REVERT: E 270 GLU cc_start: 0.7709 (mp0) cc_final: 0.7455 (mt-10) REVERT: E 285 LYS cc_start: 0.7904 (ttmm) cc_final: 0.7510 (ttmm) REVERT: E 295 VAL cc_start: 0.8433 (t) cc_final: 0.8134 (m) REVERT: E 302 ASP cc_start: 0.6712 (t0) cc_final: 0.6336 (t0) REVERT: E 314 TYR cc_start: 0.8333 (t80) cc_final: 0.6894 (t80) REVERT: E 343 ASP cc_start: 0.6566 (t0) cc_final: 0.6236 (t70) REVERT: E 354 LEU cc_start: 0.8298 (tp) cc_final: 0.8029 (tp) REVERT: E 356 ASP cc_start: 0.7687 (t0) cc_final: 0.7449 (t0) REVERT: E 371 MET cc_start: 0.8255 (mtt) cc_final: 0.8026 (mtt) REVERT: E 372 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8083 (ttmm) REVERT: E 376 LYS cc_start: 0.8196 (tptt) cc_final: 0.7856 (tptt) REVERT: E 388 GLU cc_start: 0.7399 (tp30) cc_final: 0.6942 (tp30) REVERT: E 392 ASN cc_start: 0.7698 (m-40) cc_final: 0.6778 (m-40) REVERT: E 396 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7067 (mt-10) REVERT: E 414 ASN cc_start: 0.8237 (t0) cc_final: 0.7906 (t0) REVERT: E 415 LEU cc_start: 0.8443 (mt) cc_final: 0.8152 (mt) REVERT: E 416 LEU cc_start: 0.8489 (mt) cc_final: 0.8171 (mm) REVERT: E 422 LYS cc_start: 0.7595 (mmtp) cc_final: 0.7321 (mmtp) REVERT: E 426 GLU cc_start: 0.7178 (mp0) cc_final: 0.6512 (mp0) REVERT: E 427 LYS cc_start: 0.8496 (ttpp) cc_final: 0.8082 (ttpp) REVERT: E 432 GLU cc_start: 0.7323 (tt0) cc_final: 0.6969 (tt0) REVERT: E 446 ILE cc_start: 0.8178 (mt) cc_final: 0.7946 (mm) REVERT: F 61 GLU cc_start: 0.7822 (tp30) cc_final: 0.7593 (tp30) REVERT: F 90 MET cc_start: 0.8260 (ttm) cc_final: 0.8001 (mtp) REVERT: F 107 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7356 (mt-10) REVERT: F 112 GLU cc_start: 0.6987 (tp30) cc_final: 0.6587 (tp30) REVERT: F 137 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7706 (mm) REVERT: F 160 LYS cc_start: 0.7630 (ttpt) cc_final: 0.7229 (ttpt) REVERT: F 162 THR cc_start: 0.8132 (m) cc_final: 0.7477 (p) REVERT: F 176 THR cc_start: 0.7956 (m) cc_final: 0.7713 (p) REVERT: F 179 ILE cc_start: 0.8625 (mm) cc_final: 0.8280 (mt) REVERT: F 186 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7879 (mtpp) REVERT: F 188 GLN cc_start: 0.7523 (mt0) cc_final: 0.6997 (mt0) REVERT: F 192 VAL cc_start: 0.8412 (t) cc_final: 0.8029 (p) REVERT: F 194 THR cc_start: 0.8149 (m) cc_final: 0.7480 (p) REVERT: F 196 ASP cc_start: 0.7513 (t0) cc_final: 0.7175 (t0) REVERT: F 201 LYS cc_start: 0.8180 (tttp) cc_final: 0.7755 (tttp) REVERT: F 236 LYS cc_start: 0.7091 (mmtp) cc_final: 0.6861 (mmtp) REVERT: F 264 ASP cc_start: 0.7603 (t0) cc_final: 0.7191 (t0) REVERT: F 269 LYS cc_start: 0.8098 (mmtp) cc_final: 0.7714 (mmtp) REVERT: F 274 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6715 (mm-30) REVERT: F 276 ILE cc_start: 0.8278 (mt) cc_final: 0.8050 (tp) REVERT: F 299 ASP cc_start: 0.7589 (t0) cc_final: 0.7373 (t0) REVERT: F 300 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6591 (mm-30) REVERT: F 314 ARG cc_start: 0.7534 (mmt180) cc_final: 0.6967 (mpt180) REVERT: F 317 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6881 (mt-10) REVERT: F 329 ASN cc_start: 0.8334 (p0) cc_final: 0.7928 (p0) REVERT: F 332 ILE cc_start: 0.8411 (mm) cc_final: 0.8115 (mm) REVERT: F 353 ARG cc_start: 0.7919 (mtt90) cc_final: 0.7166 (mtt90) REVERT: F 415 LYS cc_start: 0.8401 (tptt) cc_final: 0.7875 (tptt) REVERT: F 431 SER cc_start: 0.8448 (m) cc_final: 0.8084 (p) REVERT: F 444 LYS cc_start: 0.8411 (mmtp) cc_final: 0.8116 (mmtp) REVERT: F 447 GLN cc_start: 0.7601 (tp40) cc_final: 0.6875 (tp40) REVERT: G 43 GLU cc_start: 0.7521 (mp0) cc_final: 0.7284 (mp0) REVERT: G 77 THR cc_start: 0.8006 (m) cc_final: 0.7631 (p) REVERT: G 90 LYS cc_start: 0.8338 (tptm) cc_final: 0.7730 (tptp) REVERT: G 108 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7638 (mtmt) REVERT: G 110 GLU cc_start: 0.7918 (tp30) cc_final: 0.7602 (tp30) REVERT: G 113 MET cc_start: 0.7698 (tpt) cc_final: 0.7052 (tpt) REVERT: G 125 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7908 (mttm) REVERT: G 128 LYS cc_start: 0.8568 (tttt) cc_final: 0.8337 (tttp) REVERT: G 129 GLU cc_start: 0.7257 (tt0) cc_final: 0.6814 (tt0) REVERT: G 131 TYR cc_start: 0.7881 (m-80) cc_final: 0.7307 (m-80) REVERT: G 137 GLU cc_start: 0.7155 (tt0) cc_final: 0.6816 (tt0) REVERT: G 158 ILE cc_start: 0.8558 (mt) cc_final: 0.8165 (mt) REVERT: G 169 GLN cc_start: 0.7997 (mt0) cc_final: 0.7226 (mt0) REVERT: G 176 ILE cc_start: 0.8809 (tp) cc_final: 0.8536 (tp) REVERT: G 178 GLU cc_start: 0.8051 (tt0) cc_final: 0.7195 (tp30) REVERT: G 183 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7378 (mm-30) REVERT: G 192 TYR cc_start: 0.7538 (p90) cc_final: 0.6948 (p90) REVERT: G 203 GLN cc_start: 0.8138 (pt0) cc_final: 0.7905 (tt0) REVERT: G 227 ASP cc_start: 0.7623 (t0) cc_final: 0.7335 (t0) REVERT: G 229 HIS cc_start: 0.8112 (t-90) cc_final: 0.7641 (t70) REVERT: G 231 LYS cc_start: 0.8319 (ptmt) cc_final: 0.7903 (ptmt) REVERT: G 244 ASP cc_start: 0.7389 (m-30) cc_final: 0.7019 (m-30) REVERT: G 258 SER cc_start: 0.8029 (m) cc_final: 0.7648 (t) REVERT: G 265 LYS cc_start: 0.7749 (ttpt) cc_final: 0.7290 (ttpp) REVERT: G 273 ASP cc_start: 0.7440 (m-30) cc_final: 0.7182 (m-30) REVERT: G 278 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6911 (mt-10) REVERT: G 280 ASN cc_start: 0.7963 (m-40) cc_final: 0.7686 (m110) REVERT: G 295 VAL cc_start: 0.8652 (t) cc_final: 0.8434 (p) REVERT: G 303 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7084 (mm-30) REVERT: G 308 ASP cc_start: 0.7999 (p0) cc_final: 0.7076 (p0) REVERT: G 311 CYS cc_start: 0.7932 (m) cc_final: 0.7581 (m) REVERT: G 326 ILE cc_start: 0.8674 (mt) cc_final: 0.8379 (mm) REVERT: G 356 ASP cc_start: 0.7707 (t0) cc_final: 0.7382 (t0) REVERT: G 388 GLU cc_start: 0.6994 (tp30) cc_final: 0.6622 (tp30) REVERT: G 389 GLU cc_start: 0.7321 (pt0) cc_final: 0.7104 (pt0) REVERT: G 392 ASN cc_start: 0.8428 (m-40) cc_final: 0.7622 (m-40) REVERT: G 396 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7055 (mt-10) REVERT: G 404 ARG cc_start: 0.7096 (mtt90) cc_final: 0.6751 (mtt180) REVERT: G 430 VAL cc_start: 0.8552 (t) cc_final: 0.8288 (p) REVERT: G 439 ASP cc_start: 0.7536 (p0) cc_final: 0.7333 (p0) REVERT: G 445 LYS cc_start: 0.8192 (mttm) cc_final: 0.7704 (mtpp) REVERT: H 22 ILE cc_start: 0.8760 (mt) cc_final: 0.8535 (mm) REVERT: H 41 GLN cc_start: 0.8033 (tp40) cc_final: 0.7252 (tm-30) REVERT: H 94 LEU cc_start: 0.8271 (tp) cc_final: 0.7958 (tt) REVERT: H 126 SER cc_start: 0.8527 (m) cc_final: 0.7709 (t) REVERT: H 130 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7414 (ttp-110) REVERT: H 141 GLU cc_start: 0.7011 (tt0) cc_final: 0.6776 (tt0) REVERT: H 146 GLN cc_start: 0.7508 (pt0) cc_final: 0.7272 (pt0) REVERT: H 160 LYS cc_start: 0.8044 (mttt) cc_final: 0.7501 (mttt) REVERT: H 164 LYS cc_start: 0.8397 (pttt) cc_final: 0.7960 (ptmm) REVERT: H 167 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6965 (mt-10) REVERT: H 169 GLU cc_start: 0.7163 (tt0) cc_final: 0.6674 (tt0) REVERT: H 172 TYR cc_start: 0.8199 (m-80) cc_final: 0.7829 (m-80) REVERT: H 177 LYS cc_start: 0.8296 (ptpt) cc_final: 0.7971 (ptpt) REVERT: H 202 ILE cc_start: 0.8378 (mt) cc_final: 0.8135 (mm) REVERT: H 209 PHE cc_start: 0.8413 (t80) cc_final: 0.7934 (t80) REVERT: H 211 ARG cc_start: 0.7743 (ttt180) cc_final: 0.7457 (ttt180) REVERT: H 218 MET cc_start: 0.7496 (mtp) cc_final: 0.7257 (mtp) REVERT: H 234 LYS cc_start: 0.8540 (mttp) cc_final: 0.8120 (mttp) REVERT: H 236 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7528 (ttmm) REVERT: H 238 VAL cc_start: 0.8693 (t) cc_final: 0.8307 (m) REVERT: H 251 ASN cc_start: 0.8506 (m-40) cc_final: 0.8159 (m110) REVERT: H 255 GLN cc_start: 0.7673 (mm-40) cc_final: 0.7443 (tp40) REVERT: H 260 LEU cc_start: 0.8335 (mt) cc_final: 0.8131 (mt) REVERT: H 269 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7599 (mtmt) REVERT: H 271 GLU cc_start: 0.7302 (mp0) cc_final: 0.7010 (mp0) REVERT: H 282 GLU cc_start: 0.7497 (tt0) cc_final: 0.6868 (tt0) REVERT: H 286 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6676 (mt-10) REVERT: H 292 ILE cc_start: 0.8176 (mt) cc_final: 0.7869 (mt) REVERT: H 295 VAL cc_start: 0.8098 (t) cc_final: 0.7814 (t) REVERT: H 324 LEU cc_start: 0.8378 (tp) cc_final: 0.8147 (tp) REVERT: H 332 ILE cc_start: 0.7987 (mt) cc_final: 0.7731 (mt) REVERT: H 353 ARG cc_start: 0.7563 (mtt90) cc_final: 0.7249 (ttm110) REVERT: H 369 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7781 (mm-40) REVERT: H 378 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7788 (mt-10) REVERT: H 379 ASP cc_start: 0.7455 (m-30) cc_final: 0.7190 (m-30) REVERT: H 395 LEU cc_start: 0.8287 (mm) cc_final: 0.8025 (mp) REVERT: H 443 MET cc_start: 0.7928 (ttm) cc_final: 0.7721 (ttt) REVERT: H 450 PHE cc_start: 0.7408 (m-80) cc_final: 0.7001 (m-80) REVERT: I 17 SER cc_start: 0.8111 (m) cc_final: 0.7798 (p) REVERT: I 34 GLN cc_start: 0.7566 (tm-30) cc_final: 0.7340 (tm-30) REVERT: I 43 GLU cc_start: 0.7503 (mp0) cc_final: 0.6964 (mt-10) REVERT: I 74 THR cc_start: 0.8149 (p) cc_final: 0.7935 (p) REVERT: I 86 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7362 (mm-30) REVERT: I 105 GLU cc_start: 0.7456 (mt-10) cc_final: 0.6865 (mt-10) REVERT: I 114 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7187 (mt-10) REVERT: I 129 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7257 (mt-10) REVERT: I 137 GLU cc_start: 0.7029 (tt0) cc_final: 0.6631 (tt0) REVERT: I 139 THR cc_start: 0.8184 (m) cc_final: 0.7455 (p) REVERT: I 154 ILE cc_start: 0.7997 (mp) cc_final: 0.7677 (mm) REVERT: I 158 ILE cc_start: 0.8475 (mm) cc_final: 0.8267 (mt) REVERT: I 169 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7622 (mt0) REVERT: I 181 GLN cc_start: 0.7514 (mt0) cc_final: 0.7249 (mt0) REVERT: I 196 ASN cc_start: 0.8206 (p0) cc_final: 0.7913 (p0) REVERT: I 201 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7520 (ttmm) REVERT: I 209 TYR cc_start: 0.7673 (m-80) cc_final: 0.7295 (m-80) REVERT: I 221 VAL cc_start: 0.8684 (t) cc_final: 0.8298 (m) REVERT: I 230 LYS cc_start: 0.7950 (mttp) cc_final: 0.7544 (mttp) REVERT: I 242 ASP cc_start: 0.7774 (m-30) cc_final: 0.7450 (m-30) REVERT: I 268 LYS cc_start: 0.8197 (mtmt) cc_final: 0.7455 (mtmm) REVERT: I 303 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6727 (mm-30) REVERT: I 352 LEU cc_start: 0.8329 (mt) cc_final: 0.8074 (mm) REVERT: I 362 ARG cc_start: 0.8137 (tmm-80) cc_final: 0.7775 (ptm160) REVERT: I 370 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6895 (mt-10) REVERT: I 408 GLN cc_start: 0.7725 (mt0) cc_final: 0.7446 (mt0) REVERT: I 427 LYS cc_start: 0.8538 (tttt) cc_final: 0.8219 (tttm) REVERT: I 443 SER cc_start: 0.8603 (t) cc_final: 0.8212 (m) REVERT: J 38 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6610 (mm-30) REVERT: J 67 LYS cc_start: 0.8319 (mttm) cc_final: 0.8093 (mttm) REVERT: J 90 MET cc_start: 0.7793 (mtm) cc_final: 0.7535 (mtp) REVERT: J 131 ILE cc_start: 0.8484 (mt) cc_final: 0.8190 (mt) REVERT: J 134 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7073 (mt-10) REVERT: J 135 THR cc_start: 0.8120 (t) cc_final: 0.7853 (m) REVERT: J 136 GLU cc_start: 0.7394 (mt-10) cc_final: 0.6988 (mt-10) REVERT: J 139 GLU cc_start: 0.6304 (tt0) cc_final: 0.6065 (tt0) REVERT: J 141 GLU cc_start: 0.6855 (mp0) cc_final: 0.6418 (mp0) REVERT: J 164 LYS cc_start: 0.7931 (pttt) cc_final: 0.7139 (pttt) REVERT: J 167 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6924 (mt-10) REVERT: J 178 MET cc_start: 0.7835 (tpp) cc_final: 0.7240 (tpp) REVERT: J 194 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8137 (p) REVERT: J 196 ASP cc_start: 0.6789 (t0) cc_final: 0.6541 (t0) REVERT: J 234 LYS cc_start: 0.8272 (mtpt) cc_final: 0.7999 (mtpt) REVERT: J 241 THR cc_start: 0.8236 (m) cc_final: 0.7998 (t) REVERT: J 242 VAL cc_start: 0.8215 (t) cc_final: 0.7920 (p) REVERT: J 246 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7055 (mt-10) REVERT: J 251 ASN cc_start: 0.8211 (m-40) cc_final: 0.7895 (m-40) REVERT: J 273 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7108 (mtt180) REVERT: J 279 LYS cc_start: 0.8343 (tppt) cc_final: 0.8132 (tptp) REVERT: J 364 GLU cc_start: 0.7243 (tt0) cc_final: 0.7018 (tt0) REVERT: J 377 GLU cc_start: 0.7738 (tp30) cc_final: 0.7491 (tp30) REVERT: J 378 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7112 (tt0) REVERT: J 379 ASP cc_start: 0.7710 (m-30) cc_final: 0.7386 (m-30) REVERT: J 391 THR cc_start: 0.7843 (m) cc_final: 0.7465 (p) REVERT: J 404 GLN cc_start: 0.7587 (mt0) cc_final: 0.7266 (mt0) REVERT: J 405 LEU cc_start: 0.8548 (mt) cc_final: 0.8297 (mt) REVERT: J 413 CYS cc_start: 0.7621 (t) cc_final: 0.7357 (t) REVERT: J 415 LYS cc_start: 0.8573 (tptt) cc_final: 0.8322 (tppp) REVERT: J 430 TYR cc_start: 0.8175 (t80) cc_final: 0.7695 (t80) REVERT: J 436 GLU cc_start: 0.6853 (tm-30) cc_final: 0.6582 (tm-30) REVERT: J 441 GLN cc_start: 0.7101 (mt0) cc_final: 0.6721 (mt0) REVERT: J 445 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7228 (mt-10) outliers start: 93 outliers final: 67 residues processed: 1198 average time/residue: 0.2293 time to fit residues: 407.2264 Evaluate side-chains 1217 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1145 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1984 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 105 CYS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 195 ILE Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 381 GLU Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 376 LYS Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 432 GLU Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 443 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 142 optimal weight: 4.9990 chunk 329 optimal weight: 0.5980 chunk 263 optimal weight: 0.0970 chunk 274 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 351 optimal weight: 0.7980 chunk 339 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2007 GLN ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN C 174 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN F 146 GLN F 369 GLN F 404 GLN G 247 ASN G 284 ASN I 280 ASN J 78 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107780 restraints weight = 48462.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111298 restraints weight = 20864.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112642 restraints weight = 10938.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114423 restraints weight = 7605.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114959 restraints weight = 5448.523| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29053 Z= 0.181 Angle : 0.574 14.811 39245 Z= 0.286 Chirality : 0.044 0.260 4499 Planarity : 0.004 0.050 5042 Dihedral : 7.316 151.989 4020 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.15 % Allowed : 15.72 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.14), residues: 3580 helix: 1.56 (0.13), residues: 1589 sheet: 0.43 (0.20), residues: 640 loop : 0.48 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 118 TYR 0.017 0.001 TYR F 172 PHE 0.030 0.001 PHE C 248 TRP 0.007 0.001 TRP H 283 HIS 0.011 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00390 (29045) covalent geometry : angle 0.57253 (39236) hydrogen bonds : bond 0.03865 ( 1224) hydrogen bonds : angle 4.08744 ( 3483) metal coordination : bond 0.02017 ( 8) metal coordination : angle 2.88868 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1156 time to evaluate : 0.972 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: A 873 MET cc_start: 0.5881 (mmm) cc_final: 0.5321 (mmm) REVERT: A 916 PHE cc_start: 0.8379 (t80) cc_final: 0.8104 (t80) REVERT: A 933 THR cc_start: 0.8294 (m) cc_final: 0.8029 (t) REVERT: A 939 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7209 (mm-40) REVERT: A 940 ARG cc_start: 0.7370 (ptt-90) cc_final: 0.7094 (ptt90) REVERT: A 957 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7724 (mtp85) REVERT: A 1900 ARG cc_start: 0.8148 (ttp-110) cc_final: 0.7941 (ttp-110) REVERT: A 1902 GLU cc_start: 0.7676 (tp30) cc_final: 0.7409 (tp30) REVERT: A 1906 GLN cc_start: 0.7623 (mm110) cc_final: 0.7320 (mm110) REVERT: A 1926 CYS cc_start: 0.8365 (m) cc_final: 0.8021 (m) REVERT: A 1934 SER cc_start: 0.8490 (m) cc_final: 0.8052 (p) REVERT: A 1943 PRO cc_start: 0.7856 (Cg_exo) cc_final: 0.7499 (Cg_endo) REVERT: A 1951 TYR cc_start: 0.8228 (m-80) cc_final: 0.7655 (m-80) REVERT: A 1973 ILE cc_start: 0.8828 (mt) cc_final: 0.8614 (mm) REVERT: A 1991 HIS cc_start: 0.6444 (t70) cc_final: 0.6146 (t70) REVERT: A 2001 PRO cc_start: 0.8454 (Cg_exo) cc_final: 0.8228 (Cg_endo) REVERT: A 2008 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7075 (tt0) REVERT: A 2014 LEU cc_start: 0.8535 (mt) cc_final: 0.8204 (mm) REVERT: A 2017 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7532 (mtp85) REVERT: A 2019 ARG cc_start: 0.7936 (mtt180) cc_final: 0.7499 (mtt180) REVERT: A 2032 PHE cc_start: 0.8297 (m-80) cc_final: 0.8037 (m-80) REVERT: A 2071 MET cc_start: 0.6466 (tpp) cc_final: 0.5974 (tpp) REVERT: C 8 ASN cc_start: 0.7949 (t0) cc_final: 0.7524 (t0) REVERT: C 33 LYS cc_start: 0.7230 (mtmm) cc_final: 0.6930 (mtmm) REVERT: C 55 PHE cc_start: 0.8099 (t80) cc_final: 0.7826 (t80) REVERT: C 73 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7674 (mp10) REVERT: C 85 GLN cc_start: 0.8606 (pm20) cc_final: 0.8148 (pm20) REVERT: C 103 THR cc_start: 0.8326 (m) cc_final: 0.8054 (t) REVERT: C 137 ARG cc_start: 0.7343 (tpp80) cc_final: 0.7016 (tpp80) REVERT: C 138 ASP cc_start: 0.6905 (m-30) cc_final: 0.6646 (m-30) REVERT: C 142 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7090 (mm-30) REVERT: C 149 ASP cc_start: 0.7899 (t0) cc_final: 0.7610 (t0) REVERT: C 164 LYS cc_start: 0.7450 (tptm) cc_final: 0.7102 (tptm) REVERT: C 165 LYS cc_start: 0.8747 (ttpp) cc_final: 0.7883 (ptmm) REVERT: C 187 ILE cc_start: 0.8236 (mt) cc_final: 0.7888 (tp) REVERT: C 208 ASP cc_start: 0.7265 (m-30) cc_final: 0.6608 (m-30) REVERT: C 209 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8290 (p) REVERT: C 224 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8230 (ttmt) REVERT: C 230 ASN cc_start: 0.8247 (t0) cc_final: 0.7635 (t0) REVERT: C 235 ASP cc_start: 0.6745 (m-30) cc_final: 0.6520 (m-30) REVERT: C 237 VAL cc_start: 0.8841 (t) cc_final: 0.8607 (m) REVERT: C 256 VAL cc_start: 0.8527 (t) cc_final: 0.8033 (p) REVERT: C 286 ASP cc_start: 0.7326 (m-30) cc_final: 0.7106 (m-30) REVERT: C 308 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6884 (tm-30) REVERT: C 315 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7599 (ttpt) REVERT: C 326 PHE cc_start: 0.8630 (m-80) cc_final: 0.8360 (m-80) REVERT: C 341 THR cc_start: 0.8538 (t) cc_final: 0.8163 (p) REVERT: C 345 TYR cc_start: 0.7676 (m-10) cc_final: 0.7310 (m-10) REVERT: C 346 ASP cc_start: 0.7747 (m-30) cc_final: 0.7340 (m-30) REVERT: C 364 LYS cc_start: 0.8072 (ptmt) cc_final: 0.7474 (ttpp) REVERT: D 82 LYS cc_start: 0.7870 (mtmm) cc_final: 0.7549 (mtmm) REVERT: D 93 LEU cc_start: 0.8439 (tp) cc_final: 0.8200 (tp) REVERT: E 34 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7673 (tm-30) REVERT: E 40 VAL cc_start: 0.8211 (t) cc_final: 0.7590 (p) REVERT: E 43 GLU cc_start: 0.7589 (mp0) cc_final: 0.7227 (mt-10) REVERT: E 47 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6662 (mt-10) REVERT: E 60 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7819 (mtpp) REVERT: E 99 SER cc_start: 0.8701 (m) cc_final: 0.8366 (p) REVERT: E 105 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7200 (mt-10) REVERT: E 113 MET cc_start: 0.7258 (tpt) cc_final: 0.6927 (tpt) REVERT: E 168 LYS cc_start: 0.8136 (ttmt) cc_final: 0.7594 (ttmt) REVERT: E 200 VAL cc_start: 0.8296 (t) cc_final: 0.8076 (p) REVERT: E 201 LYS cc_start: 0.7884 (tptm) cc_final: 0.7260 (tptm) REVERT: E 209 TYR cc_start: 0.7894 (m-80) cc_final: 0.7165 (m-80) REVERT: E 244 ASP cc_start: 0.6867 (m-30) cc_final: 0.6588 (m-30) REVERT: E 259 MET cc_start: 0.7698 (tpt) cc_final: 0.7438 (tmm) REVERT: E 267 LYS cc_start: 0.7829 (mttp) cc_final: 0.7483 (mttp) REVERT: E 270 GLU cc_start: 0.7733 (mp0) cc_final: 0.7327 (mt-10) REVERT: E 285 LYS cc_start: 0.7873 (ttmm) cc_final: 0.7454 (ttmm) REVERT: E 295 VAL cc_start: 0.8409 (t) cc_final: 0.8105 (m) REVERT: E 302 ASP cc_start: 0.6664 (t0) cc_final: 0.6264 (t0) REVERT: E 314 TYR cc_start: 0.8312 (t80) cc_final: 0.6941 (t80) REVERT: E 343 ASP cc_start: 0.6571 (t0) cc_final: 0.6251 (t70) REVERT: E 354 LEU cc_start: 0.8292 (tp) cc_final: 0.8014 (tp) REVERT: E 356 ASP cc_start: 0.7701 (t0) cc_final: 0.7466 (t0) REVERT: E 370 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7634 (mt-10) REVERT: E 371 MET cc_start: 0.8253 (mtt) cc_final: 0.7999 (mtt) REVERT: E 372 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8079 (ttmm) REVERT: E 376 LYS cc_start: 0.8221 (tptt) cc_final: 0.7889 (tptt) REVERT: E 388 GLU cc_start: 0.7368 (tp30) cc_final: 0.7043 (tp30) REVERT: E 396 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7046 (mt-10) REVERT: E 414 ASN cc_start: 0.8193 (t0) cc_final: 0.7919 (t0) REVERT: E 415 LEU cc_start: 0.8442 (mt) cc_final: 0.8136 (mt) REVERT: E 416 LEU cc_start: 0.8471 (mt) cc_final: 0.8155 (mm) REVERT: E 418 LYS cc_start: 0.7975 (ttmm) cc_final: 0.7633 (ttmm) REVERT: E 426 GLU cc_start: 0.7252 (mp0) cc_final: 0.6585 (mp0) REVERT: E 427 LYS cc_start: 0.8484 (ttpp) cc_final: 0.8087 (ttpp) REVERT: E 432 GLU cc_start: 0.7305 (tt0) cc_final: 0.6977 (tt0) REVERT: E 446 ILE cc_start: 0.8171 (mt) cc_final: 0.7927 (mm) REVERT: F 61 GLU cc_start: 0.7806 (tp30) cc_final: 0.7591 (tp30) REVERT: F 107 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7338 (mt-10) REVERT: F 112 GLU cc_start: 0.6959 (tp30) cc_final: 0.6611 (tp30) REVERT: F 132 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7727 (mmmm) REVERT: F 137 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7727 (mm) REVERT: F 160 LYS cc_start: 0.7636 (ttpt) cc_final: 0.7370 (ttpt) REVERT: F 162 THR cc_start: 0.8134 (m) cc_final: 0.7501 (p) REVERT: F 179 ILE cc_start: 0.8651 (mm) cc_final: 0.8320 (mt) REVERT: F 180 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7274 (mm-30) REVERT: F 186 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7879 (mtpp) REVERT: F 188 GLN cc_start: 0.7528 (mt0) cc_final: 0.7100 (mt0) REVERT: F 192 VAL cc_start: 0.8435 (t) cc_final: 0.8094 (m) REVERT: F 194 THR cc_start: 0.8116 (m) cc_final: 0.7868 (t) REVERT: F 196 ASP cc_start: 0.7527 (t0) cc_final: 0.7182 (t0) REVERT: F 201 LYS cc_start: 0.8199 (tttp) cc_final: 0.7759 (tttp) REVERT: F 236 LYS cc_start: 0.7068 (mmtp) cc_final: 0.6843 (mmtp) REVERT: F 264 ASP cc_start: 0.7599 (t0) cc_final: 0.7177 (t0) REVERT: F 269 LYS cc_start: 0.8041 (mmtp) cc_final: 0.7680 (mmtp) REVERT: F 274 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6733 (mm-30) REVERT: F 300 GLU cc_start: 0.7081 (mm-30) cc_final: 0.6591 (mm-30) REVERT: F 314 ARG cc_start: 0.7530 (mmt180) cc_final: 0.6816 (mpt180) REVERT: F 317 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6832 (mt-10) REVERT: F 329 ASN cc_start: 0.8321 (p0) cc_final: 0.7948 (p0) REVERT: F 342 SER cc_start: 0.8834 (t) cc_final: 0.8426 (t) REVERT: F 353 ARG cc_start: 0.7909 (mtt90) cc_final: 0.7205 (ttp-110) REVERT: F 431 SER cc_start: 0.8438 (m) cc_final: 0.8087 (p) REVERT: F 444 LYS cc_start: 0.8420 (mmtp) cc_final: 0.8077 (mmtp) REVERT: G 43 GLU cc_start: 0.7502 (mp0) cc_final: 0.6915 (pm20) REVERT: G 59 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8440 (mtpp) REVERT: G 77 THR cc_start: 0.7957 (m) cc_final: 0.7646 (p) REVERT: G 90 LYS cc_start: 0.8273 (tptm) cc_final: 0.7661 (tptt) REVERT: G 108 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7633 (mtmt) REVERT: G 110 GLU cc_start: 0.7888 (tp30) cc_final: 0.7559 (tp30) REVERT: G 113 MET cc_start: 0.7684 (tpt) cc_final: 0.7069 (tpt) REVERT: G 123 ARG cc_start: 0.7773 (ttm-80) cc_final: 0.7513 (ttm170) REVERT: G 125 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7854 (mttm) REVERT: G 128 LYS cc_start: 0.8557 (tttt) cc_final: 0.8311 (tttp) REVERT: G 129 GLU cc_start: 0.7281 (tt0) cc_final: 0.6793 (tt0) REVERT: G 131 TYR cc_start: 0.7779 (m-80) cc_final: 0.7261 (m-80) REVERT: G 137 GLU cc_start: 0.7133 (tt0) cc_final: 0.6775 (tt0) REVERT: G 158 ILE cc_start: 0.8566 (mt) cc_final: 0.8187 (mt) REVERT: G 169 GLN cc_start: 0.7941 (mt0) cc_final: 0.7240 (mt0) REVERT: G 171 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8046 (mttm) REVERT: G 176 ILE cc_start: 0.8810 (tp) cc_final: 0.8530 (tp) REVERT: G 178 GLU cc_start: 0.8046 (tt0) cc_final: 0.7169 (tp30) REVERT: G 183 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7350 (mm-30) REVERT: G 192 TYR cc_start: 0.7577 (p90) cc_final: 0.6979 (p90) REVERT: G 203 GLN cc_start: 0.8141 (pt0) cc_final: 0.7890 (tt0) REVERT: G 216 GLU cc_start: 0.7018 (tp30) cc_final: 0.6641 (tp30) REVERT: G 227 ASP cc_start: 0.7554 (t0) cc_final: 0.7171 (t0) REVERT: G 229 HIS cc_start: 0.8107 (t-90) cc_final: 0.7637 (t70) REVERT: G 231 LYS cc_start: 0.8305 (ptmt) cc_final: 0.7896 (ptmt) REVERT: G 244 ASP cc_start: 0.7372 (m-30) cc_final: 0.6995 (m-30) REVERT: G 258 SER cc_start: 0.7996 (m) cc_final: 0.7615 (t) REVERT: G 265 LYS cc_start: 0.7704 (ttpt) cc_final: 0.7153 (ttpp) REVERT: G 273 ASP cc_start: 0.7410 (m-30) cc_final: 0.7148 (m-30) REVERT: G 278 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6884 (mt-10) REVERT: G 280 ASN cc_start: 0.8004 (m-40) cc_final: 0.7718 (m110) REVERT: G 291 ILE cc_start: 0.8575 (mt) cc_final: 0.8213 (tp) REVERT: G 295 VAL cc_start: 0.8625 (t) cc_final: 0.8301 (p) REVERT: G 302 ASP cc_start: 0.7506 (t0) cc_final: 0.7171 (t0) REVERT: G 303 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7034 (mm-30) REVERT: G 308 ASP cc_start: 0.8022 (p0) cc_final: 0.7150 (p0) REVERT: G 311 CYS cc_start: 0.7888 (m) cc_final: 0.7543 (m) REVERT: G 326 ILE cc_start: 0.8671 (mt) cc_final: 0.8365 (mm) REVERT: G 356 ASP cc_start: 0.7721 (t0) cc_final: 0.7374 (t0) REVERT: G 388 GLU cc_start: 0.6923 (tp30) cc_final: 0.6507 (tp30) REVERT: G 389 GLU cc_start: 0.7278 (pt0) cc_final: 0.7047 (pt0) REVERT: G 392 ASN cc_start: 0.8434 (m-40) cc_final: 0.7626 (m-40) REVERT: G 396 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7031 (mt-10) REVERT: G 430 VAL cc_start: 0.8534 (t) cc_final: 0.8275 (p) REVERT: G 445 LYS cc_start: 0.8126 (mttm) cc_final: 0.7684 (mtpp) REVERT: G 455 MET cc_start: 0.6400 (mmm) cc_final: 0.5946 (mmm) REVERT: H 22 ILE cc_start: 0.8792 (mt) cc_final: 0.8554 (mm) REVERT: H 41 GLN cc_start: 0.8053 (tp40) cc_final: 0.7229 (tm-30) REVERT: H 94 LEU cc_start: 0.8263 (tp) cc_final: 0.7946 (tt) REVERT: H 107 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7362 (mt-10) REVERT: H 126 SER cc_start: 0.8555 (m) cc_final: 0.7711 (t) REVERT: H 130 ARG cc_start: 0.7811 (ttp80) cc_final: 0.7377 (ttp-110) REVERT: H 136 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7233 (mm-30) REVERT: H 141 GLU cc_start: 0.7006 (tt0) cc_final: 0.6770 (tt0) REVERT: H 146 GLN cc_start: 0.7496 (pt0) cc_final: 0.7268 (pt0) REVERT: H 160 LYS cc_start: 0.8034 (mttt) cc_final: 0.7512 (mttt) REVERT: H 164 LYS cc_start: 0.8419 (pttt) cc_final: 0.7960 (ptmm) REVERT: H 167 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6962 (mt-10) REVERT: H 168 MET cc_start: 0.6786 (mtp) cc_final: 0.6543 (mtp) REVERT: H 169 GLU cc_start: 0.7170 (tt0) cc_final: 0.6689 (tt0) REVERT: H 172 TYR cc_start: 0.8170 (m-80) cc_final: 0.7846 (m-10) REVERT: H 177 LYS cc_start: 0.8301 (ptpt) cc_final: 0.7785 (ptpt) REVERT: H 202 ILE cc_start: 0.8369 (mt) cc_final: 0.8100 (mm) REVERT: H 209 PHE cc_start: 0.8421 (t80) cc_final: 0.7959 (t80) REVERT: H 211 ARG cc_start: 0.7714 (ttt180) cc_final: 0.7417 (ttt180) REVERT: H 218 MET cc_start: 0.7523 (mtp) cc_final: 0.7272 (mtp) REVERT: H 223 LYS cc_start: 0.8743 (pttm) cc_final: 0.8460 (pttm) REVERT: H 234 LYS cc_start: 0.8542 (mttp) cc_final: 0.8155 (mttp) REVERT: H 236 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7691 (ttpt) REVERT: H 238 VAL cc_start: 0.8671 (t) cc_final: 0.8292 (m) REVERT: H 251 ASN cc_start: 0.8482 (m-40) cc_final: 0.8131 (m110) REVERT: H 255 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7363 (tp40) REVERT: H 264 ASP cc_start: 0.6702 (t0) cc_final: 0.6114 (t0) REVERT: H 269 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7542 (mtmt) REVERT: H 271 GLU cc_start: 0.7304 (mp0) cc_final: 0.7059 (mp0) REVERT: H 282 GLU cc_start: 0.7487 (tt0) cc_final: 0.6824 (tt0) REVERT: H 286 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6597 (mt-10) REVERT: H 292 ILE cc_start: 0.8170 (mt) cc_final: 0.7870 (mt) REVERT: H 295 VAL cc_start: 0.8053 (t) cc_final: 0.7772 (t) REVERT: H 303 MET cc_start: 0.8346 (mmm) cc_final: 0.8131 (mmp) REVERT: H 313 ASN cc_start: 0.8170 (m-40) cc_final: 0.7941 (m-40) REVERT: H 324 LEU cc_start: 0.8358 (tp) cc_final: 0.8132 (tp) REVERT: H 332 ILE cc_start: 0.8031 (mt) cc_final: 0.7776 (mt) REVERT: H 353 ARG cc_start: 0.7567 (mtt90) cc_final: 0.7230 (mtt-85) REVERT: H 369 GLN cc_start: 0.8018 (tp-100) cc_final: 0.7792 (mm-40) REVERT: H 379 ASP cc_start: 0.7459 (m-30) cc_final: 0.7210 (m-30) REVERT: H 395 LEU cc_start: 0.8279 (mm) cc_final: 0.8031 (mp) REVERT: H 443 MET cc_start: 0.7919 (ttm) cc_final: 0.7648 (ttp) REVERT: H 450 PHE cc_start: 0.7389 (m-80) cc_final: 0.6959 (m-80) REVERT: I 34 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7369 (tm-30) REVERT: I 43 GLU cc_start: 0.7483 (mp0) cc_final: 0.6854 (mt-10) REVERT: I 52 ILE cc_start: 0.8460 (mm) cc_final: 0.8246 (mt) REVERT: I 74 THR cc_start: 0.8151 (p) cc_final: 0.7943 (p) REVERT: I 105 GLU cc_start: 0.7426 (mt-10) cc_final: 0.6878 (mt-10) REVERT: I 125 LYS cc_start: 0.8283 (ttpp) cc_final: 0.7926 (ttpp) REVERT: I 137 GLU cc_start: 0.6916 (tt0) cc_final: 0.6503 (tt0) REVERT: I 139 THR cc_start: 0.8161 (m) cc_final: 0.7392 (p) REVERT: I 154 ILE cc_start: 0.7978 (mp) cc_final: 0.7658 (mm) REVERT: I 158 ILE cc_start: 0.8460 (mm) cc_final: 0.8233 (mt) REVERT: I 177 PHE cc_start: 0.8817 (t80) cc_final: 0.8296 (t80) REVERT: I 181 GLN cc_start: 0.7491 (mt0) cc_final: 0.7048 (mt0) REVERT: I 196 ASN cc_start: 0.8214 (p0) cc_final: 0.7901 (p0) REVERT: I 201 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7470 (ttmm) REVERT: I 209 TYR cc_start: 0.7733 (m-80) cc_final: 0.7350 (m-80) REVERT: I 221 VAL cc_start: 0.8683 (t) cc_final: 0.8280 (m) REVERT: I 230 LYS cc_start: 0.7948 (mttp) cc_final: 0.7517 (mttp) REVERT: I 242 ASP cc_start: 0.7780 (m-30) cc_final: 0.7454 (m-30) REVERT: I 259 MET cc_start: 0.7408 (mtm) cc_final: 0.7153 (mpp) REVERT: I 268 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7463 (mtmm) REVERT: I 303 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6637 (mm-30) REVERT: I 352 LEU cc_start: 0.8305 (mt) cc_final: 0.8070 (mm) REVERT: I 370 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6904 (mt-10) REVERT: I 408 GLN cc_start: 0.7728 (mt0) cc_final: 0.7433 (mt0) REVERT: I 427 LYS cc_start: 0.8508 (tttt) cc_final: 0.8189 (tttm) REVERT: I 443 SER cc_start: 0.8602 (t) cc_final: 0.8193 (m) REVERT: I 455 MET cc_start: 0.6472 (mmm) cc_final: 0.6012 (mmm) REVERT: J 38 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6605 (mm-30) REVERT: J 67 LYS cc_start: 0.8305 (mttm) cc_final: 0.8092 (mttm) REVERT: J 90 MET cc_start: 0.7743 (mtm) cc_final: 0.7478 (mtp) REVERT: J 131 ILE cc_start: 0.8481 (mt) cc_final: 0.8209 (mt) REVERT: J 134 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7101 (mt-10) REVERT: J 135 THR cc_start: 0.8191 (t) cc_final: 0.7819 (m) REVERT: J 136 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6928 (mt-10) REVERT: J 139 GLU cc_start: 0.6261 (tt0) cc_final: 0.6057 (tt0) REVERT: J 164 LYS cc_start: 0.7959 (pttt) cc_final: 0.7653 (pttt) REVERT: J 178 MET cc_start: 0.7799 (tpp) cc_final: 0.7240 (tpp) REVERT: J 194 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.8179 (p) REVERT: J 196 ASP cc_start: 0.6753 (t0) cc_final: 0.6544 (t0) REVERT: J 231 GLU cc_start: 0.6659 (mm-30) cc_final: 0.6373 (mm-30) REVERT: J 234 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7999 (mtpt) REVERT: J 241 THR cc_start: 0.8218 (m) cc_final: 0.7963 (t) REVERT: J 242 VAL cc_start: 0.8231 (t) cc_final: 0.7875 (p) REVERT: J 251 ASN cc_start: 0.8222 (m-40) cc_final: 0.7890 (m-40) REVERT: J 273 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7111 (mtt180) REVERT: J 279 LYS cc_start: 0.8298 (tppt) cc_final: 0.8075 (tptp) REVERT: J 307 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6989 (mt-10) REVERT: J 364 GLU cc_start: 0.7210 (tt0) cc_final: 0.6987 (tt0) REVERT: J 377 GLU cc_start: 0.7699 (tp30) cc_final: 0.7469 (tp30) REVERT: J 379 ASP cc_start: 0.7695 (m-30) cc_final: 0.7389 (m-30) REVERT: J 384 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6745 (mm-30) REVERT: J 391 THR cc_start: 0.7846 (m) cc_final: 0.7462 (p) REVERT: J 404 GLN cc_start: 0.7540 (mt0) cc_final: 0.7202 (mt0) REVERT: J 405 LEU cc_start: 0.8511 (mt) cc_final: 0.8270 (mt) REVERT: J 413 CYS cc_start: 0.7603 (t) cc_final: 0.7343 (t) REVERT: J 415 LYS cc_start: 0.8568 (tptt) cc_final: 0.8338 (tppp) REVERT: J 430 TYR cc_start: 0.8181 (t80) cc_final: 0.7722 (t80) REVERT: J 436 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6461 (tm-30) REVERT: J 441 GLN cc_start: 0.7098 (mt0) cc_final: 0.6696 (mt0) REVERT: J 445 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7153 (mt-10) outliers start: 98 outliers final: 77 residues processed: 1192 average time/residue: 0.2166 time to fit residues: 381.6892 Evaluate side-chains 1225 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1142 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1984 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 28 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain E residue 433 ILE Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 418 LYS Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 414 ARG Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 376 LYS Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 432 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 326 MET Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 443 MET Chi-restraints excluded: chain J residue 444 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 267 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 302 optimal weight: 0.9980 chunk 285 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 326 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 252 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1945 HIS ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 HIS ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN F 404 GLN G 284 ASN I 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106285 restraints weight = 48275.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.109849 restraints weight = 20848.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.111374 restraints weight = 11002.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.113037 restraints weight = 7588.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113586 restraints weight = 5526.135| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29053 Z= 0.175 Angle : 0.584 13.116 39245 Z= 0.291 Chirality : 0.044 0.211 4499 Planarity : 0.004 0.051 5042 Dihedral : 7.317 152.462 4020 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.02 % Allowed : 16.78 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.14), residues: 3580 helix: 1.57 (0.13), residues: 1588 sheet: 0.40 (0.20), residues: 628 loop : 0.43 (0.17), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 118 TYR 0.017 0.001 TYR I 192 PHE 0.031 0.001 PHE C 248 TRP 0.006 0.001 TRP H 283 HIS 0.010 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00379 (29045) covalent geometry : angle 0.58257 (39236) hydrogen bonds : bond 0.03821 ( 1224) hydrogen bonds : angle 4.07733 ( 3483) metal coordination : bond 0.01912 ( 8) metal coordination : angle 2.85031 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1143 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 873 MET cc_start: 0.5910 (mmm) cc_final: 0.5350 (mmm) REVERT: A 933 THR cc_start: 0.8286 (m) cc_final: 0.8071 (t) REVERT: A 939 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7233 (mm-40) REVERT: A 940 ARG cc_start: 0.7359 (ptt-90) cc_final: 0.7061 (ptt90) REVERT: A 957 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7720 (mtp85) REVERT: A 966 ARG cc_start: 0.7137 (ttp80) cc_final: 0.6761 (ttp80) REVERT: A 1895 ARG cc_start: 0.7463 (ttp-170) cc_final: 0.7218 (ttp-170) REVERT: A 1900 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7938 (ttp-110) REVERT: A 1902 GLU cc_start: 0.7711 (tp30) cc_final: 0.7397 (tp30) REVERT: A 1906 GLN cc_start: 0.7612 (mm110) cc_final: 0.7301 (mm110) REVERT: A 1934 SER cc_start: 0.8480 (m) cc_final: 0.8054 (p) REVERT: A 1943 PRO cc_start: 0.7859 (Cg_exo) cc_final: 0.7498 (Cg_endo) REVERT: A 1951 TYR cc_start: 0.8228 (m-80) cc_final: 0.7680 (m-80) REVERT: A 1973 ILE cc_start: 0.8815 (mt) cc_final: 0.8611 (mm) REVERT: A 2001 PRO cc_start: 0.8443 (Cg_exo) cc_final: 0.8222 (Cg_endo) REVERT: A 2008 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7033 (tt0) REVERT: A 2014 LEU cc_start: 0.8534 (mt) cc_final: 0.8226 (mm) REVERT: A 2019 ARG cc_start: 0.7909 (mtt180) cc_final: 0.7467 (mtt180) REVERT: A 2023 ARG cc_start: 0.7253 (mmm160) cc_final: 0.6768 (mmm160) REVERT: A 2032 PHE cc_start: 0.8308 (m-80) cc_final: 0.7984 (m-80) REVERT: A 2068 MET cc_start: 0.5973 (mtt) cc_final: 0.5768 (mtt) REVERT: A 2071 MET cc_start: 0.6468 (tpp) cc_final: 0.6037 (tpp) REVERT: A 2098 ARG cc_start: 0.7457 (mtt-85) cc_final: 0.7044 (mpp80) REVERT: C 33 LYS cc_start: 0.7294 (mtmm) cc_final: 0.6997 (mtmm) REVERT: C 55 PHE cc_start: 0.8105 (t80) cc_final: 0.7854 (t80) REVERT: C 85 GLN cc_start: 0.8596 (pm20) cc_final: 0.8340 (pm20) REVERT: C 103 THR cc_start: 0.8346 (m) cc_final: 0.8052 (t) REVERT: C 137 ARG cc_start: 0.7335 (tpp80) cc_final: 0.7065 (tpp80) REVERT: C 138 ASP cc_start: 0.6908 (m-30) cc_final: 0.6654 (m-30) REVERT: C 142 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7143 (mm-30) REVERT: C 149 ASP cc_start: 0.7911 (t0) cc_final: 0.7645 (t0) REVERT: C 164 LYS cc_start: 0.7429 (tptm) cc_final: 0.7041 (tptm) REVERT: C 165 LYS cc_start: 0.8744 (ttpp) cc_final: 0.7651 (ptmm) REVERT: C 187 ILE cc_start: 0.8264 (mt) cc_final: 0.7918 (tp) REVERT: C 208 ASP cc_start: 0.7240 (m-30) cc_final: 0.6565 (m-30) REVERT: C 209 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8286 (p) REVERT: C 224 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8243 (ttmt) REVERT: C 230 ASN cc_start: 0.8255 (t0) cc_final: 0.7626 (t0) REVERT: C 234 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7907 (tp) REVERT: C 235 ASP cc_start: 0.6751 (m-30) cc_final: 0.6498 (m-30) REVERT: C 237 VAL cc_start: 0.8844 (t) cc_final: 0.8595 (m) REVERT: C 256 VAL cc_start: 0.8521 (t) cc_final: 0.8010 (p) REVERT: C 286 ASP cc_start: 0.7333 (m-30) cc_final: 0.7110 (m-30) REVERT: C 315 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7676 (ttmm) REVERT: C 316 ASN cc_start: 0.7931 (m-40) cc_final: 0.7597 (m-40) REVERT: C 326 PHE cc_start: 0.8631 (m-80) cc_final: 0.8369 (m-80) REVERT: C 341 THR cc_start: 0.8553 (t) cc_final: 0.8053 (p) REVERT: C 364 LYS cc_start: 0.8027 (ptmt) cc_final: 0.7569 (ttpp) REVERT: D 82 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7518 (mtmm) REVERT: D 93 LEU cc_start: 0.8448 (tp) cc_final: 0.8214 (tp) REVERT: E 34 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7683 (tm-30) REVERT: E 40 VAL cc_start: 0.8202 (t) cc_final: 0.7599 (p) REVERT: E 43 GLU cc_start: 0.7605 (mp0) cc_final: 0.7260 (mp0) REVERT: E 47 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6649 (mt-10) REVERT: E 60 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7788 (mtpp) REVERT: E 96 MET cc_start: 0.7507 (ptm) cc_final: 0.7228 (ttp) REVERT: E 99 SER cc_start: 0.8702 (m) cc_final: 0.8389 (p) REVERT: E 105 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7242 (mt-10) REVERT: E 113 MET cc_start: 0.7227 (tpt) cc_final: 0.6929 (tpt) REVERT: E 132 GLU cc_start: 0.7159 (tt0) cc_final: 0.6885 (tt0) REVERT: E 168 LYS cc_start: 0.8116 (ttmt) cc_final: 0.7538 (ttmt) REVERT: E 200 VAL cc_start: 0.8288 (t) cc_final: 0.8063 (p) REVERT: E 201 LYS cc_start: 0.7884 (tptm) cc_final: 0.7244 (tptm) REVERT: E 209 TYR cc_start: 0.7898 (m-80) cc_final: 0.7260 (m-80) REVERT: E 244 ASP cc_start: 0.6901 (m-30) cc_final: 0.6570 (m-30) REVERT: E 259 MET cc_start: 0.7775 (tpt) cc_final: 0.7529 (tmm) REVERT: E 267 LYS cc_start: 0.7826 (mttp) cc_final: 0.7499 (mttp) REVERT: E 270 GLU cc_start: 0.7653 (mp0) cc_final: 0.7243 (mt-10) REVERT: E 278 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6684 (mt-10) REVERT: E 284 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8071 (m-40) REVERT: E 285 LYS cc_start: 0.7907 (ttmm) cc_final: 0.7480 (ttmm) REVERT: E 295 VAL cc_start: 0.8407 (t) cc_final: 0.8124 (m) REVERT: E 302 ASP cc_start: 0.6695 (t0) cc_final: 0.6225 (t0) REVERT: E 314 TYR cc_start: 0.8300 (t80) cc_final: 0.6948 (t80) REVERT: E 343 ASP cc_start: 0.6598 (t0) cc_final: 0.6286 (t70) REVERT: E 354 LEU cc_start: 0.8248 (tp) cc_final: 0.7961 (tp) REVERT: E 356 ASP cc_start: 0.7712 (t0) cc_final: 0.7467 (t0) REVERT: E 370 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7602 (mt-10) REVERT: E 371 MET cc_start: 0.8255 (mtt) cc_final: 0.8013 (mtt) REVERT: E 372 LYS cc_start: 0.8445 (mtpt) cc_final: 0.8083 (ttmm) REVERT: E 376 LYS cc_start: 0.8209 (tptt) cc_final: 0.7872 (tptt) REVERT: E 388 GLU cc_start: 0.7343 (tp30) cc_final: 0.7071 (tp30) REVERT: E 396 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7039 (mt-10) REVERT: E 414 ASN cc_start: 0.8208 (t0) cc_final: 0.7936 (t0) REVERT: E 415 LEU cc_start: 0.8446 (mt) cc_final: 0.8159 (mt) REVERT: E 416 LEU cc_start: 0.8463 (mt) cc_final: 0.8175 (mm) REVERT: E 418 LYS cc_start: 0.7988 (ttmm) cc_final: 0.7638 (ttmm) REVERT: E 426 GLU cc_start: 0.7393 (mp0) cc_final: 0.7141 (mp0) REVERT: E 427 LYS cc_start: 0.8454 (ttpp) cc_final: 0.8068 (ttpp) REVERT: E 432 GLU cc_start: 0.7321 (tt0) cc_final: 0.6961 (tt0) REVERT: E 446 ILE cc_start: 0.8190 (mt) cc_final: 0.7919 (mm) REVERT: F 107 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7355 (mt-10) REVERT: F 112 GLU cc_start: 0.6990 (tp30) cc_final: 0.6560 (tp30) REVERT: F 132 LYS cc_start: 0.8089 (mtmm) cc_final: 0.7789 (mmmm) REVERT: F 137 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7691 (mm) REVERT: F 160 LYS cc_start: 0.7613 (ttpt) cc_final: 0.7382 (ttpt) REVERT: F 162 THR cc_start: 0.8074 (m) cc_final: 0.7574 (p) REVERT: F 176 THR cc_start: 0.7892 (m) cc_final: 0.7329 (p) REVERT: F 179 ILE cc_start: 0.8653 (mm) cc_final: 0.8344 (mt) REVERT: F 180 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7261 (mm-30) REVERT: F 186 LYS cc_start: 0.8214 (mtpp) cc_final: 0.7862 (mtpp) REVERT: F 188 GLN cc_start: 0.7563 (mt0) cc_final: 0.7155 (mt0) REVERT: F 194 THR cc_start: 0.8102 (m) cc_final: 0.7466 (p) REVERT: F 196 ASP cc_start: 0.7537 (t0) cc_final: 0.7196 (t0) REVERT: F 201 LYS cc_start: 0.8207 (tttp) cc_final: 0.7743 (tttp) REVERT: F 214 ASP cc_start: 0.7670 (p0) cc_final: 0.7368 (p0) REVERT: F 236 LYS cc_start: 0.7054 (mmtp) cc_final: 0.6850 (mmtp) REVERT: F 264 ASP cc_start: 0.7619 (t0) cc_final: 0.7172 (t0) REVERT: F 269 LYS cc_start: 0.8007 (mmtp) cc_final: 0.7635 (mmtp) REVERT: F 274 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6716 (mm-30) REVERT: F 288 LYS cc_start: 0.8177 (tttt) cc_final: 0.7628 (tttt) REVERT: F 300 GLU cc_start: 0.7063 (mm-30) cc_final: 0.6818 (mm-30) REVERT: F 314 ARG cc_start: 0.7538 (mmt180) cc_final: 0.6711 (mpt180) REVERT: F 317 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6795 (mt-10) REVERT: F 329 ASN cc_start: 0.8399 (p0) cc_final: 0.7997 (p0) REVERT: F 332 ILE cc_start: 0.8382 (mm) cc_final: 0.8055 (mm) REVERT: F 342 SER cc_start: 0.8839 (t) cc_final: 0.8433 (t) REVERT: F 353 ARG cc_start: 0.7914 (mtt90) cc_final: 0.7419 (mtt90) REVERT: F 415 LYS cc_start: 0.8389 (tptt) cc_final: 0.7878 (tptt) REVERT: F 431 SER cc_start: 0.8447 (m) cc_final: 0.8094 (p) REVERT: F 444 LYS cc_start: 0.8415 (mmtp) cc_final: 0.8069 (mmtp) REVERT: G 43 GLU cc_start: 0.7469 (mp0) cc_final: 0.7038 (mp0) REVERT: G 77 THR cc_start: 0.7966 (m) cc_final: 0.7637 (p) REVERT: G 108 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7646 (mtmt) REVERT: G 110 GLU cc_start: 0.7884 (tp30) cc_final: 0.7567 (tp30) REVERT: G 113 MET cc_start: 0.7688 (tpt) cc_final: 0.7053 (tpt) REVERT: G 125 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7831 (mttm) REVERT: G 128 LYS cc_start: 0.8558 (tttt) cc_final: 0.8340 (tttp) REVERT: G 129 GLU cc_start: 0.7298 (tt0) cc_final: 0.6791 (tt0) REVERT: G 131 TYR cc_start: 0.7749 (m-80) cc_final: 0.7262 (m-80) REVERT: G 158 ILE cc_start: 0.8553 (mt) cc_final: 0.8139 (mt) REVERT: G 171 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8067 (mttm) REVERT: G 176 ILE cc_start: 0.8799 (tp) cc_final: 0.8499 (tp) REVERT: G 178 GLU cc_start: 0.8085 (tt0) cc_final: 0.7181 (tp30) REVERT: G 183 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7367 (mm-30) REVERT: G 192 TYR cc_start: 0.7585 (p90) cc_final: 0.6964 (p90) REVERT: G 203 GLN cc_start: 0.8147 (pt0) cc_final: 0.7887 (tt0) REVERT: G 216 GLU cc_start: 0.7002 (tp30) cc_final: 0.6677 (tp30) REVERT: G 227 ASP cc_start: 0.7569 (t0) cc_final: 0.7174 (t0) REVERT: G 229 HIS cc_start: 0.8124 (t-90) cc_final: 0.7640 (t70) REVERT: G 231 LYS cc_start: 0.8309 (ptmt) cc_final: 0.7896 (ptmt) REVERT: G 244 ASP cc_start: 0.7394 (m-30) cc_final: 0.7010 (m-30) REVERT: G 258 SER cc_start: 0.7986 (m) cc_final: 0.7674 (t) REVERT: G 260 MET cc_start: 0.7175 (mmt) cc_final: 0.6632 (mmt) REVERT: G 265 LYS cc_start: 0.7728 (ttpt) cc_final: 0.7142 (ttpp) REVERT: G 273 ASP cc_start: 0.7412 (m-30) cc_final: 0.7143 (m-30) REVERT: G 278 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6892 (mt-10) REVERT: G 280 ASN cc_start: 0.8001 (m-40) cc_final: 0.7694 (m110) REVERT: G 291 ILE cc_start: 0.8559 (mt) cc_final: 0.8167 (tp) REVERT: G 295 VAL cc_start: 0.8636 (t) cc_final: 0.8347 (p) REVERT: G 302 ASP cc_start: 0.7512 (t0) cc_final: 0.7168 (t0) REVERT: G 303 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7052 (mm-30) REVERT: G 308 ASP cc_start: 0.8025 (p0) cc_final: 0.7152 (p0) REVERT: G 311 CYS cc_start: 0.7893 (m) cc_final: 0.7575 (m) REVERT: G 326 ILE cc_start: 0.8661 (mt) cc_final: 0.8367 (mm) REVERT: G 327 VAL cc_start: 0.8822 (t) cc_final: 0.8453 (m) REVERT: G 356 ASP cc_start: 0.7700 (t0) cc_final: 0.7360 (t0) REVERT: G 388 GLU cc_start: 0.6917 (tp30) cc_final: 0.6496 (tp30) REVERT: G 389 GLU cc_start: 0.7290 (pt0) cc_final: 0.7058 (pt0) REVERT: G 392 ASN cc_start: 0.8391 (m-40) cc_final: 0.7558 (m-40) REVERT: G 396 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7027 (mt-10) REVERT: G 430 VAL cc_start: 0.8529 (t) cc_final: 0.8252 (p) REVERT: G 445 LYS cc_start: 0.8108 (mttm) cc_final: 0.7692 (mtpp) REVERT: G 455 MET cc_start: 0.6330 (mmm) cc_final: 0.5932 (mmm) REVERT: H 22 ILE cc_start: 0.8757 (mt) cc_final: 0.8496 (mm) REVERT: H 41 GLN cc_start: 0.8073 (tp40) cc_final: 0.7273 (tm-30) REVERT: H 73 VAL cc_start: 0.8365 (t) cc_final: 0.8042 (p) REVERT: H 94 LEU cc_start: 0.8253 (tp) cc_final: 0.7933 (tt) REVERT: H 107 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7364 (mt-10) REVERT: H 126 SER cc_start: 0.8559 (m) cc_final: 0.7713 (t) REVERT: H 130 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7369 (ttp-110) REVERT: H 141 GLU cc_start: 0.7012 (tt0) cc_final: 0.6797 (tt0) REVERT: H 146 GLN cc_start: 0.7500 (pt0) cc_final: 0.7276 (pt0) REVERT: H 160 LYS cc_start: 0.8037 (mttt) cc_final: 0.7504 (mttt) REVERT: H 164 LYS cc_start: 0.8410 (pttt) cc_final: 0.7944 (ptmm) REVERT: H 167 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6977 (mt-10) REVERT: H 168 MET cc_start: 0.6763 (mtp) cc_final: 0.6536 (mtp) REVERT: H 169 GLU cc_start: 0.7187 (tt0) cc_final: 0.6713 (tt0) REVERT: H 172 TYR cc_start: 0.8136 (m-80) cc_final: 0.7819 (m-10) REVERT: H 177 LYS cc_start: 0.8374 (ptpt) cc_final: 0.7836 (ptpt) REVERT: H 202 ILE cc_start: 0.8375 (mt) cc_final: 0.8094 (mm) REVERT: H 209 PHE cc_start: 0.8435 (t80) cc_final: 0.7959 (t80) REVERT: H 211 ARG cc_start: 0.7721 (ttt180) cc_final: 0.7407 (ttt180) REVERT: H 218 MET cc_start: 0.7508 (mtp) cc_final: 0.7257 (mtp) REVERT: H 234 LYS cc_start: 0.8543 (mttp) cc_final: 0.8335 (mttp) REVERT: H 236 LYS cc_start: 0.8032 (ttpt) cc_final: 0.7732 (ttpt) REVERT: H 238 VAL cc_start: 0.8674 (t) cc_final: 0.8252 (m) REVERT: H 251 ASN cc_start: 0.8421 (m-40) cc_final: 0.8102 (m110) REVERT: H 255 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7378 (tp40) REVERT: H 264 ASP cc_start: 0.6702 (t0) cc_final: 0.6142 (t0) REVERT: H 267 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6807 (mt-10) REVERT: H 269 LYS cc_start: 0.7790 (mtmt) cc_final: 0.7516 (mtmt) REVERT: H 271 GLU cc_start: 0.7316 (mp0) cc_final: 0.7057 (mp0) REVERT: H 282 GLU cc_start: 0.7503 (tt0) cc_final: 0.6822 (tt0) REVERT: H 286 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6672 (mt-10) REVERT: H 292 ILE cc_start: 0.8173 (mt) cc_final: 0.7870 (mt) REVERT: H 295 VAL cc_start: 0.8059 (t) cc_final: 0.7816 (t) REVERT: H 303 MET cc_start: 0.8329 (mmm) cc_final: 0.8118 (mmp) REVERT: H 324 LEU cc_start: 0.8352 (tp) cc_final: 0.8079 (tp) REVERT: H 332 ILE cc_start: 0.8088 (mt) cc_final: 0.7832 (mt) REVERT: H 368 LYS cc_start: 0.8312 (ttmm) cc_final: 0.8094 (ttmm) REVERT: H 369 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7791 (mm-40) REVERT: H 379 ASP cc_start: 0.7497 (m-30) cc_final: 0.7215 (m-30) REVERT: H 395 LEU cc_start: 0.8303 (mm) cc_final: 0.8036 (mp) REVERT: H 443 MET cc_start: 0.7913 (ttm) cc_final: 0.7641 (ttp) REVERT: H 450 PHE cc_start: 0.7361 (m-80) cc_final: 0.6940 (m-80) REVERT: I 34 GLN cc_start: 0.7593 (tm-30) cc_final: 0.7392 (tm-30) REVERT: I 43 GLU cc_start: 0.7491 (mp0) cc_final: 0.6843 (mt-10) REVERT: I 52 ILE cc_start: 0.8456 (mm) cc_final: 0.8232 (mt) REVERT: I 74 THR cc_start: 0.8147 (p) cc_final: 0.7941 (p) REVERT: I 105 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6907 (mt-10) REVERT: I 139 THR cc_start: 0.8152 (m) cc_final: 0.7571 (p) REVERT: I 154 ILE cc_start: 0.7945 (mp) cc_final: 0.7625 (mm) REVERT: I 158 ILE cc_start: 0.8475 (mm) cc_final: 0.8215 (mt) REVERT: I 177 PHE cc_start: 0.8810 (t80) cc_final: 0.8298 (t80) REVERT: I 181 GLN cc_start: 0.7501 (mt0) cc_final: 0.7056 (mt0) REVERT: I 189 ASP cc_start: 0.8047 (m-30) cc_final: 0.7653 (m-30) REVERT: I 196 ASN cc_start: 0.8212 (p0) cc_final: 0.7907 (p0) REVERT: I 201 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7468 (ttmm) REVERT: I 209 TYR cc_start: 0.7720 (m-80) cc_final: 0.7385 (m-80) REVERT: I 221 VAL cc_start: 0.8666 (t) cc_final: 0.8272 (m) REVERT: I 230 LYS cc_start: 0.7942 (mttp) cc_final: 0.7527 (mttp) REVERT: I 242 ASP cc_start: 0.7793 (m-30) cc_final: 0.7466 (m-30) REVERT: I 268 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7491 (mtmm) REVERT: I 303 GLU cc_start: 0.6994 (mm-30) cc_final: 0.6644 (mm-30) REVERT: I 352 LEU cc_start: 0.8310 (mt) cc_final: 0.8079 (mm) REVERT: I 362 ARG cc_start: 0.8130 (tmm-80) cc_final: 0.7809 (ptm160) REVERT: I 370 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6891 (mt-10) REVERT: I 408 GLN cc_start: 0.7708 (mt0) cc_final: 0.7429 (mt0) REVERT: I 427 LYS cc_start: 0.8495 (tttt) cc_final: 0.8212 (tttm) REVERT: I 443 SER cc_start: 0.8598 (t) cc_final: 0.8190 (m) REVERT: I 455 MET cc_start: 0.6360 (mmm) cc_final: 0.5914 (mmm) REVERT: J 38 GLU cc_start: 0.6977 (mm-30) cc_final: 0.6603 (mm-30) REVERT: J 67 LYS cc_start: 0.8312 (mttm) cc_final: 0.8096 (mttm) REVERT: J 90 MET cc_start: 0.7751 (mtm) cc_final: 0.7496 (mtp) REVERT: J 131 ILE cc_start: 0.8478 (mt) cc_final: 0.8194 (mt) REVERT: J 134 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7106 (mt-10) REVERT: J 135 THR cc_start: 0.8148 (t) cc_final: 0.7836 (m) REVERT: J 136 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6898 (mt-10) REVERT: J 161 LEU cc_start: 0.8552 (tt) cc_final: 0.8313 (tp) REVERT: J 164 LYS cc_start: 0.7982 (pttt) cc_final: 0.7736 (pttt) REVERT: J 178 MET cc_start: 0.7813 (tpp) cc_final: 0.7213 (tpp) REVERT: J 182 LEU cc_start: 0.8835 (mt) cc_final: 0.8601 (mm) REVERT: J 194 THR cc_start: 0.8517 (t) cc_final: 0.8211 (p) REVERT: J 231 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6207 (mm-30) REVERT: J 234 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8050 (ttpt) REVERT: J 241 THR cc_start: 0.8205 (m) cc_final: 0.7958 (t) REVERT: J 242 VAL cc_start: 0.8231 (t) cc_final: 0.7859 (p) REVERT: J 251 ASN cc_start: 0.8225 (m-40) cc_final: 0.7894 (m-40) REVERT: J 264 ASP cc_start: 0.7463 (m-30) cc_final: 0.7153 (t0) REVERT: J 273 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7094 (mtt180) REVERT: J 279 LYS cc_start: 0.8305 (tppt) cc_final: 0.8081 (tptp) REVERT: J 364 GLU cc_start: 0.7219 (tt0) cc_final: 0.6985 (tt0) REVERT: J 377 GLU cc_start: 0.7705 (tp30) cc_final: 0.7477 (tp30) REVERT: J 379 ASP cc_start: 0.7694 (m-30) cc_final: 0.7389 (m-30) REVERT: J 384 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6749 (mm-30) REVERT: J 391 THR cc_start: 0.7848 (m) cc_final: 0.7466 (p) REVERT: J 404 GLN cc_start: 0.7508 (mt0) cc_final: 0.7186 (mt0) REVERT: J 405 LEU cc_start: 0.8502 (mt) cc_final: 0.8254 (mt) REVERT: J 413 CYS cc_start: 0.7611 (t) cc_final: 0.7340 (t) REVERT: J 415 LYS cc_start: 0.8575 (tptt) cc_final: 0.8339 (tppp) REVERT: J 430 TYR cc_start: 0.8177 (t80) cc_final: 0.7682 (t80) REVERT: J 436 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6521 (tm-30) REVERT: J 441 GLN cc_start: 0.7119 (mt0) cc_final: 0.6721 (mt0) REVERT: J 445 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7138 (mt-10) outliers start: 94 outliers final: 79 residues processed: 1176 average time/residue: 0.2237 time to fit residues: 391.7606 Evaluate side-chains 1206 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1121 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1980 MET Chi-restraints excluded: chain A residue 1984 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 284 ASN Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 418 LYS Chi-restraints excluded: chain G residue 435 GLU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 414 ARG Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 376 LYS Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 432 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 169 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 326 MET Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 443 MET Chi-restraints excluded: chain J residue 444 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 347 optimal weight: 0.9980 chunk 338 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 281 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 349 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 163 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 319 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN G 284 ASN I 280 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106526 restraints weight = 48482.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.110081 restraints weight = 20986.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111595 restraints weight = 10917.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113287 restraints weight = 7419.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113669 restraints weight = 5202.271| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29053 Z= 0.184 Angle : 0.593 13.136 39245 Z= 0.297 Chirality : 0.044 0.210 4499 Planarity : 0.004 0.095 5042 Dihedral : 7.344 154.626 4020 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.05 % Allowed : 17.30 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.14), residues: 3580 helix: 1.57 (0.13), residues: 1582 sheet: 0.44 (0.20), residues: 618 loop : 0.45 (0.17), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 972 TYR 0.017 0.001 TYR I 192 PHE 0.032 0.001 PHE C 248 TRP 0.006 0.001 TRP H 283 HIS 0.010 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00398 (29045) covalent geometry : angle 0.59164 (39236) hydrogen bonds : bond 0.03829 ( 1224) hydrogen bonds : angle 4.07339 ( 3483) metal coordination : bond 0.02121 ( 8) metal coordination : angle 2.75557 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1132 time to evaluate : 1.086 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 873 MET cc_start: 0.5918 (mmm) cc_final: 0.5352 (mmm) REVERT: A 933 THR cc_start: 0.8290 (m) cc_final: 0.8064 (t) REVERT: A 939 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7229 (mm-40) REVERT: A 966 ARG cc_start: 0.7138 (ttp80) cc_final: 0.6761 (ttp80) REVERT: A 1895 ARG cc_start: 0.7491 (ttp-170) cc_final: 0.7243 (ttp-170) REVERT: A 1900 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7914 (ttp-110) REVERT: A 1902 GLU cc_start: 0.7711 (tp30) cc_final: 0.7482 (tp30) REVERT: A 1906 GLN cc_start: 0.7623 (mm110) cc_final: 0.7291 (mm110) REVERT: A 1934 SER cc_start: 0.8482 (m) cc_final: 0.8051 (p) REVERT: A 1943 PRO cc_start: 0.7767 (Cg_exo) cc_final: 0.7396 (Cg_endo) REVERT: A 1951 TYR cc_start: 0.8226 (m-80) cc_final: 0.7620 (m-80) REVERT: A 1957 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7604 (mtm110) REVERT: A 1973 ILE cc_start: 0.8807 (mt) cc_final: 0.8568 (mm) REVERT: A 2001 PRO cc_start: 0.8424 (Cg_exo) cc_final: 0.8194 (Cg_endo) REVERT: A 2002 ARG cc_start: 0.7605 (mtm180) cc_final: 0.7237 (mtm-85) REVERT: A 2008 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7030 (tt0) REVERT: A 2013 GLU cc_start: 0.7204 (tp30) cc_final: 0.6309 (tp30) REVERT: A 2014 LEU cc_start: 0.8555 (mt) cc_final: 0.8116 (mm) REVERT: A 2019 ARG cc_start: 0.7855 (mtt180) cc_final: 0.7419 (mtt180) REVERT: A 2023 ARG cc_start: 0.7248 (mmm160) cc_final: 0.6887 (mmm160) REVERT: A 2032 PHE cc_start: 0.8308 (m-80) cc_final: 0.8017 (m-80) REVERT: A 2068 MET cc_start: 0.5956 (mtt) cc_final: 0.5739 (mtt) REVERT: A 2071 MET cc_start: 0.6463 (tpp) cc_final: 0.6035 (tpp) REVERT: C 33 LYS cc_start: 0.7381 (mtmm) cc_final: 0.7097 (mtmm) REVERT: C 55 PHE cc_start: 0.8113 (t80) cc_final: 0.7873 (t80) REVERT: C 103 THR cc_start: 0.8344 (m) cc_final: 0.8038 (t) REVERT: C 137 ARG cc_start: 0.7349 (tpp80) cc_final: 0.7060 (tpp80) REVERT: C 138 ASP cc_start: 0.6906 (m-30) cc_final: 0.6655 (m-30) REVERT: C 149 ASP cc_start: 0.7935 (t0) cc_final: 0.7674 (t0) REVERT: C 164 LYS cc_start: 0.7426 (tptm) cc_final: 0.7068 (tptm) REVERT: C 165 LYS cc_start: 0.8753 (ttpp) cc_final: 0.7571 (ptmm) REVERT: C 187 ILE cc_start: 0.8270 (mt) cc_final: 0.7918 (tp) REVERT: C 208 ASP cc_start: 0.7240 (m-30) cc_final: 0.6561 (m-30) REVERT: C 209 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8262 (p) REVERT: C 224 LYS cc_start: 0.8480 (mtpp) cc_final: 0.8215 (ttmt) REVERT: C 230 ASN cc_start: 0.8243 (t0) cc_final: 0.7588 (t0) REVERT: C 234 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7809 (tp) REVERT: C 235 ASP cc_start: 0.6735 (m-30) cc_final: 0.6433 (m-30) REVERT: C 237 VAL cc_start: 0.8824 (t) cc_final: 0.8597 (m) REVERT: C 256 VAL cc_start: 0.8530 (t) cc_final: 0.8018 (p) REVERT: C 286 ASP cc_start: 0.7348 (m-30) cc_final: 0.7105 (m-30) REVERT: C 315 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7610 (ttmm) REVERT: C 341 THR cc_start: 0.8569 (t) cc_final: 0.8032 (p) REVERT: C 364 LYS cc_start: 0.8039 (ptmt) cc_final: 0.7742 (ttpp) REVERT: D 82 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7486 (mtmm) REVERT: D 93 LEU cc_start: 0.8421 (tp) cc_final: 0.8194 (tp) REVERT: E 34 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7709 (tm-30) REVERT: E 40 VAL cc_start: 0.8208 (t) cc_final: 0.7569 (p) REVERT: E 43 GLU cc_start: 0.7628 (mp0) cc_final: 0.7338 (mp0) REVERT: E 47 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6638 (mt-10) REVERT: E 59 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8530 (ttmt) REVERT: E 60 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7797 (mtpp) REVERT: E 90 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8320 (ttmt) REVERT: E 99 SER cc_start: 0.8695 (m) cc_final: 0.8386 (p) REVERT: E 105 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7199 (mt-10) REVERT: E 113 MET cc_start: 0.7244 (tpt) cc_final: 0.6943 (tpt) REVERT: E 132 GLU cc_start: 0.7165 (tt0) cc_final: 0.6890 (tt0) REVERT: E 168 LYS cc_start: 0.8104 (ttmt) cc_final: 0.7550 (ttmt) REVERT: E 200 VAL cc_start: 0.8307 (t) cc_final: 0.8089 (p) REVERT: E 201 LYS cc_start: 0.7917 (tptm) cc_final: 0.7278 (tptm) REVERT: E 209 TYR cc_start: 0.7847 (m-80) cc_final: 0.7196 (m-80) REVERT: E 244 ASP cc_start: 0.6917 (m-30) cc_final: 0.6583 (m-30) REVERT: E 259 MET cc_start: 0.7780 (tpt) cc_final: 0.7532 (tmm) REVERT: E 270 GLU cc_start: 0.7571 (mp0) cc_final: 0.7186 (mt-10) REVERT: E 278 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6661 (mt-10) REVERT: E 285 LYS cc_start: 0.7841 (ttmm) cc_final: 0.7426 (ttmm) REVERT: E 295 VAL cc_start: 0.8438 (t) cc_final: 0.8141 (m) REVERT: E 302 ASP cc_start: 0.6676 (t0) cc_final: 0.6235 (t0) REVERT: E 314 TYR cc_start: 0.8314 (t80) cc_final: 0.6960 (t80) REVERT: E 343 ASP cc_start: 0.6614 (t0) cc_final: 0.6307 (t70) REVERT: E 354 LEU cc_start: 0.8255 (tp) cc_final: 0.7968 (tp) REVERT: E 356 ASP cc_start: 0.7700 (t0) cc_final: 0.7455 (t0) REVERT: E 364 MET cc_start: 0.7638 (mmm) cc_final: 0.7409 (mmm) REVERT: E 371 MET cc_start: 0.8253 (mtt) cc_final: 0.8008 (mtt) REVERT: E 372 LYS cc_start: 0.8445 (mtpt) cc_final: 0.8077 (ttmm) REVERT: E 376 LYS cc_start: 0.8211 (tptt) cc_final: 0.7892 (tptt) REVERT: E 388 GLU cc_start: 0.7345 (tp30) cc_final: 0.6900 (tp30) REVERT: E 396 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7036 (mt-10) REVERT: E 414 ASN cc_start: 0.8225 (t0) cc_final: 0.7953 (t0) REVERT: E 415 LEU cc_start: 0.8457 (mt) cc_final: 0.8168 (mt) REVERT: E 416 LEU cc_start: 0.8511 (mt) cc_final: 0.8187 (mm) REVERT: E 418 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7645 (ttmm) REVERT: E 426 GLU cc_start: 0.7461 (mp0) cc_final: 0.7213 (mp0) REVERT: E 427 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8074 (ttpp) REVERT: E 432 GLU cc_start: 0.7298 (tt0) cc_final: 0.6952 (tt0) REVERT: E 446 ILE cc_start: 0.8174 (mt) cc_final: 0.7920 (mm) REVERT: F 107 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7383 (mt-10) REVERT: F 112 GLU cc_start: 0.6989 (tp30) cc_final: 0.6520 (tp30) REVERT: F 124 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.8132 (mtt-85) REVERT: F 132 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7799 (mmmm) REVERT: F 160 LYS cc_start: 0.7666 (ttpt) cc_final: 0.7447 (ttpt) REVERT: F 162 THR cc_start: 0.8092 (m) cc_final: 0.7621 (p) REVERT: F 170 THR cc_start: 0.8282 (m) cc_final: 0.7823 (t) REVERT: F 180 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7200 (mm-30) REVERT: F 186 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7909 (mtpp) REVERT: F 188 GLN cc_start: 0.7565 (mt0) cc_final: 0.7180 (mt0) REVERT: F 194 THR cc_start: 0.8097 (m) cc_final: 0.7499 (p) REVERT: F 196 ASP cc_start: 0.7537 (t0) cc_final: 0.7170 (t0) REVERT: F 201 LYS cc_start: 0.8207 (tttp) cc_final: 0.7771 (tttp) REVERT: F 214 ASP cc_start: 0.7770 (p0) cc_final: 0.7542 (p0) REVERT: F 236 LYS cc_start: 0.7022 (mmtp) cc_final: 0.6815 (mmtp) REVERT: F 264 ASP cc_start: 0.7640 (t0) cc_final: 0.7077 (t0) REVERT: F 269 LYS cc_start: 0.7987 (mmtp) cc_final: 0.7629 (mmtp) REVERT: F 274 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6720 (mm-30) REVERT: F 288 LYS cc_start: 0.8186 (tttt) cc_final: 0.7611 (tttt) REVERT: F 300 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6492 (mm-30) REVERT: F 314 ARG cc_start: 0.7555 (mmt180) cc_final: 0.6701 (mpt180) REVERT: F 317 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6912 (mt-10) REVERT: F 329 ASN cc_start: 0.8395 (p0) cc_final: 0.8123 (p0) REVERT: F 332 ILE cc_start: 0.8361 (mm) cc_final: 0.8036 (mm) REVERT: F 342 SER cc_start: 0.8835 (t) cc_final: 0.8381 (t) REVERT: F 353 ARG cc_start: 0.7915 (mtt90) cc_final: 0.7431 (mtt90) REVERT: F 415 LYS cc_start: 0.8388 (tptt) cc_final: 0.7887 (tptt) REVERT: F 431 SER cc_start: 0.8442 (m) cc_final: 0.8086 (p) REVERT: F 444 LYS cc_start: 0.8426 (mmtp) cc_final: 0.8070 (mmtp) REVERT: G 43 GLU cc_start: 0.7466 (mp0) cc_final: 0.7038 (mp0) REVERT: G 77 THR cc_start: 0.7989 (m) cc_final: 0.7625 (p) REVERT: G 108 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7663 (mtmt) REVERT: G 110 GLU cc_start: 0.7887 (tp30) cc_final: 0.7575 (tp30) REVERT: G 113 MET cc_start: 0.7687 (tpt) cc_final: 0.7068 (tpt) REVERT: G 123 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7535 (ttm170) REVERT: G 125 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7842 (mttm) REVERT: G 128 LYS cc_start: 0.8588 (tttt) cc_final: 0.8018 (ttmm) REVERT: G 129 GLU cc_start: 0.7295 (tt0) cc_final: 0.6814 (tt0) REVERT: G 131 TYR cc_start: 0.7734 (m-80) cc_final: 0.7236 (m-80) REVERT: G 137 GLU cc_start: 0.7097 (tt0) cc_final: 0.6872 (tt0) REVERT: G 158 ILE cc_start: 0.8536 (mt) cc_final: 0.7654 (tp) REVERT: G 169 GLN cc_start: 0.7767 (mt0) cc_final: 0.7298 (tt0) REVERT: G 171 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8062 (mttm) REVERT: G 176 ILE cc_start: 0.8773 (tp) cc_final: 0.8145 (tp) REVERT: G 178 GLU cc_start: 0.8128 (tt0) cc_final: 0.7248 (tp30) REVERT: G 179 SER cc_start: 0.8491 (t) cc_final: 0.8106 (p) REVERT: G 183 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7365 (mm-30) REVERT: G 192 TYR cc_start: 0.7596 (p90) cc_final: 0.6980 (p90) REVERT: G 203 GLN cc_start: 0.8146 (pt0) cc_final: 0.7864 (tt0) REVERT: G 216 GLU cc_start: 0.7026 (tp30) cc_final: 0.6693 (tp30) REVERT: G 225 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7571 (tppp) REVERT: G 227 ASP cc_start: 0.7599 (t0) cc_final: 0.7160 (t0) REVERT: G 229 HIS cc_start: 0.8140 (t-90) cc_final: 0.7624 (t70) REVERT: G 231 LYS cc_start: 0.8308 (ptmt) cc_final: 0.7877 (ptmt) REVERT: G 244 ASP cc_start: 0.7397 (m-30) cc_final: 0.7019 (m-30) REVERT: G 258 SER cc_start: 0.8011 (m) cc_final: 0.7677 (t) REVERT: G 260 MET cc_start: 0.7200 (mmt) cc_final: 0.6565 (mmt) REVERT: G 265 LYS cc_start: 0.7726 (ttpt) cc_final: 0.7495 (ttpp) REVERT: G 273 ASP cc_start: 0.7412 (m-30) cc_final: 0.7149 (m-30) REVERT: G 278 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6891 (mt-10) REVERT: G 280 ASN cc_start: 0.7996 (m-40) cc_final: 0.7699 (m110) REVERT: G 291 ILE cc_start: 0.8556 (mt) cc_final: 0.8177 (tp) REVERT: G 295 VAL cc_start: 0.8666 (t) cc_final: 0.8388 (p) REVERT: G 303 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7096 (mm-30) REVERT: G 308 ASP cc_start: 0.8014 (p0) cc_final: 0.7197 (p0) REVERT: G 311 CYS cc_start: 0.7900 (m) cc_final: 0.7576 (m) REVERT: G 326 ILE cc_start: 0.8651 (mt) cc_final: 0.8356 (mm) REVERT: G 356 ASP cc_start: 0.7672 (t0) cc_final: 0.7339 (t0) REVERT: G 388 GLU cc_start: 0.6910 (tp30) cc_final: 0.6479 (tp30) REVERT: G 389 GLU cc_start: 0.7287 (pt0) cc_final: 0.7055 (pt0) REVERT: G 392 ASN cc_start: 0.8386 (m-40) cc_final: 0.7526 (m-40) REVERT: G 396 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7032 (mt-10) REVERT: G 430 VAL cc_start: 0.8545 (t) cc_final: 0.8262 (p) REVERT: G 445 LYS cc_start: 0.8109 (mttm) cc_final: 0.7701 (mtpp) REVERT: G 455 MET cc_start: 0.6304 (mmm) cc_final: 0.5892 (mmm) REVERT: H 22 ILE cc_start: 0.8739 (mt) cc_final: 0.8488 (mm) REVERT: H 41 GLN cc_start: 0.8071 (tp40) cc_final: 0.7276 (tm-30) REVERT: H 73 VAL cc_start: 0.8352 (t) cc_final: 0.8047 (p) REVERT: H 94 LEU cc_start: 0.8248 (tp) cc_final: 0.7924 (tt) REVERT: H 107 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7371 (mt-10) REVERT: H 126 SER cc_start: 0.8573 (m) cc_final: 0.7728 (t) REVERT: H 130 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7358 (ttp-110) REVERT: H 146 GLN cc_start: 0.7524 (pt0) cc_final: 0.7309 (pt0) REVERT: H 160 LYS cc_start: 0.8041 (mttt) cc_final: 0.7520 (mttt) REVERT: H 164 LYS cc_start: 0.8427 (pttt) cc_final: 0.7977 (ptmm) REVERT: H 167 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6977 (mt-10) REVERT: H 168 MET cc_start: 0.6836 (mtp) cc_final: 0.6568 (mtp) REVERT: H 169 GLU cc_start: 0.7184 (tt0) cc_final: 0.6714 (tt0) REVERT: H 172 TYR cc_start: 0.8097 (m-80) cc_final: 0.7758 (m-10) REVERT: H 177 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7878 (ptpt) REVERT: H 202 ILE cc_start: 0.8377 (mt) cc_final: 0.8093 (mm) REVERT: H 209 PHE cc_start: 0.8431 (t80) cc_final: 0.7989 (t80) REVERT: H 211 ARG cc_start: 0.7732 (ttt180) cc_final: 0.7410 (ttt180) REVERT: H 218 MET cc_start: 0.7507 (mtp) cc_final: 0.7278 (mtp) REVERT: H 223 LYS cc_start: 0.8674 (pttm) cc_final: 0.8399 (pttp) REVERT: H 236 LYS cc_start: 0.8010 (ttpt) cc_final: 0.7686 (ttpp) REVERT: H 251 ASN cc_start: 0.8406 (m-40) cc_final: 0.8093 (m110) REVERT: H 255 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7358 (tp40) REVERT: H 267 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6852 (mt-10) REVERT: H 269 LYS cc_start: 0.7861 (mtmt) cc_final: 0.7589 (mtmt) REVERT: H 271 GLU cc_start: 0.7326 (mp0) cc_final: 0.7108 (mp0) REVERT: H 282 GLU cc_start: 0.7491 (tt0) cc_final: 0.6788 (tt0) REVERT: H 286 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6586 (mt-10) REVERT: H 292 ILE cc_start: 0.8173 (mt) cc_final: 0.7877 (mt) REVERT: H 295 VAL cc_start: 0.8069 (t) cc_final: 0.7829 (t) REVERT: H 303 MET cc_start: 0.8338 (mmm) cc_final: 0.8125 (mmp) REVERT: H 313 ASN cc_start: 0.7971 (m-40) cc_final: 0.7611 (m-40) REVERT: H 332 ILE cc_start: 0.8095 (mt) cc_final: 0.7829 (mt) REVERT: H 342 SER cc_start: 0.8466 (m) cc_final: 0.8079 (t) REVERT: H 369 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7807 (mm-40) REVERT: H 379 ASP cc_start: 0.7494 (m-30) cc_final: 0.7225 (m-30) REVERT: H 395 LEU cc_start: 0.8295 (mm) cc_final: 0.8021 (mp) REVERT: I 43 GLU cc_start: 0.7509 (mp0) cc_final: 0.6828 (mt-10) REVERT: I 52 ILE cc_start: 0.8440 (mm) cc_final: 0.8216 (mt) REVERT: I 74 THR cc_start: 0.8153 (p) cc_final: 0.7941 (p) REVERT: I 105 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7090 (mt-10) REVERT: I 139 THR cc_start: 0.8159 (m) cc_final: 0.7580 (p) REVERT: I 154 ILE cc_start: 0.7957 (mp) cc_final: 0.7632 (mm) REVERT: I 158 ILE cc_start: 0.8471 (mm) cc_final: 0.8227 (mt) REVERT: I 177 PHE cc_start: 0.8808 (t80) cc_final: 0.8251 (t80) REVERT: I 181 GLN cc_start: 0.7464 (mt0) cc_final: 0.7071 (mt0) REVERT: I 196 ASN cc_start: 0.8218 (p0) cc_final: 0.7923 (p0) REVERT: I 201 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7466 (ttmm) REVERT: I 209 TYR cc_start: 0.7718 (m-80) cc_final: 0.7431 (m-80) REVERT: I 221 VAL cc_start: 0.8665 (t) cc_final: 0.8270 (m) REVERT: I 230 LYS cc_start: 0.7953 (mttp) cc_final: 0.7546 (mttp) REVERT: I 242 ASP cc_start: 0.7803 (m-30) cc_final: 0.7473 (m-30) REVERT: I 268 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7330 (mtmm) REVERT: I 303 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6707 (mm-30) REVERT: I 352 LEU cc_start: 0.8288 (mt) cc_final: 0.8055 (mm) REVERT: I 362 ARG cc_start: 0.8130 (tmm-80) cc_final: 0.7556 (ptm160) REVERT: I 370 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6875 (mt-10) REVERT: I 408 GLN cc_start: 0.7690 (mt0) cc_final: 0.7423 (mt0) REVERT: I 427 LYS cc_start: 0.8523 (tttt) cc_final: 0.8174 (tttm) REVERT: I 443 SER cc_start: 0.8604 (t) cc_final: 0.8197 (m) REVERT: I 455 MET cc_start: 0.6296 (mmm) cc_final: 0.5867 (mmm) REVERT: J 38 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6612 (mm-30) REVERT: J 67 LYS cc_start: 0.8319 (mttm) cc_final: 0.8115 (mttm) REVERT: J 90 MET cc_start: 0.7745 (mtm) cc_final: 0.7485 (mtp) REVERT: J 117 GLU cc_start: 0.7717 (tp30) cc_final: 0.6849 (mm-30) REVERT: J 131 ILE cc_start: 0.8472 (mt) cc_final: 0.8185 (mt) REVERT: J 134 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7100 (mt-10) REVERT: J 135 THR cc_start: 0.8111 (t) cc_final: 0.7834 (m) REVERT: J 136 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6903 (mt-10) REVERT: J 161 LEU cc_start: 0.8545 (tt) cc_final: 0.8335 (tp) REVERT: J 178 MET cc_start: 0.7828 (tpp) cc_final: 0.7208 (tpp) REVERT: J 182 LEU cc_start: 0.8817 (mt) cc_final: 0.8586 (mm) REVERT: J 194 THR cc_start: 0.8523 (t) cc_final: 0.8216 (p) REVERT: J 234 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8047 (ttpt) REVERT: J 241 THR cc_start: 0.8213 (m) cc_final: 0.7966 (t) REVERT: J 242 VAL cc_start: 0.8247 (t) cc_final: 0.7879 (p) REVERT: J 251 ASN cc_start: 0.8227 (m-40) cc_final: 0.7891 (m-40) REVERT: J 264 ASP cc_start: 0.7455 (m-30) cc_final: 0.7149 (t0) REVERT: J 267 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6328 (mt-10) REVERT: J 273 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6907 (mtt180) REVERT: J 364 GLU cc_start: 0.7230 (tt0) cc_final: 0.6994 (tt0) REVERT: J 377 GLU cc_start: 0.7710 (tp30) cc_final: 0.7472 (tp30) REVERT: J 379 ASP cc_start: 0.7703 (m-30) cc_final: 0.7398 (m-30) REVERT: J 384 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6753 (mm-30) REVERT: J 391 THR cc_start: 0.7851 (m) cc_final: 0.7427 (p) REVERT: J 393 ILE cc_start: 0.8497 (mt) cc_final: 0.8259 (tt) REVERT: J 404 GLN cc_start: 0.7525 (mt0) cc_final: 0.7195 (mt0) REVERT: J 413 CYS cc_start: 0.7598 (t) cc_final: 0.7338 (t) REVERT: J 415 LYS cc_start: 0.8564 (tptt) cc_final: 0.8339 (tppp) REVERT: J 430 TYR cc_start: 0.8167 (t80) cc_final: 0.7695 (t80) REVERT: J 436 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6517 (tm-30) REVERT: J 441 GLN cc_start: 0.7163 (mt0) cc_final: 0.6755 (mt0) REVERT: J 445 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7180 (mt-10) outliers start: 95 outliers final: 79 residues processed: 1167 average time/residue: 0.2097 time to fit residues: 364.6267 Evaluate side-chains 1228 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1143 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 1984 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 95 ILE Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 146 GLN Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 318 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 234 ILE Chi-restraints excluded: chain G residue 264 MET Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 418 LYS Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 177 LYS Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 301 VAL Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 414 ARG Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 263 LEU Chi-restraints excluded: chain I residue 376 LYS Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 432 GLU Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 169 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 326 MET Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 383 SER Chi-restraints excluded: chain J residue 407 THR Chi-restraints excluded: chain J residue 443 MET Chi-restraints excluded: chain J residue 444 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 282 optimal weight: 0.8980 chunk 318 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 100 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 327 optimal weight: 0.8980 chunk 86 optimal weight: 0.0570 chunk 115 optimal weight: 1.9990 chunk 142 optimal weight: 0.0070 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2153 HIS ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN F 41 GLN ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 284 ASN G 348 HIS I 34 GLN I 280 ASN I 373 GLN I 392 ASN J 78 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107716 restraints weight = 48333.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111247 restraints weight = 20769.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112721 restraints weight = 11019.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114508 restraints weight = 7429.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114911 restraints weight = 5173.445| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29053 Z= 0.127 Angle : 0.579 12.105 39245 Z= 0.288 Chirality : 0.043 0.218 4499 Planarity : 0.004 0.052 5042 Dihedral : 7.230 156.054 4020 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.60 % Allowed : 18.52 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.14), residues: 3580 helix: 1.67 (0.13), residues: 1568 sheet: 0.51 (0.21), residues: 615 loop : 0.48 (0.17), residues: 1397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 972 TYR 0.016 0.001 TYR F 172 PHE 0.032 0.001 PHE C 248 TRP 0.004 0.001 TRP H 283 HIS 0.009 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00284 (29045) covalent geometry : angle 0.57756 (39236) hydrogen bonds : bond 0.03391 ( 1224) hydrogen bonds : angle 3.97196 ( 3483) metal coordination : bond 0.01549 ( 8) metal coordination : angle 2.65117 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1146 time to evaluate : 0.686 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: A 873 MET cc_start: 0.5945 (mmm) cc_final: 0.5383 (mmm) REVERT: A 933 THR cc_start: 0.8343 (m) cc_final: 0.8069 (t) REVERT: A 939 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7196 (mm-40) REVERT: A 940 ARG cc_start: 0.7328 (ptt-90) cc_final: 0.7094 (ptt90) REVERT: A 957 ARG cc_start: 0.8087 (mtp85) cc_final: 0.7701 (mtp85) REVERT: A 961 ASP cc_start: 0.7256 (m-30) cc_final: 0.6933 (m-30) REVERT: A 1895 ARG cc_start: 0.7441 (ttp-170) cc_final: 0.7192 (ttp-170) REVERT: A 1900 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7915 (ttp-110) REVERT: A 1902 GLU cc_start: 0.7650 (tp30) cc_final: 0.7304 (tp30) REVERT: A 1906 GLN cc_start: 0.7617 (mm110) cc_final: 0.7274 (mm110) REVERT: A 1934 SER cc_start: 0.8496 (m) cc_final: 0.8058 (p) REVERT: A 1943 PRO cc_start: 0.7712 (Cg_exo) cc_final: 0.7338 (Cg_endo) REVERT: A 1951 TYR cc_start: 0.8209 (m-80) cc_final: 0.7615 (m-80) REVERT: A 2001 PRO cc_start: 0.8412 (Cg_exo) cc_final: 0.8194 (Cg_endo) REVERT: A 2008 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7026 (tt0) REVERT: A 2013 GLU cc_start: 0.7241 (tp30) cc_final: 0.6310 (tp30) REVERT: A 2014 LEU cc_start: 0.8559 (mt) cc_final: 0.8136 (mm) REVERT: A 2019 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7393 (mtt180) REVERT: A 2023 ARG cc_start: 0.7301 (mmm160) cc_final: 0.6808 (mmm160) REVERT: A 2032 PHE cc_start: 0.8285 (m-80) cc_final: 0.7984 (m-80) REVERT: A 2068 MET cc_start: 0.5909 (mtt) cc_final: 0.5663 (mtt) REVERT: A 2071 MET cc_start: 0.6361 (tpp) cc_final: 0.5953 (tpp) REVERT: A 2098 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.7030 (mpp80) REVERT: C 33 LYS cc_start: 0.7373 (mtmm) cc_final: 0.7087 (mtmm) REVERT: C 55 PHE cc_start: 0.8048 (t80) cc_final: 0.7800 (t80) REVERT: C 73 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: C 103 THR cc_start: 0.8353 (m) cc_final: 0.8023 (t) REVERT: C 133 HIS cc_start: 0.7888 (t-170) cc_final: 0.7356 (t-90) REVERT: C 137 ARG cc_start: 0.7343 (tpp80) cc_final: 0.7001 (tpp80) REVERT: C 138 ASP cc_start: 0.6864 (m-30) cc_final: 0.6609 (m-30) REVERT: C 149 ASP cc_start: 0.7908 (t0) cc_final: 0.7656 (t0) REVERT: C 158 VAL cc_start: 0.8985 (p) cc_final: 0.8696 (m) REVERT: C 165 LYS cc_start: 0.8642 (ttpp) cc_final: 0.8284 (ptmm) REVERT: C 187 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7869 (tp) REVERT: C 208 ASP cc_start: 0.7209 (m-30) cc_final: 0.6570 (m-30) REVERT: C 224 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8220 (ttmt) REVERT: C 230 ASN cc_start: 0.8244 (t0) cc_final: 0.7610 (t0) REVERT: C 235 ASP cc_start: 0.6803 (m-30) cc_final: 0.6561 (m-30) REVERT: C 237 VAL cc_start: 0.8781 (t) cc_final: 0.8551 (m) REVERT: C 286 ASP cc_start: 0.7303 (m-30) cc_final: 0.7073 (m-30) REVERT: C 315 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7628 (ttmm) REVERT: C 326 PHE cc_start: 0.8511 (m-10) cc_final: 0.8247 (m-80) REVERT: C 341 THR cc_start: 0.8480 (t) cc_final: 0.7887 (p) REVERT: C 358 TYR cc_start: 0.8305 (t80) cc_final: 0.7964 (t80) REVERT: C 364 LYS cc_start: 0.7984 (ptmt) cc_final: 0.7680 (ttpp) REVERT: D 82 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7472 (mtmm) REVERT: D 93 LEU cc_start: 0.8418 (tp) cc_final: 0.8203 (tp) REVERT: E 34 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7783 (tm-30) REVERT: E 40 VAL cc_start: 0.8232 (t) cc_final: 0.7634 (p) REVERT: E 47 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6589 (mt-10) REVERT: E 59 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8504 (ttmt) REVERT: E 60 LYS cc_start: 0.8144 (mtpp) cc_final: 0.7767 (mtpp) REVERT: E 90 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8330 (ttmt) REVERT: E 99 SER cc_start: 0.8714 (m) cc_final: 0.8371 (p) REVERT: E 113 MET cc_start: 0.7168 (tpt) cc_final: 0.6871 (tpt) REVERT: E 132 GLU cc_start: 0.7167 (tt0) cc_final: 0.6932 (tt0) REVERT: E 168 LYS cc_start: 0.8098 (ttmt) cc_final: 0.7536 (ttmt) REVERT: E 200 VAL cc_start: 0.8287 (t) cc_final: 0.8080 (p) REVERT: E 201 LYS cc_start: 0.7913 (tptm) cc_final: 0.7255 (tptm) REVERT: E 209 TYR cc_start: 0.7796 (m-80) cc_final: 0.7279 (m-80) REVERT: E 215 LEU cc_start: 0.8116 (mt) cc_final: 0.7843 (mt) REVERT: E 245 VAL cc_start: 0.8073 (t) cc_final: 0.7673 (p) REVERT: E 259 MET cc_start: 0.7774 (tpt) cc_final: 0.7536 (tmm) REVERT: E 270 GLU cc_start: 0.7426 (mp0) cc_final: 0.7033 (mt-10) REVERT: E 278 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6606 (mt-10) REVERT: E 295 VAL cc_start: 0.8429 (t) cc_final: 0.8117 (m) REVERT: E 302 ASP cc_start: 0.6662 (t0) cc_final: 0.6183 (t0) REVERT: E 303 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6616 (mm-30) REVERT: E 314 TYR cc_start: 0.8262 (t80) cc_final: 0.7052 (t80) REVERT: E 343 ASP cc_start: 0.6629 (t0) cc_final: 0.6319 (t70) REVERT: E 354 LEU cc_start: 0.8219 (tp) cc_final: 0.7936 (tp) REVERT: E 356 ASP cc_start: 0.7719 (t0) cc_final: 0.7482 (t0) REVERT: E 364 MET cc_start: 0.7612 (mmm) cc_final: 0.7409 (mmm) REVERT: E 371 MET cc_start: 0.8217 (mtt) cc_final: 0.7976 (mtt) REVERT: E 372 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8073 (ttmm) REVERT: E 376 LYS cc_start: 0.8199 (tptt) cc_final: 0.7894 (tptt) REVERT: E 388 GLU cc_start: 0.7328 (tp30) cc_final: 0.7038 (tp30) REVERT: E 396 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7000 (mt-10) REVERT: E 414 ASN cc_start: 0.8246 (t0) cc_final: 0.7951 (t0) REVERT: E 415 LEU cc_start: 0.8457 (mt) cc_final: 0.8156 (mt) REVERT: E 416 LEU cc_start: 0.8478 (mt) cc_final: 0.8211 (mm) REVERT: E 418 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7643 (ttmm) REVERT: E 426 GLU cc_start: 0.7484 (mp0) cc_final: 0.6801 (mp0) REVERT: E 427 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8092 (ttpp) REVERT: E 432 GLU cc_start: 0.7290 (tt0) cc_final: 0.6933 (tt0) REVERT: E 446 ILE cc_start: 0.8092 (mt) cc_final: 0.7836 (mm) REVERT: F 107 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7381 (mt-10) REVERT: F 112 GLU cc_start: 0.6982 (tp30) cc_final: 0.6532 (tp30) REVERT: F 124 ARG cc_start: 0.8416 (mtt-85) cc_final: 0.8100 (mtt-85) REVERT: F 132 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7762 (mmmm) REVERT: F 160 LYS cc_start: 0.7658 (ttpt) cc_final: 0.7184 (ttpt) REVERT: F 162 THR cc_start: 0.8095 (m) cc_final: 0.7685 (p) REVERT: F 170 THR cc_start: 0.8231 (m) cc_final: 0.7785 (t) REVERT: F 174 LEU cc_start: 0.7790 (mp) cc_final: 0.7589 (mp) REVERT: F 179 ILE cc_start: 0.8629 (mm) cc_final: 0.8342 (mp) REVERT: F 186 LYS cc_start: 0.8237 (mtpp) cc_final: 0.7910 (mtpp) REVERT: F 188 GLN cc_start: 0.7582 (mt0) cc_final: 0.7193 (mt0) REVERT: F 192 VAL cc_start: 0.8422 (t) cc_final: 0.8060 (m) REVERT: F 194 THR cc_start: 0.8062 (m) cc_final: 0.7831 (t) REVERT: F 196 ASP cc_start: 0.7519 (t0) cc_final: 0.7166 (t0) REVERT: F 201 LYS cc_start: 0.8219 (tttp) cc_final: 0.7698 (tttp) REVERT: F 214 ASP cc_start: 0.7808 (p0) cc_final: 0.7556 (p0) REVERT: F 236 LYS cc_start: 0.6989 (mmtp) cc_final: 0.6776 (mmtp) REVERT: F 264 ASP cc_start: 0.7609 (t0) cc_final: 0.7145 (t0) REVERT: F 269 LYS cc_start: 0.7900 (mmtp) cc_final: 0.7534 (mmtp) REVERT: F 274 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6701 (mm-30) REVERT: F 300 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6666 (mm-30) REVERT: F 314 ARG cc_start: 0.7516 (mmt180) cc_final: 0.6798 (mpt180) REVERT: F 317 GLU cc_start: 0.7329 (mt-10) cc_final: 0.6810 (mt-10) REVERT: F 329 ASN cc_start: 0.8264 (p0) cc_final: 0.7908 (p0) REVERT: F 342 SER cc_start: 0.8827 (t) cc_final: 0.8372 (t) REVERT: F 353 ARG cc_start: 0.7901 (mtt90) cc_final: 0.7342 (ttp-110) REVERT: F 382 MET cc_start: 0.7733 (mtp) cc_final: 0.7408 (mtp) REVERT: F 415 LYS cc_start: 0.8374 (tptt) cc_final: 0.7870 (tptt) REVERT: F 431 SER cc_start: 0.8433 (m) cc_final: 0.8100 (p) REVERT: F 444 LYS cc_start: 0.8424 (mmtp) cc_final: 0.8069 (mmtp) REVERT: G 43 GLU cc_start: 0.7461 (mp0) cc_final: 0.7033 (mp0) REVERT: G 77 THR cc_start: 0.7985 (m) cc_final: 0.7643 (p) REVERT: G 86 GLU cc_start: 0.7703 (tp30) cc_final: 0.7478 (tp30) REVERT: G 108 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7681 (mtmt) REVERT: G 110 GLU cc_start: 0.7858 (tp30) cc_final: 0.7565 (tp30) REVERT: G 113 MET cc_start: 0.7656 (tpt) cc_final: 0.7023 (tpt) REVERT: G 125 LYS cc_start: 0.8125 (mtpt) cc_final: 0.7756 (mttm) REVERT: G 128 LYS cc_start: 0.8571 (tttt) cc_final: 0.8211 (ttmm) REVERT: G 129 GLU cc_start: 0.7285 (tt0) cc_final: 0.6881 (tt0) REVERT: G 131 TYR cc_start: 0.7726 (m-80) cc_final: 0.7244 (m-80) REVERT: G 169 GLN cc_start: 0.7804 (mt0) cc_final: 0.7398 (tt0) REVERT: G 171 LYS cc_start: 0.8636 (mtpt) cc_final: 0.8122 (mttm) REVERT: G 176 ILE cc_start: 0.8764 (tp) cc_final: 0.8151 (tp) REVERT: G 178 GLU cc_start: 0.8115 (tt0) cc_final: 0.7408 (tp30) REVERT: G 179 SER cc_start: 0.8457 (t) cc_final: 0.8097 (p) REVERT: G 183 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7369 (mm-30) REVERT: G 192 TYR cc_start: 0.7599 (p90) cc_final: 0.6995 (p90) REVERT: G 203 GLN cc_start: 0.8187 (pt0) cc_final: 0.7862 (tt0) REVERT: G 216 GLU cc_start: 0.6977 (tp30) cc_final: 0.6655 (tp30) REVERT: G 225 LYS cc_start: 0.7918 (mmmm) cc_final: 0.7520 (tppp) REVERT: G 227 ASP cc_start: 0.7674 (t0) cc_final: 0.7404 (t70) REVERT: G 229 HIS cc_start: 0.8127 (t-90) cc_final: 0.7607 (t70) REVERT: G 231 LYS cc_start: 0.8309 (ptmt) cc_final: 0.7847 (ptmt) REVERT: G 244 ASP cc_start: 0.7373 (m-30) cc_final: 0.7007 (m-30) REVERT: G 258 SER cc_start: 0.8022 (m) cc_final: 0.7680 (t) REVERT: G 260 MET cc_start: 0.7186 (mmt) cc_final: 0.6531 (mmt) REVERT: G 265 LYS cc_start: 0.7787 (ttpt) cc_final: 0.7552 (ttpp) REVERT: G 273 ASP cc_start: 0.7389 (m-30) cc_final: 0.7109 (m-30) REVERT: G 278 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6856 (mt-10) REVERT: G 280 ASN cc_start: 0.7939 (m-40) cc_final: 0.7622 (m110) REVERT: G 291 ILE cc_start: 0.8576 (mt) cc_final: 0.8169 (tp) REVERT: G 295 VAL cc_start: 0.8638 (t) cc_final: 0.8433 (p) REVERT: G 303 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7147 (mm-30) REVERT: G 308 ASP cc_start: 0.8055 (p0) cc_final: 0.7047 (p0) REVERT: G 311 CYS cc_start: 0.7926 (m) cc_final: 0.7525 (m) REVERT: G 326 ILE cc_start: 0.8629 (mt) cc_final: 0.8343 (mm) REVERT: G 327 VAL cc_start: 0.8833 (t) cc_final: 0.8468 (m) REVERT: G 346 SER cc_start: 0.8469 (m) cc_final: 0.8178 (m) REVERT: G 356 ASP cc_start: 0.7661 (t0) cc_final: 0.7330 (t0) REVERT: G 377 ILE cc_start: 0.8451 (mt) cc_final: 0.8118 (mm) REVERT: G 388 GLU cc_start: 0.6914 (tp30) cc_final: 0.6487 (tp30) REVERT: G 389 GLU cc_start: 0.7287 (pt0) cc_final: 0.7046 (pt0) REVERT: G 392 ASN cc_start: 0.8365 (m-40) cc_final: 0.7500 (m-40) REVERT: G 396 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6799 (mt-10) REVERT: G 400 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7319 (mtmm) REVERT: G 441 LYS cc_start: 0.8143 (mttt) cc_final: 0.7838 (mtpp) REVERT: G 445 LYS cc_start: 0.8058 (mttm) cc_final: 0.7692 (mtpp) REVERT: G 455 MET cc_start: 0.6270 (mmm) cc_final: 0.5870 (mmm) REVERT: H 22 ILE cc_start: 0.8727 (mt) cc_final: 0.8454 (mm) REVERT: H 41 GLN cc_start: 0.8073 (tp40) cc_final: 0.7293 (tm-30) REVERT: H 73 VAL cc_start: 0.8320 (t) cc_final: 0.8016 (p) REVERT: H 126 SER cc_start: 0.8557 (m) cc_final: 0.7736 (t) REVERT: H 130 ARG cc_start: 0.7781 (ttp80) cc_final: 0.7371 (ttp-110) REVERT: H 146 GLN cc_start: 0.7484 (pt0) cc_final: 0.7255 (pt0) REVERT: H 160 LYS cc_start: 0.8003 (mttt) cc_final: 0.7471 (mttt) REVERT: H 164 LYS cc_start: 0.8388 (pttt) cc_final: 0.8104 (pttp) REVERT: H 167 GLU cc_start: 0.7254 (mt-10) cc_final: 0.7005 (mt-10) REVERT: H 168 MET cc_start: 0.6821 (mtp) cc_final: 0.6609 (mtp) REVERT: H 172 TYR cc_start: 0.8068 (m-80) cc_final: 0.7835 (m-10) REVERT: H 177 LYS cc_start: 0.8399 (ptpt) cc_final: 0.7831 (ptpt) REVERT: H 202 ILE cc_start: 0.8363 (mt) cc_final: 0.8059 (mm) REVERT: H 209 PHE cc_start: 0.8394 (t80) cc_final: 0.7810 (t80) REVERT: H 211 ARG cc_start: 0.7704 (ttt180) cc_final: 0.7189 (ttt180) REVERT: H 218 MET cc_start: 0.7470 (mtp) cc_final: 0.7230 (mtp) REVERT: H 236 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7733 (ttpp) REVERT: H 251 ASN cc_start: 0.8419 (m-40) cc_final: 0.8130 (m110) REVERT: H 255 GLN cc_start: 0.7600 (mm-40) cc_final: 0.7361 (tp40) REVERT: H 269 LYS cc_start: 0.7792 (mtmt) cc_final: 0.7533 (mtmt) REVERT: H 282 GLU cc_start: 0.7461 (tt0) cc_final: 0.6786 (tt0) REVERT: H 286 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6591 (mt-10) REVERT: H 313 ASN cc_start: 0.7966 (m-40) cc_final: 0.7604 (m-40) REVERT: H 332 ILE cc_start: 0.8088 (mt) cc_final: 0.7824 (mt) REVERT: H 369 GLN cc_start: 0.8029 (tp-100) cc_final: 0.7810 (mm-40) REVERT: H 378 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7748 (mt-10) REVERT: H 379 ASP cc_start: 0.7462 (m-30) cc_final: 0.7174 (m-30) REVERT: H 395 LEU cc_start: 0.8294 (mm) cc_final: 0.8028 (mp) REVERT: H 441 GLN cc_start: 0.7808 (tt0) cc_final: 0.7565 (tt0) REVERT: I 17 SER cc_start: 0.7933 (m) cc_final: 0.7635 (p) REVERT: I 43 GLU cc_start: 0.7419 (mp0) cc_final: 0.6667 (mt-10) REVERT: I 74 THR cc_start: 0.8144 (p) cc_final: 0.7932 (p) REVERT: I 105 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7006 (mt-10) REVERT: I 110 GLU cc_start: 0.7337 (tp30) cc_final: 0.7115 (tp30) REVERT: I 114 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6931 (mt-10) REVERT: I 139 THR cc_start: 0.8058 (m) cc_final: 0.7510 (p) REVERT: I 154 ILE cc_start: 0.7927 (mp) cc_final: 0.7588 (mm) REVERT: I 158 ILE cc_start: 0.8464 (mm) cc_final: 0.8209 (mt) REVERT: I 177 PHE cc_start: 0.8799 (t80) cc_final: 0.8293 (t80) REVERT: I 181 GLN cc_start: 0.7445 (mt0) cc_final: 0.6994 (mt0) REVERT: I 189 ASP cc_start: 0.7995 (m-30) cc_final: 0.7541 (m-30) REVERT: I 196 ASN cc_start: 0.8198 (p0) cc_final: 0.7895 (p0) REVERT: I 201 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7364 (ttmm) REVERT: I 209 TYR cc_start: 0.7725 (m-80) cc_final: 0.7407 (m-80) REVERT: I 221 VAL cc_start: 0.8663 (t) cc_final: 0.8274 (m) REVERT: I 230 LYS cc_start: 0.7963 (mttp) cc_final: 0.7549 (mttp) REVERT: I 242 ASP cc_start: 0.7823 (m-30) cc_final: 0.7489 (m-30) REVERT: I 268 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7410 (mtmm) REVERT: I 303 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6669 (mm-30) REVERT: I 352 LEU cc_start: 0.8259 (mt) cc_final: 0.8028 (mm) REVERT: I 362 ARG cc_start: 0.8133 (tmm-80) cc_final: 0.7791 (ptm160) REVERT: I 370 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6914 (mt-10) REVERT: I 373 GLN cc_start: 0.8126 (mt0) cc_final: 0.7919 (mt0) REVERT: I 408 GLN cc_start: 0.7755 (mt0) cc_final: 0.7473 (mt0) REVERT: I 427 LYS cc_start: 0.8469 (tttt) cc_final: 0.8174 (tttm) REVERT: I 443 SER cc_start: 0.8590 (t) cc_final: 0.8194 (m) REVERT: J 38 GLU cc_start: 0.7010 (mm-30) cc_final: 0.6579 (mm-30) REVERT: J 67 LYS cc_start: 0.8323 (mttm) cc_final: 0.8101 (mttm) REVERT: J 90 MET cc_start: 0.7682 (mtm) cc_final: 0.7431 (mtp) REVERT: J 117 GLU cc_start: 0.7688 (tp30) cc_final: 0.7104 (mm-30) REVERT: J 131 ILE cc_start: 0.8466 (mt) cc_final: 0.8190 (mt) REVERT: J 134 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7081 (mt-10) REVERT: J 135 THR cc_start: 0.8080 (t) cc_final: 0.7835 (m) REVERT: J 136 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6885 (mt-10) REVERT: J 178 MET cc_start: 0.7901 (tpp) cc_final: 0.7298 (tpp) REVERT: J 182 LEU cc_start: 0.8797 (mt) cc_final: 0.8567 (mm) REVERT: J 194 THR cc_start: 0.8529 (t) cc_final: 0.8213 (p) REVERT: J 231 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6068 (mm-30) REVERT: J 234 LYS cc_start: 0.8317 (mtpt) cc_final: 0.8062 (ttpt) REVERT: J 241 THR cc_start: 0.8196 (m) cc_final: 0.7923 (t) REVERT: J 242 VAL cc_start: 0.8192 (t) cc_final: 0.7812 (p) REVERT: J 251 ASN cc_start: 0.8194 (m-40) cc_final: 0.7861 (m-40) REVERT: J 264 ASP cc_start: 0.7404 (m-30) cc_final: 0.7105 (t0) REVERT: J 267 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6285 (mt-10) REVERT: J 273 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6968 (mtt180) REVERT: J 288 LYS cc_start: 0.8193 (mttm) cc_final: 0.7949 (mttp) REVERT: J 364 GLU cc_start: 0.7200 (tt0) cc_final: 0.6984 (tt0) REVERT: J 377 GLU cc_start: 0.7697 (tp30) cc_final: 0.7405 (tp30) REVERT: J 379 ASP cc_start: 0.7694 (m-30) cc_final: 0.7392 (m-30) REVERT: J 384 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6695 (mm-30) REVERT: J 391 THR cc_start: 0.7841 (m) cc_final: 0.7433 (p) REVERT: J 404 GLN cc_start: 0.7433 (mt0) cc_final: 0.7130 (mt0) REVERT: J 413 CYS cc_start: 0.7620 (t) cc_final: 0.7343 (t) REVERT: J 415 LYS cc_start: 0.8496 (tptt) cc_final: 0.8259 (tppp) REVERT: J 430 TYR cc_start: 0.8128 (t80) cc_final: 0.7727 (t80) REVERT: J 436 GLU cc_start: 0.6918 (tm-30) cc_final: 0.6481 (tm-30) REVERT: J 441 GLN cc_start: 0.7115 (mt0) cc_final: 0.6709 (mt0) REVERT: J 445 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7117 (mt-10) outliers start: 81 outliers final: 61 residues processed: 1174 average time/residue: 0.2086 time to fit residues: 363.4649 Evaluate side-chains 1194 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 1128 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 29 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 233 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 435 GLU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 241 THR Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 414 ARG Chi-restraints excluded: chain I residue 34 GLN Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 162 LYS Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 376 LYS Chi-restraints excluded: chain I residue 428 GLU Chi-restraints excluded: chain I residue 432 GLU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 169 GLU Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 270 SER Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 444 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 175 optimal weight: 0.9980 chunk 78 optimal weight: 0.0000 chunk 197 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 346 optimal weight: 0.2980 chunk 306 optimal weight: 0.9980 chunk 273 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 23 optimal weight: 0.0000 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN ** C 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 HIS E 348 HIS ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 GLN G 348 HIS I 280 ASN I 392 ASN J 78 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108578 restraints weight = 48086.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.112251 restraints weight = 20664.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114083 restraints weight = 10876.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115410 restraints weight = 7092.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116114 restraints weight = 5460.402| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29053 Z= 0.116 Angle : 0.586 11.635 39245 Z= 0.291 Chirality : 0.043 0.182 4499 Planarity : 0.004 0.074 5042 Dihedral : 7.161 156.148 4020 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.28 % Allowed : 19.07 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.14), residues: 3580 helix: 1.70 (0.13), residues: 1576 sheet: 0.52 (0.21), residues: 621 loop : 0.54 (0.17), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 972 TYR 0.017 0.001 TYR F 172 PHE 0.032 0.001 PHE C 248 TRP 0.006 0.001 TRP D 152 HIS 0.009 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00262 (29045) covalent geometry : angle 0.58503 (39236) hydrogen bonds : bond 0.03246 ( 1224) hydrogen bonds : angle 3.93882 ( 3483) metal coordination : bond 0.01341 ( 8) metal coordination : angle 2.36566 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7160 Ramachandran restraints generated. 3580 Oldfield, 0 Emsley, 3580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1119 time to evaluate : 0.966 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: A 873 MET cc_start: 0.5953 (mmm) cc_final: 0.5369 (mmm) REVERT: A 933 THR cc_start: 0.8321 (m) cc_final: 0.8073 (t) REVERT: A 939 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7191 (mm-40) REVERT: A 955 VAL cc_start: 0.8605 (t) cc_final: 0.8302 (p) REVERT: A 966 ARG cc_start: 0.7178 (ttp80) cc_final: 0.6897 (ttp80) REVERT: A 1895 ARG cc_start: 0.7459 (ttp-170) cc_final: 0.7204 (ttp-170) REVERT: A 1902 GLU cc_start: 0.7603 (tp30) cc_final: 0.7333 (tp30) REVERT: A 1906 GLN cc_start: 0.7621 (mm110) cc_final: 0.7290 (mm110) REVERT: A 1934 SER cc_start: 0.8476 (m) cc_final: 0.8049 (p) REVERT: A 1943 PRO cc_start: 0.7677 (Cg_exo) cc_final: 0.7308 (Cg_endo) REVERT: A 1951 TYR cc_start: 0.8184 (m-80) cc_final: 0.7612 (m-80) REVERT: A 1973 ILE cc_start: 0.8705 (mt) cc_final: 0.8453 (mm) REVERT: A 2001 PRO cc_start: 0.8388 (Cg_exo) cc_final: 0.8157 (Cg_endo) REVERT: A 2002 ARG cc_start: 0.7589 (mtm180) cc_final: 0.7229 (mtm-85) REVERT: A 2008 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6959 (tt0) REVERT: A 2013 GLU cc_start: 0.7283 (tp30) cc_final: 0.6322 (tp30) REVERT: A 2014 LEU cc_start: 0.8491 (mt) cc_final: 0.8075 (mm) REVERT: A 2019 ARG cc_start: 0.7858 (mtt180) cc_final: 0.7406 (mtt180) REVERT: A 2023 ARG cc_start: 0.7331 (mmm160) cc_final: 0.6955 (mmm160) REVERT: A 2032 PHE cc_start: 0.8281 (m-80) cc_final: 0.7997 (m-80) REVERT: A 2068 MET cc_start: 0.5908 (mtt) cc_final: 0.5681 (mtt) REVERT: A 2071 MET cc_start: 0.6379 (tpp) cc_final: 0.5977 (tpp) REVERT: C 33 LYS cc_start: 0.7402 (mtmm) cc_final: 0.7119 (mtmm) REVERT: C 55 PHE cc_start: 0.8038 (t80) cc_final: 0.7800 (t80) REVERT: C 73 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: C 103 THR cc_start: 0.8348 (m) cc_final: 0.8047 (t) REVERT: C 133 HIS cc_start: 0.7882 (t-170) cc_final: 0.7365 (t-90) REVERT: C 137 ARG cc_start: 0.7343 (tpp80) cc_final: 0.7009 (tpp80) REVERT: C 138 ASP cc_start: 0.6893 (m-30) cc_final: 0.6634 (m-30) REVERT: C 149 ASP cc_start: 0.7908 (t0) cc_final: 0.7647 (t0) REVERT: C 158 VAL cc_start: 0.9000 (p) cc_final: 0.8772 (m) REVERT: C 165 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8352 (ptmm) REVERT: C 187 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7792 (tp) REVERT: C 208 ASP cc_start: 0.7234 (m-30) cc_final: 0.6575 (m-30) REVERT: C 224 LYS cc_start: 0.8410 (mtpp) cc_final: 0.8181 (ttmt) REVERT: C 230 ASN cc_start: 0.8234 (t0) cc_final: 0.7588 (t0) REVERT: C 234 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7779 (tp) REVERT: C 235 ASP cc_start: 0.6764 (m-30) cc_final: 0.6493 (m-30) REVERT: C 237 VAL cc_start: 0.8749 (t) cc_final: 0.8495 (m) REVERT: C 286 ASP cc_start: 0.7305 (m-30) cc_final: 0.7061 (m-30) REVERT: C 315 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7666 (ttmm) REVERT: C 341 THR cc_start: 0.8447 (t) cc_final: 0.7835 (p) REVERT: C 358 TYR cc_start: 0.8300 (t80) cc_final: 0.7984 (t80) REVERT: C 364 LYS cc_start: 0.7964 (ptmt) cc_final: 0.7711 (ttpp) REVERT: C 373 GLU cc_start: 0.7440 (mp0) cc_final: 0.7238 (pm20) REVERT: D 82 LYS cc_start: 0.7772 (mtmm) cc_final: 0.7464 (mtmm) REVERT: D 93 LEU cc_start: 0.8429 (tp) cc_final: 0.8183 (tp) REVERT: E 34 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7752 (tm-30) REVERT: E 40 VAL cc_start: 0.8217 (t) cc_final: 0.7653 (p) REVERT: E 47 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6665 (mt-10) REVERT: E 59 LYS cc_start: 0.8739 (mtpt) cc_final: 0.8488 (ttmt) REVERT: E 60 LYS cc_start: 0.8218 (mtpp) cc_final: 0.7845 (mtpp) REVERT: E 61 MET cc_start: 0.7814 (mmm) cc_final: 0.7582 (mmm) REVERT: E 99 SER cc_start: 0.8713 (m) cc_final: 0.8361 (p) REVERT: E 105 GLU cc_start: 0.7351 (mt-10) cc_final: 0.7120 (mt-10) REVERT: E 113 MET cc_start: 0.7132 (tpt) cc_final: 0.6857 (tpt) REVERT: E 132 GLU cc_start: 0.7178 (tt0) cc_final: 0.6938 (tt0) REVERT: E 168 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7539 (ttmt) REVERT: E 201 LYS cc_start: 0.7847 (tptm) cc_final: 0.7174 (tptm) REVERT: E 209 TYR cc_start: 0.7767 (m-80) cc_final: 0.7211 (m-80) REVERT: E 215 LEU cc_start: 0.8105 (mt) cc_final: 0.7849 (mt) REVERT: E 259 MET cc_start: 0.7807 (tpt) cc_final: 0.7526 (tmm) REVERT: E 270 GLU cc_start: 0.7430 (mp0) cc_final: 0.7035 (mt-10) REVERT: E 278 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6602 (mt-10) REVERT: E 295 VAL cc_start: 0.8398 (t) cc_final: 0.8085 (m) REVERT: E 302 ASP cc_start: 0.6620 (t0) cc_final: 0.6113 (t0) REVERT: E 303 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6625 (mm-30) REVERT: E 314 TYR cc_start: 0.8231 (t80) cc_final: 0.7004 (t80) REVERT: E 343 ASP cc_start: 0.6679 (t0) cc_final: 0.6351 (t70) REVERT: E 354 LEU cc_start: 0.8187 (tp) cc_final: 0.7920 (tp) REVERT: E 371 MET cc_start: 0.8196 (mtt) cc_final: 0.7956 (mtt) REVERT: E 372 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8053 (ttmm) REVERT: E 376 LYS cc_start: 0.8187 (tptt) cc_final: 0.7930 (tptt) REVERT: E 386 ILE cc_start: 0.8538 (tt) cc_final: 0.7988 (pt) REVERT: E 388 GLU cc_start: 0.7320 (tp30) cc_final: 0.6891 (tp30) REVERT: E 396 GLU cc_start: 0.7269 (mt-10) cc_final: 0.6868 (mt-10) REVERT: E 399 THR cc_start: 0.7925 (m) cc_final: 0.7598 (p) REVERT: E 414 ASN cc_start: 0.8293 (t0) cc_final: 0.7943 (t0) REVERT: E 415 LEU cc_start: 0.8456 (mt) cc_final: 0.8164 (mt) REVERT: E 416 LEU cc_start: 0.8477 (mt) cc_final: 0.8117 (mm) REVERT: E 422 LYS cc_start: 0.7521 (mmtp) cc_final: 0.7193 (mmtp) REVERT: E 426 GLU cc_start: 0.7500 (mp0) cc_final: 0.6916 (mp0) REVERT: E 427 LYS cc_start: 0.8446 (ttpp) cc_final: 0.8080 (ttpp) REVERT: E 432 GLU cc_start: 0.7312 (tt0) cc_final: 0.6913 (tt0) REVERT: E 445 LYS cc_start: 0.7721 (mttp) cc_final: 0.7500 (mmtp) REVERT: F 44 GLN cc_start: 0.7900 (mt0) cc_final: 0.7700 (mt0) REVERT: F 107 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7383 (mt-10) REVERT: F 112 GLU cc_start: 0.6939 (tp30) cc_final: 0.6440 (tp30) REVERT: F 124 ARG cc_start: 0.8380 (mtt-85) cc_final: 0.8066 (mtt-85) REVERT: F 132 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7757 (mmmm) REVERT: F 160 LYS cc_start: 0.7667 (ttpt) cc_final: 0.7174 (ttpt) REVERT: F 162 THR cc_start: 0.8086 (m) cc_final: 0.7692 (p) REVERT: F 170 THR cc_start: 0.8218 (m) cc_final: 0.7751 (t) REVERT: F 179 ILE cc_start: 0.8645 (mm) cc_final: 0.8388 (mt) REVERT: F 186 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7894 (mtpp) REVERT: F 188 GLN cc_start: 0.7586 (mt0) cc_final: 0.7252 (mt0) REVERT: F 192 VAL cc_start: 0.8395 (t) cc_final: 0.8028 (m) REVERT: F 194 THR cc_start: 0.7999 (m) cc_final: 0.7399 (p) REVERT: F 196 ASP cc_start: 0.7318 (t0) cc_final: 0.7022 (t0) REVERT: F 201 LYS cc_start: 0.8349 (tttp) cc_final: 0.7873 (tttp) REVERT: F 214 ASP cc_start: 0.7837 (p0) cc_final: 0.7582 (p0) REVERT: F 236 LYS cc_start: 0.7004 (mmtp) cc_final: 0.6760 (mmtp) REVERT: F 262 SER cc_start: 0.8225 (p) cc_final: 0.7892 (t) REVERT: F 264 ASP cc_start: 0.7603 (t0) cc_final: 0.7142 (t0) REVERT: F 269 LYS cc_start: 0.7848 (mmtp) cc_final: 0.7488 (mmtp) REVERT: F 274 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6711 (mm-30) REVERT: F 300 GLU cc_start: 0.7000 (mm-30) cc_final: 0.6534 (mm-30) REVERT: F 314 ARG cc_start: 0.7478 (mmt180) cc_final: 0.6763 (mpt180) REVERT: F 317 GLU cc_start: 0.7284 (mt-10) cc_final: 0.6767 (mt-10) REVERT: F 342 SER cc_start: 0.8819 (t) cc_final: 0.8386 (t) REVERT: F 353 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7322 (ttp-110) REVERT: F 369 GLN cc_start: 0.7968 (tt0) cc_final: 0.7605 (tt0) REVERT: F 382 MET cc_start: 0.7671 (mtp) cc_final: 0.7394 (mtp) REVERT: F 384 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7235 (mm-30) REVERT: F 415 LYS cc_start: 0.8365 (tptt) cc_final: 0.7858 (tptt) REVERT: F 431 SER cc_start: 0.8417 (m) cc_final: 0.8095 (p) REVERT: F 444 LYS cc_start: 0.8424 (mmtp) cc_final: 0.8060 (mmtp) REVERT: G 43 GLU cc_start: 0.7433 (mp0) cc_final: 0.6847 (pm20) REVERT: G 77 THR cc_start: 0.7989 (m) cc_final: 0.7647 (p) REVERT: G 86 GLU cc_start: 0.7718 (tp30) cc_final: 0.7480 (tp30) REVERT: G 108 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7603 (mtmt) REVERT: G 110 GLU cc_start: 0.7858 (tp30) cc_final: 0.7584 (tp30) REVERT: G 113 MET cc_start: 0.7668 (tpt) cc_final: 0.7033 (tpt) REVERT: G 125 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7515 (mmtt) REVERT: G 128 LYS cc_start: 0.8550 (tttt) cc_final: 0.8229 (ttmm) REVERT: G 129 GLU cc_start: 0.7285 (tt0) cc_final: 0.6858 (tt0) REVERT: G 131 TYR cc_start: 0.7712 (m-80) cc_final: 0.7232 (m-80) REVERT: G 169 GLN cc_start: 0.7643 (mt0) cc_final: 0.7392 (mt0) REVERT: G 171 LYS cc_start: 0.8622 (mtpt) cc_final: 0.8079 (mttm) REVERT: G 176 ILE cc_start: 0.8757 (tp) cc_final: 0.8455 (tp) REVERT: G 178 GLU cc_start: 0.8141 (tt0) cc_final: 0.7381 (tp30) REVERT: G 183 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7336 (mm-30) REVERT: G 192 TYR cc_start: 0.7608 (p90) cc_final: 0.6999 (p90) REVERT: G 203 GLN cc_start: 0.8188 (pt0) cc_final: 0.7854 (tt0) REVERT: G 216 GLU cc_start: 0.6958 (tp30) cc_final: 0.6631 (tp30) REVERT: G 225 LYS cc_start: 0.7907 (mmmm) cc_final: 0.7508 (tppp) REVERT: G 227 ASP cc_start: 0.7659 (t0) cc_final: 0.7360 (t70) REVERT: G 229 HIS cc_start: 0.8051 (t-90) cc_final: 0.7474 (t70) REVERT: G 231 LYS cc_start: 0.8329 (ptmt) cc_final: 0.7889 (ptmt) REVERT: G 233 GLU cc_start: 0.7404 (tt0) cc_final: 0.7101 (tt0) REVERT: G 244 ASP cc_start: 0.7386 (m-30) cc_final: 0.7023 (m-30) REVERT: G 258 SER cc_start: 0.7979 (m) cc_final: 0.7663 (t) REVERT: G 260 MET cc_start: 0.7228 (mmt) cc_final: 0.6648 (mmt) REVERT: G 265 LYS cc_start: 0.7809 (ttpt) cc_final: 0.7549 (ttpp) REVERT: G 273 ASP cc_start: 0.7404 (m-30) cc_final: 0.7118 (m-30) REVERT: G 278 GLU cc_start: 0.7231 (mt-10) cc_final: 0.6829 (mt-10) REVERT: G 280 ASN cc_start: 0.7920 (m-40) cc_final: 0.7604 (m110) REVERT: G 291 ILE cc_start: 0.8580 (mt) cc_final: 0.8211 (tp) REVERT: G 295 VAL cc_start: 0.8626 (t) cc_final: 0.8423 (p) REVERT: G 303 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7240 (mm-30) REVERT: G 311 CYS cc_start: 0.7947 (m) cc_final: 0.7583 (m) REVERT: G 326 ILE cc_start: 0.8638 (mt) cc_final: 0.8309 (mm) REVERT: G 327 VAL cc_start: 0.8821 (t) cc_final: 0.8468 (m) REVERT: G 346 SER cc_start: 0.8368 (m) cc_final: 0.7521 (p) REVERT: G 356 ASP cc_start: 0.7656 (t0) cc_final: 0.7231 (t0) REVERT: G 377 ILE cc_start: 0.8432 (mt) cc_final: 0.8096 (mm) REVERT: G 388 GLU cc_start: 0.6953 (tp30) cc_final: 0.6499 (tp30) REVERT: G 389 GLU cc_start: 0.7311 (pt0) cc_final: 0.7061 (pt0) REVERT: G 392 ASN cc_start: 0.8396 (m-40) cc_final: 0.7552 (m-40) REVERT: G 396 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6700 (mt-10) REVERT: G 400 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7303 (mtmm) REVERT: G 441 LYS cc_start: 0.8211 (mttt) cc_final: 0.7907 (mtpp) REVERT: G 445 LYS cc_start: 0.8031 (mttm) cc_final: 0.7628 (mtpp) REVERT: G 455 MET cc_start: 0.6252 (mmm) cc_final: 0.5826 (mmm) REVERT: H 22 ILE cc_start: 0.8721 (mt) cc_final: 0.8462 (mm) REVERT: H 73 VAL cc_start: 0.8290 (t) cc_final: 0.7963 (p) REVERT: H 94 LEU cc_start: 0.8213 (tp) cc_final: 0.7886 (tt) REVERT: H 107 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7358 (mt-10) REVERT: H 126 SER cc_start: 0.8498 (m) cc_final: 0.7674 (t) REVERT: H 130 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7342 (ttp-110) REVERT: H 146 GLN cc_start: 0.7477 (pt0) cc_final: 0.7229 (pt0) REVERT: H 164 LYS cc_start: 0.8382 (pttt) cc_final: 0.8099 (pttp) REVERT: H 172 TYR cc_start: 0.8108 (m-80) cc_final: 0.7804 (m-10) REVERT: H 177 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7820 (ptpt) REVERT: H 202 ILE cc_start: 0.8342 (mt) cc_final: 0.7999 (mm) REVERT: H 207 ARG cc_start: 0.8206 (ptp90) cc_final: 0.7486 (mtm-85) REVERT: H 209 PHE cc_start: 0.8400 (t80) cc_final: 0.7840 (t80) REVERT: H 211 ARG cc_start: 0.7703 (ttt180) cc_final: 0.7188 (ttt180) REVERT: H 218 MET cc_start: 0.7462 (mtp) cc_final: 0.7194 (mtp) REVERT: H 234 LYS cc_start: 0.8689 (mttt) cc_final: 0.8238 (mttt) REVERT: H 236 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7693 (ttpp) REVERT: H 255 GLN cc_start: 0.7640 (mm-40) cc_final: 0.7386 (tp40) REVERT: H 267 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6740 (mt-10) REVERT: H 269 LYS cc_start: 0.7657 (mtmt) cc_final: 0.7409 (mtmt) REVERT: H 282 GLU cc_start: 0.7487 (tt0) cc_final: 0.6808 (tt0) REVERT: H 283 TRP cc_start: 0.8350 (m-10) cc_final: 0.8084 (m-10) REVERT: H 286 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6595 (mt-10) REVERT: H 292 ILE cc_start: 0.8198 (mt) cc_final: 0.7985 (mt) REVERT: H 313 ASN cc_start: 0.7948 (m-40) cc_final: 0.7680 (m-40) REVERT: H 332 ILE cc_start: 0.7966 (mt) cc_final: 0.7724 (mt) REVERT: H 369 GLN cc_start: 0.8035 (tp-100) cc_final: 0.7816 (mm-40) REVERT: H 379 ASP cc_start: 0.7459 (m-30) cc_final: 0.7174 (m-30) REVERT: H 381 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: H 395 LEU cc_start: 0.8304 (mm) cc_final: 0.8018 (mp) REVERT: I 43 GLU cc_start: 0.7389 (mp0) cc_final: 0.6670 (mt-10) REVERT: I 105 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7012 (mt-10) REVERT: I 114 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6977 (mt-10) REVERT: I 139 THR cc_start: 0.8038 (m) cc_final: 0.7490 (p) REVERT: I 154 ILE cc_start: 0.7921 (mp) cc_final: 0.7571 (mm) REVERT: I 158 ILE cc_start: 0.8436 (mm) cc_final: 0.8207 (mt) REVERT: I 177 PHE cc_start: 0.8790 (t80) cc_final: 0.8292 (t80) REVERT: I 181 GLN cc_start: 0.7429 (mt0) cc_final: 0.6995 (mt0) REVERT: I 189 ASP cc_start: 0.7972 (m-30) cc_final: 0.7555 (m-30) REVERT: I 196 ASN cc_start: 0.8191 (p0) cc_final: 0.7863 (p0) REVERT: I 201 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7375 (ttmm) REVERT: I 209 TYR cc_start: 0.7740 (m-80) cc_final: 0.7408 (m-80) REVERT: I 221 VAL cc_start: 0.8662 (t) cc_final: 0.8263 (m) REVERT: I 230 LYS cc_start: 0.7984 (mttp) cc_final: 0.7562 (mttp) REVERT: I 242 ASP cc_start: 0.7803 (m-30) cc_final: 0.7528 (m-30) REVERT: I 268 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7395 (mtmm) REVERT: I 303 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6672 (mm-30) REVERT: I 352 LEU cc_start: 0.8230 (mt) cc_final: 0.7996 (mm) REVERT: I 362 ARG cc_start: 0.8157 (tmm-80) cc_final: 0.7738 (ptm160) REVERT: I 370 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6884 (mt-10) REVERT: I 373 GLN cc_start: 0.8141 (mt0) cc_final: 0.7933 (mt0) REVERT: I 408 GLN cc_start: 0.7774 (mt0) cc_final: 0.7512 (mt0) REVERT: I 427 LYS cc_start: 0.8442 (tttt) cc_final: 0.8144 (ttmm) REVERT: I 443 SER cc_start: 0.8591 (t) cc_final: 0.8159 (m) REVERT: J 38 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6654 (mm-30) REVERT: J 67 LYS cc_start: 0.8327 (mttm) cc_final: 0.8123 (mttm) REVERT: J 117 GLU cc_start: 0.7651 (tp30) cc_final: 0.7006 (mm-30) REVERT: J 131 ILE cc_start: 0.8461 (mt) cc_final: 0.8187 (mt) REVERT: J 134 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7085 (mt-10) REVERT: J 135 THR cc_start: 0.8094 (t) cc_final: 0.7839 (m) REVERT: J 136 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6913 (mt-10) REVERT: J 178 MET cc_start: 0.7938 (tpp) cc_final: 0.7329 (tpp) REVERT: J 182 LEU cc_start: 0.8813 (mt) cc_final: 0.8608 (mm) REVERT: J 194 THR cc_start: 0.8524 (t) cc_final: 0.8217 (p) REVERT: J 231 GLU cc_start: 0.6377 (mm-30) cc_final: 0.6078 (mm-30) REVERT: J 234 LYS cc_start: 0.8292 (mtpt) cc_final: 0.8056 (ttpt) REVERT: J 241 THR cc_start: 0.8172 (m) cc_final: 0.7908 (t) REVERT: J 242 VAL cc_start: 0.8167 (t) cc_final: 0.7781 (p) REVERT: J 251 ASN cc_start: 0.8204 (m-40) cc_final: 0.7898 (m-40) REVERT: J 264 ASP cc_start: 0.7354 (m-30) cc_final: 0.7033 (t0) REVERT: J 267 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6081 (mt-10) REVERT: J 273 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.6838 (mtt180) REVERT: J 288 LYS cc_start: 0.8191 (mttm) cc_final: 0.7941 (mttp) REVERT: J 364 GLU cc_start: 0.7226 (tt0) cc_final: 0.6977 (tt0) REVERT: J 377 GLU cc_start: 0.7692 (tp30) cc_final: 0.7397 (tp30) REVERT: J 379 ASP cc_start: 0.7706 (m-30) cc_final: 0.7404 (m-30) REVERT: J 384 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6620 (mm-30) REVERT: J 391 THR cc_start: 0.7827 (m) cc_final: 0.7439 (p) REVERT: J 404 GLN cc_start: 0.7427 (mt0) cc_final: 0.7108 (mt0) REVERT: J 413 CYS cc_start: 0.7623 (t) cc_final: 0.7362 (t) REVERT: J 415 LYS cc_start: 0.8530 (tptt) cc_final: 0.8284 (tppp) REVERT: J 430 TYR cc_start: 0.8067 (t80) cc_final: 0.7585 (t80) REVERT: J 436 GLU cc_start: 0.6926 (tm-30) cc_final: 0.6475 (tm-30) REVERT: J 441 GLN cc_start: 0.7114 (mt0) cc_final: 0.6706 (mt0) REVERT: J 445 GLU cc_start: 0.7353 (mt-10) cc_final: 0.7089 (mt-10) outliers start: 71 outliers final: 54 residues processed: 1145 average time/residue: 0.2137 time to fit residues: 363.5968 Evaluate side-chains 1168 residues out of total 3110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 1106 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 339 CYS Chi-restraints excluded: chain C residue 383 GLU Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 129 GLU Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 400 LYS Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 96 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 228 VAL Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 435 GLU Chi-restraints excluded: chain G residue 447 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 171 ILE Chi-restraints excluded: chain H residue 177 LYS Chi-restraints excluded: chain H residue 265 THR Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 381 GLU Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 405 LEU Chi-restraints excluded: chain H residue 414 ARG Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 89 SER Chi-restraints excluded: chain I residue 159 ILE Chi-restraints excluded: chain I residue 162 LYS Chi-restraints excluded: chain I residue 203 GLN Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 376 LYS Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 248 ASP Chi-restraints excluded: chain J residue 273 ARG Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 348 ILE Chi-restraints excluded: chain J residue 444 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 93 optimal weight: 0.1980 chunk 108 optimal weight: 0.9980 chunk 276 optimal weight: 0.9980 chunk 186 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 16 optimal weight: 0.0980 chunk 349 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 307 optimal weight: 0.9990 chunk 236 optimal weight: 0.5980 chunk 181 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2009 GLN ** C 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN ** C 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 174 ASN E 316 HIS E 450 GLN F 121 GLN ** F 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 441 GLN G 85 GLN G 348 HIS ** H 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 ASN I 335 ASN I 392 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109074 restraints weight = 48528.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.112355 restraints weight = 20164.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114401 restraints weight = 10712.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.115607 restraints weight = 6897.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.116425 restraints weight = 5236.471| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29053 Z= 0.126 Angle : 0.590 12.303 39245 Z= 0.293 Chirality : 0.043 0.180 4499 Planarity : 0.004 0.049 5042 Dihedral : 7.141 156.438 4020 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.15 % Allowed : 19.84 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.14), residues: 3580 helix: 1.71 (0.13), residues: 1570 sheet: 0.55 (0.21), residues: 610 loop : 0.53 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 972 TYR 0.020 0.001 TYR C 190 PHE 0.033 0.001 PHE C 248 TRP 0.004 0.001 TRP D 152 HIS 0.009 0.001 HIS I 316 Details of bonding type rmsd covalent geometry : bond 0.00285 (29045) covalent geometry : angle 0.58920 (39236) hydrogen bonds : bond 0.03297 ( 1224) hydrogen bonds : angle 3.94314 ( 3483) metal coordination : bond 0.01505 ( 8) metal coordination : angle 2.31107 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6836.53 seconds wall clock time: 117 minutes 58.08 seconds (7078.08 seconds total)