Starting phenix.real_space_refine on Tue Sep 15 15:44:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfx_49376/09_2026/9nfx_49376.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfx_49376/09_2026/9nfx_49376.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nfx_49376/09_2026/9nfx_49376.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfx_49376/09_2026/9nfx_49376.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nfx_49376/09_2026/9nfx_49376.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfx_49376/09_2026/9nfx_49376.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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 234 5.49 5 Mg 5 5.21 5 S 178 5.16 5 C 24701 2.51 5 N 7170 2.21 5 O 8064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40354 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 5767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 703, 5767 Classifications: {'peptide': 703} Link IDs: {'PTRANS': 47, 'TRANS': 655} Chain breaks: 2 Chain: "B" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1015 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 12, 'TRANS': 111} Chain breaks: 3 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: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 570 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 66} 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: "P" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 525 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "S" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "T" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "U" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "V" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 576 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "W" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "X" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "Y" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2207 Classifications: {'DNA': 108} Link IDs: {'rna3p': 107} Chain: "Z" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 2221 Classifications: {'DNA': 108} Link IDs: {'rna3p': 107} Chain: "A" 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: "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 10373 SG CYS D 128 75.216 116.981 64.543 1.00 87.26 S ATOM 10392 SG CYS D 131 71.918 118.361 63.352 1.00 73.92 S ATOM 10532 SG CYS D 149 75.232 120.043 62.274 1.00 95.90 S ATOM 10295 SG CYS D 117 72.670 109.155 56.589 1.00 76.18 S ATOM 10313 SG CYS D 120 73.012 106.806 53.641 1.00 88.56 S ATOM 10430 SG CYS D 136 75.033 106.127 56.691 1.00 73.57 S ATOM 10461 SG CYS D 140 75.851 109.237 54.666 1.00 85.75 S Time building chain proxies: 8.52, per 1000 atoms: 0.21 Number of scatterers: 40354 At special positions: 0 Unit cell: (172.2, 180.4, 162.975, 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 178 16.00 P 234 15.00 Mg 5 11.99 O 8064 8.00 N 7170 7.00 C 24701 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: 3.86 Conformation dependent library (CDL) restraints added in 1.9 seconds 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 128 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 131 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 149 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 117 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 136 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 120 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 140 " Number of angles added : 9 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8430 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 40 sheets defined 51.7% alpha, 11.0% beta 108 base pairs and 197 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 619 through 635 Processing helix chain 'A' and resid 648 through 663 Processing helix chain 'A' and resid 677 through 690 removed outlier: 4.037A pdb=" N ASN A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 731 through 738 removed outlier: 3.930A pdb=" N ARG A 737 " --> pdb=" O GLN A 733 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 756 through 764 removed outlier: 4.397A pdb=" N ASN A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 793 removed outlier: 4.074A pdb=" N LEU A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 removed outlier: 3.705A pdb=" N PHE A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 816 Processing helix chain 'A' and resid 822 through 834 Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'A' and resid 862 through 875 removed outlier: 4.011A pdb=" N GLN A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 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: 3.858A pdb=" N ARG A 945 " --> pdb=" O ASP A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 952 removed outlier: 3.530A pdb=" N GLU A 952 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 962 Processing helix chain 'A' and resid 962 through 968 removed outlier: 3.855A 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 1912 removed outlier: 3.547A pdb=" N GLY A1912 " --> pdb=" O SER A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1918 through 1927 removed outlier: 4.249A pdb=" N VAL A1922 " --> pdb=" O TYR A1918 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 1998 through 2015 Processing helix chain 'A' and resid 2016 through 2020 removed outlier: 3.602A 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 2028 Processing helix chain 'A' and resid 2036 through 2041 Processing helix chain 'A' and resid 2042 through 2058 Processing helix chain 'A' and resid 2068 through 2083 removed outlier: 3.806A pdb=" N LEU A2072 " --> pdb=" O MET A2068 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP A2073 " --> pdb=" O THR A2069 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A2074 " --> pdb=" O ARG A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2108 Processing helix chain 'A' and resid 2141 through 2154 removed outlier: 3.739A pdb=" N ASP A2145 " --> pdb=" O ASN A2141 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS A2152 " --> pdb=" O ALA A2148 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS A2153 " --> pdb=" O GLN A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2191 removed outlier: 3.820A pdb=" N ASN A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET A2185 " --> pdb=" O ASN A2181 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A2186 " --> pdb=" O GLN A2182 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A2187 " --> pdb=" O LYS A2183 " (cutoff:3.500A) Processing helix chain 'A' and resid 2198 through 2203 removed outlier: 3.715A pdb=" N LYS A2202 " --> pdb=" O THR A2198 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 194 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: 3.812A 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 126 through 139 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 Processing helix chain 'C' and resid 251 through 255 Processing helix chain 'C' and resid 272 through 277 removed outlier: 3.766A pdb=" N VAL C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 4.207A 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: 3.674A 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 Processing helix chain 'C' and resid 371 through 376 removed outlier: 3.594A pdb=" N MET C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 394 removed outlier: 4.182A pdb=" N GLU C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N HIS C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N SER C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU C 391 " --> pdb=" O HIS C 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 137 through 148 Processing helix chain 'E' and resid 42 through 59 removed outlier: 3.763A 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: 3.589A pdb=" N VAL E 101 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 3.791A 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: 3.567A 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: 3.850A 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: 3.556A 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 126 removed outlier: 3.521A pdb=" N SER F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 186 Processing helix chain 'F' and resid 244 through 253 removed outlier: 4.118A pdb=" N ARG F 253 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 263 removed outlier: 3.527A pdb=" N ALA F 259 " --> pdb=" O GLN F 255 " (cutoff:3.500A) removed outlier: 4.305A 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: 3.775A 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: 3.897A 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: 3.700A 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: 4.248A 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: 3.596A pdb=" N HIS G 316 " --> pdb=" O PHE G 312 " (cutoff:3.500A) removed outlier: 4.107A 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 removed outlier: 3.516A pdb=" N LYS G 400 " --> pdb=" O GLU G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 409 removed outlier: 3.603A 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 Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 210 through 214 removed outlier: 3.865A pdb=" N ASP H 214 " --> pdb=" O ARG H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 253 removed outlier: 4.176A pdb=" N ARG H 253 " --> pdb=" O VAL H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 269 through 286 Processing helix chain 'H' and resid 301 through 304 Processing helix chain 'H' and resid 305 through 316 removed outlier: 3.755A 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: 3.708A 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 'H' and resid 447 through 450 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: 3.785A 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: 4.019A pdb=" N SER I 179 " --> pdb=" O SER I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 210 No H-bonds generated for 'chain 'I' and resid 208 through 210' Processing helix chain 'I' and resid 240 through 247 Processing helix chain 'I' and resid 255 through 264 removed outlier: 3.592A pdb=" N GLN I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU I 263 " --> pdb=" O MET I 259 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET I 264 " --> pdb=" O MET I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 289 Processing helix chain 'I' and resid 303 through 307 Processing helix chain 'I' and resid 308 through 320 removed outlier: 3.586A pdb=" N ARG I 317 " --> pdb=" O THR I 313 " (cutoff:3.500A) removed outlier: 3.721A 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 Processing helix chain 'J' and resid 175 through 185 Processing helix chain 'J' and resid 244 through 253 removed outlier: 4.097A pdb=" N ARG J 253 " --> pdb=" O VAL J 249 " (cutoff:3.500A) 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: 3.699A 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: 4.141A pdb=" N THR J 407 " --> pdb=" O ILE J 403 " (cutoff:3.500A) removed outlier: 3.602A 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 helix chain 'P' and resid 239 through 256 Processing helix chain 'P' and resid 257 through 267 Processing helix chain 'P' and resid 270 through 297 Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.358A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'S' and resid 90 through 97 Processing helix chain 'S' and resid 112 through 116 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'T' and resid 55 through 84 Processing helix chain 'T' and resid 90 through 102 Processing helix chain 'T' and resid 103 through 125 removed outlier: 3.707A pdb=" N ALA T 107 " --> pdb=" O PRO T 103 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS T 108 " --> pdb=" O GLY T 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 55 Processing helix chain 'U' and resid 63 through 79 removed outlier: 4.050A pdb=" N ASP U 77 " --> pdb=" O GLU U 73 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE U 78 " --> pdb=" O ILE U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 114 Processing helix chain 'U' and resid 120 through 132 removed outlier: 3.538A pdb=" N ILE U 124 " --> pdb=" O MET U 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 24 through 29 removed outlier: 3.901A pdb=" N GLN V 27 " --> pdb=" O ASP V 24 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 41 Processing helix chain 'V' and resid 49 through 76 removed outlier: 3.737A pdb=" N GLU V 53 " --> pdb=" O LEU V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 93 Processing helix chain 'W' and resid 44 through 57 Processing helix chain 'W' and resid 63 through 79 removed outlier: 4.241A pdb=" N ASP W 77 " --> pdb=" O GLU W 73 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE W 78 " --> pdb=" O ILE W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 85 through 113 Processing helix chain 'W' and resid 120 through 132 Processing helix chain 'X' and resid 24 through 29 removed outlier: 3.768A pdb=" N GLN X 27 " --> pdb=" O ASP X 24 " (cutoff:3.500A) Processing helix chain 'X' and resid 30 through 41 Processing helix chain 'X' and resid 49 through 76 removed outlier: 3.691A pdb=" N GLU X 53 " --> pdb=" O LEU X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 695 through 697 removed outlier: 6.498A pdb=" N HIS A 670 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N THR A 723 " --> pdb=" O HIS A 670 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 672 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG A 741 " --> pdb=" O ARG A 769 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N LEU A 771 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU A 743 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N LEU A 773 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU A 745 " --> pdb=" O LEU A 773 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY A 639 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG A 840 " --> pdb=" O ALA A 642 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 852 through 859 removed outlier: 6.332A pdb=" N TYR A 853 " --> pdb=" O ILE A2163 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ARG A2165 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N HIS A 855 " --> pdb=" O ARG A2165 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N ILE A2167 " --> pdb=" O HIS A 855 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE A 857 " --> pdb=" O ILE A2167 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A2133 " --> pdb=" O TYR A2164 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N LEU A2166 " --> pdb=" O VAL A2133 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE A2135 " --> pdb=" O LEU A2166 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N SER A2168 " --> pdb=" O PHE A2135 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A2063 " --> pdb=" O VAL A2134 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A2062 " --> pdb=" O PHE A2114 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LEU A2116 " --> pdb=" O VAL A2062 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A2064 " --> pdb=" O LEU A2116 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER A2117 " --> pdb=" O LEU A2089 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 916 through 917 removed outlier: 5.955A pdb=" N PHE A 916 " --> pdb=" O GLU A1984 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 922 through 924 Processing sheet with id=AA5, 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: 4.378A 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: 3.796A 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: 5.349A pdb=" N VAL G 221 " --> pdb=" O GLN G 203 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG G 205 " --> pdb=" O VAL G 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AA7, first strand: chain 'C' and resid 23 through 26 removed outlier: 4.482A pdb=" N ASN C 8 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 121 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 41 Processing sheet with id=AA9, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AB1, first strand: chain 'C' and resid 171 through 173 removed outlier: 6.415A pdb=" N ILE C 146 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 320 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL C 148 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 317 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 248 through 249 removed outlier: 3.542A pdb=" N PHE C 248 " --> pdb=" O VAL C 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 126 through 127 Processing sheet with id=AB4, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.236A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER E 331 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU E 68 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ALA E 65 " --> pdb=" O MET E 359 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE E 361 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU E 67 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 121 through 141 removed outlier: 5.782A pdb=" N VAL E 135 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS E 162 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU E 137 " --> pdb=" O GLY E 160 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 157 " --> pdb=" O LEU E 172 " (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: 5.460A pdb=" N VAL E 221 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARG E 205 " --> pdb=" O VAL E 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 336 through 337 Processing sheet with id=AB7, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB8, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.595A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY F 77 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR F 359 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA F 76 " --> pdb=" O THR F 359 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 332 through 334 Processing sheet with id=AC1, first strand: chain 'G' and resid 35 through 36 Processing sheet with id=AC2, first strand: chain 'G' and resid 93 through 97 removed outlier: 6.394A pdb=" N CYS G 94 " --> pdb=" O PHE G 300 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP G 302 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N MET G 96 " --> pdb=" O ASP G 302 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL G 66 " --> pdb=" O PHE G 329 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N SER G 331 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU G 68 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA G 65 " --> pdb=" O MET G 359 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE G 361 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU G 67 " --> pdb=" O ILE G 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 336 through 337 Processing sheet with id=AC4, first strand: chain 'H' and resid 42 through 43 Processing sheet with id=AC5, first strand: chain 'H' and resid 100 through 104 removed outlier: 6.377A pdb=" N THR H 101 " --> pdb=" O PHE H 297 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASP H 299 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE H 103 " --> pdb=" O ASP H 299 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY H 77 " --> pdb=" O THR H 328 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA H 72 " --> pdb=" O LEU H 355 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL H 357 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU H 74 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR H 359 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA H 76 " --> pdb=" O THR H 359 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 127 through 148 removed outlier: 6.751A pdb=" N THR H 162 " --> pdb=" O VAL H 143 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE H 145 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS H 160 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ILE H 147 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N VAL H 158 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.878A 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=AC7, first strand: chain 'H' and resid 333 through 334 Processing sheet with id=AC8, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AC9, first strand: chain 'I' and resid 93 through 97 removed outlier: 6.176A pdb=" N CYS I 94 " --> pdb=" O PHE I 300 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ASP I 302 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N MET I 96 " --> pdb=" O ASP I 302 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL I 66 " --> pdb=" O PHE I 329 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N SER I 331 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU I 68 " --> pdb=" O SER I 331 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA I 65 " --> pdb=" O MET I 359 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ILE I 361 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU I 67 " --> pdb=" O ILE I 361 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 121 through 141 removed outlier: 6.256A pdb=" N GLY I 160 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU I 138 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE I 158 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 6.867A 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: 5.141A pdb=" N VAL I 221 " --> pdb=" O GLN I 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ARG I 205 " --> pdb=" O VAL I 221 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 336 through 337 Processing sheet with id=AD3, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AD4, first strand: chain 'J' and resid 100 through 104 removed outlier: 6.452A pdb=" N THR J 101 " --> pdb=" O PHE J 297 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP J 299 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE J 103 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU J 296 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N ALA J 327 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE J 298 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA J 72 " --> pdb=" O LEU J 355 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N VAL J 357 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU J 74 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR J 359 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA J 76 " --> pdb=" O THR J 359 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 127 through 148 removed outlier: 6.717A pdb=" N THR J 162 " --> pdb=" O VAL J 143 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE J 145 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS J 160 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N ILE J 147 " --> pdb=" O VAL J 158 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL J 158 " --> pdb=" O ILE J 147 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 169 through 173 current: chain 'J' and resid 202 through 207 Processing sheet with id=AD6, first strand: chain 'J' and resid 333 through 334 Processing sheet with id=AD7, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.407A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'S' and resid 77 through 78 Processing sheet with id=AD9, first strand: chain 'S' and resid 101 through 102 removed outlier: 6.972A pdb=" N THR S 101 " --> pdb=" O TYR X 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'U' and resid 83 through 84 removed outlier: 7.177A pdb=" N ARG U 83 " --> pdb=" O VAL V 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'U' and resid 118 through 119 Processing sheet with id=AE3, first strand: chain 'W' and resid 83 through 84 removed outlier: 6.983A pdb=" N ARG W 83 " --> pdb=" O VAL X 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'W' and resid 118 through 119 1673 hydrogen bonds defined for protein. 4812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 562 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 197 stacking parallelities Total time for adding SS restraints: 12.19 Time building geometry restraints manager: 4.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 13251 1.36 - 1.51: 11603 1.51 - 1.65: 16324 1.65 - 1.80: 167 1.80 - 1.95: 126 Bond restraints: 41471 Sorted by residual: bond pdb=" O3B AGS A3301 " pdb=" PB AGS A3301 " ideal model delta sigma weight residual 1.673 1.571 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" O3B AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C3' DC Y -64 " pdb=" C2' DC Y -64 " ideal model delta sigma weight residual 1.516 1.552 -0.036 8.00e-03 1.56e+04 2.08e+01 bond pdb=" O3A AGS A3301 " pdb=" PA AGS A3301 " ideal model delta sigma weight residual 1.664 1.577 0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" O3A AGS C 401 " pdb=" PA AGS C 401 " ideal model delta sigma weight residual 1.664 1.579 0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 41466 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.92: 56467 2.92 - 5.84: 398 5.84 - 8.76: 25 8.76 - 11.68: 22 11.68 - 14.60: 10 Bond angle restraints: 56922 Sorted by residual: angle pdb=" O4' DG Z -33 " pdb=" C4' DG Z -33 " pdb=" C3' DG Z -33 " ideal model delta sigma weight residual 106.00 102.28 3.72 6.00e-01 2.78e+00 3.84e+01 angle pdb=" O4' DC Z -20 " pdb=" C1' DC Z -20 " pdb=" N1 DC Z -20 " ideal model delta sigma weight residual 108.00 112.27 -4.27 7.00e-01 2.04e+00 3.72e+01 angle pdb=" O5' DG Z -19 " pdb=" C5' DG Z -19 " pdb=" C4' DG Z -19 " ideal model delta sigma weight residual 109.40 114.21 -4.81 8.00e-01 1.56e+00 3.62e+01 angle pdb=" O5' DG Z -18 " pdb=" C5' DG Z -18 " pdb=" C4' DG Z -18 " ideal model delta sigma weight residual 109.40 113.94 -4.54 8.00e-01 1.56e+00 3.22e+01 angle pdb=" O5' DA Y -69 " pdb=" C5' DA Y -69 " pdb=" C4' DA Y -69 " ideal model delta sigma weight residual 109.40 113.55 -4.15 8.00e-01 1.56e+00 2.69e+01 ... (remaining 56917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 23478 35.20 - 70.41: 1287 70.41 - 105.61: 59 105.61 - 140.82: 4 140.82 - 176.02: 10 Dihedral angle restraints: 24838 sinusoidal: 11789 harmonic: 13049 Sorted by residual: dihedral pdb=" O1B ADP J 501 " pdb=" O3A ADP J 501 " pdb=" PB ADP J 501 " pdb=" PA ADP J 501 " ideal model delta sinusoidal sigma weight residual -60.00 109.55 -169.55 1 2.00e+01 2.50e-03 4.76e+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 300.00 157.50 142.51 1 2.00e+01 2.50e-03 4.30e+01 dihedral pdb=" O1B ADP H 501 " pdb=" O3A ADP H 501 " pdb=" PB ADP H 501 " pdb=" PA ADP H 501 " ideal model delta sinusoidal sigma weight residual 300.00 161.32 138.68 1 2.00e+01 2.50e-03 4.20e+01 ... (remaining 24835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 6255 0.111 - 0.223: 198 0.223 - 0.334: 9 0.334 - 0.445: 12 0.445 - 0.556: 5 Chirality restraints: 6479 Sorted by residual: chirality pdb=" P DT Z -23 " pdb=" OP1 DT Z -23 " pdb=" OP2 DT Z -23 " pdb=" O5' DT Z -23 " both_signs ideal model delta sigma weight residual True 2.34 -2.89 -0.56 2.00e-01 2.50e+01 7.74e+00 chirality pdb=" P DT Y 31 " pdb=" OP1 DT Y 31 " pdb=" OP2 DT Y 31 " pdb=" O5' DT Y 31 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.75e+00 chirality pdb=" P DT Z -29 " pdb=" OP1 DT Z -29 " pdb=" OP2 DT Z -29 " pdb=" O5' DT Z -29 " both_signs ideal model delta sigma weight residual True 2.34 -2.84 -0.51 2.00e-01 2.50e+01 6.45e+00 ... (remaining 6476 not shown) Planarity restraints: 6519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC Y 21 " -0.035 2.00e-02 2.50e+03 2.53e-02 1.44e+01 pdb=" N1 DC Y 21 " 0.062 2.00e-02 2.50e+03 pdb=" C2 DC Y 21 " -0.024 2.00e-02 2.50e+03 pdb=" O2 DC Y 21 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DC Y 21 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC Y 21 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC Y 21 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC Y 21 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DC Y 21 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT Y 31 " -0.047 2.00e-02 2.50e+03 2.32e-02 1.34e+01 pdb=" N1 DT Y 31 " 0.052 2.00e-02 2.50e+03 pdb=" C2 DT Y 31 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT Y 31 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DT Y 31 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT Y 31 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT Y 31 " -0.015 2.00e-02 2.50e+03 pdb=" C5 DT Y 31 " -0.003 2.00e-02 2.50e+03 pdb=" C7 DT Y 31 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT Y 31 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA Y 23 " 0.011 2.00e-02 2.50e+03 2.16e-02 1.28e+01 pdb=" N9 DA Y 23 " -0.056 2.00e-02 2.50e+03 pdb=" C8 DA Y 23 " 0.042 2.00e-02 2.50e+03 pdb=" N7 DA Y 23 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DA Y 23 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA Y 23 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA Y 23 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA Y 23 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DA Y 23 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DA Y 23 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DA Y 23 " 0.001 2.00e-02 2.50e+03 ... (remaining 6516 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 135 2.53 - 3.12: 29820 3.12 - 3.72: 65137 3.72 - 4.31: 93176 4.31 - 4.90: 150405 Nonbonded interactions: 338673 Sorted by model distance: nonbonded pdb=" O2G AGS A3301 " pdb="MG MG A3302 " model vdw 1.940 2.170 nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 1.960 2.170 nonbonded pdb=" O2B ADP F 501 " pdb="MG MG F 502 " model vdw 1.961 2.170 nonbonded pdb=" O1B ADP J 501 " pdb="MG MG J 502 " model vdw 2.002 2.170 nonbonded pdb=" OG1 THR F 84 " pdb="MG MG F 502 " model vdw 2.013 2.170 ... (remaining 338668 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)) } ncs_group { reference = (chain 'U' and resid 39 through 134) selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 49.480 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.004 0.102 41479 Z= 0.306 Angle : 0.688 14.605 56931 Z= 0.445 Chirality : 0.052 0.556 6479 Planarity : 0.007 0.100 6519 Dihedral : 18.651 176.020 16408 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.03 % Allowed : 0.15 % Favored : 99.82 % 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 are not related in a simple way. whole: 1.37 (0.12), residues: 4461 helix: 1.40 (0.11), residues: 2156 sheet: 0.75 (0.20), residues: 679 loop : 0.50 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.002 ARG A2154 TYR 0.026 0.002 TYR D 126 PHE 0.053 0.001 PHE H 123 TRP 0.027 0.002 TRP A 712 HIS 0.005 0.001 HIS X 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.31 (41471) covalent geometry : angle 0.68718 / 0.44 (56922) hydrogen bonds : bond 0.14187 / 9.31 ( 1954) hydrogen bonds : angle 4.87276 / 3.50 ( 5374) metal coordination : bond 0.01090 / 0.50 ( 8) metal coordination : angle 2.28850 / 1.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1600 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1599 time to evaluate : 1.494 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 628 TRP cc_start: 0.8559 (t60) cc_final: 0.7889 (t60) REVERT: A 632 MET cc_start: 0.8180 (mmm) cc_final: 0.7634 (mmm) REVERT: A 636 LYS cc_start: 0.8403 (mttt) cc_final: 0.8196 (mttt) REVERT: A 640 ILE cc_start: 0.8256 (mt) cc_final: 0.7974 (mp) REVERT: A 643 ASP cc_start: 0.7642 (m-30) cc_final: 0.7330 (m-30) REVERT: A 644 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7629 (mp0) REVERT: A 659 HIS cc_start: 0.8545 (t-90) cc_final: 0.8073 (t70) REVERT: A 694 LYS cc_start: 0.8421 (mttt) cc_final: 0.8015 (mttt) REVERT: A 703 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8196 (mtpp) REVERT: A 704 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6890 (mt-10) REVERT: A 719 HIS cc_start: 0.8004 (m170) cc_final: 0.7472 (m90) REVERT: A 746 ASP cc_start: 0.8916 (t0) cc_final: 0.8710 (t0) REVERT: A 764 ASN cc_start: 0.8801 (m-40) cc_final: 0.8254 (t0) REVERT: A 768 GLN cc_start: 0.8430 (mt0) cc_final: 0.8080 (mt0) REVERT: A 789 MET cc_start: 0.7630 (mmp) cc_final: 0.7165 (mmp) REVERT: A 792 LEU cc_start: 0.8150 (mt) cc_final: 0.7895 (mt) REVERT: A 830 HIS cc_start: 0.7050 (m90) cc_final: 0.6829 (m90) REVERT: A 851 LYS cc_start: 0.8940 (mmtp) cc_final: 0.8571 (mmtp) REVERT: A 870 ASP cc_start: 0.8712 (t0) cc_final: 0.8397 (t0) REVERT: A 871 ASP cc_start: 0.8550 (t0) cc_final: 0.8055 (t70) REVERT: A 892 ASN cc_start: 0.8482 (m110) cc_final: 0.8216 (m110) REVERT: A 947 ASP cc_start: 0.7976 (t0) cc_final: 0.7758 (t0) REVERT: A 958 TYR cc_start: 0.8239 (t80) cc_final: 0.7737 (t80) REVERT: A 964 LEU cc_start: 0.8574 (mt) cc_final: 0.8328 (mm) REVERT: A 966 ARG cc_start: 0.8126 (mtp85) cc_final: 0.7798 (mtp-110) REVERT: A 975 LEU cc_start: 0.8163 (mt) cc_final: 0.7911 (mt) REVERT: A 992 MET cc_start: 0.2668 (ttm) cc_final: 0.1892 (ttm) REVERT: A 1891 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 1893 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7858 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8302 (ptpp) cc_final: 0.7872 (ptpp) REVERT: A 1897 ARG cc_start: 0.8171 (ttp-170) cc_final: 0.7764 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8136 (ttm110) cc_final: 0.7923 (ttp-170) REVERT: A 1934 SER cc_start: 0.8273 (m) cc_final: 0.7888 (p) REVERT: A 1936 ILE cc_start: 0.8861 (mm) cc_final: 0.8267 (mt) REVERT: A 1948 PHE cc_start: 0.8666 (t80) cc_final: 0.8401 (t80) REVERT: A 1953 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7466 (mm-30) REVERT: A 1957 ARG cc_start: 0.8184 (mtp180) cc_final: 0.7964 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7747 (tp30) cc_final: 0.6927 (tp30) REVERT: A 2025 VAL cc_start: 0.8163 (t) cc_final: 0.7871 (m) REVERT: A 2026 CYS cc_start: 0.8282 (m) cc_final: 0.7853 (m) REVERT: A 2028 MET cc_start: 0.8362 (mtt) cc_final: 0.8127 (mtp) REVERT: A 2041 ASP cc_start: 0.8377 (m-30) cc_final: 0.8170 (m-30) REVERT: A 2058 GLU cc_start: 0.7372 (pt0) cc_final: 0.7090 (pt0) REVERT: A 2094 ARG cc_start: 0.7705 (mtp85) cc_final: 0.7305 (mtm-85) REVERT: A 2104 ARG cc_start: 0.8426 (ttp80) cc_final: 0.8199 (mtp85) REVERT: A 2160 ASP cc_start: 0.8245 (m-30) cc_final: 0.7951 (m-30) REVERT: A 2164 TYR cc_start: 0.8880 (m-80) cc_final: 0.8677 (m-80) REVERT: A 2169 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7741 (mt-10) REVERT: A 2179 LYS cc_start: 0.8511 (tppp) cc_final: 0.8120 (ttmm) REVERT: A 2185 MET cc_start: 0.6853 (ttm) cc_final: 0.6515 (ttm) REVERT: A 2196 PHE cc_start: 0.7866 (m-80) cc_final: 0.7601 (m-80) REVERT: B 133 MET cc_start: 0.6084 (mmt) cc_final: 0.5495 (mmt) REVERT: C 12 ASN cc_start: 0.8522 (m-40) cc_final: 0.8305 (m110) REVERT: C 14 LYS cc_start: 0.8612 (mppt) cc_final: 0.8217 (mppt) REVERT: C 38 LYS cc_start: 0.7817 (tttt) cc_final: 0.7341 (tttt) REVERT: C 55 PHE cc_start: 0.7464 (t80) cc_final: 0.7003 (t80) REVERT: C 67 ASN cc_start: 0.8947 (t0) cc_final: 0.8676 (t0) REVERT: C 71 GLN cc_start: 0.7964 (tp40) cc_final: 0.7574 (tp-100) REVERT: C 72 ARG cc_start: 0.8744 (tpp80) cc_final: 0.8192 (tpp80) REVERT: C 76 ASP cc_start: 0.8225 (m-30) cc_final: 0.7751 (m-30) REVERT: C 86 VAL cc_start: 0.8753 (t) cc_final: 0.8296 (m) REVERT: C 90 ASP cc_start: 0.8399 (t0) cc_final: 0.7572 (t0) REVERT: C 92 ASN cc_start: 0.8295 (m-40) cc_final: 0.8018 (m-40) REVERT: C 103 THR cc_start: 0.8760 (m) cc_final: 0.8488 (p) REVERT: C 116 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7876 (mp0) REVERT: C 164 LYS cc_start: 0.7718 (tptm) cc_final: 0.7476 (tptm) REVERT: C 196 MET cc_start: 0.8360 (mmm) cc_final: 0.7568 (mmm) REVERT: C 204 GLN cc_start: 0.8731 (tp40) cc_final: 0.8025 (tp40) REVERT: C 208 ASP cc_start: 0.8046 (m-30) cc_final: 0.7607 (m-30) REVERT: C 218 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7523 (ttp80) REVERT: C 229 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8306 (pt0) REVERT: C 230 ASN cc_start: 0.8575 (t0) cc_final: 0.8139 (t0) REVERT: C 233 MET cc_start: 0.8022 (ttp) cc_final: 0.7248 (ttp) REVERT: C 235 ASP cc_start: 0.8767 (m-30) cc_final: 0.8521 (m-30) REVERT: C 250 LYS cc_start: 0.8971 (mtpp) cc_final: 0.8606 (mtpp) REVERT: C 252 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7775 (mtp85) REVERT: C 255 MET cc_start: 0.7702 (ttm) cc_final: 0.7455 (ttm) REVERT: C 366 ILE cc_start: 0.9030 (tt) cc_final: 0.8781 (tt) REVERT: E 15 ILE cc_start: 0.8652 (mm) cc_final: 0.8389 (mm) REVERT: E 17 SER cc_start: 0.8168 (m) cc_final: 0.7931 (p) REVERT: E 22 LYS cc_start: 0.8287 (mmtp) cc_final: 0.7948 (mmtp) REVERT: E 28 GLU cc_start: 0.7637 (mp0) cc_final: 0.7073 (mp0) REVERT: E 57 LYS cc_start: 0.8360 (mttt) cc_final: 0.8072 (mttp) REVERT: E 85 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8111 (mm-40) REVERT: E 96 MET cc_start: 0.8561 (ptm) cc_final: 0.8323 (ptm) REVERT: E 105 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8103 (mt-10) REVERT: E 134 GLU cc_start: 0.7466 (tt0) cc_final: 0.7193 (tt0) REVERT: E 137 GLU cc_start: 0.7917 (tt0) cc_final: 0.7716 (tt0) REVERT: E 158 ILE cc_start: 0.8422 (mt) cc_final: 0.8197 (mm) REVERT: E 162 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7797 (ptmm) REVERT: E 165 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7620 (mmtt) REVERT: E 167 THR cc_start: 0.8290 (m) cc_final: 0.7914 (p) REVERT: E 168 LYS cc_start: 0.8295 (ttmt) cc_final: 0.7836 (ttmt) REVERT: E 178 GLU cc_start: 0.8037 (tt0) cc_final: 0.7761 (tt0) REVERT: E 181 GLN cc_start: 0.7929 (mt0) cc_final: 0.7622 (mt0) REVERT: E 182 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7617 (mtmt) REVERT: E 183 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7728 (mm-30) REVERT: E 184 ARG cc_start: 0.7595 (mtm-85) cc_final: 0.7180 (mtm-85) REVERT: E 212 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7437 (mm-30) REVERT: E 214 ASP cc_start: 0.7981 (m-30) cc_final: 0.7767 (m-30) REVERT: E 230 LYS cc_start: 0.8277 (mttt) cc_final: 0.8030 (mttt) REVERT: E 236 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8359 (mm110) REVERT: E 262 GLN cc_start: 0.7433 (mt0) cc_final: 0.7124 (mm-40) REVERT: E 286 TYR cc_start: 0.8271 (m-10) cc_final: 0.7799 (m-80) REVERT: E 314 TYR cc_start: 0.8150 (t80) cc_final: 0.7773 (t80) REVERT: E 356 ASP cc_start: 0.7708 (t0) cc_final: 0.7356 (t0) REVERT: E 357 ARG cc_start: 0.8165 (mtt90) cc_final: 0.7934 (mtt90) REVERT: E 370 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7900 (mt-10) REVERT: E 389 GLU cc_start: 0.7617 (tt0) cc_final: 0.7338 (tt0) REVERT: E 397 ILE cc_start: 0.8068 (mt) cc_final: 0.7862 (tt) REVERT: E 400 LYS cc_start: 0.7921 (ptpt) cc_final: 0.7673 (mtmm) REVERT: E 405 TYR cc_start: 0.8663 (t80) cc_final: 0.8417 (t80) REVERT: E 408 GLN cc_start: 0.7856 (mt0) cc_final: 0.7543 (mt0) REVERT: E 426 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7632 (mm-30) REVERT: E 439 ASP cc_start: 0.7357 (p0) cc_final: 0.6947 (p0) REVERT: E 441 LYS cc_start: 0.8234 (mttt) cc_final: 0.7872 (mttt) REVERT: E 445 LYS cc_start: 0.7745 (mmtp) cc_final: 0.7462 (mmtp) REVERT: F 40 ARG cc_start: 0.8136 (mtt90) cc_final: 0.7822 (mtt90) REVERT: F 112 GLU cc_start: 0.7863 (tp30) cc_final: 0.7535 (tp30) REVERT: F 117 GLU cc_start: 0.8195 (tp30) cc_final: 0.7514 (mm-30) REVERT: F 142 VAL cc_start: 0.8196 (t) cc_final: 0.7759 (m) REVERT: F 160 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7898 (mtpt) REVERT: F 163 LEU cc_start: 0.8035 (mt) cc_final: 0.7715 (mt) REVERT: F 178 MET cc_start: 0.7971 (tpp) cc_final: 0.7601 (tpp) REVERT: F 182 LEU cc_start: 0.8891 (mt) cc_final: 0.8601 (mm) REVERT: F 192 VAL cc_start: 0.8479 (t) cc_final: 0.8031 (p) REVERT: F 201 LYS cc_start: 0.8457 (tttp) cc_final: 0.8222 (tttp) REVERT: F 248 ASP cc_start: 0.7831 (m-30) cc_final: 0.7619 (m-30) REVERT: F 267 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7152 (mt-10) REVERT: F 268 ILE cc_start: 0.8347 (mt) cc_final: 0.8085 (mt) REVERT: F 269 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8372 (mmtp) REVERT: F 271 GLU cc_start: 0.7741 (mp0) cc_final: 0.7527 (mp0) REVERT: F 274 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7620 (mm-30) REVERT: F 279 LYS cc_start: 0.8549 (tppp) cc_final: 0.8339 (tppt) REVERT: F 286 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7782 (pt0) REVERT: F 303 MET cc_start: 0.8574 (mmm) cc_final: 0.8205 (mmp) REVERT: F 317 GLU cc_start: 0.7593 (mt-10) cc_final: 0.6992 (mt-10) REVERT: F 320 MET cc_start: 0.8021 (mmt) cc_final: 0.7780 (mmp) REVERT: F 326 MET cc_start: 0.8241 (mtt) cc_final: 0.8025 (mtm) REVERT: F 341 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8101 (mt0) REVERT: F 392 ARG cc_start: 0.8091 (ttp-110) cc_final: 0.7867 (ttp-170) REVERT: F 415 LYS cc_start: 0.8345 (tptt) cc_final: 0.8084 (tppt) REVERT: F 441 GLN cc_start: 0.7465 (mm-40) cc_final: 0.7264 (mm-40) REVERT: F 446 TYR cc_start: 0.7973 (m-80) cc_final: 0.7592 (m-80) REVERT: G 15 ILE cc_start: 0.8926 (mt) cc_final: 0.8673 (mm) REVERT: G 34 GLN cc_start: 0.8308 (tm-30) cc_final: 0.8064 (tm-30) REVERT: G 61 MET cc_start: 0.8568 (mmt) cc_final: 0.8124 (mmm) REVERT: G 85 GLN cc_start: 0.8421 (mm110) cc_final: 0.8197 (mm-40) REVERT: G 86 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7746 (mm-30) REVERT: G 89 SER cc_start: 0.8236 (m) cc_final: 0.7932 (t) REVERT: G 90 LYS cc_start: 0.8460 (tptm) cc_final: 0.8162 (tptm) REVERT: G 96 MET cc_start: 0.7883 (ttp) cc_final: 0.7603 (ttt) REVERT: G 102 TYR cc_start: 0.8406 (m-80) cc_final: 0.8040 (m-80) REVERT: G 110 GLU cc_start: 0.8170 (tp30) cc_final: 0.7707 (mm-30) REVERT: G 113 MET cc_start: 0.8349 (tpt) cc_final: 0.8106 (tpp) REVERT: G 125 LYS cc_start: 0.8270 (mtmt) cc_final: 0.7831 (mtmt) REVERT: G 126 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7380 (mt-10) REVERT: G 128 LYS cc_start: 0.8207 (tttt) cc_final: 0.7929 (tttt) REVERT: G 129 GLU cc_start: 0.7106 (tt0) cc_final: 0.6876 (tt0) REVERT: G 147 MET cc_start: 0.6411 (mtp) cc_final: 0.5960 (mtp) REVERT: G 162 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8191 (ttmm) REVERT: G 169 GLN cc_start: 0.8453 (mt0) cc_final: 0.8248 (mt0) REVERT: G 171 LYS cc_start: 0.7809 (mtpt) cc_final: 0.7396 (tttp) REVERT: G 178 GLU cc_start: 0.7950 (tt0) cc_final: 0.7345 (tt0) REVERT: G 186 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7613 (mt-10) REVERT: G 193 ILE cc_start: 0.8604 (mt) cc_final: 0.8265 (mm) REVERT: G 209 TYR cc_start: 0.8312 (m-80) cc_final: 0.7984 (m-10) REVERT: G 227 ASP cc_start: 0.7685 (t0) cc_final: 0.7466 (t0) REVERT: G 233 GLU cc_start: 0.8021 (tt0) cc_final: 0.7319 (tt0) REVERT: G 244 ASP cc_start: 0.7412 (m-30) cc_final: 0.7141 (m-30) REVERT: G 268 LYS cc_start: 0.7867 (mttt) cc_final: 0.7643 (mttt) REVERT: G 280 ASN cc_start: 0.8016 (m-40) cc_final: 0.7812 (m-40) REVERT: G 323 ILE cc_start: 0.8748 (mt) cc_final: 0.8504 (mm) REVERT: G 362 ARG cc_start: 0.8264 (ttp80) cc_final: 0.8021 (ttt-90) REVERT: G 385 ASN cc_start: 0.8135 (m-40) cc_final: 0.7927 (m-40) REVERT: G 408 GLN cc_start: 0.7969 (mt0) cc_final: 0.7733 (mt0) REVERT: G 420 ASN cc_start: 0.7936 (t0) cc_final: 0.7721 (t0) REVERT: G 428 GLU cc_start: 0.7984 (mp0) cc_final: 0.7729 (mp0) REVERT: G 455 MET cc_start: 0.7159 (mmm) cc_final: 0.6852 (mmm) REVERT: H 18 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7333 (mtp85) REVERT: H 26 SER cc_start: 0.8760 (m) cc_final: 0.8456 (p) REVERT: H 33 LEU cc_start: 0.8389 (mt) cc_final: 0.8152 (mt) REVERT: H 38 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7575 (mm-30) REVERT: H 83 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8299 (mtmm) REVERT: H 132 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8166 (ttmm) REVERT: H 144 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7453 (mm-30) REVERT: H 160 LYS cc_start: 0.8245 (mttt) cc_final: 0.7948 (mttt) REVERT: H 186 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8190 (ttpt) REVERT: H 201 LYS cc_start: 0.8590 (ptmt) cc_final: 0.8366 (ptmt) REVERT: H 204 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8523 (mtmm) REVERT: H 214 ASP cc_start: 0.7329 (p0) cc_final: 0.7105 (p0) REVERT: H 237 GLU cc_start: 0.7974 (tt0) cc_final: 0.7740 (tt0) REVERT: H 238 VAL cc_start: 0.8171 (t) cc_final: 0.7873 (p) REVERT: H 264 ASP cc_start: 0.7977 (t0) cc_final: 0.7696 (t0) REVERT: H 269 LYS cc_start: 0.8364 (mtmt) cc_final: 0.8088 (mtmt) REVERT: H 271 GLU cc_start: 0.7897 (mp0) cc_final: 0.7692 (mp0) REVERT: H 275 GLN cc_start: 0.8233 (mm110) cc_final: 0.7995 (mm110) REVERT: H 277 ASN cc_start: 0.8652 (m-40) cc_final: 0.8299 (m-40) REVERT: H 279 LYS cc_start: 0.8471 (tppt) cc_final: 0.8249 (tptp) REVERT: H 285 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7532 (mt-10) REVERT: H 303 MET cc_start: 0.8068 (mmp) cc_final: 0.7810 (mmm) REVERT: H 305 ASP cc_start: 0.7563 (m-30) cc_final: 0.7338 (m-30) REVERT: H 307 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7486 (mm-30) REVERT: H 314 ARG cc_start: 0.7392 (mmt180) cc_final: 0.6940 (mmt180) REVERT: H 317 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7357 (mt-10) REVERT: H 326 MET cc_start: 0.8348 (mtm) cc_final: 0.8124 (mtp) REVERT: H 369 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8184 (mt0) REVERT: H 417 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8238 (mtmt) REVERT: H 443 MET cc_start: 0.8371 (ttm) cc_final: 0.8154 (ttm) REVERT: H 452 PHE cc_start: 0.8579 (m-80) cc_final: 0.8205 (m-80) REVERT: I 17 SER cc_start: 0.8622 (m) cc_final: 0.8265 (t) REVERT: I 31 LEU cc_start: 0.8074 (mt) cc_final: 0.7831 (mm) REVERT: I 43 GLU cc_start: 0.8183 (mp0) cc_final: 0.7909 (mp0) REVERT: I 61 MET cc_start: 0.8276 (mmm) cc_final: 0.7883 (mmm) REVERT: I 105 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7608 (mt-10) REVERT: I 125 LYS cc_start: 0.8634 (ttpp) cc_final: 0.8317 (ttmm) REVERT: I 134 GLU cc_start: 0.7890 (tt0) cc_final: 0.7631 (tt0) REVERT: I 139 THR cc_start: 0.8727 (m) cc_final: 0.8293 (p) REVERT: I 171 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8530 (ttmm) REVERT: I 184 ARG cc_start: 0.8381 (mtt180) cc_final: 0.8179 (mtt180) REVERT: I 218 GLU cc_start: 0.7839 (tp30) cc_final: 0.7612 (tp30) REVERT: I 225 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7753 (mtpp) REVERT: I 231 LYS cc_start: 0.8377 (mttt) cc_final: 0.8118 (mtpp) REVERT: I 249 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7740 (mtp85) REVERT: I 259 MET cc_start: 0.8486 (mtp) cc_final: 0.8186 (mtp) REVERT: I 269 THR cc_start: 0.8470 (p) cc_final: 0.8215 (p) REVERT: I 270 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7473 (mt-10) REVERT: I 281 LYS cc_start: 0.8723 (mttt) cc_final: 0.8492 (mtmt) REVERT: I 288 ASP cc_start: 0.7499 (m-30) cc_final: 0.6982 (m-30) REVERT: I 302 ASP cc_start: 0.8219 (t0) cc_final: 0.7676 (t0) REVERT: I 308 ASP cc_start: 0.8138 (p0) cc_final: 0.7801 (p0) REVERT: I 310 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7834 (mt-10) REVERT: I 322 SER cc_start: 0.8627 (p) cc_final: 0.8116 (t) REVERT: I 336 CYS cc_start: 0.8727 (p) cc_final: 0.8502 (p) REVERT: I 415 LEU cc_start: 0.8154 (mt) cc_final: 0.7943 (mt) REVERT: I 426 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7608 (mm-30) REVERT: I 438 TYR cc_start: 0.8361 (m-80) cc_final: 0.7901 (m-80) REVERT: I 439 ASP cc_start: 0.8158 (p0) cc_final: 0.7821 (p0) REVERT: I 441 LYS cc_start: 0.8247 (mttm) cc_final: 0.7747 (mtmm) REVERT: I 445 LYS cc_start: 0.8217 (tppt) cc_final: 0.7270 (tppt) REVERT: J 17 THR cc_start: 0.8222 (m) cc_final: 0.7953 (t) REVERT: J 38 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7403 (tp30) REVERT: J 78 GLN cc_start: 0.8510 (mt0) cc_final: 0.8309 (mt0) REVERT: J 86 ILE cc_start: 0.8643 (mm) cc_final: 0.8353 (mp) REVERT: J 90 MET cc_start: 0.8502 (mtm) cc_final: 0.8271 (mtm) REVERT: J 92 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8107 (mm-40) REVERT: J 115 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7935 (mttp) REVERT: J 133 GLU cc_start: 0.8056 (pt0) cc_final: 0.7845 (pt0) REVERT: J 136 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7418 (mt-10) REVERT: J 139 GLU cc_start: 0.7958 (tt0) cc_final: 0.7743 (tt0) REVERT: J 144 GLU cc_start: 0.8016 (tt0) cc_final: 0.7811 (tt0) REVERT: J 180 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7164 (mt-10) REVERT: J 183 THR cc_start: 0.8259 (m) cc_final: 0.8012 (p) REVERT: J 184 LYS cc_start: 0.7994 (mttp) cc_final: 0.7718 (mttp) REVERT: J 185 ASP cc_start: 0.7287 (t0) cc_final: 0.7013 (t0) REVERT: J 192 VAL cc_start: 0.8681 (t) cc_final: 0.8250 (p) REVERT: J 201 LYS cc_start: 0.8306 (tptm) cc_final: 0.8071 (tmtt) REVERT: J 225 VAL cc_start: 0.8520 (t) cc_final: 0.8189 (p) REVERT: J 231 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7141 (mm-30) REVERT: J 234 LYS cc_start: 0.8555 (mtpt) cc_final: 0.8299 (ttmm) REVERT: J 236 LYS cc_start: 0.8397 (mtpt) cc_final: 0.8110 (mmmm) REVERT: J 255 GLN cc_start: 0.8336 (mm110) cc_final: 0.8083 (mm-40) REVERT: J 267 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7300 (mt-10) REVERT: J 270 SER cc_start: 0.8278 (p) cc_final: 0.8029 (t) REVERT: J 279 LYS cc_start: 0.8498 (tppt) cc_final: 0.8277 (tppp) REVERT: J 320 MET cc_start: 0.7877 (mmt) cc_final: 0.7673 (mmt) REVERT: J 326 MET cc_start: 0.8402 (mtm) cc_final: 0.8160 (mtp) REVERT: J 353 ARG cc_start: 0.7759 (mtt-85) cc_final: 0.7511 (mtm-85) REVERT: J 368 LYS cc_start: 0.8537 (ttmt) cc_final: 0.8216 (ttmm) REVERT: J 376 GLU cc_start: 0.7980 (tt0) cc_final: 0.7755 (tt0) REVERT: J 377 GLU cc_start: 0.7920 (tp30) cc_final: 0.7499 (tp30) REVERT: J 382 MET cc_start: 0.8492 (mtt) cc_final: 0.8238 (mtt) REVERT: J 430 TYR cc_start: 0.8687 (t80) cc_final: 0.8427 (t80) REVERT: J 436 GLU cc_start: 0.7002 (tm-30) cc_final: 0.6480 (tm-30) REVERT: J 443 MET cc_start: 0.8119 (ttp) cc_final: 0.7916 (ttp) REVERT: J 444 LYS cc_start: 0.8355 (mttm) cc_final: 0.8059 (mttm) REVERT: J 447 GLN cc_start: 0.8158 (pt0) cc_final: 0.7927 (pt0) REVERT: P 250 SER cc_start: 0.8890 (m) cc_final: 0.8227 (p) REVERT: P 252 LYS cc_start: 0.8582 (mttt) cc_final: 0.8215 (mttp) REVERT: P 254 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7316 (mt-10) REVERT: S 77 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.7775 (mtt90) REVERT: S 87 VAL cc_start: 0.8908 (t) cc_final: 0.8643 (p) REVERT: S 95 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8875 (ttmt) REVERT: T 43 LYS cc_start: 0.8691 (mttt) cc_final: 0.8471 (mtmm) REVERT: T 68 ASP cc_start: 0.8064 (t0) cc_final: 0.7616 (t0) REVERT: T 79 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7477 (mtm110) REVERT: T 115 THR cc_start: 0.8487 (t) cc_final: 0.8169 (p) REVERT: T 120 LYS cc_start: 0.8481 (tttp) cc_final: 0.8248 (tttp) REVERT: U 93 GLN cc_start: 0.8966 (tt0) cc_final: 0.8714 (tt0) REVERT: U 106 ASP cc_start: 0.8241 (m-30) cc_final: 0.7779 (m-30) REVERT: V 57 VAL cc_start: 0.9151 (t) cc_final: 0.8911 (p) REVERT: V 58 LEU cc_start: 0.9160 (tp) cc_final: 0.8946 (tp) REVERT: V 64 ASN cc_start: 0.8794 (m-40) cc_final: 0.8462 (m-40) REVERT: V 68 ASP cc_start: 0.8736 (m-30) cc_final: 0.8410 (m-30) REVERT: V 87 VAL cc_start: 0.9026 (t) cc_final: 0.8757 (m) REVERT: W 54 TYR cc_start: 0.8592 (m-80) cc_final: 0.8286 (m-10) REVERT: W 56 LYS cc_start: 0.8733 (mttp) cc_final: 0.8523 (tppp) REVERT: W 90 MET cc_start: 0.8444 (mmm) cc_final: 0.8213 (mmp) REVERT: W 120 MET cc_start: 0.8320 (mtt) cc_final: 0.7808 (mtp) REVERT: W 123 ASP cc_start: 0.8230 (m-30) cc_final: 0.8014 (m-30) REVERT: W 128 ARG cc_start: 0.8831 (mtp180) cc_final: 0.8624 (mtp-110) REVERT: X 39 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8440 (mmt-90) REVERT: X 40 ARG cc_start: 0.9022 (ttm170) cc_final: 0.8792 (ttm170) REVERT: X 84 MET cc_start: 0.8308 (tpt) cc_final: 0.8010 (mmm) REVERT: X 91 LYS cc_start: 0.8756 (tttt) cc_final: 0.8555 (ttmm) outliers start: 1 outliers final: 0 residues processed: 1599 average time/residue: 0.3007 time to fit residues: 746.0842 Evaluate side-chains 1432 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1432 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 432 optimal weight: 0.8980 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 0.5980 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 702 GLN A 739 ASN D 91 GLN E 115 ASN E 169 GLN E 289 GLN ** E 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 GLN F 188 GLN F 277 ASN G 262 GLN G 316 HIS G 380 GLN G 414 ASN H 240 HIS ** H 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 GLN I 247 ASN I 385 ASN I 408 GLN J 341 GLN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 GLN T 63 ASN U 108 ASN W 39 HIS X 27 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.119829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.100577 restraints weight = 65927.713| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.83 r_work: 0.3114 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41479 Z= 0.160 Angle : 0.606 7.290 56931 Z= 0.324 Chirality : 0.045 0.331 6479 Planarity : 0.004 0.061 6519 Dihedral : 20.861 178.218 7413 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.36 % Allowed : 10.28 % Favored : 88.36 % 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 are not related in a simple way. whole: 1.73 (0.13), residues: 4461 helix: 1.79 (0.11), residues: 2178 sheet: 0.77 (0.20), residues: 670 loop : 0.57 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 314 TYR 0.014 0.001 TYR A2136 PHE 0.025 0.001 PHE A 718 TRP 0.026 0.001 TRP C 360 HIS 0.006 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (41471) covalent geometry : angle 0.60556 / 0.32 (56922) hydrogen bonds : bond 0.04674 / 3.15 ( 1954) hydrogen bonds : angle 4.03126 / 2.91 ( 5374) metal coordination : bond 0.00681 / 0.29 ( 8) metal coordination : angle 1.16460 / 0.63 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1504 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1451 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 ARG cc_start: 0.8336 (ttm110) cc_final: 0.8092 (mtt-85) REVERT: A 643 ASP cc_start: 0.7695 (m-30) cc_final: 0.7463 (m-30) REVERT: A 694 LYS cc_start: 0.8577 (mttt) cc_final: 0.8259 (mttt) REVERT: A 704 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6577 (mt-10) REVERT: A 719 HIS cc_start: 0.7985 (m170) cc_final: 0.7585 (m-70) REVERT: A 722 ILE cc_start: 0.8220 (mt) cc_final: 0.7917 (mm) REVERT: A 727 LEU cc_start: 0.9039 (mt) cc_final: 0.8735 (mm) REVERT: A 747 GLU cc_start: 0.8104 (mp0) cc_final: 0.7796 (mm-30) REVERT: A 749 GLN cc_start: 0.8463 (pm20) cc_final: 0.8020 (pm20) REVERT: A 751 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8479 (tp) REVERT: A 764 ASN cc_start: 0.8667 (m-40) cc_final: 0.8433 (t0) REVERT: A 789 MET cc_start: 0.7373 (mmp) cc_final: 0.7042 (mmm) REVERT: A 792 LEU cc_start: 0.8160 (mt) cc_final: 0.7938 (mt) REVERT: A 851 LYS cc_start: 0.9022 (mmtp) cc_final: 0.8709 (mmtp) REVERT: A 870 ASP cc_start: 0.8698 (t0) cc_final: 0.8415 (t0) REVERT: A 871 ASP cc_start: 0.8347 (t0) cc_final: 0.8017 (t70) REVERT: A 892 ASN cc_start: 0.8689 (m110) cc_final: 0.8393 (m110) REVERT: A 918 THR cc_start: 0.8564 (p) cc_final: 0.8318 (m) REVERT: A 958 TYR cc_start: 0.8427 (t80) cc_final: 0.8128 (t80) REVERT: A 966 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7819 (mtp-110) REVERT: A 975 LEU cc_start: 0.8452 (mt) cc_final: 0.8169 (mt) REVERT: A 992 MET cc_start: 0.2489 (ttm) cc_final: 0.1675 (ttm) REVERT: A 1891 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7620 (tm-30) REVERT: A 1893 ARG cc_start: 0.8484 (mtt180) cc_final: 0.8103 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8528 (ptpp) cc_final: 0.8153 (ptpp) REVERT: A 1895 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7860 (ttp-170) REVERT: A 1897 ARG cc_start: 0.8199 (ttp-170) cc_final: 0.7847 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8241 (ttp-170) REVERT: A 1921 GLU cc_start: 0.8215 (mp0) cc_final: 0.7842 (mp0) REVERT: A 1934 SER cc_start: 0.8437 (m) cc_final: 0.8197 (p) REVERT: A 1936 ILE cc_start: 0.8984 (mm) cc_final: 0.8430 (mt) REVERT: A 1953 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7674 (mm-30) REVERT: A 1957 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8132 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7869 (tp30) cc_final: 0.7057 (tp30) REVERT: A 2026 CYS cc_start: 0.8447 (m) cc_final: 0.8089 (m) REVERT: A 2028 MET cc_start: 0.8588 (mtt) cc_final: 0.8366 (mtp) REVERT: A 2036 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7752 (ttp80) REVERT: A 2150 ASP cc_start: 0.8014 (m-30) cc_final: 0.7572 (m-30) REVERT: A 2185 MET cc_start: 0.6825 (ttm) cc_final: 0.6277 (ppp) REVERT: A 2189 MET cc_start: 0.7749 (mtt) cc_final: 0.7021 (mtt) REVERT: A 2196 PHE cc_start: 0.7852 (m-80) cc_final: 0.7602 (m-80) REVERT: B 133 MET cc_start: 0.5886 (mmt) cc_final: 0.5378 (mmt) REVERT: C 2 THR cc_start: 0.7643 (t) cc_final: 0.7194 (m) REVERT: C 14 LYS cc_start: 0.8759 (mppt) cc_final: 0.8213 (mppt) REVERT: C 67 ASN cc_start: 0.8937 (t0) cc_final: 0.8715 (t0) REVERT: C 72 ARG cc_start: 0.8731 (tpp80) cc_final: 0.8070 (tpp80) REVERT: C 76 ASP cc_start: 0.8143 (m-30) cc_final: 0.7612 (m-30) REVERT: C 83 MET cc_start: 0.8323 (mmm) cc_final: 0.8031 (mmm) REVERT: C 86 VAL cc_start: 0.8781 (t) cc_final: 0.8437 (m) REVERT: C 90 ASP cc_start: 0.7971 (t0) cc_final: 0.7313 (t0) REVERT: C 103 THR cc_start: 0.8697 (m) cc_final: 0.8357 (p) REVERT: C 107 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7889 (mm-30) REVERT: C 115 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8022 (mt-10) REVERT: C 120 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7884 (tm-30) REVERT: C 164 LYS cc_start: 0.7684 (tptm) cc_final: 0.7469 (tptm) REVERT: C 204 GLN cc_start: 0.8566 (tp40) cc_final: 0.7883 (tp40) REVERT: C 208 ASP cc_start: 0.7965 (m-30) cc_final: 0.7547 (m-30) REVERT: C 220 MET cc_start: 0.8316 (tpp) cc_final: 0.8092 (mmt) REVERT: C 230 ASN cc_start: 0.8577 (t0) cc_final: 0.8056 (t0) REVERT: C 250 LYS cc_start: 0.8909 (mtpp) cc_final: 0.8579 (mtpp) REVERT: C 252 ARG cc_start: 0.8328 (tpp80) cc_final: 0.7952 (mtp85) REVERT: C 366 ILE cc_start: 0.9054 (tt) cc_final: 0.8817 (tt) REVERT: C 371 ASP cc_start: 0.7881 (t0) cc_final: 0.7400 (t0) REVERT: C 373 GLU cc_start: 0.7876 (pm20) cc_final: 0.7539 (pm20) REVERT: C 379 ARG cc_start: 0.8307 (ptm-80) cc_final: 0.7853 (ttp80) REVERT: C 392 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7869 (pp20) REVERT: D 92 ASN cc_start: 0.8664 (t0) cc_final: 0.8094 (t0) REVERT: E 15 ILE cc_start: 0.8746 (mm) cc_final: 0.8482 (mm) REVERT: E 17 SER cc_start: 0.8470 (m) cc_final: 0.8249 (p) REVERT: E 22 LYS cc_start: 0.8424 (mmtp) cc_final: 0.8068 (mmtp) REVERT: E 28 GLU cc_start: 0.7823 (mp0) cc_final: 0.7372 (mp0) REVERT: E 64 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8014 (mmt-90) REVERT: E 85 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8277 (mm-40) REVERT: E 105 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8084 (mt-10) REVERT: E 118 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8116 (mtp-110) REVERT: E 134 GLU cc_start: 0.7501 (tt0) cc_final: 0.7294 (tt0) REVERT: E 162 LYS cc_start: 0.8346 (ptmt) cc_final: 0.7819 (ptmm) REVERT: E 165 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7696 (mmtt) REVERT: E 167 THR cc_start: 0.8299 (m) cc_final: 0.7943 (p) REVERT: E 168 LYS cc_start: 0.8402 (ttmt) cc_final: 0.8043 (ttmt) REVERT: E 178 GLU cc_start: 0.7861 (tt0) cc_final: 0.7555 (tt0) REVERT: E 182 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7742 (mtmt) REVERT: E 183 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7836 (mm-30) REVERT: E 184 ARG cc_start: 0.7657 (mtm-85) cc_final: 0.7309 (mtm-85) REVERT: E 194 GLU cc_start: 0.7888 (tt0) cc_final: 0.7607 (tt0) REVERT: E 209 TYR cc_start: 0.8414 (m-80) cc_final: 0.8094 (m-80) REVERT: E 212 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7654 (mm-30) REVERT: E 214 ASP cc_start: 0.7982 (m-30) cc_final: 0.7748 (m-30) REVERT: E 227 ASP cc_start: 0.7701 (t0) cc_final: 0.7403 (t0) REVERT: E 230 LYS cc_start: 0.8363 (mttt) cc_final: 0.8108 (mttt) REVERT: E 236 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8190 (mm110) REVERT: E 262 GLN cc_start: 0.7329 (mt0) cc_final: 0.7116 (mm-40) REVERT: E 286 TYR cc_start: 0.8410 (m-10) cc_final: 0.7971 (m-80) REVERT: E 356 ASP cc_start: 0.7982 (t0) cc_final: 0.7622 (t70) REVERT: E 370 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7990 (mt-10) REVERT: E 389 GLU cc_start: 0.7791 (tt0) cc_final: 0.7541 (tt0) REVERT: E 397 ILE cc_start: 0.8291 (mt) cc_final: 0.8055 (tt) REVERT: E 408 GLN cc_start: 0.7968 (mt0) cc_final: 0.7685 (mt0) REVERT: E 418 LYS cc_start: 0.7976 (ttmm) cc_final: 0.7737 (ttmm) REVERT: E 439 ASP cc_start: 0.7602 (p0) cc_final: 0.7392 (p0) REVERT: E 441 LYS cc_start: 0.8297 (mttt) cc_final: 0.8009 (mttt) REVERT: E 445 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7666 (mmtp) REVERT: F 19 ILE cc_start: 0.8651 (tt) cc_final: 0.8000 (tp) REVERT: F 40 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7871 (mtt90) REVERT: F 83 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7854 (mtmt) REVERT: F 112 GLU cc_start: 0.7991 (tp30) cc_final: 0.7653 (tp30) REVERT: F 117 GLU cc_start: 0.8247 (tp30) cc_final: 0.7632 (mm-30) REVERT: F 142 VAL cc_start: 0.8215 (t) cc_final: 0.7778 (m) REVERT: F 160 LYS cc_start: 0.8311 (ttpt) cc_final: 0.7906 (mtpt) REVERT: F 178 MET cc_start: 0.8004 (tpp) cc_final: 0.7604 (tpp) REVERT: F 182 LEU cc_start: 0.8851 (mt) cc_final: 0.8614 (mm) REVERT: F 192 VAL cc_start: 0.8472 (t) cc_final: 0.7999 (p) REVERT: F 218 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6629 (mpp) REVERT: F 267 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7156 (mt-10) REVERT: F 269 LYS cc_start: 0.8331 (mmtp) cc_final: 0.8011 (mmtp) REVERT: F 271 GLU cc_start: 0.7780 (mp0) cc_final: 0.7445 (mp0) REVERT: F 274 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7815 (mm-30) REVERT: F 279 LYS cc_start: 0.8437 (tppp) cc_final: 0.8224 (tppt) REVERT: F 282 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7419 (mt-10) REVERT: F 286 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7727 (pt0) REVERT: F 303 MET cc_start: 0.8677 (mmm) cc_final: 0.8372 (mmp) REVERT: F 392 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7957 (ttp-170) REVERT: F 436 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7465 (tm-30) REVERT: F 441 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7521 (mm-40) REVERT: F 445 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7624 (mm-30) REVERT: G 15 ILE cc_start: 0.8885 (mt) cc_final: 0.8643 (mm) REVERT: G 86 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7709 (mm-30) REVERT: G 89 SER cc_start: 0.8213 (m) cc_final: 0.7931 (t) REVERT: G 90 LYS cc_start: 0.8526 (tptm) cc_final: 0.7620 (tptm) REVERT: G 102 TYR cc_start: 0.8387 (m-80) cc_final: 0.8094 (m-10) REVERT: G 110 GLU cc_start: 0.8271 (tp30) cc_final: 0.8017 (tp30) REVERT: G 113 MET cc_start: 0.8354 (tpt) cc_final: 0.8034 (tpp) REVERT: G 123 ARG cc_start: 0.8327 (ttm170) cc_final: 0.7150 (ttt90) REVERT: G 125 LYS cc_start: 0.8282 (mtmt) cc_final: 0.7890 (mtmt) REVERT: G 126 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7267 (mt-10) REVERT: G 128 LYS cc_start: 0.8278 (tttt) cc_final: 0.7953 (tttt) REVERT: G 129 GLU cc_start: 0.7413 (tt0) cc_final: 0.7156 (tt0) REVERT: G 137 GLU cc_start: 0.7863 (tt0) cc_final: 0.7521 (tp30) REVERT: G 147 MET cc_start: 0.6400 (mtp) cc_final: 0.5736 (mtp) REVERT: G 162 LYS cc_start: 0.8375 (ttmt) cc_final: 0.8065 (ttmm) REVERT: G 171 LYS cc_start: 0.8447 (mtpt) cc_final: 0.7953 (tttp) REVERT: G 178 GLU cc_start: 0.8078 (tt0) cc_final: 0.7363 (tt0) REVERT: G 193 ILE cc_start: 0.8601 (mt) cc_final: 0.8244 (mm) REVERT: G 209 TYR cc_start: 0.8495 (m-80) cc_final: 0.8158 (m-10) REVERT: G 225 LYS cc_start: 0.8335 (mmpt) cc_final: 0.7921 (mmpt) REVERT: G 227 ASP cc_start: 0.7785 (t0) cc_final: 0.7505 (t0) REVERT: G 233 GLU cc_start: 0.8093 (tt0) cc_final: 0.7365 (tt0) REVERT: G 244 ASP cc_start: 0.7444 (m-30) cc_final: 0.7146 (m-30) REVERT: G 247 ASN cc_start: 0.8404 (m-40) cc_final: 0.8184 (m110) REVERT: G 249 ARG cc_start: 0.7802 (ttt-90) cc_final: 0.7520 (ttt-90) REVERT: G 268 LYS cc_start: 0.7887 (mttt) cc_final: 0.7599 (mttt) REVERT: G 302 ASP cc_start: 0.7865 (t0) cc_final: 0.7656 (t0) REVERT: G 323 ILE cc_start: 0.8814 (mt) cc_final: 0.8536 (mm) REVERT: G 370 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7739 (mt-10) REVERT: G 385 ASN cc_start: 0.8136 (m-40) cc_final: 0.7903 (m-40) REVERT: G 408 GLN cc_start: 0.7909 (mt0) cc_final: 0.7699 (mt0) REVERT: G 420 ASN cc_start: 0.7969 (t0) cc_final: 0.7733 (t0) REVERT: G 428 GLU cc_start: 0.8302 (mp0) cc_final: 0.7963 (mp0) REVERT: G 446 ILE cc_start: 0.8666 (mt) cc_final: 0.8287 (mm) REVERT: G 455 MET cc_start: 0.7317 (mmm) cc_final: 0.6986 (mmm) REVERT: H 18 ARG cc_start: 0.7681 (mtp85) cc_final: 0.7397 (mtp85) REVERT: H 26 SER cc_start: 0.8773 (m) cc_final: 0.8484 (p) REVERT: H 33 LEU cc_start: 0.8327 (mt) cc_final: 0.8107 (mt) REVERT: H 38 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7726 (mm-30) REVERT: H 64 ARG cc_start: 0.8296 (mtt180) cc_final: 0.7997 (mtt-85) REVERT: H 83 LYS cc_start: 0.8773 (mtmm) cc_final: 0.8403 (mtmm) REVERT: H 144 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7510 (mm-30) REVERT: H 145 ILE cc_start: 0.8334 (mt) cc_final: 0.8121 (tp) REVERT: H 160 LYS cc_start: 0.8309 (mttt) cc_final: 0.8082 (mttt) REVERT: H 174 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8126 (mp) REVERT: H 186 LYS cc_start: 0.8360 (ttpt) cc_final: 0.7957 (ttpt) REVERT: H 201 LYS cc_start: 0.8476 (ptmt) cc_final: 0.8221 (ptmt) REVERT: H 204 LYS cc_start: 0.8870 (mtpt) cc_final: 0.8521 (mtpt) REVERT: H 238 VAL cc_start: 0.8245 (t) cc_final: 0.7982 (p) REVERT: H 267 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7955 (mt-10) REVERT: H 274 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7850 (mt-10) REVERT: H 275 GLN cc_start: 0.8261 (mm110) cc_final: 0.7975 (mm110) REVERT: H 277 ASN cc_start: 0.8620 (m-40) cc_final: 0.8246 (m-40) REVERT: H 279 LYS cc_start: 0.8500 (tppt) cc_final: 0.8276 (tptp) REVERT: H 285 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7774 (mt-10) REVERT: H 303 MET cc_start: 0.8123 (mmp) cc_final: 0.7919 (mmm) REVERT: H 314 ARG cc_start: 0.7495 (mmt180) cc_final: 0.6870 (mmt180) REVERT: H 317 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7410 (mt-10) REVERT: H 384 GLU cc_start: 0.8338 (mp0) cc_final: 0.8038 (mm-30) REVERT: H 452 PHE cc_start: 0.8520 (m-80) cc_final: 0.8184 (m-80) REVERT: I 17 SER cc_start: 0.8690 (m) cc_final: 0.8384 (t) REVERT: I 64 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.7953 (tpp80) REVERT: I 105 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7277 (mt-10) REVERT: I 125 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8299 (ttmm) REVERT: I 139 THR cc_start: 0.8724 (m) cc_final: 0.8364 (p) REVERT: I 184 ARG cc_start: 0.8656 (mtt180) cc_final: 0.8423 (mtt180) REVERT: I 216 GLU cc_start: 0.7881 (tt0) cc_final: 0.7529 (tp30) REVERT: I 227 ASP cc_start: 0.7595 (t0) cc_final: 0.7332 (t0) REVERT: I 231 LYS cc_start: 0.8353 (mttt) cc_final: 0.8135 (mtpp) REVERT: I 244 ASP cc_start: 0.7741 (m-30) cc_final: 0.7424 (t0) REVERT: I 249 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7799 (mtp85) REVERT: I 269 THR cc_start: 0.8456 (p) cc_final: 0.8211 (p) REVERT: I 270 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7610 (mt-10) REVERT: I 281 LYS cc_start: 0.8763 (mttt) cc_final: 0.8538 (mtmt) REVERT: I 288 ASP cc_start: 0.7739 (m-30) cc_final: 0.7402 (m-30) REVERT: I 310 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7795 (mt-10) REVERT: I 322 SER cc_start: 0.8645 (p) cc_final: 0.8274 (t) REVERT: I 353 ASP cc_start: 0.7689 (m-30) cc_final: 0.7366 (m-30) REVERT: I 438 TYR cc_start: 0.8327 (m-80) cc_final: 0.7874 (m-80) REVERT: I 439 ASP cc_start: 0.8254 (p0) cc_final: 0.7939 (p0) REVERT: I 441 LYS cc_start: 0.8380 (mttm) cc_final: 0.7912 (mtmm) REVERT: I 445 LYS cc_start: 0.8246 (tppt) cc_final: 0.7272 (tppt) REVERT: J 17 THR cc_start: 0.8219 (m) cc_final: 0.7987 (t) REVERT: J 37 LEU cc_start: 0.8324 (mp) cc_final: 0.8032 (mt) REVERT: J 38 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7846 (mm-30) REVERT: J 61 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7845 (mm-30) REVERT: J 90 MET cc_start: 0.8578 (mtm) cc_final: 0.8311 (mtm) REVERT: J 133 GLU cc_start: 0.7810 (pt0) cc_final: 0.7585 (pt0) REVERT: J 136 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7452 (mt-10) REVERT: J 139 GLU cc_start: 0.7920 (tt0) cc_final: 0.7718 (tt0) REVERT: J 144 GLU cc_start: 0.8121 (tt0) cc_final: 0.7918 (tt0) REVERT: J 146 GLN cc_start: 0.7698 (tt0) cc_final: 0.7082 (tm-30) REVERT: J 164 LYS cc_start: 0.8376 (pttt) cc_final: 0.7851 (ptmm) REVERT: J 180 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7006 (mt-10) REVERT: J 183 THR cc_start: 0.8333 (m) cc_final: 0.8067 (p) REVERT: J 184 LYS cc_start: 0.8173 (mttp) cc_final: 0.7928 (mttp) REVERT: J 185 ASP cc_start: 0.7469 (t0) cc_final: 0.7187 (t0) REVERT: J 192 VAL cc_start: 0.8727 (t) cc_final: 0.8407 (p) REVERT: J 225 VAL cc_start: 0.8401 (t) cc_final: 0.8084 (p) REVERT: J 231 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7474 (mm-30) REVERT: J 234 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8440 (ttmm) REVERT: J 236 LYS cc_start: 0.8524 (mtpt) cc_final: 0.8205 (mtpt) REVERT: J 267 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7387 (mt-10) REVERT: J 270 SER cc_start: 0.8342 (p) cc_final: 0.7998 (t) REVERT: J 368 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8290 (ttmm) REVERT: J 377 GLU cc_start: 0.7870 (tp30) cc_final: 0.7481 (tp30) REVERT: J 382 MET cc_start: 0.8619 (mtt) cc_final: 0.8406 (mtt) REVERT: J 430 TYR cc_start: 0.8706 (t80) cc_final: 0.8456 (t80) REVERT: J 436 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6481 (tm-30) REVERT: J 444 LYS cc_start: 0.8269 (mttm) cc_final: 0.7913 (mttm) REVERT: S 20 ARG cc_start: 0.8441 (mtt-85) cc_final: 0.7849 (ttm110) REVERT: S 31 HIS cc_start: 0.8560 (t-170) cc_final: 0.8200 (t70) REVERT: S 35 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7708 (ttm110) REVERT: S 77 ARG cc_start: 0.8390 (mtm-85) cc_final: 0.8185 (mtm-85) REVERT: S 87 VAL cc_start: 0.9023 (t) cc_final: 0.8803 (p) REVERT: T 43 LYS cc_start: 0.8794 (mttt) cc_final: 0.8585 (mtmm) REVERT: T 68 ASP cc_start: 0.8098 (t0) cc_final: 0.7640 (t0) REVERT: T 79 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7824 (mtm110) REVERT: T 93 GLU cc_start: 0.7871 (mp0) cc_final: 0.7589 (mp0) REVERT: U 106 ASP cc_start: 0.8359 (m-30) cc_final: 0.7883 (m-30) REVERT: V 84 MET cc_start: 0.8475 (mmm) cc_final: 0.8238 (tpt) REVERT: V 87 VAL cc_start: 0.9187 (t) cc_final: 0.8931 (m) REVERT: W 107 THR cc_start: 0.8834 (m) cc_final: 0.8622 (t) REVERT: X 39 ARG cc_start: 0.8950 (mmt-90) cc_final: 0.8659 (mmt-90) REVERT: X 55 ARG cc_start: 0.8744 (mtt90) cc_final: 0.8463 (mtt90) REVERT: X 67 ARG cc_start: 0.8384 (ttm110) cc_final: 0.7922 (ttm110) REVERT: X 84 MET cc_start: 0.8586 (tpt) cc_final: 0.8367 (mmm) REVERT: X 91 LYS cc_start: 0.8848 (tttt) cc_final: 0.8623 (ttmm) outliers start: 53 outliers final: 30 residues processed: 1461 average time/residue: 0.2914 time to fit residues: 657.6589 Evaluate side-chains 1425 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 1391 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 2019 ARG Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 397 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 174 LEU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 165 LYS Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain J residue 226 GLN Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain S residue 35 ARG Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain W residue 124 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 431 optimal weight: 0.9990 chunk 414 optimal weight: 3.9990 chunk 196 optimal weight: 0.5980 chunk 319 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 326 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 86 optimal weight: 0.0970 chunk 269 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 GLN C 12 ASN C 92 ASN D 91 GLN D 113 GLN ** E 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 380 GLN F 188 GLN F 277 ASN F 341 GLN G 280 ASN ** H 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 262 GLN I 289 GLN I 335 ASN I 385 ASN I 408 GLN ** S 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 GLN T 63 ASN X 27 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.119252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.100144 restraints weight = 66195.924| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.85 r_work: 0.3109 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41479 Z= 0.137 Angle : 0.572 8.686 56931 Z= 0.304 Chirality : 0.044 0.353 6479 Planarity : 0.004 0.051 6519 Dihedral : 20.902 179.847 7413 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.85 % Allowed : 12.26 % Favored : 85.89 % 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 are not related in a simple way. whole: 1.79 (0.13), residues: 4461 helix: 1.90 (0.11), residues: 2177 sheet: 0.74 (0.19), residues: 685 loop : 0.54 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 202 TYR 0.024 0.001 TYR E 220 PHE 0.026 0.001 PHE A 718 TRP 0.039 0.002 TRP C 360 HIS 0.004 0.001 HIS A2060 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (41471) covalent geometry : angle 0.57233 / 0.30 (56922) hydrogen bonds : bond 0.04126 / 2.78 ( 1954) hydrogen bonds : angle 3.83415 / 2.77 ( 5374) metal coordination : bond 0.00586 / 0.23 ( 8) metal coordination : angle 1.00337 / 0.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1468 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1396 time to evaluate : 1.495 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: A 619 ARG cc_start: 0.8397 (ttm110) cc_final: 0.8192 (mtt-85) REVERT: A 628 TRP cc_start: 0.8392 (t60) cc_final: 0.7941 (t60) REVERT: A 659 HIS cc_start: 0.8736 (t-90) cc_final: 0.8508 (t70) REVERT: A 660 LEU cc_start: 0.9058 (mp) cc_final: 0.8771 (mp) REVERT: A 678 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8447 (m) REVERT: A 684 MET cc_start: 0.8490 (tpp) cc_final: 0.8232 (tpt) REVERT: A 694 LYS cc_start: 0.8645 (mttt) cc_final: 0.8304 (mmtp) REVERT: A 704 GLU cc_start: 0.6951 (mt-10) cc_final: 0.6640 (mt-10) REVERT: A 719 HIS cc_start: 0.8049 (m170) cc_final: 0.7405 (m-70) REVERT: A 727 LEU cc_start: 0.9016 (mt) cc_final: 0.8762 (mm) REVERT: A 747 GLU cc_start: 0.8218 (mp0) cc_final: 0.7909 (mm-30) REVERT: A 749 GLN cc_start: 0.8471 (pm20) cc_final: 0.8009 (pm20) REVERT: A 751 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8539 (tp) REVERT: A 764 ASN cc_start: 0.8584 (m-40) cc_final: 0.8375 (t0) REVERT: A 792 LEU cc_start: 0.8113 (mt) cc_final: 0.7786 (mt) REVERT: A 867 CYS cc_start: 0.8499 (m) cc_final: 0.8130 (m) REVERT: A 871 ASP cc_start: 0.8397 (t0) cc_final: 0.8078 (t70) REVERT: A 892 ASN cc_start: 0.8724 (m110) cc_final: 0.8409 (m110) REVERT: A 918 THR cc_start: 0.8594 (p) cc_final: 0.8346 (m) REVERT: A 958 TYR cc_start: 0.8417 (t80) cc_final: 0.8171 (t80) REVERT: A 966 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7871 (mtp-110) REVERT: A 973 VAL cc_start: 0.8749 (t) cc_final: 0.8525 (p) REVERT: A 975 LEU cc_start: 0.8440 (mt) cc_final: 0.8164 (mt) REVERT: A 992 MET cc_start: 0.2561 (ttm) cc_final: 0.1772 (ttm) REVERT: A 1891 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7630 (tm-30) REVERT: A 1893 ARG cc_start: 0.8468 (mtt180) cc_final: 0.8135 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8519 (ptpp) cc_final: 0.8120 (ptpp) REVERT: A 1895 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7857 (ttp-170) REVERT: A 1897 ARG cc_start: 0.8294 (ttp-170) cc_final: 0.7931 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8539 (ttm110) cc_final: 0.8296 (ttp-170) REVERT: A 1921 GLU cc_start: 0.8184 (mp0) cc_final: 0.7825 (mp0) REVERT: A 1934 SER cc_start: 0.8393 (m) cc_final: 0.8115 (p) REVERT: A 1936 ILE cc_start: 0.8988 (mm) cc_final: 0.8427 (mt) REVERT: A 1953 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 1957 ARG cc_start: 0.8376 (mtp180) cc_final: 0.8136 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7953 (tp30) cc_final: 0.7204 (tp30) REVERT: A 2026 CYS cc_start: 0.8505 (m) cc_final: 0.8154 (m) REVERT: A 2139 ASP cc_start: 0.8157 (t0) cc_final: 0.7560 (t0) REVERT: A 2141 ASN cc_start: 0.8747 (t0) cc_final: 0.8291 (t0) REVERT: A 2144 MET cc_start: 0.7698 (mpp) cc_final: 0.7323 (mpp) REVERT: A 2150 ASP cc_start: 0.8048 (m-30) cc_final: 0.7628 (m-30) REVERT: A 2185 MET cc_start: 0.6866 (ttm) cc_final: 0.6357 (ppp) REVERT: A 2189 MET cc_start: 0.7774 (mtt) cc_final: 0.7104 (mtt) REVERT: A 2196 PHE cc_start: 0.7903 (m-80) cc_final: 0.7620 (m-80) REVERT: B 133 MET cc_start: 0.5854 (mmt) cc_final: 0.5340 (mmt) REVERT: C 2 THR cc_start: 0.7633 (t) cc_final: 0.7399 (m) REVERT: C 23 SER cc_start: 0.7952 (m) cc_final: 0.7500 (p) REVERT: C 71 GLN cc_start: 0.8138 (tp-100) cc_final: 0.7639 (tp-100) REVERT: C 72 ARG cc_start: 0.8763 (tpp80) cc_final: 0.8114 (tpp80) REVERT: C 75 TRP cc_start: 0.8944 (m-10) cc_final: 0.8696 (m-10) REVERT: C 76 ASP cc_start: 0.8211 (m-30) cc_final: 0.7677 (m-30) REVERT: C 83 MET cc_start: 0.8311 (mmm) cc_final: 0.8065 (mmm) REVERT: C 88 PHE cc_start: 0.8682 (m-80) cc_final: 0.8306 (m-10) REVERT: C 90 ASP cc_start: 0.8039 (t0) cc_final: 0.7438 (t0) REVERT: C 97 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7464 (mm-30) REVERT: C 103 THR cc_start: 0.8732 (m) cc_final: 0.8433 (p) REVERT: C 107 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7924 (mm-30) REVERT: C 109 MET cc_start: 0.8962 (tpp) cc_final: 0.8529 (ttm) REVERT: C 115 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8041 (mt-10) REVERT: C 116 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7750 (mp0) REVERT: C 120 GLN cc_start: 0.8214 (tm-30) cc_final: 0.7783 (tm-30) REVERT: C 164 LYS cc_start: 0.7730 (tptm) cc_final: 0.7514 (tptm) REVERT: C 204 GLN cc_start: 0.8580 (tp40) cc_final: 0.7899 (tp40) REVERT: C 208 ASP cc_start: 0.7982 (m-30) cc_final: 0.7550 (m-30) REVERT: C 220 MET cc_start: 0.8305 (tpp) cc_final: 0.8072 (mmt) REVERT: C 229 GLU cc_start: 0.8197 (pt0) cc_final: 0.7832 (pt0) REVERT: C 230 ASN cc_start: 0.8512 (t0) cc_final: 0.8006 (t0) REVERT: C 250 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8603 (mtpp) REVERT: C 254 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8212 (mt-10) REVERT: C 366 ILE cc_start: 0.9054 (tt) cc_final: 0.8833 (tt) REVERT: C 369 ASN cc_start: 0.8568 (t0) cc_final: 0.7978 (t0) REVERT: C 375 MET cc_start: 0.8525 (mtt) cc_final: 0.8167 (mtt) REVERT: C 379 ARG cc_start: 0.8347 (ptm-80) cc_final: 0.7855 (ttp80) REVERT: D 92 ASN cc_start: 0.8671 (t0) cc_final: 0.8132 (t0) REVERT: E 15 ILE cc_start: 0.8745 (mm) cc_final: 0.8472 (mm) REVERT: E 17 SER cc_start: 0.8487 (m) cc_final: 0.8227 (p) REVERT: E 22 LYS cc_start: 0.8446 (mmtp) cc_final: 0.8231 (mmtp) REVERT: E 28 GLU cc_start: 0.7946 (mp0) cc_final: 0.7442 (mp0) REVERT: E 64 ARG cc_start: 0.8357 (mtp85) cc_final: 0.8054 (mmt-90) REVERT: E 162 LYS cc_start: 0.8324 (ptmt) cc_final: 0.8089 (ptmm) REVERT: E 165 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7675 (mmtt) REVERT: E 167 THR cc_start: 0.8268 (m) cc_final: 0.7931 (p) REVERT: E 168 LYS cc_start: 0.8388 (ttmt) cc_final: 0.8031 (ttmt) REVERT: E 178 GLU cc_start: 0.7870 (tt0) cc_final: 0.7619 (tt0) REVERT: E 182 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7779 (mtmt) REVERT: E 183 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7826 (mm-30) REVERT: E 184 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7317 (mtm-85) REVERT: E 194 GLU cc_start: 0.7910 (tt0) cc_final: 0.7599 (tt0) REVERT: E 212 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7511 (mm-30) REVERT: E 214 ASP cc_start: 0.8013 (m-30) cc_final: 0.7775 (m-30) REVERT: E 230 LYS cc_start: 0.8373 (mttt) cc_final: 0.8124 (mttt) REVERT: E 231 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8281 (mtpp) REVERT: E 262 GLN cc_start: 0.7366 (mt0) cc_final: 0.7151 (mm110) REVERT: E 268 LYS cc_start: 0.8293 (mttt) cc_final: 0.8082 (mttt) REVERT: E 286 TYR cc_start: 0.8421 (m-10) cc_final: 0.7984 (m-80) REVERT: E 320 GLU cc_start: 0.7873 (mt-10) cc_final: 0.6841 (mt-10) REVERT: E 345 THR cc_start: 0.8756 (m) cc_final: 0.8405 (p) REVERT: E 356 ASP cc_start: 0.8043 (t0) cc_final: 0.7694 (t70) REVERT: E 357 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7625 (mtt-85) REVERT: E 370 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8190 (mt-10) REVERT: E 389 GLU cc_start: 0.7833 (tt0) cc_final: 0.7563 (tt0) REVERT: E 418 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7762 (ttmm) REVERT: E 439 ASP cc_start: 0.7519 (p0) cc_final: 0.7274 (p0) REVERT: E 441 LYS cc_start: 0.8261 (mttt) cc_final: 0.7969 (mttt) REVERT: E 445 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7606 (mmtp) REVERT: E 446 ILE cc_start: 0.8346 (mm) cc_final: 0.8067 (mt) REVERT: F 19 ILE cc_start: 0.8705 (tt) cc_final: 0.7974 (tp) REVERT: F 40 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7847 (mtt90) REVERT: F 83 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7860 (mtmt) REVERT: F 112 GLU cc_start: 0.8062 (tp30) cc_final: 0.7723 (tp30) REVERT: F 117 GLU cc_start: 0.8250 (tp30) cc_final: 0.7651 (mm-30) REVERT: F 160 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7946 (mtpt) REVERT: F 177 LYS cc_start: 0.8183 (mttt) cc_final: 0.7949 (mttt) REVERT: F 178 MET cc_start: 0.8030 (tpp) cc_final: 0.7626 (tpp) REVERT: F 182 LEU cc_start: 0.8861 (mt) cc_final: 0.8627 (mm) REVERT: F 192 VAL cc_start: 0.8454 (t) cc_final: 0.7934 (p) REVERT: F 218 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6673 (mpp) REVERT: F 233 GLN cc_start: 0.7657 (tt0) cc_final: 0.7365 (tp40) REVERT: F 248 ASP cc_start: 0.7915 (m-30) cc_final: 0.7620 (m-30) REVERT: F 267 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7155 (mt-10) REVERT: F 269 LYS cc_start: 0.8246 (mmtp) cc_final: 0.7863 (mmtp) REVERT: F 271 GLU cc_start: 0.7853 (mp0) cc_final: 0.7558 (mp0) REVERT: F 274 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7889 (mm-30) REVERT: F 303 MET cc_start: 0.8710 (mmm) cc_final: 0.8411 (mmp) REVERT: F 314 ARG cc_start: 0.7895 (mmt180) cc_final: 0.7638 (mmp-170) REVERT: F 392 ARG cc_start: 0.8217 (ttp-110) cc_final: 0.7971 (ttp-170) REVERT: F 436 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7293 (tm-30) REVERT: F 441 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7524 (mm-40) REVERT: F 445 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7608 (mm-30) REVERT: G 15 ILE cc_start: 0.8880 (mt) cc_final: 0.8632 (mm) REVERT: G 27 ASP cc_start: 0.7391 (t70) cc_final: 0.7163 (t70) REVERT: G 34 GLN cc_start: 0.8276 (tm-30) cc_final: 0.8031 (tm-30) REVERT: G 43 GLU cc_start: 0.7915 (mp0) cc_final: 0.7641 (mp0) REVERT: G 89 SER cc_start: 0.8205 (m) cc_final: 0.7930 (t) REVERT: G 90 LYS cc_start: 0.8560 (tptm) cc_final: 0.7548 (tptm) REVERT: G 102 TYR cc_start: 0.8338 (m-80) cc_final: 0.8045 (m-10) REVERT: G 113 MET cc_start: 0.8398 (tpt) cc_final: 0.8099 (tpp) REVERT: G 123 ARG cc_start: 0.8340 (ttm170) cc_final: 0.7152 (ttt90) REVERT: G 126 GLU cc_start: 0.7669 (mt-10) cc_final: 0.6640 (mt-10) REVERT: G 129 GLU cc_start: 0.7476 (tt0) cc_final: 0.6902 (tt0) REVERT: G 134 GLU cc_start: 0.7426 (tt0) cc_final: 0.6994 (tm-30) REVERT: G 137 GLU cc_start: 0.7853 (tt0) cc_final: 0.7534 (tp30) REVERT: G 147 MET cc_start: 0.6371 (mtp) cc_final: 0.5704 (mtp) REVERT: G 162 LYS cc_start: 0.8404 (ttmt) cc_final: 0.8028 (ttmm) REVERT: G 171 LYS cc_start: 0.8542 (mtpt) cc_final: 0.7981 (tttp) REVERT: G 178 GLU cc_start: 0.8121 (tt0) cc_final: 0.7412 (tt0) REVERT: G 193 ILE cc_start: 0.8604 (mt) cc_final: 0.8201 (mm) REVERT: G 202 ARG cc_start: 0.8811 (ttt-90) cc_final: 0.8601 (ttt-90) REVERT: G 209 TYR cc_start: 0.8447 (m-80) cc_final: 0.8107 (m-10) REVERT: G 225 LYS cc_start: 0.8338 (mmpt) cc_final: 0.7895 (mmpt) REVERT: G 227 ASP cc_start: 0.7824 (t0) cc_final: 0.7510 (t0) REVERT: G 244 ASP cc_start: 0.7434 (m-30) cc_final: 0.7149 (m-30) REVERT: G 247 ASN cc_start: 0.8435 (m-40) cc_final: 0.8210 (m-40) REVERT: G 249 ARG cc_start: 0.7759 (ttt-90) cc_final: 0.7483 (ttt-90) REVERT: G 302 ASP cc_start: 0.7834 (t0) cc_final: 0.7621 (t0) REVERT: G 323 ILE cc_start: 0.8868 (mt) cc_final: 0.8509 (mm) REVERT: G 371 MET cc_start: 0.8207 (mtp) cc_final: 0.7939 (mtm) REVERT: G 376 LYS cc_start: 0.8838 (tptt) cc_final: 0.8570 (tptm) REVERT: G 408 GLN cc_start: 0.7915 (mt0) cc_final: 0.7700 (mt0) REVERT: G 420 ASN cc_start: 0.7969 (t0) cc_final: 0.7278 (t0) REVERT: G 422 LYS cc_start: 0.8345 (mttp) cc_final: 0.8071 (mptt) REVERT: G 428 GLU cc_start: 0.8290 (mp0) cc_final: 0.7901 (mp0) REVERT: G 435 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7960 (tp30) REVERT: G 455 MET cc_start: 0.7249 (mmm) cc_final: 0.6513 (mmm) REVERT: H 26 SER cc_start: 0.8737 (m) cc_final: 0.8467 (p) REVERT: H 38 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7741 (mm-30) REVERT: H 64 ARG cc_start: 0.8311 (mtt180) cc_final: 0.8035 (mtt-85) REVERT: H 83 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8430 (mtmm) REVERT: H 117 GLU cc_start: 0.8135 (tp30) cc_final: 0.7874 (tp30) REVERT: H 144 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7507 (mm-30) REVERT: H 145 ILE cc_start: 0.8317 (mt) cc_final: 0.8081 (tp) REVERT: H 160 LYS cc_start: 0.8277 (mttt) cc_final: 0.8066 (mttt) REVERT: H 168 MET cc_start: 0.7461 (ttm) cc_final: 0.5877 (ttm) REVERT: H 186 LYS cc_start: 0.8345 (ttpt) cc_final: 0.7930 (ttpt) REVERT: H 201 LYS cc_start: 0.8549 (ptmt) cc_final: 0.8267 (ptmt) REVERT: H 211 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8100 (ttt180) REVERT: H 214 ASP cc_start: 0.7429 (p0) cc_final: 0.7226 (p0) REVERT: H 231 GLU cc_start: 0.7880 (tt0) cc_final: 0.7193 (tp30) REVERT: H 238 VAL cc_start: 0.8241 (t) cc_final: 0.7978 (p) REVERT: H 267 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7939 (mt-10) REVERT: H 273 ARG cc_start: 0.8501 (mtt90) cc_final: 0.7970 (mtt90) REVERT: H 274 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7874 (mt-10) REVERT: H 275 GLN cc_start: 0.8264 (mm110) cc_final: 0.7959 (mm110) REVERT: H 277 ASN cc_start: 0.8638 (m-40) cc_final: 0.8233 (m110) REVERT: H 279 LYS cc_start: 0.8503 (tppt) cc_final: 0.8274 (tptp) REVERT: H 285 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7785 (mt-10) REVERT: H 303 MET cc_start: 0.8137 (mmp) cc_final: 0.7927 (mmm) REVERT: H 307 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7442 (mm-30) REVERT: H 314 ARG cc_start: 0.7497 (mmt180) cc_final: 0.6820 (mmt180) REVERT: H 452 PHE cc_start: 0.8539 (m-80) cc_final: 0.8251 (m-80) REVERT: I 17 SER cc_start: 0.8707 (m) cc_final: 0.8359 (t) REVERT: I 43 GLU cc_start: 0.8067 (mp0) cc_final: 0.7837 (mp0) REVERT: I 64 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7909 (tpp80) REVERT: I 105 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7291 (mt-10) REVERT: I 125 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8304 (ttmm) REVERT: I 134 GLU cc_start: 0.7694 (tt0) cc_final: 0.7444 (tt0) REVERT: I 139 THR cc_start: 0.8767 (m) cc_final: 0.8391 (p) REVERT: I 184 ARG cc_start: 0.8666 (mtt180) cc_final: 0.8420 (mtt180) REVERT: I 216 GLU cc_start: 0.7899 (tt0) cc_final: 0.7516 (tp30) REVERT: I 227 ASP cc_start: 0.7685 (t0) cc_final: 0.7464 (t0) REVERT: I 231 LYS cc_start: 0.8351 (mttt) cc_final: 0.8109 (mtpp) REVERT: I 236 GLN cc_start: 0.8611 (tt0) cc_final: 0.8387 (tt0) REVERT: I 249 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7805 (mtp85) REVERT: I 270 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7615 (mt-10) REVERT: I 281 LYS cc_start: 0.8748 (mttt) cc_final: 0.8514 (mtmt) REVERT: I 322 SER cc_start: 0.8623 (p) cc_final: 0.8253 (t) REVERT: I 353 ASP cc_start: 0.7683 (m-30) cc_final: 0.6701 (m-30) REVERT: I 438 TYR cc_start: 0.8341 (m-80) cc_final: 0.7841 (m-80) REVERT: I 439 ASP cc_start: 0.8264 (p0) cc_final: 0.7925 (p0) REVERT: I 441 LYS cc_start: 0.8378 (mttm) cc_final: 0.7908 (mtmm) REVERT: I 445 LYS cc_start: 0.8235 (tppt) cc_final: 0.7243 (tppt) REVERT: J 17 THR cc_start: 0.8202 (m) cc_final: 0.7986 (t) REVERT: J 38 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7833 (mm-30) REVERT: J 71 ARG cc_start: 0.8462 (tpp80) cc_final: 0.8250 (tpp-160) REVERT: J 90 MET cc_start: 0.8620 (mtm) cc_final: 0.8378 (mtm) REVERT: J 133 GLU cc_start: 0.7809 (pt0) cc_final: 0.7568 (pt0) REVERT: J 139 GLU cc_start: 0.7963 (tt0) cc_final: 0.7737 (tt0) REVERT: J 146 GLN cc_start: 0.7768 (tt0) cc_final: 0.7053 (tm-30) REVERT: J 164 LYS cc_start: 0.8400 (pttt) cc_final: 0.7786 (ptmm) REVERT: J 168 MET cc_start: 0.8818 (ptm) cc_final: 0.8382 (ptm) REVERT: J 172 TYR cc_start: 0.8570 (m-80) cc_final: 0.7901 (m-80) REVERT: J 180 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7007 (mt-10) REVERT: J 183 THR cc_start: 0.8312 (m) cc_final: 0.8046 (p) REVERT: J 184 LYS cc_start: 0.8219 (mttp) cc_final: 0.7967 (mttp) REVERT: J 185 ASP cc_start: 0.7467 (t0) cc_final: 0.7178 (t0) REVERT: J 192 VAL cc_start: 0.8708 (t) cc_final: 0.8421 (p) REVERT: J 225 VAL cc_start: 0.8354 (t) cc_final: 0.8042 (p) REVERT: J 231 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7426 (mm-30) REVERT: J 234 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8387 (ttmm) REVERT: J 267 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7495 (mt-10) REVERT: J 270 SER cc_start: 0.8344 (p) cc_final: 0.7993 (t) REVERT: J 368 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8341 (ttmt) REVERT: J 377 GLU cc_start: 0.7815 (tp30) cc_final: 0.7431 (tp30) REVERT: J 430 TYR cc_start: 0.8668 (t80) cc_final: 0.8420 (t80) REVERT: J 436 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6437 (tm-30) REVERT: J 444 LYS cc_start: 0.8258 (mttm) cc_final: 0.7899 (mttm) REVERT: P 254 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7637 (mp0) REVERT: S 20 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8312 (ttm110) REVERT: S 31 HIS cc_start: 0.8557 (t-170) cc_final: 0.8222 (t70) REVERT: S 35 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7816 (ttm110) REVERT: S 61 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8004 (mm-30) REVERT: S 87 VAL cc_start: 0.9007 (t) cc_final: 0.8797 (p) REVERT: T 40 TYR cc_start: 0.8694 (m-80) cc_final: 0.8484 (m-80) REVERT: T 43 LYS cc_start: 0.8808 (mttt) cc_final: 0.8580 (mtmm) REVERT: T 68 ASP cc_start: 0.8131 (t0) cc_final: 0.7687 (t0) REVERT: T 79 ARG cc_start: 0.8289 (mtm110) cc_final: 0.7745 (mtm110) REVERT: U 106 ASP cc_start: 0.8385 (m-30) cc_final: 0.7902 (m-30) REVERT: V 67 ARG cc_start: 0.8522 (ttp80) cc_final: 0.8253 (ttp80) REVERT: V 84 MET cc_start: 0.8524 (mmm) cc_final: 0.8308 (tpt) REVERT: V 87 VAL cc_start: 0.9176 (t) cc_final: 0.8963 (m) REVERT: W 78 PHE cc_start: 0.7718 (m-80) cc_final: 0.7398 (m-10) REVERT: X 67 ARG cc_start: 0.8402 (ttm110) cc_final: 0.7770 (ttm110) REVERT: X 84 MET cc_start: 0.8637 (tpt) cc_final: 0.8412 (mmm) REVERT: X 91 LYS cc_start: 0.8901 (tttt) cc_final: 0.8642 (ttmm) outliers start: 72 outliers final: 44 residues processed: 1413 average time/residue: 0.2956 time to fit residues: 643.1368 Evaluate side-chains 1397 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 1348 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1980 MET Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 397 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 409 LEU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 165 LYS Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 264 MET Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 364 MET Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain S residue 35 ARG Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain X residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 154 optimal weight: 0.9980 chunk 438 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 chunk 168 optimal weight: 0.6980 chunk 170 optimal weight: 0.0980 chunk 212 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 HIS D 91 GLN E 181 GLN E 420 ASN F 277 ASN G 169 GLN G 262 GLN G 280 ASN G 380 GLN H 240 HIS H 453 ASN ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 262 GLN I 289 GLN I 408 GLN S 31 HIS ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.119646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.100606 restraints weight = 65909.338| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.85 r_work: 0.3116 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 41479 Z= 0.124 Angle : 0.559 9.220 56931 Z= 0.296 Chirality : 0.043 0.357 6479 Planarity : 0.004 0.075 6519 Dihedral : 20.891 179.307 7413 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.36 % Allowed : 13.85 % Favored : 83.78 % 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 are not related in a simple way. whole: 1.83 (0.13), residues: 4461 helix: 1.95 (0.11), residues: 2177 sheet: 0.72 (0.19), residues: 695 loop : 0.55 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 284 TYR 0.019 0.001 TYR E 209 PHE 0.017 0.001 PHE E 177 TRP 0.054 0.002 TRP C 360 HIS 0.008 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (41471) covalent geometry : angle 0.55928 / 0.30 (56922) hydrogen bonds : bond 0.03871 / 2.61 ( 1954) hydrogen bonds : angle 3.73937 / 2.70 ( 5374) metal coordination : bond 0.00526 / 0.19 ( 8) metal coordination : angle 1.06802 / 0.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1390 time to evaluate : 1.476 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 660 LEU cc_start: 0.9047 (mp) cc_final: 0.8765 (mp) REVERT: A 678 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8469 (m) REVERT: A 704 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6737 (mt-10) REVERT: A 727 LEU cc_start: 0.8993 (mt) cc_final: 0.8748 (mm) REVERT: A 747 GLU cc_start: 0.8186 (mp0) cc_final: 0.7894 (mm-30) REVERT: A 749 GLN cc_start: 0.8492 (pm20) cc_final: 0.8040 (pm20) REVERT: A 751 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8529 (tp) REVERT: A 789 MET cc_start: 0.7387 (mmt) cc_final: 0.7083 (mmm) REVERT: A 830 HIS cc_start: 0.6973 (m90) cc_final: 0.6698 (m90) REVERT: A 867 CYS cc_start: 0.8460 (m) cc_final: 0.8142 (m) REVERT: A 871 ASP cc_start: 0.8390 (t0) cc_final: 0.8030 (t70) REVERT: A 892 ASN cc_start: 0.8709 (m110) cc_final: 0.8392 (m110) REVERT: A 918 THR cc_start: 0.8588 (p) cc_final: 0.8342 (m) REVERT: A 966 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7830 (mtp-110) REVERT: A 973 VAL cc_start: 0.8732 (t) cc_final: 0.8506 (p) REVERT: A 975 LEU cc_start: 0.8415 (mt) cc_final: 0.8144 (mt) REVERT: A 992 MET cc_start: 0.2553 (ttm) cc_final: 0.1808 (ttm) REVERT: A 1891 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 1893 ARG cc_start: 0.8427 (mtt180) cc_final: 0.8100 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8524 (ptpp) cc_final: 0.8094 (ptpp) REVERT: A 1897 ARG cc_start: 0.8316 (ttp-170) cc_final: 0.7937 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8520 (ttm110) cc_final: 0.8155 (ttp-170) REVERT: A 1934 SER cc_start: 0.8397 (m) cc_final: 0.8115 (p) REVERT: A 1936 ILE cc_start: 0.9003 (mm) cc_final: 0.8447 (mt) REVERT: A 1957 ARG cc_start: 0.8368 (mtp180) cc_final: 0.8135 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7976 (tp30) cc_final: 0.7260 (tp30) REVERT: A 2026 CYS cc_start: 0.8519 (m) cc_final: 0.8159 (m) REVERT: A 2139 ASP cc_start: 0.8101 (t0) cc_final: 0.7614 (t0) REVERT: A 2141 ASN cc_start: 0.8714 (t0) cc_final: 0.8223 (t0) REVERT: A 2144 MET cc_start: 0.7667 (mpp) cc_final: 0.7230 (mpp) REVERT: A 2185 MET cc_start: 0.6814 (ttm) cc_final: 0.6298 (ppp) REVERT: A 2189 MET cc_start: 0.7724 (mtt) cc_final: 0.7079 (mtt) REVERT: A 2196 PHE cc_start: 0.7918 (m-80) cc_final: 0.7658 (m-80) REVERT: B 133 MET cc_start: 0.5851 (mmt) cc_final: 0.5319 (mmt) REVERT: C 1 MET cc_start: 0.4339 (tmm) cc_final: 0.4050 (tmm) REVERT: C 2 THR cc_start: 0.7623 (t) cc_final: 0.7177 (m) REVERT: C 14 LYS cc_start: 0.8755 (mppt) cc_final: 0.8329 (mptp) REVERT: C 67 ASN cc_start: 0.8944 (t0) cc_final: 0.8722 (t0) REVERT: C 71 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7628 (tp-100) REVERT: C 72 ARG cc_start: 0.8733 (tpp80) cc_final: 0.8111 (tpp80) REVERT: C 75 TRP cc_start: 0.8948 (m-10) cc_final: 0.8665 (m-10) REVERT: C 76 ASP cc_start: 0.8218 (m-30) cc_final: 0.7646 (m-30) REVERT: C 90 ASP cc_start: 0.7873 (t0) cc_final: 0.7235 (t0) REVERT: C 103 THR cc_start: 0.8701 (m) cc_final: 0.8409 (p) REVERT: C 107 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7920 (mm-30) REVERT: C 115 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8060 (mt-10) REVERT: C 116 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7780 (mp0) REVERT: C 164 LYS cc_start: 0.7716 (tptm) cc_final: 0.7495 (tptm) REVERT: C 196 MET cc_start: 0.8257 (mmm) cc_final: 0.7695 (mmm) REVERT: C 204 GLN cc_start: 0.8574 (tp40) cc_final: 0.7877 (tp40) REVERT: C 208 ASP cc_start: 0.7987 (m-30) cc_final: 0.7539 (m-30) REVERT: C 230 ASN cc_start: 0.8568 (t0) cc_final: 0.8132 (t0) REVERT: C 250 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8565 (mtpp) REVERT: C 254 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8145 (mt-10) REVERT: C 369 ASN cc_start: 0.8685 (t0) cc_final: 0.8420 (t0) REVERT: C 379 ARG cc_start: 0.8373 (ptm-80) cc_final: 0.7871 (ttp80) REVERT: D 92 ASN cc_start: 0.8680 (t0) cc_final: 0.8143 (t0) REVERT: E 15 ILE cc_start: 0.8743 (mm) cc_final: 0.8468 (mt) REVERT: E 17 SER cc_start: 0.8508 (m) cc_final: 0.8209 (p) REVERT: E 22 LYS cc_start: 0.8436 (mmtp) cc_final: 0.8223 (mmtp) REVERT: E 28 GLU cc_start: 0.7853 (mp0) cc_final: 0.7372 (mp0) REVERT: E 43 GLU cc_start: 0.8191 (mp0) cc_final: 0.7963 (mp0) REVERT: E 64 ARG cc_start: 0.8332 (mtp85) cc_final: 0.8040 (mmt-90) REVERT: E 162 LYS cc_start: 0.8293 (ptmt) cc_final: 0.7849 (ptmm) REVERT: E 163 THR cc_start: 0.8199 (t) cc_final: 0.7923 (m) REVERT: E 165 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7684 (mmtt) REVERT: E 167 THR cc_start: 0.8244 (m) cc_final: 0.7910 (p) REVERT: E 168 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8023 (ttmt) REVERT: E 173 ASP cc_start: 0.7942 (m-30) cc_final: 0.7741 (m-30) REVERT: E 178 GLU cc_start: 0.7855 (tt0) cc_final: 0.7548 (tt0) REVERT: E 182 LYS cc_start: 0.8077 (mtmt) cc_final: 0.7763 (mtmt) REVERT: E 183 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7840 (mm-30) REVERT: E 184 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7348 (mtm-85) REVERT: E 194 GLU cc_start: 0.7913 (tt0) cc_final: 0.7585 (tt0) REVERT: E 212 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7514 (mm-30) REVERT: E 214 ASP cc_start: 0.7983 (m-30) cc_final: 0.7758 (m-30) REVERT: E 227 ASP cc_start: 0.7698 (t0) cc_final: 0.7289 (t0) REVERT: E 230 LYS cc_start: 0.8376 (mttt) cc_final: 0.8099 (mttt) REVERT: E 231 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8346 (mtpp) REVERT: E 268 LYS cc_start: 0.8324 (mttt) cc_final: 0.8099 (mttt) REVERT: E 286 TYR cc_start: 0.8438 (m-10) cc_final: 0.8007 (m-80) REVERT: E 314 TYR cc_start: 0.8193 (t80) cc_final: 0.7968 (t80) REVERT: E 320 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7258 (mt-10) REVERT: E 342 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7042 (mm-30) REVERT: E 345 THR cc_start: 0.8770 (m) cc_final: 0.8399 (p) REVERT: E 356 ASP cc_start: 0.8059 (t0) cc_final: 0.7811 (t70) REVERT: E 357 ARG cc_start: 0.8164 (mtt90) cc_final: 0.7932 (mtt-85) REVERT: E 370 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8158 (mt-10) REVERT: E 389 GLU cc_start: 0.7819 (tt0) cc_final: 0.7558 (tt0) REVERT: E 418 LYS cc_start: 0.8003 (ttmm) cc_final: 0.7768 (ttmm) REVERT: E 439 ASP cc_start: 0.7501 (p0) cc_final: 0.7260 (p0) REVERT: E 441 LYS cc_start: 0.8254 (mttt) cc_final: 0.7985 (mttt) REVERT: E 445 LYS cc_start: 0.7831 (mmtp) cc_final: 0.7582 (mmtp) REVERT: E 446 ILE cc_start: 0.8326 (mm) cc_final: 0.8035 (mt) REVERT: F 19 ILE cc_start: 0.8702 (tt) cc_final: 0.8046 (tp) REVERT: F 40 ARG cc_start: 0.8191 (mtt90) cc_final: 0.7836 (mtt90) REVERT: F 71 ARG cc_start: 0.7889 (mmt90) cc_final: 0.7582 (mmm-85) REVERT: F 83 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7924 (mtmt) REVERT: F 112 GLU cc_start: 0.8074 (tp30) cc_final: 0.7689 (tp30) REVERT: F 117 GLU cc_start: 0.8241 (tp30) cc_final: 0.7648 (mm-30) REVERT: F 160 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7962 (mtpt) REVERT: F 170 THR cc_start: 0.8160 (m) cc_final: 0.7896 (t) REVERT: F 177 LYS cc_start: 0.8174 (mttt) cc_final: 0.7890 (mttt) REVERT: F 178 MET cc_start: 0.8018 (tpp) cc_final: 0.7616 (tpp) REVERT: F 182 LEU cc_start: 0.8850 (mt) cc_final: 0.8623 (mm) REVERT: F 192 VAL cc_start: 0.8449 (t) cc_final: 0.7912 (p) REVERT: F 218 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6697 (mpp) REVERT: F 233 GLN cc_start: 0.7609 (tt0) cc_final: 0.7335 (tp40) REVERT: F 235 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7375 (mtp85) REVERT: F 248 ASP cc_start: 0.7870 (m-30) cc_final: 0.7538 (m-30) REVERT: F 269 LYS cc_start: 0.8197 (mmtp) cc_final: 0.7847 (mmtp) REVERT: F 271 GLU cc_start: 0.7797 (mp0) cc_final: 0.7523 (mp0) REVERT: F 274 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7837 (mm-30) REVERT: F 303 MET cc_start: 0.8690 (mmm) cc_final: 0.8423 (mmp) REVERT: F 314 ARG cc_start: 0.7864 (mmt180) cc_final: 0.7641 (mmp-170) REVERT: F 392 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7938 (ttp-170) REVERT: F 436 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7242 (tm-30) REVERT: F 441 GLN cc_start: 0.7775 (mm-40) cc_final: 0.7540 (mm-40) REVERT: F 445 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7620 (mm-30) REVERT: G 15 ILE cc_start: 0.8875 (mt) cc_final: 0.8634 (mm) REVERT: G 34 GLN cc_start: 0.8269 (tm-30) cc_final: 0.8028 (tm-30) REVERT: G 43 GLU cc_start: 0.7862 (mp0) cc_final: 0.7642 (mp0) REVERT: G 89 SER cc_start: 0.8202 (m) cc_final: 0.7946 (t) REVERT: G 90 LYS cc_start: 0.8568 (tptm) cc_final: 0.7526 (tptm) REVERT: G 102 TYR cc_start: 0.8345 (m-80) cc_final: 0.8083 (m-10) REVERT: G 113 MET cc_start: 0.8376 (tpt) cc_final: 0.8069 (tpp) REVERT: G 123 ARG cc_start: 0.8331 (ttm170) cc_final: 0.7146 (ttt90) REVERT: G 125 LYS cc_start: 0.8285 (mtmt) cc_final: 0.7795 (mmmt) REVERT: G 126 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6967 (mt-10) REVERT: G 129 GLU cc_start: 0.7286 (tt0) cc_final: 0.7004 (tt0) REVERT: G 134 GLU cc_start: 0.7426 (tt0) cc_final: 0.6999 (tm-30) REVERT: G 137 GLU cc_start: 0.7809 (tt0) cc_final: 0.7470 (tp30) REVERT: G 147 MET cc_start: 0.6258 (mtp) cc_final: 0.5592 (mtp) REVERT: G 162 LYS cc_start: 0.8425 (ttmt) cc_final: 0.8052 (ttmm) REVERT: G 169 GLN cc_start: 0.8539 (tt0) cc_final: 0.8330 (tt0) REVERT: G 171 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8002 (tttp) REVERT: G 178 GLU cc_start: 0.8132 (tt0) cc_final: 0.7413 (tt0) REVERT: G 193 ILE cc_start: 0.8591 (mt) cc_final: 0.8209 (mm) REVERT: G 209 TYR cc_start: 0.8445 (m-80) cc_final: 0.8151 (m-10) REVERT: G 225 LYS cc_start: 0.8367 (mmpt) cc_final: 0.7908 (mmpt) REVERT: G 227 ASP cc_start: 0.7851 (t0) cc_final: 0.7539 (t0) REVERT: G 233 GLU cc_start: 0.7346 (tp30) cc_final: 0.6679 (tp30) REVERT: G 244 ASP cc_start: 0.7453 (m-30) cc_final: 0.7191 (m-30) REVERT: G 247 ASN cc_start: 0.8445 (m-40) cc_final: 0.8207 (m-40) REVERT: G 249 ARG cc_start: 0.7787 (ttt-90) cc_final: 0.7520 (ttt-90) REVERT: G 255 ASP cc_start: 0.7626 (p0) cc_final: 0.7423 (p0) REVERT: G 302 ASP cc_start: 0.7822 (t0) cc_final: 0.7086 (t0) REVERT: G 303 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7452 (mp0) REVERT: G 323 ILE cc_start: 0.8853 (mt) cc_final: 0.8533 (mm) REVERT: G 371 MET cc_start: 0.8207 (mtp) cc_final: 0.7957 (mtm) REVERT: G 408 GLN cc_start: 0.7929 (mt0) cc_final: 0.7703 (mt0) REVERT: G 420 ASN cc_start: 0.7970 (t0) cc_final: 0.7223 (t0) REVERT: G 422 LYS cc_start: 0.8358 (mttp) cc_final: 0.8060 (mptt) REVERT: G 428 GLU cc_start: 0.8276 (mp0) cc_final: 0.7861 (mp0) REVERT: G 435 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7938 (tp30) REVERT: H 26 SER cc_start: 0.8727 (m) cc_final: 0.8431 (p) REVERT: H 38 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7803 (mm-30) REVERT: H 64 ARG cc_start: 0.8253 (mtt180) cc_final: 0.7977 (mtt-85) REVERT: H 83 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8428 (mtmm) REVERT: H 117 GLU cc_start: 0.8137 (tp30) cc_final: 0.7753 (tp30) REVERT: H 144 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7459 (mm-30) REVERT: H 145 ILE cc_start: 0.8347 (mt) cc_final: 0.8097 (tp) REVERT: H 160 LYS cc_start: 0.8269 (mttt) cc_final: 0.7963 (mttt) REVERT: H 168 MET cc_start: 0.7382 (ttm) cc_final: 0.5839 (ttt) REVERT: H 186 LYS cc_start: 0.8351 (ttpt) cc_final: 0.7921 (ttpt) REVERT: H 201 LYS cc_start: 0.8508 (ptmt) cc_final: 0.8207 (ptmt) REVERT: H 214 ASP cc_start: 0.7424 (p0) cc_final: 0.7187 (p0) REVERT: H 231 GLU cc_start: 0.7859 (tt0) cc_final: 0.7195 (tp30) REVERT: H 238 VAL cc_start: 0.8259 (t) cc_final: 0.7988 (p) REVERT: H 253 ARG cc_start: 0.8091 (ptm-80) cc_final: 0.7816 (ptm-80) REVERT: H 267 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7975 (mt-10) REVERT: H 273 ARG cc_start: 0.8482 (mtt90) cc_final: 0.7929 (mtt90) REVERT: H 274 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7848 (mt-10) REVERT: H 275 GLN cc_start: 0.8261 (mm110) cc_final: 0.7950 (mm110) REVERT: H 277 ASN cc_start: 0.8625 (m-40) cc_final: 0.8243 (m110) REVERT: H 279 LYS cc_start: 0.8483 (tppt) cc_final: 0.8236 (tptp) REVERT: H 285 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7748 (mt-10) REVERT: H 303 MET cc_start: 0.8127 (mmp) cc_final: 0.7912 (mmm) REVERT: H 307 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7458 (mm-30) REVERT: H 314 ARG cc_start: 0.7481 (mmt180) cc_final: 0.6755 (mmt180) REVERT: H 452 PHE cc_start: 0.8532 (m-80) cc_final: 0.8239 (m-80) REVERT: I 17 SER cc_start: 0.8701 (m) cc_final: 0.8359 (t) REVERT: I 64 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7849 (tpp80) REVERT: I 105 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7234 (mt-10) REVERT: I 125 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8267 (ttmm) REVERT: I 134 GLU cc_start: 0.7682 (tt0) cc_final: 0.7403 (tt0) REVERT: I 139 THR cc_start: 0.8748 (m) cc_final: 0.8391 (p) REVERT: I 184 ARG cc_start: 0.8654 (mtt180) cc_final: 0.8373 (mtt180) REVERT: I 216 GLU cc_start: 0.7941 (tt0) cc_final: 0.7559 (tp30) REVERT: I 231 LYS cc_start: 0.8333 (mttt) cc_final: 0.8061 (mtpp) REVERT: I 236 GLN cc_start: 0.8626 (tt0) cc_final: 0.8302 (tt0) REVERT: I 249 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7774 (mtp85) REVERT: I 281 LYS cc_start: 0.8734 (mttt) cc_final: 0.8501 (mtmt) REVERT: I 322 SER cc_start: 0.8634 (p) cc_final: 0.8275 (t) REVERT: I 353 ASP cc_start: 0.7674 (m-30) cc_final: 0.7362 (m-30) REVERT: I 438 TYR cc_start: 0.8322 (m-80) cc_final: 0.7828 (m-80) REVERT: I 439 ASP cc_start: 0.8254 (p0) cc_final: 0.7921 (p0) REVERT: I 441 LYS cc_start: 0.8379 (mttm) cc_final: 0.7920 (mtmm) REVERT: I 445 LYS cc_start: 0.8184 (tppt) cc_final: 0.7147 (tppt) REVERT: I 447 LEU cc_start: 0.7450 (mp) cc_final: 0.7229 (mt) REVERT: J 17 THR cc_start: 0.8215 (m) cc_final: 0.7997 (t) REVERT: J 61 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7795 (mm-30) REVERT: J 90 MET cc_start: 0.8610 (mtm) cc_final: 0.8269 (mtp) REVERT: J 92 GLN cc_start: 0.8420 (mm-40) cc_final: 0.8176 (mm-40) REVERT: J 133 GLU cc_start: 0.7771 (pt0) cc_final: 0.7534 (pt0) REVERT: J 139 GLU cc_start: 0.7954 (tt0) cc_final: 0.7735 (tt0) REVERT: J 142 VAL cc_start: 0.8612 (t) cc_final: 0.8274 (m) REVERT: J 164 LYS cc_start: 0.8410 (pttt) cc_final: 0.8108 (ptmm) REVERT: J 172 TYR cc_start: 0.8561 (m-80) cc_final: 0.7871 (m-80) REVERT: J 180 GLU cc_start: 0.7698 (mt-10) cc_final: 0.6997 (mt-10) REVERT: J 183 THR cc_start: 0.8297 (m) cc_final: 0.8026 (p) REVERT: J 184 LYS cc_start: 0.8218 (mttp) cc_final: 0.7959 (mttp) REVERT: J 185 ASP cc_start: 0.7449 (t0) cc_final: 0.7176 (t0) REVERT: J 192 VAL cc_start: 0.8713 (t) cc_final: 0.8395 (p) REVERT: J 207 ARG cc_start: 0.7738 (ttm170) cc_final: 0.7453 (ttm-80) REVERT: J 225 VAL cc_start: 0.8325 (t) cc_final: 0.8011 (p) REVERT: J 234 LYS cc_start: 0.8727 (mtpt) cc_final: 0.8373 (ttmm) REVERT: J 267 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7583 (mt-10) REVERT: J 270 SER cc_start: 0.8327 (p) cc_final: 0.7989 (t) REVERT: J 328 THR cc_start: 0.8293 (t) cc_final: 0.7977 (m) REVERT: J 368 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8311 (ttmt) REVERT: J 377 GLU cc_start: 0.7773 (tp30) cc_final: 0.7397 (tp30) REVERT: J 378 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7915 (mt-10) REVERT: J 382 MET cc_start: 0.8607 (mtt) cc_final: 0.8400 (mtm) REVERT: J 430 TYR cc_start: 0.8659 (t80) cc_final: 0.8395 (t80) REVERT: J 436 GLU cc_start: 0.6902 (tm-30) cc_final: 0.6430 (tm-30) REVERT: J 444 LYS cc_start: 0.8271 (mttm) cc_final: 0.8058 (mttm) REVERT: S 20 ARG cc_start: 0.8558 (mtt-85) cc_final: 0.8176 (ttm110) REVERT: S 31 HIS cc_start: 0.8432 (t-90) cc_final: 0.8194 (t70) REVERT: S 59 THR cc_start: 0.9147 (m) cc_final: 0.8843 (p) REVERT: S 87 VAL cc_start: 0.9000 (t) cc_final: 0.8799 (p) REVERT: T 40 TYR cc_start: 0.8686 (m-80) cc_final: 0.8455 (m-80) REVERT: T 68 ASP cc_start: 0.8115 (t0) cc_final: 0.7647 (t0) REVERT: T 79 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7436 (mtm110) REVERT: T 93 GLU cc_start: 0.7895 (mp0) cc_final: 0.7567 (mp0) REVERT: U 106 ASP cc_start: 0.8396 (m-30) cc_final: 0.7916 (m-30) REVERT: V 67 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8261 (ttp80) REVERT: V 87 VAL cc_start: 0.9165 (t) cc_final: 0.8961 (m) REVERT: X 67 ARG cc_start: 0.8391 (ttm110) cc_final: 0.7921 (ttp80) REVERT: X 84 MET cc_start: 0.8682 (tpt) cc_final: 0.8442 (mmm) REVERT: X 91 LYS cc_start: 0.8905 (tttt) cc_final: 0.8644 (ttmm) outliers start: 92 outliers final: 60 residues processed: 1418 average time/residue: 0.2926 time to fit residues: 640.1468 Evaluate side-chains 1434 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1370 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 1980 MET Chi-restraints excluded: chain A residue 2019 ARG Chi-restraints excluded: chain A residue 2058 GLU Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain E residue 396 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain G residue 313 THR Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 397 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 264 MET Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 364 MET Chi-restraints excluded: chain J residue 226 GLN Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain X residue 70 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 179 optimal weight: 0.4980 chunk 454 optimal weight: 6.9990 chunk 324 optimal weight: 4.9990 chunk 453 optimal weight: 30.0000 chunk 289 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 389 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN D 91 GLN E 420 ASN F 277 ASN G 203 GLN G 262 GLN G 280 ASN G 380 GLN H 453 ASN I 262 GLN I 289 GLN I 305 HIS I 348 HIS J 78 GLN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 93 GLN ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.116894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097892 restraints weight = 66024.081| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.84 r_work: 0.3071 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 41479 Z= 0.231 Angle : 0.617 12.898 56931 Z= 0.323 Chirality : 0.046 0.361 6479 Planarity : 0.004 0.054 6519 Dihedral : 20.991 179.497 7413 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.70 % Allowed : 14.60 % Favored : 82.70 % 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 are not related in a simple way. whole: 1.66 (0.13), residues: 4461 helix: 1.82 (0.11), residues: 2185 sheet: 0.63 (0.20), residues: 680 loop : 0.44 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG V 78 TYR 0.034 0.002 TYR C 382 PHE 0.020 0.002 PHE E 177 TRP 0.072 0.003 TRP C 360 HIS 0.006 0.001 HIS A 623 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 (41471) covalent geometry : angle 0.61646 / 0.32 (56922) hydrogen bonds : bond 0.04460 / 3.00 ( 1954) hydrogen bonds : angle 3.80623 / 2.75 ( 5374) metal coordination : bond 0.01495 / 0.63 ( 8) metal coordination : angle 1.87702 / 0.88 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1418 time to evaluate : 1.383 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 660 LEU cc_start: 0.9015 (mp) cc_final: 0.8783 (mp) REVERT: A 678 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8556 (m) REVERT: A 699 TYR cc_start: 0.7986 (p90) cc_final: 0.7761 (p90) REVERT: A 704 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6788 (mt-10) REVERT: A 727 LEU cc_start: 0.9011 (mt) cc_final: 0.8800 (mm) REVERT: A 747 GLU cc_start: 0.8264 (mp0) cc_final: 0.7999 (mm-30) REVERT: A 749 GLN cc_start: 0.8505 (pm20) cc_final: 0.8030 (pm20) REVERT: A 751 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8579 (tp) REVERT: A 771 LEU cc_start: 0.9008 (tp) cc_final: 0.8756 (tp) REVERT: A 789 MET cc_start: 0.7500 (mmt) cc_final: 0.7214 (mmm) REVERT: A 854 GLU cc_start: 0.8084 (pm20) cc_final: 0.7619 (pm20) REVERT: A 864 ARG cc_start: 0.8464 (mtp85) cc_final: 0.8167 (mtp85) REVERT: A 871 ASP cc_start: 0.8441 (t0) cc_final: 0.8059 (t70) REVERT: A 892 ASN cc_start: 0.8669 (m110) cc_final: 0.8371 (m110) REVERT: A 966 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7823 (mtp-110) REVERT: A 973 VAL cc_start: 0.8758 (t) cc_final: 0.8523 (p) REVERT: A 992 MET cc_start: 0.2527 (ttm) cc_final: 0.1792 (ttm) REVERT: A 1891 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7743 (tm-30) REVERT: A 1893 ARG cc_start: 0.8466 (mtt180) cc_final: 0.8134 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8568 (ptpp) cc_final: 0.8153 (ptpp) REVERT: A 1897 ARG cc_start: 0.8319 (ttp-170) cc_final: 0.7945 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8575 (ttm110) cc_final: 0.8320 (ttp-170) REVERT: A 1934 SER cc_start: 0.8505 (m) cc_final: 0.8278 (p) REVERT: A 1936 ILE cc_start: 0.9016 (mm) cc_final: 0.8476 (mt) REVERT: A 1953 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 1957 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8208 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7884 (tp30) cc_final: 0.7133 (tp30) REVERT: A 2026 CYS cc_start: 0.8547 (m) cc_final: 0.8204 (m) REVERT: A 2041 ASP cc_start: 0.8415 (m-30) cc_final: 0.8025 (m-30) REVERT: A 2139 ASP cc_start: 0.8109 (t0) cc_final: 0.7878 (t0) REVERT: A 2141 ASN cc_start: 0.8790 (t0) cc_final: 0.8510 (t0) REVERT: A 2144 MET cc_start: 0.7730 (mpp) cc_final: 0.7393 (mpp) REVERT: A 2150 ASP cc_start: 0.8293 (m-30) cc_final: 0.7922 (m-30) REVERT: A 2185 MET cc_start: 0.6778 (ttm) cc_final: 0.6523 (ttm) REVERT: A 2196 PHE cc_start: 0.7975 (m-80) cc_final: 0.7703 (m-80) REVERT: B 133 MET cc_start: 0.5906 (mmt) cc_final: 0.5386 (mmt) REVERT: C 2 THR cc_start: 0.7738 (t) cc_final: 0.7303 (m) REVERT: C 14 LYS cc_start: 0.8787 (mppt) cc_final: 0.8445 (mptp) REVERT: C 67 ASN cc_start: 0.8958 (t0) cc_final: 0.8738 (t0) REVERT: C 71 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7968 (tp-100) REVERT: C 72 ARG cc_start: 0.8760 (tpp80) cc_final: 0.8039 (tpp80) REVERT: C 76 ASP cc_start: 0.8259 (m-30) cc_final: 0.7680 (m-30) REVERT: C 83 MET cc_start: 0.8374 (mmp) cc_final: 0.8046 (mmm) REVERT: C 103 THR cc_start: 0.8732 (m) cc_final: 0.8431 (p) REVERT: C 107 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7973 (mm-30) REVERT: C 111 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7063 (tm-30) REVERT: C 115 GLU cc_start: 0.8462 (mt-10) cc_final: 0.7457 (mt-10) REVERT: C 116 GLU cc_start: 0.8280 (mm-30) cc_final: 0.8079 (mm-30) REVERT: C 164 LYS cc_start: 0.7764 (tptm) cc_final: 0.7550 (tptm) REVERT: C 196 MET cc_start: 0.8286 (mmm) cc_final: 0.7684 (mmm) REVERT: C 204 GLN cc_start: 0.8620 (tp40) cc_final: 0.8089 (tp40) REVERT: C 208 ASP cc_start: 0.8003 (m-30) cc_final: 0.7543 (m-30) REVERT: C 225 LEU cc_start: 0.8511 (mt) cc_final: 0.8274 (mt) REVERT: C 229 GLU cc_start: 0.8217 (pt0) cc_final: 0.7972 (pt0) REVERT: C 230 ASN cc_start: 0.8559 (t0) cc_final: 0.8196 (t0) REVERT: C 250 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8647 (mtpp) REVERT: C 254 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8128 (mt-10) REVERT: C 369 ASN cc_start: 0.8766 (t0) cc_final: 0.8386 (t0) REVERT: C 372 PHE cc_start: 0.8584 (t80) cc_final: 0.8123 (t80) REVERT: D 92 ASN cc_start: 0.8803 (t0) cc_final: 0.8353 (t0) REVERT: E 15 ILE cc_start: 0.8700 (mm) cc_final: 0.8441 (mt) REVERT: E 17 SER cc_start: 0.8578 (m) cc_final: 0.8248 (p) REVERT: E 28 GLU cc_start: 0.7893 (mp0) cc_final: 0.7461 (mp0) REVERT: E 85 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8490 (mm-40) REVERT: E 162 LYS cc_start: 0.8295 (ptmt) cc_final: 0.8001 (ptmm) REVERT: E 165 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7682 (mmtt) REVERT: E 167 THR cc_start: 0.8277 (m) cc_final: 0.7989 (p) REVERT: E 168 LYS cc_start: 0.8416 (ttmt) cc_final: 0.8060 (ttmt) REVERT: E 178 GLU cc_start: 0.7852 (tt0) cc_final: 0.7575 (tt0) REVERT: E 182 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7812 (mtmt) REVERT: E 183 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7796 (mm-30) REVERT: E 194 GLU cc_start: 0.7871 (tt0) cc_final: 0.7523 (tt0) REVERT: E 214 ASP cc_start: 0.8002 (m-30) cc_final: 0.7732 (m-30) REVERT: E 236 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8099 (mm-40) REVERT: E 244 ASP cc_start: 0.7964 (m-30) cc_final: 0.7648 (m-30) REVERT: E 255 ASP cc_start: 0.7492 (p0) cc_final: 0.7225 (p0) REVERT: E 268 LYS cc_start: 0.8320 (mttt) cc_final: 0.8069 (mttt) REVERT: E 286 TYR cc_start: 0.8435 (m-10) cc_final: 0.8026 (m-80) REVERT: E 352 LEU cc_start: 0.8374 (mt) cc_final: 0.8095 (mm) REVERT: E 356 ASP cc_start: 0.8113 (t0) cc_final: 0.7641 (t0) REVERT: E 370 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8188 (mt-10) REVERT: E 389 GLU cc_start: 0.7917 (tt0) cc_final: 0.7625 (tt0) REVERT: E 397 ILE cc_start: 0.8271 (tt) cc_final: 0.8027 (tt) REVERT: E 415 LEU cc_start: 0.8595 (mt) cc_final: 0.8350 (mm) REVERT: E 418 LYS cc_start: 0.8088 (ttmm) cc_final: 0.7856 (ttmm) REVERT: E 439 ASP cc_start: 0.7616 (p0) cc_final: 0.7380 (p0) REVERT: E 441 LYS cc_start: 0.8259 (mttt) cc_final: 0.7921 (mttt) REVERT: E 445 LYS cc_start: 0.7866 (mmtp) cc_final: 0.7611 (mmtp) REVERT: E 446 ILE cc_start: 0.8367 (mm) cc_final: 0.8073 (mt) REVERT: F 19 ILE cc_start: 0.8691 (tt) cc_final: 0.8014 (tp) REVERT: F 40 ARG cc_start: 0.8215 (mtt90) cc_final: 0.7856 (mtt90) REVERT: F 71 ARG cc_start: 0.7915 (mmt90) cc_final: 0.7593 (mmm-85) REVERT: F 83 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7843 (mtmt) REVERT: F 112 GLU cc_start: 0.8033 (tp30) cc_final: 0.7693 (tp30) REVERT: F 117 GLU cc_start: 0.8249 (tp30) cc_final: 0.7613 (mm-30) REVERT: F 142 VAL cc_start: 0.8257 (t) cc_final: 0.7937 (m) REVERT: F 160 LYS cc_start: 0.8371 (ttpt) cc_final: 0.7977 (mtpt) REVERT: F 162 THR cc_start: 0.7962 (m) cc_final: 0.7534 (p) REVERT: F 170 THR cc_start: 0.8134 (m) cc_final: 0.7880 (t) REVERT: F 177 LYS cc_start: 0.8293 (mttt) cc_final: 0.7986 (mttt) REVERT: F 181 SER cc_start: 0.8626 (m) cc_final: 0.8215 (p) REVERT: F 192 VAL cc_start: 0.8381 (t) cc_final: 0.7855 (p) REVERT: F 218 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6883 (tpp) REVERT: F 233 GLN cc_start: 0.7683 (tt0) cc_final: 0.7370 (tp40) REVERT: F 235 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7350 (mtp85) REVERT: F 248 ASP cc_start: 0.7890 (m-30) cc_final: 0.7605 (m-30) REVERT: F 269 LYS cc_start: 0.8302 (mmtp) cc_final: 0.7873 (mmtp) REVERT: F 271 GLU cc_start: 0.7860 (mp0) cc_final: 0.7601 (mp0) REVERT: F 274 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7841 (mm-30) REVERT: F 303 MET cc_start: 0.8736 (mmm) cc_final: 0.8439 (mmp) REVERT: F 329 ASN cc_start: 0.8233 (p0) cc_final: 0.7876 (p0) REVERT: F 392 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.7931 (ttp-170) REVERT: F 436 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7277 (tm-30) REVERT: F 441 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7549 (mm-40) REVERT: F 445 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7701 (mm-30) REVERT: G 15 ILE cc_start: 0.8851 (mt) cc_final: 0.8634 (mm) REVERT: G 34 GLN cc_start: 0.8343 (tm-30) cc_final: 0.8037 (tm-30) REVERT: G 43 GLU cc_start: 0.7987 (mp0) cc_final: 0.7676 (mp0) REVERT: G 61 MET cc_start: 0.8751 (mmm) cc_final: 0.8143 (mmm) REVERT: G 89 SER cc_start: 0.8355 (m) cc_final: 0.8078 (t) REVERT: G 90 LYS cc_start: 0.8602 (tptm) cc_final: 0.7678 (tptm) REVERT: G 102 TYR cc_start: 0.8322 (m-80) cc_final: 0.8085 (m-10) REVERT: G 113 MET cc_start: 0.8454 (tpt) cc_final: 0.8194 (tpp) REVERT: G 123 ARG cc_start: 0.8325 (ttm170) cc_final: 0.7554 (ttt180) REVERT: G 126 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7065 (mt-10) REVERT: G 129 GLU cc_start: 0.7393 (tt0) cc_final: 0.7173 (tt0) REVERT: G 134 GLU cc_start: 0.7460 (tt0) cc_final: 0.7002 (tm-30) REVERT: G 137 GLU cc_start: 0.7837 (tt0) cc_final: 0.7493 (tp30) REVERT: G 147 MET cc_start: 0.6229 (mtp) cc_final: 0.5605 (mtp) REVERT: G 162 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8111 (ttmm) REVERT: G 171 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8190 (mtpp) REVERT: G 178 GLU cc_start: 0.8174 (tt0) cc_final: 0.7568 (tt0) REVERT: G 183 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8227 (mm-30) REVERT: G 186 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7620 (mm-30) REVERT: G 193 ILE cc_start: 0.8610 (mt) cc_final: 0.8257 (mm) REVERT: G 209 TYR cc_start: 0.8464 (m-80) cc_final: 0.8167 (m-10) REVERT: G 225 LYS cc_start: 0.8394 (mmpt) cc_final: 0.7904 (mmpt) REVERT: G 227 ASP cc_start: 0.7892 (t0) cc_final: 0.7623 (t0) REVERT: G 244 ASP cc_start: 0.7503 (m-30) cc_final: 0.7256 (m-30) REVERT: G 247 ASN cc_start: 0.8457 (m-40) cc_final: 0.8255 (m110) REVERT: G 249 ARG cc_start: 0.7830 (ttt-90) cc_final: 0.7554 (ttt-90) REVERT: G 255 ASP cc_start: 0.7659 (p0) cc_final: 0.7449 (p0) REVERT: G 303 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7679 (mp0) REVERT: G 323 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8297 (mm) REVERT: G 371 MET cc_start: 0.8290 (mtp) cc_final: 0.8066 (mtm) REVERT: G 376 LYS cc_start: 0.8772 (tptt) cc_final: 0.8531 (tptm) REVERT: G 408 GLN cc_start: 0.8027 (mt0) cc_final: 0.7813 (mt0) REVERT: G 422 LYS cc_start: 0.8390 (mttp) cc_final: 0.8057 (mtpp) REVERT: G 428 GLU cc_start: 0.8369 (mp0) cc_final: 0.7922 (mp0) REVERT: G 435 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7987 (tp30) REVERT: G 455 MET cc_start: 0.7201 (mmm) cc_final: 0.6733 (mmm) REVERT: H 26 SER cc_start: 0.8741 (m) cc_final: 0.8487 (p) REVERT: H 38 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7806 (mm-30) REVERT: H 64 ARG cc_start: 0.8261 (mtt180) cc_final: 0.7951 (mtt-85) REVERT: H 83 LYS cc_start: 0.8821 (mtmm) cc_final: 0.8457 (mtmm) REVERT: H 88 MET cc_start: 0.8116 (mmp) cc_final: 0.7817 (mmm) REVERT: H 117 GLU cc_start: 0.8152 (tp30) cc_final: 0.7787 (tp30) REVERT: H 139 GLU cc_start: 0.7574 (tt0) cc_final: 0.7373 (tt0) REVERT: H 144 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7482 (mm-30) REVERT: H 145 ILE cc_start: 0.8363 (mt) cc_final: 0.8149 (tp) REVERT: H 160 LYS cc_start: 0.8286 (mttt) cc_final: 0.8040 (mttt) REVERT: H 201 LYS cc_start: 0.8538 (ptmt) cc_final: 0.8254 (ptmt) REVERT: H 214 ASP cc_start: 0.7534 (p0) cc_final: 0.7285 (p0) REVERT: H 238 VAL cc_start: 0.8276 (t) cc_final: 0.7966 (p) REVERT: H 253 ARG cc_start: 0.8129 (ptm-80) cc_final: 0.7837 (ptm-80) REVERT: H 267 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8022 (mt-10) REVERT: H 273 ARG cc_start: 0.8492 (mtt90) cc_final: 0.7984 (mtt90) REVERT: H 274 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7871 (mt-10) REVERT: H 275 GLN cc_start: 0.8258 (mm110) cc_final: 0.7917 (mm-40) REVERT: H 277 ASN cc_start: 0.8613 (m-40) cc_final: 0.8205 (m110) REVERT: H 279 LYS cc_start: 0.8519 (tppt) cc_final: 0.8268 (tptp) REVERT: H 285 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7708 (mt-10) REVERT: H 303 MET cc_start: 0.8207 (mmp) cc_final: 0.7998 (mmm) REVERT: H 307 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7462 (mm-30) REVERT: H 313 ASN cc_start: 0.8097 (m-40) cc_final: 0.7785 (m-40) REVERT: H 314 ARG cc_start: 0.7517 (mmt180) cc_final: 0.7051 (mmt180) REVERT: H 452 PHE cc_start: 0.8563 (m-80) cc_final: 0.8351 (m-80) REVERT: I 17 SER cc_start: 0.8677 (m) cc_final: 0.8419 (t) REVERT: I 105 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7280 (mt-10) REVERT: I 125 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8288 (ttmm) REVERT: I 137 GLU cc_start: 0.8023 (tt0) cc_final: 0.7756 (tt0) REVERT: I 139 THR cc_start: 0.8773 (m) cc_final: 0.8348 (p) REVERT: I 184 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8350 (mtt180) REVERT: I 216 GLU cc_start: 0.7908 (tt0) cc_final: 0.7560 (tp30) REVERT: I 231 LYS cc_start: 0.8450 (mttt) cc_final: 0.8176 (mtpp) REVERT: I 244 ASP cc_start: 0.7718 (m-30) cc_final: 0.7380 (t0) REVERT: I 249 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7797 (mtp85) REVERT: I 281 LYS cc_start: 0.8745 (mttt) cc_final: 0.8490 (mtmt) REVERT: I 322 SER cc_start: 0.8556 (p) cc_final: 0.8291 (t) REVERT: I 353 ASP cc_start: 0.7645 (m-30) cc_final: 0.7256 (m-30) REVERT: I 438 TYR cc_start: 0.8426 (m-80) cc_final: 0.7907 (m-80) REVERT: I 439 ASP cc_start: 0.8286 (p0) cc_final: 0.8052 (p0) REVERT: I 441 LYS cc_start: 0.8398 (mttm) cc_final: 0.8013 (mtmm) REVERT: I 445 LYS cc_start: 0.8200 (tppt) cc_final: 0.7195 (tppt) REVERT: J 17 THR cc_start: 0.8248 (m) cc_final: 0.8042 (t) REVERT: J 71 ARG cc_start: 0.8405 (tpp80) cc_final: 0.8186 (tpp-160) REVERT: J 90 MET cc_start: 0.8643 (mtm) cc_final: 0.8380 (mtp) REVERT: J 92 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8143 (mm-40) REVERT: J 133 GLU cc_start: 0.7787 (pt0) cc_final: 0.7566 (pt0) REVERT: J 142 VAL cc_start: 0.8656 (t) cc_final: 0.8380 (m) REVERT: J 164 LYS cc_start: 0.8404 (pttt) cc_final: 0.8063 (ptmm) REVERT: J 180 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7102 (mt-10) REVERT: J 183 THR cc_start: 0.8333 (m) cc_final: 0.8073 (p) REVERT: J 184 LYS cc_start: 0.8273 (mttp) cc_final: 0.8041 (mttp) REVERT: J 192 VAL cc_start: 0.8731 (t) cc_final: 0.8401 (p) REVERT: J 207 ARG cc_start: 0.7853 (ttm170) cc_final: 0.7527 (ttm170) REVERT: J 225 VAL cc_start: 0.8371 (t) cc_final: 0.8071 (p) REVERT: J 234 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8358 (ttmm) REVERT: J 267 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7518 (mt-10) REVERT: J 270 SER cc_start: 0.8360 (p) cc_final: 0.8042 (t) REVERT: J 368 LYS cc_start: 0.8539 (ttmt) cc_final: 0.8257 (ttmm) REVERT: J 377 GLU cc_start: 0.7747 (tp30) cc_final: 0.7383 (tp30) REVERT: J 427 LYS cc_start: 0.8539 (mttm) cc_final: 0.8331 (mmtm) REVERT: J 430 TYR cc_start: 0.8764 (t80) cc_final: 0.8526 (t80) REVERT: J 444 LYS cc_start: 0.8301 (mttm) cc_final: 0.8082 (mttm) REVERT: P 247 ASP cc_start: 0.8452 (t0) cc_final: 0.8213 (t0) REVERT: P 254 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7773 (mp0) REVERT: P 275 LYS cc_start: 0.8302 (mtpt) cc_final: 0.7872 (mtpt) REVERT: S 20 ARG cc_start: 0.8568 (mtt-85) cc_final: 0.8127 (mtt-85) REVERT: S 31 HIS cc_start: 0.8626 (t-90) cc_final: 0.8423 (t70) REVERT: S 59 THR cc_start: 0.9165 (m) cc_final: 0.8865 (p) REVERT: S 73 ASN cc_start: 0.8844 (m110) cc_final: 0.8490 (t0) REVERT: T 40 TYR cc_start: 0.8735 (m-80) cc_final: 0.8524 (m-80) REVERT: T 43 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8621 (mtmm) REVERT: T 44 VAL cc_start: 0.9244 (t) cc_final: 0.8998 (p) REVERT: T 63 ASN cc_start: 0.9151 (t0) cc_final: 0.8942 (t0) REVERT: T 68 ASP cc_start: 0.8153 (t0) cc_final: 0.7709 (t0) REVERT: T 79 ARG cc_start: 0.8293 (mtm110) cc_final: 0.7540 (mtm110) REVERT: T 93 GLU cc_start: 0.7868 (mp0) cc_final: 0.7548 (mp0) REVERT: U 106 ASP cc_start: 0.8399 (m-30) cc_final: 0.7921 (m-30) REVERT: V 78 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8342 (mtm180) REVERT: V 87 VAL cc_start: 0.9201 (t) cc_final: 0.8985 (m) REVERT: X 67 ARG cc_start: 0.8479 (ttm110) cc_final: 0.8049 (ttp80) REVERT: X 84 MET cc_start: 0.8744 (tpt) cc_final: 0.8536 (mmm) REVERT: X 91 LYS cc_start: 0.8955 (tttt) cc_final: 0.8678 (ttmm) outliers start: 105 outliers final: 65 residues processed: 1442 average time/residue: 0.2905 time to fit residues: 647.6587 Evaluate side-chains 1447 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1378 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 2019 ARG Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2068 MET Chi-restraints excluded: chain A residue 2128 THR Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 323 ILE Chi-restraints excluded: chain G residue 353 ASP Chi-restraints excluded: chain G residue 365 LEU Chi-restraints excluded: chain G residue 377 ILE Chi-restraints excluded: chain G residue 397 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 199 THR Chi-restraints excluded: chain H residue 339 SER Chi-restraints excluded: chain H residue 379 ASP Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 264 MET Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 396 GLU Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain J residue 417 LYS Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 124 ILE Chi-restraints excluded: chain X residue 70 VAL Chi-restraints excluded: chain X residue 81 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 302 optimal weight: 2.9990 chunk 383 optimal weight: 0.6980 chunk 190 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 159 optimal weight: 0.5980 chunk 428 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 0.1980 chunk 117 optimal weight: 0.0370 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN C 110 ASN E 380 GLN E 408 GLN E 420 ASN F 277 ASN G 262 GLN H 41 GLN H 453 ASN I 408 GLN ** T 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 93 GLN ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.118687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.099609 restraints weight = 65980.737| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.85 r_work: 0.3101 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41479 Z= 0.127 Angle : 0.572 10.652 56931 Z= 0.300 Chirality : 0.043 0.362 6479 Planarity : 0.004 0.056 6519 Dihedral : 20.926 179.025 7413 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.11 % Allowed : 15.73 % Favored : 82.16 % 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 are not related in a simple way. whole: 1.74 (0.13), residues: 4461 helix: 1.93 (0.11), residues: 2178 sheet: 0.63 (0.20), residues: 661 loop : 0.45 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 92 TYR 0.032 0.001 TYR C 382 PHE 0.028 0.001 PHE W 78 TRP 0.092 0.002 TRP C 360 HIS 0.006 0.001 HIS I 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (41471) covalent geometry : angle 0.57187 / 0.30 (56922) hydrogen bonds : bond 0.03789 / 2.53 ( 1954) hydrogen bonds : angle 3.66759 / 2.66 ( 5374) metal coordination : bond 0.00745 / 0.25 ( 8) metal coordination : angle 1.35128 / 0.72 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1492 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1410 time to evaluate : 1.714 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 660 LEU cc_start: 0.8998 (mp) cc_final: 0.8753 (mp) REVERT: A 678 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8544 (m) REVERT: A 704 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6750 (mt-10) REVERT: A 727 LEU cc_start: 0.8962 (mt) cc_final: 0.8758 (mm) REVERT: A 747 GLU cc_start: 0.8189 (mp0) cc_final: 0.7945 (mm-30) REVERT: A 749 GLN cc_start: 0.8494 (pm20) cc_final: 0.8039 (pm20) REVERT: A 751 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8558 (tp) REVERT: A 789 MET cc_start: 0.7437 (mmt) cc_final: 0.7113 (mmm) REVERT: A 854 GLU cc_start: 0.8060 (pm20) cc_final: 0.7582 (pm20) REVERT: A 864 ARG cc_start: 0.8402 (mtp85) cc_final: 0.8100 (mtp85) REVERT: A 867 CYS cc_start: 0.8481 (m) cc_final: 0.8092 (m) REVERT: A 871 ASP cc_start: 0.8364 (t0) cc_final: 0.8028 (t70) REVERT: A 966 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7832 (mtp-110) REVERT: A 973 VAL cc_start: 0.8749 (t) cc_final: 0.8527 (p) REVERT: A 975 LEU cc_start: 0.8417 (mt) cc_final: 0.8150 (mt) REVERT: A 992 MET cc_start: 0.2498 (ttm) cc_final: 0.1753 (ttm) REVERT: A 1891 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7668 (tm-30) REVERT: A 1893 ARG cc_start: 0.8420 (mtt180) cc_final: 0.8085 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8147 (ptpp) REVERT: A 1895 ARG cc_start: 0.8168 (ttp-170) cc_final: 0.7864 (ttp-170) REVERT: A 1897 ARG cc_start: 0.8339 (ttp-170) cc_final: 0.7977 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8555 (ttm110) cc_final: 0.8278 (ttp-170) REVERT: A 1934 SER cc_start: 0.8471 (m) cc_final: 0.8183 (p) REVERT: A 1936 ILE cc_start: 0.8993 (mm) cc_final: 0.8450 (mt) REVERT: A 1953 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7642 (mm-30) REVERT: A 1957 ARG cc_start: 0.8399 (mtp180) cc_final: 0.8193 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7954 (tp30) cc_final: 0.7204 (tp30) REVERT: A 2026 CYS cc_start: 0.8567 (m) cc_final: 0.8197 (m) REVERT: A 2038 ILE cc_start: 0.8801 (tt) cc_final: 0.8590 (tp) REVERT: A 2041 ASP cc_start: 0.8349 (m-30) cc_final: 0.7899 (m-30) REVERT: A 2094 ARG cc_start: 0.8207 (ptp90) cc_final: 0.7518 (mtm-85) REVERT: A 2141 ASN cc_start: 0.8757 (t0) cc_final: 0.8503 (t0) REVERT: A 2144 MET cc_start: 0.7644 (mpp) cc_final: 0.7389 (mpp) REVERT: A 2150 ASP cc_start: 0.8287 (m-30) cc_final: 0.7949 (m-30) REVERT: A 2185 MET cc_start: 0.6753 (ttm) cc_final: 0.6260 (ppp) REVERT: A 2189 MET cc_start: 0.7698 (mtt) cc_final: 0.7115 (mtt) REVERT: A 2196 PHE cc_start: 0.7951 (m-80) cc_final: 0.7685 (m-80) REVERT: B 133 MET cc_start: 0.5988 (mmt) cc_final: 0.5454 (mmt) REVERT: C 2 THR cc_start: 0.7712 (t) cc_final: 0.7476 (m) REVERT: C 14 LYS cc_start: 0.8741 (mppt) cc_final: 0.7991 (mtmm) REVERT: C 44 GLN cc_start: 0.8538 (mt0) cc_final: 0.8166 (mt0) REVERT: C 71 GLN cc_start: 0.8185 (tp-100) cc_final: 0.7721 (tp-100) REVERT: C 72 ARG cc_start: 0.8758 (tpp80) cc_final: 0.7893 (ttm110) REVERT: C 76 ASP cc_start: 0.8233 (m-30) cc_final: 0.7678 (m-30) REVERT: C 83 MET cc_start: 0.8385 (mmp) cc_final: 0.8072 (mmm) REVERT: C 90 ASP cc_start: 0.8049 (t0) cc_final: 0.7292 (t0) REVERT: C 97 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7886 (mm-30) REVERT: C 103 THR cc_start: 0.8693 (m) cc_final: 0.8407 (p) REVERT: C 107 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7961 (mm-30) REVERT: C 110 ASN cc_start: 0.8773 (m-40) cc_final: 0.8544 (m110) REVERT: C 111 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7023 (tm-30) REVERT: C 115 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7505 (mt-10) REVERT: C 116 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8055 (mm-30) REVERT: C 135 TYR cc_start: 0.8925 (t80) cc_final: 0.8579 (t80) REVERT: C 142 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7689 (mp0) REVERT: C 164 LYS cc_start: 0.7822 (tptm) cc_final: 0.7599 (tptm) REVERT: C 196 MET cc_start: 0.8229 (mmm) cc_final: 0.7626 (mmm) REVERT: C 204 GLN cc_start: 0.8657 (tp40) cc_final: 0.8080 (tp-100) REVERT: C 208 ASP cc_start: 0.7992 (m-30) cc_final: 0.7562 (m-30) REVERT: C 220 MET cc_start: 0.8139 (tpp) cc_final: 0.7883 (tpp) REVERT: C 229 GLU cc_start: 0.8345 (pt0) cc_final: 0.7768 (pt0) REVERT: C 230 ASN cc_start: 0.8566 (t0) cc_final: 0.8176 (t0) REVERT: C 250 LYS cc_start: 0.8949 (mtpp) cc_final: 0.8583 (mtpp) REVERT: C 254 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8104 (mt-10) REVERT: C 369 ASN cc_start: 0.8779 (t0) cc_final: 0.8360 (t0) REVERT: C 372 PHE cc_start: 0.8479 (t80) cc_final: 0.8080 (t80) REVERT: C 374 ASP cc_start: 0.8208 (m-30) cc_final: 0.7932 (m-30) REVERT: C 382 TYR cc_start: 0.8148 (t80) cc_final: 0.7799 (t80) REVERT: D 92 ASN cc_start: 0.8737 (t0) cc_final: 0.8417 (t0) REVERT: E 15 ILE cc_start: 0.8718 (mm) cc_final: 0.8456 (mt) REVERT: E 17 SER cc_start: 0.8602 (m) cc_final: 0.8269 (p) REVERT: E 28 GLU cc_start: 0.7857 (mp0) cc_final: 0.7453 (mp0) REVERT: E 64 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7997 (mmt-90) REVERT: E 100 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7895 (mt-10) REVERT: E 162 LYS cc_start: 0.8300 (ptmt) cc_final: 0.8091 (ptmm) REVERT: E 165 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7674 (mmtt) REVERT: E 167 THR cc_start: 0.8240 (m) cc_final: 0.7933 (p) REVERT: E 168 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8032 (ttmt) REVERT: E 178 GLU cc_start: 0.7812 (tt0) cc_final: 0.7538 (tt0) REVERT: E 182 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7781 (mtmt) REVERT: E 183 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7828 (mm-30) REVERT: E 194 GLU cc_start: 0.7866 (tt0) cc_final: 0.7584 (tt0) REVERT: E 214 ASP cc_start: 0.7997 (m-30) cc_final: 0.7712 (m-30) REVERT: E 227 ASP cc_start: 0.7805 (t0) cc_final: 0.7412 (t0) REVERT: E 255 ASP cc_start: 0.7385 (p0) cc_final: 0.7173 (p0) REVERT: E 262 GLN cc_start: 0.7480 (mm-40) cc_final: 0.7258 (mm110) REVERT: E 285 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7802 (mtpp) REVERT: E 286 TYR cc_start: 0.8423 (m-10) cc_final: 0.8012 (m-80) REVERT: E 342 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6986 (mm-30) REVERT: E 352 LEU cc_start: 0.8358 (mt) cc_final: 0.8069 (mm) REVERT: E 356 ASP cc_start: 0.8135 (t0) cc_final: 0.7924 (t70) REVERT: E 370 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8242 (mt-10) REVERT: E 389 GLU cc_start: 0.7854 (tt0) cc_final: 0.7586 (tt0) REVERT: E 397 ILE cc_start: 0.8273 (tt) cc_final: 0.8001 (tt) REVERT: E 415 LEU cc_start: 0.8589 (mt) cc_final: 0.8342 (mm) REVERT: E 418 LYS cc_start: 0.8115 (ttmm) cc_final: 0.7912 (ttmm) REVERT: E 439 ASP cc_start: 0.7546 (p0) cc_final: 0.7294 (p0) REVERT: E 441 LYS cc_start: 0.8278 (mttt) cc_final: 0.7957 (mttt) REVERT: E 445 LYS cc_start: 0.7846 (mmtp) cc_final: 0.7551 (mmmm) REVERT: E 446 ILE cc_start: 0.8345 (mm) cc_final: 0.8059 (mt) REVERT: F 19 ILE cc_start: 0.8699 (tt) cc_final: 0.8405 (tp) REVERT: F 40 ARG cc_start: 0.8195 (mtt90) cc_final: 0.7827 (mtt90) REVERT: F 71 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7604 (mmm-85) REVERT: F 83 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7875 (mtmt) REVERT: F 112 GLU cc_start: 0.7894 (tp30) cc_final: 0.7562 (tp30) REVERT: F 117 GLU cc_start: 0.8225 (tp30) cc_final: 0.7580 (mm-30) REVERT: F 142 VAL cc_start: 0.8245 (t) cc_final: 0.7923 (m) REVERT: F 160 LYS cc_start: 0.8382 (ttpt) cc_final: 0.7980 (mtpt) REVERT: F 170 THR cc_start: 0.8119 (m) cc_final: 0.7900 (t) REVERT: F 177 LYS cc_start: 0.8254 (mttt) cc_final: 0.7926 (mttt) REVERT: F 181 SER cc_start: 0.8653 (m) cc_final: 0.8231 (p) REVERT: F 182 LEU cc_start: 0.8872 (mt) cc_final: 0.8663 (mm) REVERT: F 192 VAL cc_start: 0.8349 (t) cc_final: 0.7810 (p) REVERT: F 218 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6848 (tpp) REVERT: F 233 GLN cc_start: 0.7667 (tt0) cc_final: 0.7357 (tp40) REVERT: F 235 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7357 (mtp85) REVERT: F 248 ASP cc_start: 0.7880 (m-30) cc_final: 0.7586 (m-30) REVERT: F 269 LYS cc_start: 0.8213 (mmtp) cc_final: 0.7908 (mmtp) REVERT: F 274 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7817 (mm-30) REVERT: F 285 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: F 303 MET cc_start: 0.8721 (mmm) cc_final: 0.8456 (mmp) REVERT: F 329 ASN cc_start: 0.8127 (p0) cc_final: 0.7736 (p0) REVERT: F 389 VAL cc_start: 0.8568 (t) cc_final: 0.8360 (p) REVERT: F 392 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.7934 (ttp-170) REVERT: F 436 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7254 (tm-30) REVERT: F 441 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7499 (mm-40) REVERT: F 445 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7652 (mm-30) REVERT: G 15 ILE cc_start: 0.8830 (mt) cc_final: 0.8608 (mm) REVERT: G 34 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8035 (tm-30) REVERT: G 43 GLU cc_start: 0.7954 (mp0) cc_final: 0.7668 (mp0) REVERT: G 61 MET cc_start: 0.8723 (mmm) cc_final: 0.8116 (mmm) REVERT: G 89 SER cc_start: 0.8301 (m) cc_final: 0.8032 (t) REVERT: G 90 LYS cc_start: 0.8563 (tptm) cc_final: 0.7281 (tptm) REVERT: G 102 TYR cc_start: 0.8318 (m-80) cc_final: 0.8044 (m-10) REVERT: G 113 MET cc_start: 0.8388 (tpt) cc_final: 0.8143 (tpp) REVERT: G 123 ARG cc_start: 0.8334 (ttm170) cc_final: 0.7499 (ttt90) REVERT: G 126 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7076 (mt-10) REVERT: G 134 GLU cc_start: 0.7457 (tt0) cc_final: 0.7022 (tm-30) REVERT: G 137 GLU cc_start: 0.7825 (tt0) cc_final: 0.7469 (tp30) REVERT: G 147 MET cc_start: 0.6174 (mtp) cc_final: 0.5576 (mtp) REVERT: G 162 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8093 (ttmm) REVERT: G 171 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8124 (mtpp) REVERT: G 178 GLU cc_start: 0.8162 (tt0) cc_final: 0.7543 (tt0) REVERT: G 186 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7461 (mm-30) REVERT: G 193 ILE cc_start: 0.8614 (mt) cc_final: 0.8273 (mm) REVERT: G 209 TYR cc_start: 0.8430 (m-80) cc_final: 0.8191 (m-10) REVERT: G 225 LYS cc_start: 0.8393 (mmpt) cc_final: 0.7956 (mmpt) REVERT: G 227 ASP cc_start: 0.7859 (t0) cc_final: 0.7580 (t0) REVERT: G 244 ASP cc_start: 0.7480 (m-30) cc_final: 0.7234 (m-30) REVERT: G 247 ASN cc_start: 0.8465 (m-40) cc_final: 0.8226 (m110) REVERT: G 249 ARG cc_start: 0.7779 (ttt-90) cc_final: 0.7522 (ttt-90) REVERT: G 268 LYS cc_start: 0.8228 (mttt) cc_final: 0.7991 (mttt) REVERT: G 302 ASP cc_start: 0.7821 (t0) cc_final: 0.7598 (t0) REVERT: G 369 GLN cc_start: 0.7892 (mp10) cc_final: 0.7674 (mp-120) REVERT: G 371 MET cc_start: 0.8215 (mtp) cc_final: 0.8009 (mtm) REVERT: G 376 LYS cc_start: 0.8807 (tptt) cc_final: 0.8578 (tptm) REVERT: G 408 GLN cc_start: 0.7972 (mt0) cc_final: 0.7754 (mt0) REVERT: G 422 LYS cc_start: 0.8250 (mttp) cc_final: 0.7960 (mptt) REVERT: G 428 GLU cc_start: 0.8339 (mp0) cc_final: 0.7889 (mp0) REVERT: G 435 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7942 (tp30) REVERT: G 455 MET cc_start: 0.7130 (mmm) cc_final: 0.6649 (mmm) REVERT: H 18 ARG cc_start: 0.7564 (mtp85) cc_final: 0.7339 (mtp180) REVERT: H 26 SER cc_start: 0.8663 (m) cc_final: 0.8441 (p) REVERT: H 38 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7758 (mm-30) REVERT: H 64 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7937 (mtt-85) REVERT: H 83 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8496 (mtmm) REVERT: H 88 MET cc_start: 0.8147 (mmp) cc_final: 0.7849 (mmm) REVERT: H 117 GLU cc_start: 0.8117 (tp30) cc_final: 0.7843 (tp30) REVERT: H 144 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7419 (mm-30) REVERT: H 145 ILE cc_start: 0.8317 (mt) cc_final: 0.8090 (tp) REVERT: H 160 LYS cc_start: 0.8293 (mttt) cc_final: 0.8053 (mttt) REVERT: H 201 LYS cc_start: 0.8496 (ptmt) cc_final: 0.8220 (ptmt) REVERT: H 214 ASP cc_start: 0.7444 (p0) cc_final: 0.7221 (p0) REVERT: H 238 VAL cc_start: 0.8277 (t) cc_final: 0.7979 (p) REVERT: H 253 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7789 (ptm-80) REVERT: H 267 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7465 (tt0) REVERT: H 273 ARG cc_start: 0.8472 (mtt90) cc_final: 0.7970 (mtt90) REVERT: H 274 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7856 (mt-10) REVERT: H 275 GLN cc_start: 0.8267 (mm110) cc_final: 0.7925 (mm-40) REVERT: H 277 ASN cc_start: 0.8580 (m-40) cc_final: 0.8133 (m110) REVERT: H 279 LYS cc_start: 0.8493 (tppt) cc_final: 0.8277 (tptp) REVERT: H 285 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7672 (mt-10) REVERT: H 307 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7405 (mm-30) REVERT: H 313 ASN cc_start: 0.8124 (m-40) cc_final: 0.7875 (m-40) REVERT: H 314 ARG cc_start: 0.7520 (mmt180) cc_final: 0.6855 (mmt180) REVERT: H 404 GLN cc_start: 0.8341 (mt0) cc_final: 0.8064 (mt0) REVERT: H 452 PHE cc_start: 0.8584 (m-80) cc_final: 0.8378 (m-80) REVERT: I 13 GLN cc_start: 0.8086 (tp40) cc_final: 0.7880 (mm-40) REVERT: I 17 SER cc_start: 0.8674 (m) cc_final: 0.8378 (t) REVERT: I 105 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7343 (mt-10) REVERT: I 125 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8256 (ttmm) REVERT: I 134 GLU cc_start: 0.7675 (tt0) cc_final: 0.7425 (tt0) REVERT: I 137 GLU cc_start: 0.8018 (tt0) cc_final: 0.7650 (tt0) REVERT: I 139 THR cc_start: 0.8744 (m) cc_final: 0.8318 (p) REVERT: I 184 ARG cc_start: 0.8634 (mtt180) cc_final: 0.8351 (mtt180) REVERT: I 216 GLU cc_start: 0.7919 (tt0) cc_final: 0.7567 (tp30) REVERT: I 219 GLU cc_start: 0.7854 (tp30) cc_final: 0.7578 (tp30) REVERT: I 231 LYS cc_start: 0.8376 (mttt) cc_final: 0.8101 (mtpp) REVERT: I 249 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7799 (mtp85) REVERT: I 281 LYS cc_start: 0.8737 (mttt) cc_final: 0.8498 (mtmt) REVERT: I 322 SER cc_start: 0.8572 (p) cc_final: 0.8330 (t) REVERT: I 438 TYR cc_start: 0.8362 (m-80) cc_final: 0.7862 (m-80) REVERT: I 439 ASP cc_start: 0.8245 (p0) cc_final: 0.7902 (p0) REVERT: I 441 LYS cc_start: 0.8431 (mttm) cc_final: 0.7958 (mtmm) REVERT: I 445 LYS cc_start: 0.8172 (tppt) cc_final: 0.7171 (tppt) REVERT: J 90 MET cc_start: 0.8664 (mtm) cc_final: 0.8366 (mtp) REVERT: J 92 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8175 (mm-40) REVERT: J 142 VAL cc_start: 0.8609 (t) cc_final: 0.8342 (m) REVERT: J 164 LYS cc_start: 0.8387 (pttt) cc_final: 0.8065 (ptmm) REVERT: J 172 TYR cc_start: 0.8601 (m-80) cc_final: 0.7740 (m-80) REVERT: J 183 THR cc_start: 0.8311 (m) cc_final: 0.8072 (p) REVERT: J 184 LYS cc_start: 0.8301 (mttp) cc_final: 0.8085 (mttp) REVERT: J 192 VAL cc_start: 0.8712 (t) cc_final: 0.8416 (p) REVERT: J 207 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7483 (ttm170) REVERT: J 225 VAL cc_start: 0.8308 (t) cc_final: 0.8014 (p) REVERT: J 234 LYS cc_start: 0.8719 (mtpt) cc_final: 0.8346 (ttmm) REVERT: J 267 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7556 (mt-10) REVERT: J 270 SER cc_start: 0.8291 (p) cc_final: 0.7997 (t) REVERT: J 377 GLU cc_start: 0.7696 (tp30) cc_final: 0.7322 (tp30) REVERT: J 427 LYS cc_start: 0.8550 (mttm) cc_final: 0.8328 (mmtm) REVERT: J 430 TYR cc_start: 0.8711 (t80) cc_final: 0.8433 (t80) REVERT: J 444 LYS cc_start: 0.8319 (mttm) cc_final: 0.8106 (mttm) REVERT: P 254 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7795 (mp0) REVERT: P 275 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7853 (mtpt) REVERT: S 31 HIS cc_start: 0.8537 (t-90) cc_final: 0.8292 (t70) REVERT: S 59 THR cc_start: 0.9148 (m) cc_final: 0.8828 (p) REVERT: T 43 LYS cc_start: 0.8913 (mtmm) cc_final: 0.8610 (mtmm) REVERT: T 44 VAL cc_start: 0.9237 (t) cc_final: 0.8987 (p) REVERT: T 63 ASN cc_start: 0.9132 (t0) cc_final: 0.8916 (t0) REVERT: T 68 ASP cc_start: 0.8159 (t0) cc_final: 0.7685 (t0) REVERT: T 76 GLU cc_start: 0.8374 (tp30) cc_final: 0.7904 (tp30) REVERT: T 93 GLU cc_start: 0.7807 (mp0) cc_final: 0.7538 (mp0) REVERT: T 120 LYS cc_start: 0.8673 (tttp) cc_final: 0.8161 (ttpp) REVERT: U 106 ASP cc_start: 0.8356 (m-30) cc_final: 0.7889 (m-30) REVERT: V 87 VAL cc_start: 0.9169 (t) cc_final: 0.8957 (m) REVERT: W 42 ARG cc_start: 0.8366 (mtm180) cc_final: 0.7955 (ttm-80) REVERT: X 84 MET cc_start: 0.8666 (tpt) cc_final: 0.8461 (mmm) REVERT: X 91 LYS cc_start: 0.8920 (tttt) cc_final: 0.8669 (ttmm) outliers start: 82 outliers final: 45 residues processed: 1433 average time/residue: 0.2942 time to fit residues: 652.9606 Evaluate side-chains 1416 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 1367 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 2019 ARG Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2068 MET Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 285 GLU Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 397 ILE Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 264 MET Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain W residue 51 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 135 optimal weight: 0.0980 chunk 305 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 376 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 323 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 125 optimal weight: 0.0770 chunk 64 optimal weight: 0.9980 chunk 273 optimal weight: 0.8980 chunk 109 optimal weight: 0.5980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 659 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A1991 HIS ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN D 91 GLN E 420 ASN F 277 ASN G 262 GLN I 289 GLN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 39 HIS ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.119150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.100105 restraints weight = 65869.044| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.85 r_work: 0.3108 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 41479 Z= 0.120 Angle : 0.579 11.085 56931 Z= 0.301 Chirality : 0.043 0.358 6479 Planarity : 0.004 0.073 6519 Dihedral : 20.891 179.820 7413 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.13 % Allowed : 16.27 % Favored : 81.60 % 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 are not related in a simple way. whole: 1.74 (0.13), residues: 4461 helix: 1.93 (0.11), residues: 2181 sheet: 0.60 (0.20), residues: 663 loop : 0.46 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 858 TYR 0.026 0.001 TYR C 382 PHE 0.029 0.001 PHE W 78 TRP 0.082 0.002 TRP C 360 HIS 0.005 0.001 HIS I 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (41471) covalent geometry : angle 0.57896 / 0.30 (56922) hydrogen bonds : bond 0.03734 / 2.52 ( 1954) hydrogen bonds : angle 3.62535 / 2.64 ( 5374) metal coordination : bond 0.00632 / 0.21 ( 8) metal coordination : angle 1.30391 / 0.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1474 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1391 time to evaluate : 1.507 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 628 TRP cc_start: 0.8539 (t60) cc_final: 0.8260 (t60) REVERT: A 660 LEU cc_start: 0.8953 (mp) cc_final: 0.8715 (mp) REVERT: A 678 VAL cc_start: 0.8820 (OUTLIER) cc_final: 0.8552 (m) REVERT: A 704 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6753 (mt-10) REVERT: A 719 HIS cc_start: 0.8044 (m170) cc_final: 0.7754 (m-70) REVERT: A 727 LEU cc_start: 0.8966 (mt) cc_final: 0.8762 (mm) REVERT: A 747 GLU cc_start: 0.8220 (mp0) cc_final: 0.7971 (mm-30) REVERT: A 749 GLN cc_start: 0.8515 (pm20) cc_final: 0.8033 (pm20) REVERT: A 751 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8562 (tp) REVERT: A 783 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7812 (mmm) REVERT: A 789 MET cc_start: 0.7463 (mmt) cc_final: 0.7179 (mmm) REVERT: A 797 PHE cc_start: 0.7747 (m-80) cc_final: 0.7399 (m-80) REVERT: A 854 GLU cc_start: 0.8065 (pm20) cc_final: 0.7580 (pm20) REVERT: A 864 ARG cc_start: 0.8415 (mtp85) cc_final: 0.8096 (mtp85) REVERT: A 867 CYS cc_start: 0.8491 (m) cc_final: 0.8127 (m) REVERT: A 871 ASP cc_start: 0.8311 (t0) cc_final: 0.7993 (t70) REVERT: A 966 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7793 (mtp-110) REVERT: A 973 VAL cc_start: 0.8757 (t) cc_final: 0.8441 (p) REVERT: A 992 MET cc_start: 0.2462 (ttm) cc_final: 0.1717 (ttm) REVERT: A 1891 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 1893 ARG cc_start: 0.8422 (mtt180) cc_final: 0.8084 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8552 (ptpp) cc_final: 0.8120 (ptpp) REVERT: A 1895 ARG cc_start: 0.8144 (ttp-170) cc_final: 0.7829 (ttp-170) REVERT: A 1897 ARG cc_start: 0.8297 (ttp-170) cc_final: 0.7939 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8566 (ttm110) cc_final: 0.8257 (ttp-170) REVERT: A 1934 SER cc_start: 0.8381 (m) cc_final: 0.8109 (p) REVERT: A 1936 ILE cc_start: 0.8996 (mm) cc_final: 0.8446 (mt) REVERT: A 1953 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7694 (mm-30) REVERT: A 1957 ARG cc_start: 0.8406 (mtp180) cc_final: 0.8185 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7957 (tp30) cc_final: 0.7262 (tp30) REVERT: A 2026 CYS cc_start: 0.8508 (m) cc_final: 0.8147 (m) REVERT: A 2038 ILE cc_start: 0.8782 (tt) cc_final: 0.8574 (tp) REVERT: A 2041 ASP cc_start: 0.8344 (m-30) cc_final: 0.7875 (m-30) REVERT: A 2139 ASP cc_start: 0.8148 (t0) cc_final: 0.7441 (t0) REVERT: A 2141 ASN cc_start: 0.8703 (t0) cc_final: 0.8084 (t0) REVERT: A 2150 ASP cc_start: 0.8320 (m-30) cc_final: 0.7980 (m-30) REVERT: A 2169 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 2185 MET cc_start: 0.6771 (ttm) cc_final: 0.6520 (ttm) REVERT: A 2196 PHE cc_start: 0.7952 (m-80) cc_final: 0.7673 (m-80) REVERT: B 133 MET cc_start: 0.6080 (mmt) cc_final: 0.5546 (mmt) REVERT: C 2 THR cc_start: 0.7671 (t) cc_final: 0.7432 (m) REVERT: C 14 LYS cc_start: 0.8700 (mppt) cc_final: 0.8212 (mtmm) REVERT: C 44 GLN cc_start: 0.8563 (mt0) cc_final: 0.8205 (mt0) REVERT: C 55 PHE cc_start: 0.7490 (t80) cc_final: 0.7115 (t80) REVERT: C 72 ARG cc_start: 0.8733 (tpp80) cc_final: 0.7780 (ttm110) REVERT: C 76 ASP cc_start: 0.8241 (m-30) cc_final: 0.7648 (m-30) REVERT: C 83 MET cc_start: 0.8361 (mmp) cc_final: 0.8060 (mmm) REVERT: C 90 ASP cc_start: 0.7999 (t0) cc_final: 0.7245 (t0) REVERT: C 97 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7870 (mp0) REVERT: C 103 THR cc_start: 0.8670 (m) cc_final: 0.8430 (p) REVERT: C 107 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7969 (mm-30) REVERT: C 110 ASN cc_start: 0.8714 (m-40) cc_final: 0.8465 (m110) REVERT: C 111 GLU cc_start: 0.8115 (tm-30) cc_final: 0.6910 (tm-30) REVERT: C 115 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7643 (mt-10) REVERT: C 116 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8072 (mm-30) REVERT: C 135 TYR cc_start: 0.8916 (t80) cc_final: 0.8609 (t80) REVERT: C 142 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7624 (mp0) REVERT: C 164 LYS cc_start: 0.7785 (tptm) cc_final: 0.7567 (tptm) REVERT: C 196 MET cc_start: 0.8301 (mmm) cc_final: 0.7733 (mmm) REVERT: C 204 GLN cc_start: 0.8657 (tp40) cc_final: 0.8088 (tp-100) REVERT: C 208 ASP cc_start: 0.8009 (m-30) cc_final: 0.7561 (m-30) REVERT: C 220 MET cc_start: 0.8090 (tpp) cc_final: 0.7889 (tpp) REVERT: C 229 GLU cc_start: 0.8226 (pt0) cc_final: 0.7946 (pt0) REVERT: C 248 PHE cc_start: 0.8577 (p90) cc_final: 0.8328 (p90) REVERT: C 250 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8584 (mtpp) REVERT: C 369 ASN cc_start: 0.8768 (t0) cc_final: 0.8346 (t0) REVERT: C 372 PHE cc_start: 0.8471 (t80) cc_final: 0.8143 (t80) REVERT: C 382 TYR cc_start: 0.8146 (t80) cc_final: 0.7930 (t80) REVERT: D 91 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8517 (tp40) REVERT: D 92 ASN cc_start: 0.8634 (t0) cc_final: 0.8207 (t0) REVERT: E 15 ILE cc_start: 0.8714 (mm) cc_final: 0.8453 (mt) REVERT: E 17 SER cc_start: 0.8637 (m) cc_final: 0.8283 (p) REVERT: E 28 GLU cc_start: 0.7898 (mp0) cc_final: 0.7457 (mp0) REVERT: E 61 MET cc_start: 0.8659 (mmm) cc_final: 0.8416 (mmm) REVERT: E 64 ARG cc_start: 0.8331 (mtp85) cc_final: 0.7945 (mmt-90) REVERT: E 100 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7846 (mt-10) REVERT: E 138 LEU cc_start: 0.8304 (mp) cc_final: 0.8094 (mp) REVERT: E 165 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7632 (mmtt) REVERT: E 167 THR cc_start: 0.8250 (m) cc_final: 0.7935 (p) REVERT: E 168 LYS cc_start: 0.8365 (ttmt) cc_final: 0.8008 (ttmt) REVERT: E 171 LYS cc_start: 0.7779 (tttt) cc_final: 0.7323 (tttp) REVERT: E 173 ASP cc_start: 0.7881 (m-30) cc_final: 0.7677 (m-30) REVERT: E 178 GLU cc_start: 0.7820 (tt0) cc_final: 0.7556 (tt0) REVERT: E 182 LYS cc_start: 0.8093 (mtmt) cc_final: 0.7765 (mtmt) REVERT: E 183 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7770 (mm-30) REVERT: E 184 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7425 (mtm-85) REVERT: E 194 GLU cc_start: 0.7852 (tt0) cc_final: 0.7575 (tt0) REVERT: E 214 ASP cc_start: 0.7983 (m-30) cc_final: 0.7707 (m-30) REVERT: E 227 ASP cc_start: 0.7837 (t0) cc_final: 0.7624 (t0) REVERT: E 260 MET cc_start: 0.8239 (mmp) cc_final: 0.8039 (mmm) REVERT: E 262 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7190 (mm110) REVERT: E 285 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7783 (mtpp) REVERT: E 286 TYR cc_start: 0.8413 (m-10) cc_final: 0.8026 (m-80) REVERT: E 342 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6896 (mm-30) REVERT: E 352 LEU cc_start: 0.8395 (mt) cc_final: 0.8111 (mm) REVERT: E 356 ASP cc_start: 0.8130 (t0) cc_final: 0.7665 (t0) REVERT: E 370 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8086 (mt-10) REVERT: E 389 GLU cc_start: 0.7894 (tt0) cc_final: 0.7618 (tt0) REVERT: E 397 ILE cc_start: 0.8259 (tt) cc_final: 0.7988 (tt) REVERT: E 415 LEU cc_start: 0.8658 (mt) cc_final: 0.8436 (mm) REVERT: E 439 ASP cc_start: 0.7451 (p0) cc_final: 0.7177 (p0) REVERT: E 441 LYS cc_start: 0.8253 (mttt) cc_final: 0.7922 (mttt) REVERT: E 445 LYS cc_start: 0.7850 (mmtp) cc_final: 0.7559 (mmmm) REVERT: E 446 ILE cc_start: 0.8361 (mm) cc_final: 0.8064 (mt) REVERT: F 19 ILE cc_start: 0.8713 (tt) cc_final: 0.8328 (tp) REVERT: F 40 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7824 (mtt90) REVERT: F 71 ARG cc_start: 0.7896 (mmt90) cc_final: 0.7622 (mmm-85) REVERT: F 83 LYS cc_start: 0.8113 (mtmt) cc_final: 0.7859 (mtmt) REVERT: F 112 GLU cc_start: 0.7970 (tp30) cc_final: 0.7711 (tp30) REVERT: F 117 GLU cc_start: 0.8192 (tp30) cc_final: 0.7559 (mm-30) REVERT: F 142 VAL cc_start: 0.8237 (t) cc_final: 0.7910 (m) REVERT: F 160 LYS cc_start: 0.8357 (ttpt) cc_final: 0.7943 (mtpt) REVERT: F 170 THR cc_start: 0.8116 (m) cc_final: 0.7894 (t) REVERT: F 177 LYS cc_start: 0.8237 (mttt) cc_final: 0.7928 (mttt) REVERT: F 181 SER cc_start: 0.8650 (m) cc_final: 0.8227 (p) REVERT: F 182 LEU cc_start: 0.8913 (mt) cc_final: 0.8663 (mm) REVERT: F 192 VAL cc_start: 0.8338 (t) cc_final: 0.7786 (p) REVERT: F 218 MET cc_start: 0.7267 (OUTLIER) cc_final: 0.6862 (tpp) REVERT: F 233 GLN cc_start: 0.7636 (tt0) cc_final: 0.7405 (tp40) REVERT: F 248 ASP cc_start: 0.7898 (m-30) cc_final: 0.7619 (m-30) REVERT: F 285 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7513 (mp0) REVERT: F 303 MET cc_start: 0.8732 (mmm) cc_final: 0.8483 (mmp) REVERT: F 319 ASP cc_start: 0.8078 (p0) cc_final: 0.7850 (p0) REVERT: F 329 ASN cc_start: 0.8156 (p0) cc_final: 0.7754 (p0) REVERT: F 389 VAL cc_start: 0.8597 (t) cc_final: 0.8382 (p) REVERT: F 392 ARG cc_start: 0.8228 (ttp-110) cc_final: 0.7921 (ttp-170) REVERT: F 441 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7509 (mm-40) REVERT: F 445 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7732 (mm-30) REVERT: G 15 ILE cc_start: 0.8828 (mt) cc_final: 0.8605 (mm) REVERT: G 34 GLN cc_start: 0.8292 (tm-30) cc_final: 0.8043 (tm-30) REVERT: G 43 GLU cc_start: 0.7943 (mp0) cc_final: 0.7728 (mp0) REVERT: G 61 MET cc_start: 0.8716 (mmm) cc_final: 0.8117 (mmm) REVERT: G 89 SER cc_start: 0.8284 (m) cc_final: 0.8019 (t) REVERT: G 90 LYS cc_start: 0.8580 (tptm) cc_final: 0.8053 (tptm) REVERT: G 102 TYR cc_start: 0.8305 (m-80) cc_final: 0.8068 (m-10) REVERT: G 113 MET cc_start: 0.8375 (tpt) cc_final: 0.8138 (tpp) REVERT: G 126 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7034 (mt-10) REVERT: G 128 LYS cc_start: 0.8314 (tttt) cc_final: 0.8019 (tttt) REVERT: G 134 GLU cc_start: 0.7507 (tt0) cc_final: 0.7052 (tm-30) REVERT: G 137 GLU cc_start: 0.7796 (tt0) cc_final: 0.7426 (tp30) REVERT: G 147 MET cc_start: 0.6271 (mtp) cc_final: 0.5643 (mtp) REVERT: G 162 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8155 (ttmm) REVERT: G 171 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8121 (mtpp) REVERT: G 178 GLU cc_start: 0.8159 (tt0) cc_final: 0.7541 (tt0) REVERT: G 183 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8064 (mm-30) REVERT: G 186 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7474 (mm-30) REVERT: G 193 ILE cc_start: 0.8634 (mt) cc_final: 0.8288 (mm) REVERT: G 209 TYR cc_start: 0.8418 (m-80) cc_final: 0.8161 (m-10) REVERT: G 212 GLU cc_start: 0.7880 (pm20) cc_final: 0.7643 (pm20) REVERT: G 225 LYS cc_start: 0.8391 (mmpt) cc_final: 0.7909 (mmpt) REVERT: G 227 ASP cc_start: 0.7856 (t0) cc_final: 0.7539 (t0) REVERT: G 229 HIS cc_start: 0.8463 (t-90) cc_final: 0.8212 (t70) REVERT: G 244 ASP cc_start: 0.7466 (m-30) cc_final: 0.7218 (m-30) REVERT: G 247 ASN cc_start: 0.8464 (m-40) cc_final: 0.8225 (m-40) REVERT: G 249 ARG cc_start: 0.7785 (ttt-90) cc_final: 0.7531 (ttt-90) REVERT: G 302 ASP cc_start: 0.7830 (t0) cc_final: 0.7608 (t0) REVERT: G 369 GLN cc_start: 0.7903 (mp10) cc_final: 0.7691 (mp-120) REVERT: G 376 LYS cc_start: 0.8824 (tptt) cc_final: 0.8584 (tptm) REVERT: G 408 GLN cc_start: 0.7966 (mt0) cc_final: 0.7734 (mt0) REVERT: G 422 LYS cc_start: 0.8291 (mttp) cc_final: 0.8041 (mptt) REVERT: G 428 GLU cc_start: 0.8311 (mp0) cc_final: 0.7855 (mp0) REVERT: G 435 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7945 (tp30) REVERT: G 455 MET cc_start: 0.7018 (mmm) cc_final: 0.6459 (mmm) REVERT: H 18 ARG cc_start: 0.7648 (mtp85) cc_final: 0.7410 (mtp180) REVERT: H 38 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7775 (mm-30) REVERT: H 64 ARG cc_start: 0.8209 (mtt180) cc_final: 0.7934 (mtt-85) REVERT: H 83 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8310 (mttp) REVERT: H 88 MET cc_start: 0.8097 (mmp) cc_final: 0.7808 (mmm) REVERT: H 117 GLU cc_start: 0.8139 (tp30) cc_final: 0.7823 (tp30) REVERT: H 135 THR cc_start: 0.7973 (m) cc_final: 0.7766 (p) REVERT: H 144 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7398 (mm-30) REVERT: H 145 ILE cc_start: 0.8314 (mt) cc_final: 0.8076 (tp) REVERT: H 160 LYS cc_start: 0.8275 (mttt) cc_final: 0.8037 (mttt) REVERT: H 201 LYS cc_start: 0.8490 (ptmt) cc_final: 0.8207 (ptmt) REVERT: H 214 ASP cc_start: 0.7411 (p0) cc_final: 0.7192 (p0) REVERT: H 225 VAL cc_start: 0.8563 (m) cc_final: 0.8093 (p) REVERT: H 238 VAL cc_start: 0.8281 (t) cc_final: 0.7982 (p) REVERT: H 253 ARG cc_start: 0.8090 (ptm-80) cc_final: 0.7753 (ptm-80) REVERT: H 267 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7980 (mt-10) REVERT: H 273 ARG cc_start: 0.8468 (mtt90) cc_final: 0.7941 (mtt90) REVERT: H 274 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7882 (mt-10) REVERT: H 275 GLN cc_start: 0.8258 (mm110) cc_final: 0.7917 (mm-40) REVERT: H 277 ASN cc_start: 0.8594 (m-40) cc_final: 0.8127 (m110) REVERT: H 279 LYS cc_start: 0.8502 (tppt) cc_final: 0.8287 (tptp) REVERT: H 285 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7648 (mt-10) REVERT: H 313 ASN cc_start: 0.8115 (m-40) cc_final: 0.7882 (m-40) REVERT: H 314 ARG cc_start: 0.7531 (mmt180) cc_final: 0.6863 (mmt180) REVERT: H 452 PHE cc_start: 0.8607 (m-80) cc_final: 0.8390 (m-80) REVERT: I 13 GLN cc_start: 0.8093 (tp40) cc_final: 0.7891 (mm-40) REVERT: I 105 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7330 (mt-10) REVERT: I 125 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8280 (ttmm) REVERT: I 134 GLU cc_start: 0.7682 (tt0) cc_final: 0.7433 (tt0) REVERT: I 137 GLU cc_start: 0.7976 (tt0) cc_final: 0.7631 (tt0) REVERT: I 139 THR cc_start: 0.8687 (m) cc_final: 0.8279 (p) REVERT: I 184 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8342 (mtt180) REVERT: I 216 GLU cc_start: 0.7892 (tt0) cc_final: 0.7549 (tp30) REVERT: I 219 GLU cc_start: 0.7826 (tp30) cc_final: 0.7538 (tp30) REVERT: I 231 LYS cc_start: 0.8345 (mttt) cc_final: 0.8054 (mtpp) REVERT: I 249 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7807 (mtp85) REVERT: I 259 MET cc_start: 0.8197 (ptp) cc_final: 0.7978 (ptp) REVERT: I 267 LYS cc_start: 0.8231 (tptm) cc_final: 0.8028 (tttp) REVERT: I 281 LYS cc_start: 0.8745 (mttt) cc_final: 0.8507 (mtmt) REVERT: I 322 SER cc_start: 0.8575 (p) cc_final: 0.8348 (t) REVERT: I 359 MET cc_start: 0.8146 (mtp) cc_final: 0.7912 (mtp) REVERT: I 438 TYR cc_start: 0.8371 (m-80) cc_final: 0.7818 (m-80) REVERT: I 439 ASP cc_start: 0.8258 (p0) cc_final: 0.7892 (p0) REVERT: I 441 LYS cc_start: 0.8401 (mttm) cc_final: 0.7937 (mtmm) REVERT: I 445 LYS cc_start: 0.8148 (tppt) cc_final: 0.7176 (tppt) REVERT: I 446 ILE cc_start: 0.8193 (mt) cc_final: 0.7983 (mp) REVERT: I 447 LEU cc_start: 0.7407 (mp) cc_final: 0.7190 (mt) REVERT: J 38 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7745 (tp30) REVERT: J 90 MET cc_start: 0.8615 (mtm) cc_final: 0.8327 (mtp) REVERT: J 92 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8153 (mm-40) REVERT: J 142 VAL cc_start: 0.8640 (t) cc_final: 0.8401 (m) REVERT: J 164 LYS cc_start: 0.8421 (pttt) cc_final: 0.8082 (ptmm) REVERT: J 172 TYR cc_start: 0.8576 (m-80) cc_final: 0.7727 (m-80) REVERT: J 183 THR cc_start: 0.8290 (m) cc_final: 0.8050 (p) REVERT: J 184 LYS cc_start: 0.8283 (mttp) cc_final: 0.8049 (mttp) REVERT: J 192 VAL cc_start: 0.8731 (t) cc_final: 0.8425 (p) REVERT: J 207 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7494 (ttm170) REVERT: J 225 VAL cc_start: 0.8310 (t) cc_final: 0.8033 (p) REVERT: J 267 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7557 (mt-10) REVERT: J 270 SER cc_start: 0.8264 (p) cc_final: 0.7930 (t) REVERT: J 377 GLU cc_start: 0.7594 (tp30) cc_final: 0.7214 (tp30) REVERT: J 378 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7728 (mt-10) REVERT: J 427 LYS cc_start: 0.8520 (mttm) cc_final: 0.8291 (mmtm) REVERT: J 430 TYR cc_start: 0.8662 (t80) cc_final: 0.8400 (t80) REVERT: J 436 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6516 (tm-30) REVERT: J 444 LYS cc_start: 0.8318 (mttm) cc_final: 0.8105 (mttm) REVERT: P 252 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8582 (mtmm) REVERT: P 254 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7779 (mp0) REVERT: S 31 HIS cc_start: 0.8517 (t-90) cc_final: 0.8267 (t70) REVERT: S 59 THR cc_start: 0.9131 (m) cc_final: 0.8815 (p) REVERT: S 73 ASN cc_start: 0.8805 (m110) cc_final: 0.8458 (t0) REVERT: S 112 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7959 (mt0) REVERT: T 43 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8620 (mtmm) REVERT: T 44 VAL cc_start: 0.9240 (t) cc_final: 0.8989 (p) REVERT: T 63 ASN cc_start: 0.9124 (t0) cc_final: 0.8899 (t0) REVERT: T 68 ASP cc_start: 0.8147 (t0) cc_final: 0.7671 (t0) REVERT: T 76 GLU cc_start: 0.8380 (tp30) cc_final: 0.7908 (tp30) REVERT: T 120 LYS cc_start: 0.8685 (tttp) cc_final: 0.8167 (ttpp) REVERT: U 106 ASP cc_start: 0.8354 (m-30) cc_final: 0.7887 (m-30) REVERT: V 35 ARG cc_start: 0.8812 (mtp85) cc_final: 0.8595 (mtp85) REVERT: V 87 VAL cc_start: 0.9175 (t) cc_final: 0.8968 (m) REVERT: W 42 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7968 (ttm-80) REVERT: X 67 ARG cc_start: 0.8411 (ttm110) cc_final: 0.8166 (ttm110) outliers start: 83 outliers final: 52 residues processed: 1412 average time/residue: 0.2938 time to fit residues: 642.2763 Evaluate side-chains 1432 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1375 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 2019 ARG Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2068 MET Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain G residue 377 ILE Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 420 ASN Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 226 GLN Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain S residue 35 ARG Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain U residue 86 SER Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 92 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 353 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 373 optimal weight: 1.9990 chunk 285 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 333 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 348 optimal weight: 2.9990 chunk 11 optimal weight: 0.2980 chunk 271 optimal weight: 0.0470 chunk 401 optimal weight: 4.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 659 HIS A 730 GLN ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN E 392 ASN E 420 ASN F 277 ASN G 262 GLN ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.099416 restraints weight = 65766.753| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.85 r_work: 0.3108 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41479 Z= 0.142 Angle : 0.592 12.279 56931 Z= 0.307 Chirality : 0.044 0.357 6479 Planarity : 0.004 0.078 6519 Dihedral : 20.898 179.806 7413 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.98 % Allowed : 17.48 % Favored : 80.54 % 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 are not related in a simple way. whole: 1.70 (0.13), residues: 4461 helix: 1.90 (0.11), residues: 2180 sheet: 0.54 (0.20), residues: 675 loop : 0.45 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG W 63 TYR 0.026 0.001 TYR C 382 PHE 0.028 0.001 PHE W 78 TRP 0.088 0.002 TRP C 360 HIS 0.008 0.001 HIS I 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (41471) covalent geometry : angle 0.59195 / 0.31 (56922) hydrogen bonds : bond 0.03812 / 2.57 ( 1954) hydrogen bonds : angle 3.62786 / 2.64 ( 5374) metal coordination : bond 0.00795 / 0.28 ( 8) metal coordination : angle 1.33349 / 0.67 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1462 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1385 time to evaluate : 1.435 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: A 628 TRP cc_start: 0.8509 (t60) cc_final: 0.8236 (t60) REVERT: A 660 LEU cc_start: 0.8967 (mp) cc_final: 0.8750 (mp) REVERT: A 678 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8573 (m) REVERT: A 704 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6702 (mt-10) REVERT: A 719 HIS cc_start: 0.8018 (m170) cc_final: 0.7812 (m-70) REVERT: A 747 GLU cc_start: 0.8060 (mp0) cc_final: 0.7845 (mm-30) REVERT: A 749 GLN cc_start: 0.8517 (pm20) cc_final: 0.7924 (pm20) REVERT: A 751 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8557 (tp) REVERT: A 783 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7821 (mmm) REVERT: A 789 MET cc_start: 0.7482 (mmt) cc_final: 0.7190 (mmm) REVERT: A 854 GLU cc_start: 0.8069 (pm20) cc_final: 0.7584 (pm20) REVERT: A 864 ARG cc_start: 0.8437 (mtp85) cc_final: 0.8143 (mtp85) REVERT: A 867 CYS cc_start: 0.8456 (m) cc_final: 0.8110 (m) REVERT: A 966 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7806 (mtp-110) REVERT: A 973 VAL cc_start: 0.8765 (t) cc_final: 0.8319 (p) REVERT: A 976 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 992 MET cc_start: 0.2471 (ttm) cc_final: 0.1723 (ttm) REVERT: A 1891 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7682 (tm-30) REVERT: A 1893 ARG cc_start: 0.8425 (mtt180) cc_final: 0.8083 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8581 (ptpp) cc_final: 0.8154 (ptpp) REVERT: A 1895 ARG cc_start: 0.8145 (ttp-170) cc_final: 0.7833 (ttp-170) REVERT: A 1897 ARG cc_start: 0.8318 (ttp-170) cc_final: 0.7960 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8572 (ttm110) cc_final: 0.8238 (ttp-170) REVERT: A 1934 SER cc_start: 0.8385 (m) cc_final: 0.8117 (p) REVERT: A 1936 ILE cc_start: 0.8989 (mm) cc_final: 0.8454 (mt) REVERT: A 1953 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7707 (mm-30) REVERT: A 1957 ARG cc_start: 0.8402 (mtp180) cc_final: 0.8191 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7975 (tp30) cc_final: 0.7281 (tp30) REVERT: A 2026 CYS cc_start: 0.8511 (m) cc_final: 0.8172 (m) REVERT: A 2038 ILE cc_start: 0.8782 (tt) cc_final: 0.8565 (tp) REVERT: A 2041 ASP cc_start: 0.8365 (m-30) cc_final: 0.7872 (m-30) REVERT: A 2054 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 2139 ASP cc_start: 0.8079 (t0) cc_final: 0.7762 (t0) REVERT: A 2150 ASP cc_start: 0.8331 (m-30) cc_final: 0.8052 (m-30) REVERT: A 2169 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 2185 MET cc_start: 0.6825 (ttm) cc_final: 0.6559 (ttm) REVERT: A 2196 PHE cc_start: 0.7964 (m-80) cc_final: 0.7676 (m-80) REVERT: B 133 MET cc_start: 0.6061 (mmt) cc_final: 0.5516 (mmt) REVERT: C 2 THR cc_start: 0.7706 (t) cc_final: 0.7474 (m) REVERT: C 14 LYS cc_start: 0.8695 (mppt) cc_final: 0.8308 (mptp) REVERT: C 44 GLN cc_start: 0.8563 (mt0) cc_final: 0.8147 (mt0) REVERT: C 55 PHE cc_start: 0.7493 (t80) cc_final: 0.7091 (t80) REVERT: C 65 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8415 (tp) REVERT: C 71 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7883 (tp-100) REVERT: C 72 ARG cc_start: 0.8778 (tpp80) cc_final: 0.7945 (ttm110) REVERT: C 76 ASP cc_start: 0.8274 (m-30) cc_final: 0.7735 (m-30) REVERT: C 83 MET cc_start: 0.8390 (mmp) cc_final: 0.8071 (mmm) REVERT: C 90 ASP cc_start: 0.8049 (t0) cc_final: 0.7266 (t0) REVERT: C 103 THR cc_start: 0.8662 (m) cc_final: 0.8428 (p) REVERT: C 107 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7949 (mm-30) REVERT: C 111 GLU cc_start: 0.8139 (tm-30) cc_final: 0.6905 (tm-30) REVERT: C 115 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 135 TYR cc_start: 0.8918 (t80) cc_final: 0.8608 (t80) REVERT: C 142 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7619 (mp0) REVERT: C 164 LYS cc_start: 0.7798 (tptm) cc_final: 0.7577 (tptm) REVERT: C 204 GLN cc_start: 0.8670 (tp40) cc_final: 0.8061 (tp-100) REVERT: C 208 ASP cc_start: 0.8018 (m-30) cc_final: 0.7557 (m-30) REVERT: C 220 MET cc_start: 0.8095 (tpp) cc_final: 0.7875 (tpp) REVERT: C 226 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.6641 (mttt) REVERT: C 229 GLU cc_start: 0.8212 (pt0) cc_final: 0.7931 (pm20) REVERT: C 250 LYS cc_start: 0.8930 (mtpp) cc_final: 0.8586 (mtpp) REVERT: C 254 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8073 (mt-10) REVERT: C 369 ASN cc_start: 0.8793 (t0) cc_final: 0.8318 (t0) REVERT: C 372 PHE cc_start: 0.8473 (t80) cc_final: 0.8150 (t80) REVERT: C 382 TYR cc_start: 0.8327 (t80) cc_final: 0.7794 (t80) REVERT: D 91 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8275 (tp40) REVERT: D 92 ASN cc_start: 0.8595 (t0) cc_final: 0.8238 (t0) REVERT: E 15 ILE cc_start: 0.8708 (mm) cc_final: 0.8448 (mt) REVERT: E 17 SER cc_start: 0.8650 (m) cc_final: 0.8296 (p) REVERT: E 28 GLU cc_start: 0.7929 (mp0) cc_final: 0.7494 (mp0) REVERT: E 61 MET cc_start: 0.8653 (mmm) cc_final: 0.8419 (mmm) REVERT: E 64 ARG cc_start: 0.8336 (mtp85) cc_final: 0.7945 (mmt-90) REVERT: E 85 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8353 (mm-40) REVERT: E 100 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7850 (mt-10) REVERT: E 165 LYS cc_start: 0.7948 (mmtt) cc_final: 0.7647 (mmtt) REVERT: E 167 THR cc_start: 0.8246 (m) cc_final: 0.7943 (p) REVERT: E 168 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8019 (ttmt) REVERT: E 173 ASP cc_start: 0.7892 (m-30) cc_final: 0.7676 (m-30) REVERT: E 178 GLU cc_start: 0.7834 (tt0) cc_final: 0.7563 (tt0) REVERT: E 182 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7781 (mtmt) REVERT: E 183 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7786 (mm-30) REVERT: E 184 ARG cc_start: 0.7742 (mtm-85) cc_final: 0.7434 (mtm-85) REVERT: E 194 GLU cc_start: 0.7854 (tt0) cc_final: 0.7573 (tt0) REVERT: E 214 ASP cc_start: 0.8007 (m-30) cc_final: 0.7741 (m-30) REVERT: E 260 MET cc_start: 0.8211 (mmp) cc_final: 0.7906 (mmm) REVERT: E 285 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7781 (mtpp) REVERT: E 286 TYR cc_start: 0.8413 (m-10) cc_final: 0.8086 (m-80) REVERT: E 352 LEU cc_start: 0.8411 (mt) cc_final: 0.8130 (mm) REVERT: E 356 ASP cc_start: 0.8143 (t0) cc_final: 0.7658 (t0) REVERT: E 370 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8223 (mt-10) REVERT: E 389 GLU cc_start: 0.7910 (tt0) cc_final: 0.7599 (tt0) REVERT: E 397 ILE cc_start: 0.8250 (tt) cc_final: 0.7991 (tt) REVERT: E 415 LEU cc_start: 0.8738 (mt) cc_final: 0.8517 (mm) REVERT: E 439 ASP cc_start: 0.7467 (p0) cc_final: 0.7202 (p0) REVERT: E 441 LYS cc_start: 0.8276 (mttt) cc_final: 0.7950 (mttt) REVERT: E 445 LYS cc_start: 0.7864 (mmtp) cc_final: 0.7575 (mmmm) REVERT: E 446 ILE cc_start: 0.8387 (mm) cc_final: 0.8095 (mt) REVERT: F 19 ILE cc_start: 0.8653 (tt) cc_final: 0.8357 (tp) REVERT: F 40 ARG cc_start: 0.8190 (mtt90) cc_final: 0.7807 (mtt90) REVERT: F 71 ARG cc_start: 0.7909 (mmt90) cc_final: 0.7626 (mmm-85) REVERT: F 83 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7863 (mtmt) REVERT: F 112 GLU cc_start: 0.8007 (tp30) cc_final: 0.7765 (tp30) REVERT: F 117 GLU cc_start: 0.8188 (tp30) cc_final: 0.7528 (mm-30) REVERT: F 142 VAL cc_start: 0.8178 (t) cc_final: 0.7865 (m) REVERT: F 160 LYS cc_start: 0.8351 (ttpt) cc_final: 0.7930 (mtpt) REVERT: F 170 THR cc_start: 0.8113 (m) cc_final: 0.7900 (t) REVERT: F 177 LYS cc_start: 0.8239 (mttt) cc_final: 0.7921 (mttt) REVERT: F 181 SER cc_start: 0.8648 (m) cc_final: 0.8228 (p) REVERT: F 182 LEU cc_start: 0.8915 (mt) cc_final: 0.8667 (mm) REVERT: F 192 VAL cc_start: 0.8337 (t) cc_final: 0.7788 (p) REVERT: F 197 LYS cc_start: 0.7771 (mtpt) cc_final: 0.6950 (mtpt) REVERT: F 218 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6868 (tpp) REVERT: F 233 GLN cc_start: 0.7660 (tt0) cc_final: 0.6780 (tp40) REVERT: F 235 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7566 (mtp85) REVERT: F 248 ASP cc_start: 0.7911 (m-30) cc_final: 0.7643 (m-30) REVERT: F 267 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7054 (mt-10) REVERT: F 285 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7492 (mp0) REVERT: F 303 MET cc_start: 0.8727 (mmm) cc_final: 0.8453 (mmp) REVERT: F 319 ASP cc_start: 0.8113 (p0) cc_final: 0.7871 (p0) REVERT: F 329 ASN cc_start: 0.8214 (p0) cc_final: 0.7827 (p0) REVERT: F 389 VAL cc_start: 0.8605 (t) cc_final: 0.8382 (p) REVERT: F 392 ARG cc_start: 0.8230 (ttp-110) cc_final: 0.7925 (ttp-170) REVERT: F 441 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7494 (mm-40) REVERT: F 445 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7772 (mm-30) REVERT: G 15 ILE cc_start: 0.8836 (mt) cc_final: 0.8611 (mm) REVERT: G 43 GLU cc_start: 0.7958 (mp0) cc_final: 0.7747 (mp0) REVERT: G 61 MET cc_start: 0.8711 (mmm) cc_final: 0.8074 (mmm) REVERT: G 89 SER cc_start: 0.8304 (m) cc_final: 0.8029 (t) REVERT: G 90 LYS cc_start: 0.8571 (tptm) cc_final: 0.8053 (tptm) REVERT: G 113 MET cc_start: 0.8429 (tpt) cc_final: 0.8186 (tpp) REVERT: G 125 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7866 (mmmt) REVERT: G 126 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7053 (mt-10) REVERT: G 134 GLU cc_start: 0.7474 (tt0) cc_final: 0.7033 (tm-30) REVERT: G 137 GLU cc_start: 0.7796 (tt0) cc_final: 0.7445 (tp30) REVERT: G 147 MET cc_start: 0.6271 (mtp) cc_final: 0.5649 (mtp) REVERT: G 162 LYS cc_start: 0.8491 (ttmt) cc_final: 0.8162 (ttmm) REVERT: G 171 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8147 (mtpp) REVERT: G 178 GLU cc_start: 0.8170 (tt0) cc_final: 0.7550 (tt0) REVERT: G 183 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8066 (mm-30) REVERT: G 186 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7534 (mm-30) REVERT: G 193 ILE cc_start: 0.8626 (mt) cc_final: 0.8292 (mm) REVERT: G 209 TYR cc_start: 0.8439 (m-80) cc_final: 0.8236 (m-10) REVERT: G 225 LYS cc_start: 0.8395 (mmpt) cc_final: 0.7927 (mmpt) REVERT: G 227 ASP cc_start: 0.7861 (t0) cc_final: 0.7553 (t0) REVERT: G 229 HIS cc_start: 0.8453 (t-90) cc_final: 0.8208 (t70) REVERT: G 244 ASP cc_start: 0.7462 (m-30) cc_final: 0.7219 (m-30) REVERT: G 247 ASN cc_start: 0.8488 (m-40) cc_final: 0.8255 (m-40) REVERT: G 249 ARG cc_start: 0.7817 (ttt-90) cc_final: 0.7562 (ttt-90) REVERT: G 302 ASP cc_start: 0.7845 (t0) cc_final: 0.7624 (t0) REVERT: G 376 LYS cc_start: 0.8827 (tptt) cc_final: 0.8573 (tptm) REVERT: G 408 GLN cc_start: 0.7958 (mt0) cc_final: 0.7742 (mt0) REVERT: G 422 LYS cc_start: 0.8296 (mttp) cc_final: 0.8040 (mptt) REVERT: G 428 GLU cc_start: 0.8320 (mp0) cc_final: 0.7858 (mp0) REVERT: G 435 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8013 (tp30) REVERT: H 18 ARG cc_start: 0.7691 (mtp85) cc_final: 0.7465 (mtp180) REVERT: H 38 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7786 (mm-30) REVERT: H 64 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7929 (mtt-85) REVERT: H 83 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8318 (mttp) REVERT: H 88 MET cc_start: 0.8064 (mmp) cc_final: 0.7793 (mmm) REVERT: H 90 MET cc_start: 0.8351 (mtp) cc_final: 0.8137 (mtp) REVERT: H 135 THR cc_start: 0.7963 (m) cc_final: 0.7751 (p) REVERT: H 144 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7415 (mm-30) REVERT: H 145 ILE cc_start: 0.8329 (mt) cc_final: 0.8078 (tp) REVERT: H 160 LYS cc_start: 0.8288 (mttt) cc_final: 0.8068 (mttt) REVERT: H 201 LYS cc_start: 0.8503 (ptmt) cc_final: 0.8228 (ptmt) REVERT: H 214 ASP cc_start: 0.7436 (p0) cc_final: 0.7225 (p0) REVERT: H 238 VAL cc_start: 0.8222 (t) cc_final: 0.7924 (p) REVERT: H 253 ARG cc_start: 0.8089 (ptm-80) cc_final: 0.7755 (ptm-80) REVERT: H 267 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7984 (mt-10) REVERT: H 273 ARG cc_start: 0.8473 (mtt90) cc_final: 0.7867 (mtt90) REVERT: H 274 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7903 (mt-10) REVERT: H 275 GLN cc_start: 0.8248 (mm110) cc_final: 0.7903 (mm-40) REVERT: H 277 ASN cc_start: 0.8605 (m-40) cc_final: 0.8122 (m110) REVERT: H 279 LYS cc_start: 0.8515 (tppt) cc_final: 0.8300 (tptp) REVERT: H 285 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7650 (mt-10) REVERT: H 307 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7358 (mm-30) REVERT: H 313 ASN cc_start: 0.8112 (m-40) cc_final: 0.7882 (m-40) REVERT: H 314 ARG cc_start: 0.7541 (mmt180) cc_final: 0.6894 (mmt180) REVERT: H 452 PHE cc_start: 0.8607 (m-80) cc_final: 0.8392 (m-80) REVERT: I 13 GLN cc_start: 0.8086 (tp40) cc_final: 0.7877 (mm-40) REVERT: I 105 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7359 (mt-10) REVERT: I 125 LYS cc_start: 0.8594 (ttpp) cc_final: 0.8289 (ttmm) REVERT: I 134 GLU cc_start: 0.7697 (tt0) cc_final: 0.7445 (tt0) REVERT: I 137 GLU cc_start: 0.7967 (tt0) cc_final: 0.7618 (tt0) REVERT: I 139 THR cc_start: 0.8713 (m) cc_final: 0.8303 (p) REVERT: I 184 ARG cc_start: 0.8626 (mtt180) cc_final: 0.8348 (mtt180) REVERT: I 216 GLU cc_start: 0.8016 (tt0) cc_final: 0.7677 (tp30) REVERT: I 219 GLU cc_start: 0.7817 (tp30) cc_final: 0.7543 (tp30) REVERT: I 231 LYS cc_start: 0.8360 (mttt) cc_final: 0.8073 (mtpp) REVERT: I 249 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7797 (mtp85) REVERT: I 259 MET cc_start: 0.8190 (ptp) cc_final: 0.7894 (ptm) REVERT: I 267 LYS cc_start: 0.8244 (tptm) cc_final: 0.8038 (tttp) REVERT: I 281 LYS cc_start: 0.8758 (mttt) cc_final: 0.8519 (mtmt) REVERT: I 322 SER cc_start: 0.8577 (p) cc_final: 0.8349 (t) REVERT: I 359 MET cc_start: 0.8153 (mtp) cc_final: 0.7929 (mtp) REVERT: I 438 TYR cc_start: 0.8388 (m-80) cc_final: 0.7893 (m-80) REVERT: I 439 ASP cc_start: 0.8245 (p0) cc_final: 0.7884 (p0) REVERT: I 441 LYS cc_start: 0.8407 (mttm) cc_final: 0.7943 (mtmm) REVERT: I 445 LYS cc_start: 0.8161 (tppt) cc_final: 0.7181 (tppt) REVERT: I 446 ILE cc_start: 0.8200 (mt) cc_final: 0.7989 (mp) REVERT: I 447 LEU cc_start: 0.7463 (mp) cc_final: 0.7224 (mt) REVERT: J 38 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7757 (tp30) REVERT: J 90 MET cc_start: 0.8630 (mtm) cc_final: 0.8340 (mtp) REVERT: J 92 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8159 (mm-40) REVERT: J 142 VAL cc_start: 0.8648 (t) cc_final: 0.8416 (m) REVERT: J 164 LYS cc_start: 0.8424 (pttt) cc_final: 0.8070 (ptmm) REVERT: J 183 THR cc_start: 0.8294 (m) cc_final: 0.8064 (p) REVERT: J 184 LYS cc_start: 0.8273 (mttp) cc_final: 0.8041 (mttp) REVERT: J 192 VAL cc_start: 0.8747 (t) cc_final: 0.8419 (p) REVERT: J 207 ARG cc_start: 0.7806 (ttm170) cc_final: 0.7500 (ttm170) REVERT: J 267 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7439 (mt-10) REVERT: J 270 SER cc_start: 0.8267 (p) cc_final: 0.7973 (t) REVERT: J 334 ARG cc_start: 0.8374 (ttp80) cc_final: 0.8030 (ttp80) REVERT: J 377 GLU cc_start: 0.7590 (tp30) cc_final: 0.7211 (tp30) REVERT: J 378 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7744 (mt-10) REVERT: J 427 LYS cc_start: 0.8522 (mttm) cc_final: 0.8300 (mmtm) REVERT: J 430 TYR cc_start: 0.8677 (t80) cc_final: 0.8408 (t80) REVERT: J 444 LYS cc_start: 0.8318 (mttm) cc_final: 0.8106 (mttm) REVERT: P 249 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8068 (mm-30) REVERT: P 252 LYS cc_start: 0.8890 (mtmt) cc_final: 0.8656 (mtmt) REVERT: P 254 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7774 (mp0) REVERT: P 272 ILE cc_start: 0.8516 (OUTLIER) cc_final: 0.8250 (mm) REVERT: S 31 HIS cc_start: 0.8563 (t-90) cc_final: 0.8314 (t70) REVERT: S 59 THR cc_start: 0.9135 (m) cc_final: 0.8820 (p) REVERT: S 73 ASN cc_start: 0.8782 (m110) cc_final: 0.8441 (t0) REVERT: S 112 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7965 (mt0) REVERT: T 43 LYS cc_start: 0.8924 (mtmm) cc_final: 0.8632 (mtmm) REVERT: T 44 VAL cc_start: 0.9250 (t) cc_final: 0.8999 (p) REVERT: T 68 ASP cc_start: 0.8184 (t0) cc_final: 0.7701 (t0) REVERT: T 76 GLU cc_start: 0.8372 (tp30) cc_final: 0.7640 (tp30) REVERT: T 79 ARG cc_start: 0.8197 (mtm110) cc_final: 0.7494 (mtm110) REVERT: T 120 LYS cc_start: 0.8702 (tttp) cc_final: 0.8170 (ttpp) REVERT: U 106 ASP cc_start: 0.8371 (m-30) cc_final: 0.7889 (m-30) REVERT: V 88 TYR cc_start: 0.8438 (m-80) cc_final: 0.7830 (m-80) REVERT: W 42 ARG cc_start: 0.8411 (mtm180) cc_final: 0.8012 (ttm-80) REVERT: X 67 ARG cc_start: 0.8425 (ttm110) cc_final: 0.8208 (ttm110) outliers start: 77 outliers final: 56 residues processed: 1408 average time/residue: 0.2906 time to fit residues: 633.3211 Evaluate side-chains 1433 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 1370 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 721 CYS Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 2019 ARG Chi-restraints excluded: chain A residue 2068 MET Chi-restraints excluded: chain A residue 2117 SER Chi-restraints excluded: chain C residue 33 LYS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 226 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 400 LYS Chi-restraints excluded: chain G residue 420 ASN Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 364 MET Chi-restraints excluded: chain I residue 371 MET Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 226 GLN Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 92 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 97 optimal weight: 0.9990 chunk 226 optimal weight: 5.9990 chunk 428 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 309 optimal weight: 0.0060 chunk 301 optimal weight: 3.9990 chunk 349 optimal weight: 0.9980 chunk 416 optimal weight: 0.7980 chunk 305 optimal weight: 0.7980 chunk 430 optimal weight: 1.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 GLN ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 110 ASN E 380 GLN E 420 ASN F 277 ASN ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099540 restraints weight = 66151.945| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.85 r_work: 0.3102 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41479 Z= 0.151 Angle : 0.599 10.087 56931 Z= 0.312 Chirality : 0.044 0.356 6479 Planarity : 0.004 0.083 6519 Dihedral : 20.910 179.090 7413 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.08 % Allowed : 17.76 % Favored : 80.16 % 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 are not related in a simple way. whole: 1.67 (0.13), residues: 4461 helix: 1.88 (0.11), residues: 2179 sheet: 0.55 (0.20), residues: 674 loop : 0.43 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 64 TYR 0.029 0.001 TYR C 382 PHE 0.023 0.001 PHE C 248 TRP 0.084 0.002 TRP C 360 HIS 0.008 0.001 HIS I 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (41471) covalent geometry : angle 0.59914 / 0.31 (56922) hydrogen bonds : bond 0.03889 / 2.63 ( 1954) hydrogen bonds : angle 3.65822 / 2.66 ( 5374) metal coordination : bond 0.00913 / 0.33 ( 8) metal coordination : angle 1.47886 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1464 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1383 time to evaluate : 1.487 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: A 628 TRP cc_start: 0.8494 (t60) cc_final: 0.8267 (t60) REVERT: A 660 LEU cc_start: 0.9022 (mp) cc_final: 0.8768 (mp) REVERT: A 678 VAL cc_start: 0.8853 (OUTLIER) cc_final: 0.8584 (m) REVERT: A 687 LYS cc_start: 0.8857 (mttt) cc_final: 0.8501 (mttm) REVERT: A 704 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6743 (mt-10) REVERT: A 749 GLN cc_start: 0.8524 (pm20) cc_final: 0.8034 (pm20) REVERT: A 751 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8485 (tp) REVERT: A 771 LEU cc_start: 0.8907 (tp) cc_final: 0.8663 (tp) REVERT: A 783 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7824 (mmm) REVERT: A 789 MET cc_start: 0.7467 (mmt) cc_final: 0.7184 (mmm) REVERT: A 797 PHE cc_start: 0.7725 (m-80) cc_final: 0.7336 (m-80) REVERT: A 854 GLU cc_start: 0.8083 (pm20) cc_final: 0.7592 (pm20) REVERT: A 864 ARG cc_start: 0.8444 (mtp85) cc_final: 0.8242 (mtp85) REVERT: A 867 CYS cc_start: 0.8455 (m) cc_final: 0.8132 (m) REVERT: A 871 ASP cc_start: 0.8358 (t0) cc_final: 0.8075 (t0) REVERT: A 966 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7878 (mtp-110) REVERT: A 973 VAL cc_start: 0.8744 (t) cc_final: 0.8321 (p) REVERT: A 976 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 992 MET cc_start: 0.2469 (ttm) cc_final: 0.1690 (ttm) REVERT: A 1891 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 1893 ARG cc_start: 0.8444 (mtt180) cc_final: 0.8095 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8588 (ptpp) cc_final: 0.8179 (ptpp) REVERT: A 1895 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7856 (ttp-170) REVERT: A 1897 ARG cc_start: 0.8344 (ttp-170) cc_final: 0.7981 (ttp-170) REVERT: A 1934 SER cc_start: 0.8406 (m) cc_final: 0.8141 (p) REVERT: A 1936 ILE cc_start: 0.8993 (mm) cc_final: 0.8459 (mt) REVERT: A 1953 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7688 (mm-30) REVERT: A 1957 ARG cc_start: 0.8409 (mtp180) cc_final: 0.8205 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7918 (tp30) cc_final: 0.7216 (tp30) REVERT: A 2026 CYS cc_start: 0.8495 (m) cc_final: 0.8162 (m) REVERT: A 2038 ILE cc_start: 0.8777 (tt) cc_final: 0.8547 (tp) REVERT: A 2054 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7684 (tm-30) REVERT: A 2094 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7818 (ptp90) REVERT: A 2137 ASP cc_start: 0.8328 (p0) cc_final: 0.8068 (p0) REVERT: A 2150 ASP cc_start: 0.8311 (m-30) cc_final: 0.7982 (m-30) REVERT: A 2151 ARG cc_start: 0.7392 (mtt180) cc_final: 0.7070 (mtt180) REVERT: A 2169 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7833 (mm-30) REVERT: A 2185 MET cc_start: 0.6788 (ttm) cc_final: 0.6508 (ttm) REVERT: A 2196 PHE cc_start: 0.7980 (m-80) cc_final: 0.7690 (m-80) REVERT: B 133 MET cc_start: 0.6030 (mmt) cc_final: 0.5493 (mmt) REVERT: C 14 LYS cc_start: 0.8678 (mppt) cc_final: 0.8253 (mtmm) REVERT: C 44 GLN cc_start: 0.8533 (mt0) cc_final: 0.8228 (mt0) REVERT: C 55 PHE cc_start: 0.7536 (t80) cc_final: 0.7149 (t80) REVERT: C 65 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8455 (tp) REVERT: C 72 ARG cc_start: 0.8785 (tpp80) cc_final: 0.8009 (tpp80) REVERT: C 76 ASP cc_start: 0.8262 (m-30) cc_final: 0.7698 (m-30) REVERT: C 83 MET cc_start: 0.8375 (mmp) cc_final: 0.8085 (mmm) REVERT: C 103 THR cc_start: 0.8682 (m) cc_final: 0.8462 (p) REVERT: C 107 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7936 (mm-30) REVERT: C 111 GLU cc_start: 0.8091 (tm-30) cc_final: 0.6798 (tm-30) REVERT: C 115 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7715 (mt-10) REVERT: C 124 ARG cc_start: 0.8516 (mtm110) cc_final: 0.8290 (mtm180) REVERT: C 142 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7654 (mp0) REVERT: C 164 LYS cc_start: 0.7841 (tptm) cc_final: 0.7616 (tptm) REVERT: C 196 MET cc_start: 0.8391 (mmm) cc_final: 0.8018 (mmp) REVERT: C 220 MET cc_start: 0.8099 (tpp) cc_final: 0.7888 (tpp) REVERT: C 230 ASN cc_start: 0.8434 (t0) cc_final: 0.7835 (t0) REVERT: C 237 VAL cc_start: 0.8740 (t) cc_final: 0.8482 (p) REVERT: C 250 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8548 (mtpp) REVERT: C 369 ASN cc_start: 0.8800 (t0) cc_final: 0.8328 (t0) REVERT: C 372 PHE cc_start: 0.8500 (t80) cc_final: 0.8161 (t80) REVERT: C 379 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8167 (mtm110) REVERT: D 92 ASN cc_start: 0.8659 (t0) cc_final: 0.8304 (t0) REVERT: E 15 ILE cc_start: 0.8707 (mm) cc_final: 0.8472 (mt) REVERT: E 17 SER cc_start: 0.8672 (m) cc_final: 0.8299 (p) REVERT: E 28 GLU cc_start: 0.7899 (mp0) cc_final: 0.7462 (mp0) REVERT: E 61 MET cc_start: 0.8658 (mmm) cc_final: 0.8367 (mmm) REVERT: E 64 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7925 (mmt-90) REVERT: E 100 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7854 (mt-10) REVERT: E 105 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7845 (mt-10) REVERT: E 165 LYS cc_start: 0.7928 (mmtt) cc_final: 0.7691 (mmtt) REVERT: E 167 THR cc_start: 0.8257 (m) cc_final: 0.7963 (p) REVERT: E 168 LYS cc_start: 0.8400 (ttmt) cc_final: 0.8031 (ttmt) REVERT: E 171 LYS cc_start: 0.7828 (tttt) cc_final: 0.7558 (tttt) REVERT: E 178 GLU cc_start: 0.7796 (tt0) cc_final: 0.7519 (tt0) REVERT: E 182 LYS cc_start: 0.8099 (mtmt) cc_final: 0.7765 (mtmt) REVERT: E 183 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7748 (mm-30) REVERT: E 184 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: E 194 GLU cc_start: 0.7827 (tt0) cc_final: 0.7545 (tt0) REVERT: E 214 ASP cc_start: 0.7994 (m-30) cc_final: 0.7722 (m-30) REVERT: E 260 MET cc_start: 0.8221 (mmp) cc_final: 0.7925 (mmm) REVERT: E 262 GLN cc_start: 0.7463 (mm-40) cc_final: 0.7227 (mm110) REVERT: E 285 LYS cc_start: 0.8092 (ttmm) cc_final: 0.7803 (mtpp) REVERT: E 286 TYR cc_start: 0.8409 (m-10) cc_final: 0.8081 (m-80) REVERT: E 352 LEU cc_start: 0.8427 (mt) cc_final: 0.8152 (mm) REVERT: E 356 ASP cc_start: 0.8140 (t0) cc_final: 0.7669 (t0) REVERT: E 370 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8238 (mt-10) REVERT: E 389 GLU cc_start: 0.7905 (tt0) cc_final: 0.7620 (tt0) REVERT: E 397 ILE cc_start: 0.8237 (tt) cc_final: 0.7991 (tt) REVERT: E 415 LEU cc_start: 0.8750 (mt) cc_final: 0.8532 (mm) REVERT: E 439 ASP cc_start: 0.7480 (p0) cc_final: 0.7221 (p0) REVERT: E 441 LYS cc_start: 0.8267 (mttt) cc_final: 0.7942 (mttt) REVERT: E 445 LYS cc_start: 0.7876 (mmtp) cc_final: 0.7578 (mmmm) REVERT: E 446 ILE cc_start: 0.8386 (mm) cc_final: 0.8093 (mt) REVERT: F 19 ILE cc_start: 0.8643 (tt) cc_final: 0.8343 (tp) REVERT: F 40 ARG cc_start: 0.8182 (mtt90) cc_final: 0.7804 (mtt90) REVERT: F 71 ARG cc_start: 0.7867 (mmt90) cc_final: 0.7577 (mmm-85) REVERT: F 83 LYS cc_start: 0.8141 (mtmt) cc_final: 0.7867 (mtmt) REVERT: F 112 GLU cc_start: 0.7997 (tp30) cc_final: 0.7741 (tp30) REVERT: F 117 GLU cc_start: 0.8180 (tp30) cc_final: 0.7522 (mm-30) REVERT: F 142 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7870 (m) REVERT: F 160 LYS cc_start: 0.8363 (ttpt) cc_final: 0.7938 (mtpt) REVERT: F 170 THR cc_start: 0.8131 (m) cc_final: 0.7930 (t) REVERT: F 177 LYS cc_start: 0.8238 (mttt) cc_final: 0.7909 (mttt) REVERT: F 181 SER cc_start: 0.8631 (m) cc_final: 0.8232 (p) REVERT: F 192 VAL cc_start: 0.8327 (t) cc_final: 0.7767 (p) REVERT: F 197 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7001 (mtpt) REVERT: F 204 LYS cc_start: 0.8239 (mtmt) cc_final: 0.7880 (mtmt) REVERT: F 218 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6859 (tpp) REVERT: F 233 GLN cc_start: 0.7703 (tt0) cc_final: 0.6851 (tp40) REVERT: F 248 ASP cc_start: 0.7903 (m-30) cc_final: 0.7636 (m-30) REVERT: F 267 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7031 (mt-10) REVERT: F 285 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7505 (mp0) REVERT: F 303 MET cc_start: 0.8724 (mmm) cc_final: 0.8447 (mmp) REVERT: F 319 ASP cc_start: 0.8085 (p0) cc_final: 0.7868 (p0) REVERT: F 329 ASN cc_start: 0.8219 (p0) cc_final: 0.7830 (p0) REVERT: F 389 VAL cc_start: 0.8610 (t) cc_final: 0.8392 (p) REVERT: F 392 ARG cc_start: 0.8235 (ttp-110) cc_final: 0.7927 (ttp-170) REVERT: F 415 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8101 (tppt) REVERT: F 441 GLN cc_start: 0.7747 (mm-40) cc_final: 0.7484 (mm-40) REVERT: F 445 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7767 (mm-30) REVERT: G 15 ILE cc_start: 0.8822 (mt) cc_final: 0.8599 (mm) REVERT: G 61 MET cc_start: 0.8707 (mmm) cc_final: 0.7933 (mmm) REVERT: G 86 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7710 (mm-30) REVERT: G 89 SER cc_start: 0.8313 (m) cc_final: 0.8027 (t) REVERT: G 90 LYS cc_start: 0.8565 (tptm) cc_final: 0.8065 (tptm) REVERT: G 110 GLU cc_start: 0.8310 (tp30) cc_final: 0.8029 (mm-30) REVERT: G 113 MET cc_start: 0.8382 (tpt) cc_final: 0.8152 (tpp) REVERT: G 125 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7875 (mmmt) REVERT: G 126 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7028 (mt-10) REVERT: G 128 LYS cc_start: 0.8344 (tttt) cc_final: 0.7925 (tttt) REVERT: G 137 GLU cc_start: 0.7822 (tt0) cc_final: 0.7424 (tp30) REVERT: G 147 MET cc_start: 0.6433 (mtp) cc_final: 0.5918 (mtp) REVERT: G 162 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8213 (ttmm) REVERT: G 171 LYS cc_start: 0.8541 (mtpt) cc_final: 0.8225 (mttm) REVERT: G 178 GLU cc_start: 0.8176 (tt0) cc_final: 0.7619 (tt0) REVERT: G 193 ILE cc_start: 0.8635 (mt) cc_final: 0.8316 (mm) REVERT: G 225 LYS cc_start: 0.8398 (mmpt) cc_final: 0.7919 (mmpt) REVERT: G 227 ASP cc_start: 0.7873 (t0) cc_final: 0.7553 (t0) REVERT: G 229 HIS cc_start: 0.8447 (t-90) cc_final: 0.8216 (t70) REVERT: G 244 ASP cc_start: 0.7452 (m-30) cc_final: 0.7203 (m-30) REVERT: G 247 ASN cc_start: 0.8481 (m-40) cc_final: 0.8254 (m-40) REVERT: G 249 ARG cc_start: 0.7881 (ttt-90) cc_final: 0.7632 (ttt-90) REVERT: G 302 ASP cc_start: 0.7839 (t0) cc_final: 0.7602 (t0) REVERT: G 376 LYS cc_start: 0.8825 (tptt) cc_final: 0.8567 (tptm) REVERT: G 408 GLN cc_start: 0.7947 (mt0) cc_final: 0.7730 (mt0) REVERT: G 428 GLU cc_start: 0.8290 (mp0) cc_final: 0.7900 (mp0) REVERT: H 18 ARG cc_start: 0.7702 (mtp85) cc_final: 0.7445 (mtp180) REVERT: H 38 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7788 (mm-30) REVERT: H 64 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7936 (mtt-85) REVERT: H 83 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8326 (mttp) REVERT: H 88 MET cc_start: 0.8045 (mmp) cc_final: 0.7833 (mmp) REVERT: H 145 ILE cc_start: 0.8336 (mt) cc_final: 0.8108 (tp) REVERT: H 160 LYS cc_start: 0.8303 (mttt) cc_final: 0.8081 (mttt) REVERT: H 164 LYS cc_start: 0.8448 (pttt) cc_final: 0.7999 (pttm) REVERT: H 201 LYS cc_start: 0.8483 (ptmt) cc_final: 0.8205 (ptmt) REVERT: H 238 VAL cc_start: 0.8224 (t) cc_final: 0.7916 (p) REVERT: H 246 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7574 (mt-10) REVERT: H 253 ARG cc_start: 0.8079 (ptm-80) cc_final: 0.7730 (ptm-80) REVERT: H 267 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7437 (tt0) REVERT: H 273 ARG cc_start: 0.8502 (mtt90) cc_final: 0.7892 (mtt90) REVERT: H 274 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7917 (mt-10) REVERT: H 275 GLN cc_start: 0.8242 (mm110) cc_final: 0.7893 (mm-40) REVERT: H 277 ASN cc_start: 0.8585 (m-40) cc_final: 0.8095 (m110) REVERT: H 279 LYS cc_start: 0.8507 (tppt) cc_final: 0.8289 (tptp) REVERT: H 285 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7646 (mt-10) REVERT: H 307 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7294 (mm-30) REVERT: H 313 ASN cc_start: 0.8104 (m-40) cc_final: 0.7885 (m-40) REVERT: H 314 ARG cc_start: 0.7552 (mmt180) cc_final: 0.6915 (mmt180) REVERT: H 452 PHE cc_start: 0.8613 (m-80) cc_final: 0.8389 (m-80) REVERT: I 13 GLN cc_start: 0.8111 (tp40) cc_final: 0.7900 (mm-40) REVERT: I 105 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7425 (mt-10) REVERT: I 125 LYS cc_start: 0.8607 (ttpp) cc_final: 0.8301 (ttmm) REVERT: I 137 GLU cc_start: 0.8001 (tt0) cc_final: 0.7638 (tt0) REVERT: I 139 THR cc_start: 0.8686 (m) cc_final: 0.8294 (p) REVERT: I 184 ARG cc_start: 0.8633 (mtt180) cc_final: 0.8340 (mtt180) REVERT: I 216 GLU cc_start: 0.8032 (tt0) cc_final: 0.7769 (tp30) REVERT: I 219 GLU cc_start: 0.7815 (tp30) cc_final: 0.7540 (tp30) REVERT: I 231 LYS cc_start: 0.8379 (mttt) cc_final: 0.8090 (mtpp) REVERT: I 249 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7780 (mtp85) REVERT: I 259 MET cc_start: 0.8199 (ptp) cc_final: 0.7902 (ptm) REVERT: I 267 LYS cc_start: 0.8220 (tptm) cc_final: 0.8014 (tttp) REVERT: I 281 LYS cc_start: 0.8757 (mttt) cc_final: 0.8518 (mtmt) REVERT: I 322 SER cc_start: 0.8578 (p) cc_final: 0.8356 (t) REVERT: I 359 MET cc_start: 0.8163 (mtp) cc_final: 0.7939 (mtp) REVERT: I 438 TYR cc_start: 0.8387 (m-80) cc_final: 0.7891 (m-80) REVERT: I 439 ASP cc_start: 0.8245 (p0) cc_final: 0.7884 (p0) REVERT: I 441 LYS cc_start: 0.8401 (mttm) cc_final: 0.7932 (mtmm) REVERT: I 445 LYS cc_start: 0.8151 (tppt) cc_final: 0.7202 (tppt) REVERT: I 446 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7957 (mp) REVERT: J 38 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7777 (tp30) REVERT: J 90 MET cc_start: 0.8647 (mtm) cc_final: 0.8351 (mtp) REVERT: J 92 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8164 (mm-40) REVERT: J 117 GLU cc_start: 0.7735 (tp30) cc_final: 0.7493 (tp30) REVERT: J 142 VAL cc_start: 0.8645 (t) cc_final: 0.8419 (m) REVERT: J 164 LYS cc_start: 0.8427 (pttt) cc_final: 0.7749 (ptmm) REVERT: J 183 THR cc_start: 0.8299 (m) cc_final: 0.8062 (p) REVERT: J 184 LYS cc_start: 0.8297 (mttp) cc_final: 0.8081 (mttp) REVERT: J 192 VAL cc_start: 0.8752 (t) cc_final: 0.8420 (p) REVERT: J 207 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7540 (ttm170) REVERT: J 267 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7650 (mt-10) REVERT: J 270 SER cc_start: 0.8256 (p) cc_final: 0.7969 (t) REVERT: J 377 GLU cc_start: 0.7550 (tp30) cc_final: 0.7185 (tp30) REVERT: J 427 LYS cc_start: 0.8530 (mttm) cc_final: 0.8300 (mmtm) REVERT: J 430 TYR cc_start: 0.8697 (t80) cc_final: 0.8415 (t80) REVERT: J 444 LYS cc_start: 0.8319 (mttm) cc_final: 0.8109 (mttm) REVERT: P 254 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: S 31 HIS cc_start: 0.8590 (t-90) cc_final: 0.8364 (t70) REVERT: S 59 THR cc_start: 0.9111 (m) cc_final: 0.8827 (p) REVERT: S 73 ASN cc_start: 0.8779 (m110) cc_final: 0.8464 (t0) REVERT: S 112 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7938 (mt0) REVERT: T 43 LYS cc_start: 0.8923 (mtmm) cc_final: 0.8642 (mtmm) REVERT: T 44 VAL cc_start: 0.9251 (t) cc_final: 0.9011 (p) REVERT: T 63 ASN cc_start: 0.9109 (t0) cc_final: 0.8881 (t0) REVERT: T 68 ASP cc_start: 0.8206 (t0) cc_final: 0.7736 (t0) REVERT: T 76 GLU cc_start: 0.8369 (tp30) cc_final: 0.7664 (tp30) REVERT: T 79 ARG cc_start: 0.8226 (mtm110) cc_final: 0.7501 (mtm110) REVERT: T 120 LYS cc_start: 0.8724 (tttp) cc_final: 0.8180 (ttpp) REVERT: U 106 ASP cc_start: 0.8378 (m-30) cc_final: 0.7895 (m-30) REVERT: V 88 TYR cc_start: 0.8444 (m-80) cc_final: 0.7868 (m-80) REVERT: X 67 ARG cc_start: 0.8425 (ttm110) cc_final: 0.8224 (ttm110) REVERT: X 84 MET cc_start: 0.8806 (mmm) cc_final: 0.8597 (tmm) outliers start: 81 outliers final: 58 residues processed: 1404 average time/residue: 0.3012 time to fit residues: 652.8992 Evaluate side-chains 1430 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1362 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 2019 ARG Chi-restraints excluded: chain A residue 2068 MET Chi-restraints excluded: chain A residue 2117 SER Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 415 LYS Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 389 GLU Chi-restraints excluded: chain G residue 420 ASN Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 165 LYS Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 364 MET Chi-restraints excluded: chain I residue 371 MET Chi-restraints excluded: chain I residue 446 ILE Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain P residue 254 GLU Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 92 ARG Chi-restraints excluded: chain X residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 329 optimal weight: 0.0020 chunk 9 optimal weight: 0.8980 chunk 258 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 317 optimal weight: 2.9990 chunk 449 optimal weight: 8.9990 chunk 326 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 GLN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN E 420 ASN F 277 ASN H 453 ASN ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 18 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099442 restraints weight = 65512.514| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.84 r_work: 0.3098 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41479 Z= 0.152 Angle : 0.611 10.968 56931 Z= 0.317 Chirality : 0.044 0.375 6479 Planarity : 0.004 0.088 6519 Dihedral : 20.917 178.880 7413 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.98 % Allowed : 18.38 % 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 are not related in a simple way. whole: 1.67 (0.13), residues: 4461 helix: 1.88 (0.11), residues: 2169 sheet: 0.53 (0.20), residues: 675 loop : 0.43 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 64 TYR 0.034 0.001 TYR C 382 PHE 0.029 0.001 PHE A 718 TRP 0.076 0.002 TRP C 360 HIS 0.007 0.001 HIS I 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (41471) covalent geometry : angle 0.61067 / 0.32 (56922) hydrogen bonds : bond 0.03899 / 2.63 ( 1954) hydrogen bonds : angle 3.66311 / 2.67 ( 5374) metal coordination : bond 0.00994 / 0.38 ( 8) metal coordination : angle 2.04587 / 0.98 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1476 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1399 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 628 TRP cc_start: 0.8504 (t60) cc_final: 0.8301 (t60) REVERT: A 660 LEU cc_start: 0.9057 (mp) cc_final: 0.8785 (mp) REVERT: A 678 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8587 (m) REVERT: A 687 LYS cc_start: 0.8851 (mttt) cc_final: 0.8490 (mttm) REVERT: A 749 GLN cc_start: 0.8528 (pm20) cc_final: 0.8069 (pm20) REVERT: A 751 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8500 (tp) REVERT: A 771 LEU cc_start: 0.8925 (tp) cc_final: 0.8678 (tp) REVERT: A 783 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7856 (mmm) REVERT: A 789 MET cc_start: 0.7487 (mmt) cc_final: 0.7191 (mmm) REVERT: A 797 PHE cc_start: 0.7685 (m-80) cc_final: 0.7327 (m-80) REVERT: A 864 ARG cc_start: 0.8516 (mtp85) cc_final: 0.8280 (mtp85) REVERT: A 867 CYS cc_start: 0.8417 (m) cc_final: 0.8097 (m) REVERT: A 871 ASP cc_start: 0.8327 (t0) cc_final: 0.8030 (t0) REVERT: A 918 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8379 (m) REVERT: A 966 ARG cc_start: 0.8122 (mtp85) cc_final: 0.7857 (mtp-110) REVERT: A 973 VAL cc_start: 0.8778 (t) cc_final: 0.8334 (p) REVERT: A 976 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7593 (mt-10) REVERT: A 992 MET cc_start: 0.2398 (ttm) cc_final: 0.1633 (ttm) REVERT: A 1891 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 1893 ARG cc_start: 0.8442 (mtt180) cc_final: 0.8087 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8595 (ptpp) cc_final: 0.8195 (ptpp) REVERT: A 1895 ARG cc_start: 0.8146 (ttp-170) cc_final: 0.7845 (ttp-170) REVERT: A 1897 ARG cc_start: 0.8323 (ttp-170) cc_final: 0.7984 (ttp-170) REVERT: A 1934 SER cc_start: 0.8404 (m) cc_final: 0.8126 (p) REVERT: A 1936 ILE cc_start: 0.8990 (mm) cc_final: 0.8454 (mt) REVERT: A 1953 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 1957 ARG cc_start: 0.8423 (mtp180) cc_final: 0.8218 (mtm-85) REVERT: A 2026 CYS cc_start: 0.8482 (m) cc_final: 0.8141 (m) REVERT: A 2041 ASP cc_start: 0.8326 (m-30) cc_final: 0.8093 (m-30) REVERT: A 2137 ASP cc_start: 0.8347 (p0) cc_final: 0.8101 (p0) REVERT: A 2150 ASP cc_start: 0.8294 (m-30) cc_final: 0.7893 (m-30) REVERT: A 2169 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7809 (mm-30) REVERT: A 2185 MET cc_start: 0.6757 (ttm) cc_final: 0.6478 (ttm) REVERT: A 2196 PHE cc_start: 0.7975 (m-80) cc_final: 0.7692 (m-80) REVERT: B 133 MET cc_start: 0.6023 (mmt) cc_final: 0.5495 (mmt) REVERT: C 14 LYS cc_start: 0.8693 (mppt) cc_final: 0.8070 (mtmm) REVERT: C 44 GLN cc_start: 0.8575 (mt0) cc_final: 0.8265 (mt0) REVERT: C 55 PHE cc_start: 0.7519 (t80) cc_final: 0.7155 (t80) REVERT: C 71 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7956 (tp-100) REVERT: C 72 ARG cc_start: 0.8772 (tpp80) cc_final: 0.8072 (ttm-80) REVERT: C 76 ASP cc_start: 0.8293 (m-30) cc_final: 0.7756 (m-30) REVERT: C 83 MET cc_start: 0.8423 (mmp) cc_final: 0.8127 (mmm) REVERT: C 90 ASP cc_start: 0.8073 (t0) cc_final: 0.7424 (t0) REVERT: C 103 THR cc_start: 0.8741 (m) cc_final: 0.8472 (p) REVERT: C 107 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7944 (mm-30) REVERT: C 110 ASN cc_start: 0.8734 (m-40) cc_final: 0.8397 (m110) REVERT: C 111 GLU cc_start: 0.8208 (tm-30) cc_final: 0.6948 (tm-30) REVERT: C 115 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7725 (mt-10) REVERT: C 124 ARG cc_start: 0.8468 (mtm110) cc_final: 0.8209 (mtm-85) REVERT: C 142 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7632 (mp0) REVERT: C 164 LYS cc_start: 0.7862 (tptm) cc_final: 0.7645 (tptm) REVERT: C 196 MET cc_start: 0.8387 (mmm) cc_final: 0.8003 (mmp) REVERT: C 220 MET cc_start: 0.8091 (tpp) cc_final: 0.7883 (tpp) REVERT: C 230 ASN cc_start: 0.8386 (t0) cc_final: 0.7707 (t0) REVERT: C 237 VAL cc_start: 0.8751 (t) cc_final: 0.8497 (p) REVERT: C 250 LYS cc_start: 0.8879 (mtpp) cc_final: 0.8541 (mtpp) REVERT: C 366 ILE cc_start: 0.9079 (tt) cc_final: 0.8720 (tt) REVERT: C 369 ASN cc_start: 0.8804 (t0) cc_final: 0.8316 (t0) REVERT: C 372 PHE cc_start: 0.8536 (t80) cc_final: 0.8199 (t80) REVERT: C 379 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8129 (mtm110) REVERT: C 382 TYR cc_start: 0.8185 (t80) cc_final: 0.7909 (t80) REVERT: C 393 LYS cc_start: 0.8829 (tttp) cc_final: 0.8524 (tttp) REVERT: D 92 ASN cc_start: 0.8624 (t0) cc_final: 0.8287 (t0) REVERT: E 15 ILE cc_start: 0.8734 (mm) cc_final: 0.8463 (mt) REVERT: E 17 SER cc_start: 0.8663 (m) cc_final: 0.8300 (p) REVERT: E 28 GLU cc_start: 0.7911 (mp0) cc_final: 0.7475 (mp0) REVERT: E 64 ARG cc_start: 0.8337 (mtp85) cc_final: 0.8028 (mmt-90) REVERT: E 100 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7853 (mt-10) REVERT: E 105 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7836 (mt-10) REVERT: E 165 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7694 (mmtt) REVERT: E 167 THR cc_start: 0.8253 (m) cc_final: 0.7959 (p) REVERT: E 168 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8019 (ttmt) REVERT: E 171 LYS cc_start: 0.7838 (tttt) cc_final: 0.7415 (tttp) REVERT: E 178 GLU cc_start: 0.7779 (tt0) cc_final: 0.7500 (tt0) REVERT: E 182 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7783 (mtmt) REVERT: E 183 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7768 (mm-30) REVERT: E 184 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7452 (mtm-85) REVERT: E 194 GLU cc_start: 0.7827 (tt0) cc_final: 0.7553 (tt0) REVERT: E 214 ASP cc_start: 0.7995 (m-30) cc_final: 0.7735 (m-30) REVERT: E 260 MET cc_start: 0.8216 (mmp) cc_final: 0.7933 (mmm) REVERT: E 262 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7254 (mm110) REVERT: E 285 LYS cc_start: 0.8087 (ttmm) cc_final: 0.7795 (mtpp) REVERT: E 286 TYR cc_start: 0.8405 (m-10) cc_final: 0.8055 (m-80) REVERT: E 352 LEU cc_start: 0.8426 (mt) cc_final: 0.8154 (mm) REVERT: E 356 ASP cc_start: 0.8153 (t0) cc_final: 0.7688 (t0) REVERT: E 370 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8268 (mt-10) REVERT: E 389 GLU cc_start: 0.7932 (tt0) cc_final: 0.7651 (tt0) REVERT: E 397 ILE cc_start: 0.8276 (tt) cc_final: 0.8045 (tt) REVERT: E 415 LEU cc_start: 0.8761 (mt) cc_final: 0.8553 (mm) REVERT: E 441 LYS cc_start: 0.8275 (mttt) cc_final: 0.7974 (mttt) REVERT: E 445 LYS cc_start: 0.7907 (mmtp) cc_final: 0.7605 (mmmm) REVERT: E 446 ILE cc_start: 0.8417 (mm) cc_final: 0.8123 (mt) REVERT: F 19 ILE cc_start: 0.8660 (tt) cc_final: 0.8367 (tp) REVERT: F 40 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7796 (mtt90) REVERT: F 71 ARG cc_start: 0.7862 (mmt90) cc_final: 0.7570 (mmm-85) REVERT: F 83 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7856 (mtmt) REVERT: F 112 GLU cc_start: 0.7980 (tp30) cc_final: 0.7737 (tp30) REVERT: F 117 GLU cc_start: 0.8189 (tp30) cc_final: 0.7533 (mm-30) REVERT: F 142 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7884 (m) REVERT: F 160 LYS cc_start: 0.8359 (ttpt) cc_final: 0.7933 (mtpt) REVERT: F 170 THR cc_start: 0.8127 (m) cc_final: 0.7924 (t) REVERT: F 177 LYS cc_start: 0.8239 (mttt) cc_final: 0.7904 (mttt) REVERT: F 181 SER cc_start: 0.8630 (m) cc_final: 0.8217 (p) REVERT: F 182 LEU cc_start: 0.8960 (mt) cc_final: 0.8711 (mm) REVERT: F 192 VAL cc_start: 0.8306 (t) cc_final: 0.7728 (p) REVERT: F 197 LYS cc_start: 0.7795 (mtpt) cc_final: 0.6963 (mtpt) REVERT: F 204 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7907 (mtmt) REVERT: F 218 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6872 (tpp) REVERT: F 233 GLN cc_start: 0.7700 (tt0) cc_final: 0.6853 (tp40) REVERT: F 248 ASP cc_start: 0.7887 (m-30) cc_final: 0.7625 (m-30) REVERT: F 267 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7021 (mt-10) REVERT: F 285 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7521 (mp0) REVERT: F 303 MET cc_start: 0.8717 (mmm) cc_final: 0.8447 (mmp) REVERT: F 319 ASP cc_start: 0.8073 (p0) cc_final: 0.7862 (p0) REVERT: F 329 ASN cc_start: 0.8214 (p0) cc_final: 0.7819 (p0) REVERT: F 389 VAL cc_start: 0.8614 (t) cc_final: 0.8400 (p) REVERT: F 392 ARG cc_start: 0.8202 (ttp-110) cc_final: 0.7902 (ttp-170) REVERT: F 415 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8099 (tppt) REVERT: F 441 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7497 (mm-40) REVERT: F 445 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7770 (mm-30) REVERT: G 15 ILE cc_start: 0.8839 (mt) cc_final: 0.8599 (mm) REVERT: G 19 SER cc_start: 0.8554 (m) cc_final: 0.8335 (m) REVERT: G 34 GLN cc_start: 0.8322 (tm-30) cc_final: 0.8080 (tm-30) REVERT: G 61 MET cc_start: 0.8701 (mmm) cc_final: 0.7938 (mmm) REVERT: G 86 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7716 (mm-30) REVERT: G 89 SER cc_start: 0.8323 (m) cc_final: 0.8037 (t) REVERT: G 90 LYS cc_start: 0.8569 (tptm) cc_final: 0.8058 (tptm) REVERT: G 110 GLU cc_start: 0.8276 (tp30) cc_final: 0.7737 (mm-30) REVERT: G 113 MET cc_start: 0.8433 (tpt) cc_final: 0.8204 (tpp) REVERT: G 125 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7884 (mmmt) REVERT: G 126 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7068 (mt-10) REVERT: G 128 LYS cc_start: 0.8330 (tttt) cc_final: 0.7913 (tttt) REVERT: G 137 GLU cc_start: 0.7782 (tt0) cc_final: 0.7415 (tp30) REVERT: G 147 MET cc_start: 0.6533 (mtp) cc_final: 0.6000 (mtp) REVERT: G 162 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8217 (ttmm) REVERT: G 171 LYS cc_start: 0.8551 (mtpt) cc_final: 0.8258 (mtpp) REVERT: G 178 GLU cc_start: 0.8127 (tt0) cc_final: 0.7566 (tt0) REVERT: G 193 ILE cc_start: 0.8649 (mt) cc_final: 0.8314 (mm) REVERT: G 225 LYS cc_start: 0.8393 (mmpt) cc_final: 0.7914 (mmpt) REVERT: G 227 ASP cc_start: 0.7874 (t0) cc_final: 0.7563 (t0) REVERT: G 229 HIS cc_start: 0.8474 (t-90) cc_final: 0.8253 (t70) REVERT: G 244 ASP cc_start: 0.7491 (m-30) cc_final: 0.7255 (m-30) REVERT: G 247 ASN cc_start: 0.8484 (m-40) cc_final: 0.8256 (m-40) REVERT: G 249 ARG cc_start: 0.7893 (ttt-90) cc_final: 0.7645 (ttt-90) REVERT: G 302 ASP cc_start: 0.7837 (t0) cc_final: 0.7610 (t0) REVERT: G 376 LYS cc_start: 0.8815 (tptt) cc_final: 0.8557 (tptm) REVERT: G 408 GLN cc_start: 0.7934 (mt0) cc_final: 0.7727 (mt0) REVERT: G 428 GLU cc_start: 0.8270 (mp0) cc_final: 0.7887 (mp0) REVERT: H 18 ARG cc_start: 0.7662 (mtp85) cc_final: 0.7404 (mtp180) REVERT: H 38 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7784 (mm-30) REVERT: H 64 ARG cc_start: 0.8240 (mtt180) cc_final: 0.7954 (mtt-85) REVERT: H 83 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8286 (mttp) REVERT: H 88 MET cc_start: 0.8060 (mmp) cc_final: 0.7844 (mmp) REVERT: H 117 GLU cc_start: 0.8162 (tp30) cc_final: 0.7800 (tp30) REVERT: H 145 ILE cc_start: 0.8334 (mt) cc_final: 0.8108 (tp) REVERT: H 160 LYS cc_start: 0.8286 (mttt) cc_final: 0.8071 (mttt) REVERT: H 164 LYS cc_start: 0.8446 (pttt) cc_final: 0.7961 (pttm) REVERT: H 201 LYS cc_start: 0.8480 (ptmt) cc_final: 0.8227 (ptmt) REVERT: H 238 VAL cc_start: 0.8212 (t) cc_final: 0.7906 (p) REVERT: H 246 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7704 (mt-10) REVERT: H 253 ARG cc_start: 0.8080 (ptm-80) cc_final: 0.7721 (ptm-80) REVERT: H 267 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7782 (tt0) REVERT: H 273 ARG cc_start: 0.8519 (mtt90) cc_final: 0.7889 (mtt90) REVERT: H 274 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7915 (mt-10) REVERT: H 275 GLN cc_start: 0.8248 (mm110) cc_final: 0.7895 (mm-40) REVERT: H 277 ASN cc_start: 0.8597 (m-40) cc_final: 0.8121 (m110) REVERT: H 279 LYS cc_start: 0.8521 (tppt) cc_final: 0.8310 (tptp) REVERT: H 285 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7636 (mt-10) REVERT: H 313 ASN cc_start: 0.8114 (m-40) cc_final: 0.7879 (m-40) REVERT: H 314 ARG cc_start: 0.7571 (mmt180) cc_final: 0.6933 (mmt180) REVERT: H 404 GLN cc_start: 0.8374 (mt0) cc_final: 0.8086 (mt0) REVERT: H 452 PHE cc_start: 0.8625 (m-80) cc_final: 0.8392 (m-80) REVERT: I 13 GLN cc_start: 0.8083 (tp40) cc_final: 0.7868 (mm-40) REVERT: I 105 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7400 (mt-10) REVERT: I 125 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8290 (ttmm) REVERT: I 137 GLU cc_start: 0.8016 (tt0) cc_final: 0.7663 (tt0) REVERT: I 139 THR cc_start: 0.8683 (m) cc_final: 0.8295 (p) REVERT: I 184 ARG cc_start: 0.8596 (mtt180) cc_final: 0.8344 (mtm-85) REVERT: I 216 GLU cc_start: 0.8050 (tt0) cc_final: 0.7795 (tp30) REVERT: I 219 GLU cc_start: 0.7833 (tp30) cc_final: 0.7560 (tp30) REVERT: I 231 LYS cc_start: 0.8356 (mttt) cc_final: 0.8080 (mtpp) REVERT: I 249 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7787 (mtp85) REVERT: I 259 MET cc_start: 0.8210 (ptp) cc_final: 0.7864 (ptm) REVERT: I 281 LYS cc_start: 0.8764 (mttt) cc_final: 0.8526 (mtmt) REVERT: I 322 SER cc_start: 0.8571 (p) cc_final: 0.8345 (t) REVERT: I 359 MET cc_start: 0.8171 (mtp) cc_final: 0.7937 (mtp) REVERT: I 438 TYR cc_start: 0.8396 (m-80) cc_final: 0.7899 (m-80) REVERT: I 439 ASP cc_start: 0.8243 (p0) cc_final: 0.7884 (p0) REVERT: I 441 LYS cc_start: 0.8362 (mttm) cc_final: 0.7892 (mtmm) REVERT: I 445 LYS cc_start: 0.8190 (tppt) cc_final: 0.7232 (tppt) REVERT: I 446 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.8030 (mp) REVERT: J 38 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7739 (tp30) REVERT: J 90 MET cc_start: 0.8652 (mtm) cc_final: 0.8352 (mtp) REVERT: J 92 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8163 (mm-40) REVERT: J 117 GLU cc_start: 0.7753 (tp30) cc_final: 0.7525 (tp30) REVERT: J 142 VAL cc_start: 0.8644 (t) cc_final: 0.8442 (m) REVERT: J 164 LYS cc_start: 0.8427 (pttt) cc_final: 0.8105 (ptmm) REVERT: J 183 THR cc_start: 0.8295 (m) cc_final: 0.8082 (p) REVERT: J 192 VAL cc_start: 0.8730 (t) cc_final: 0.8391 (p) REVERT: J 207 ARG cc_start: 0.7807 (ttm170) cc_final: 0.7540 (ttm170) REVERT: J 232 LEU cc_start: 0.8743 (tp) cc_final: 0.8491 (tp) REVERT: J 267 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7620 (mt-10) REVERT: J 270 SER cc_start: 0.8252 (p) cc_final: 0.7969 (t) REVERT: J 353 ARG cc_start: 0.7501 (ttm-80) cc_final: 0.7178 (mtm-85) REVERT: J 378 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7878 (mt-10) REVERT: J 427 LYS cc_start: 0.8517 (mttm) cc_final: 0.8285 (mmtm) REVERT: J 430 TYR cc_start: 0.8701 (t80) cc_final: 0.8416 (t80) REVERT: J 436 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6682 (tm-30) REVERT: J 444 LYS cc_start: 0.8346 (mttm) cc_final: 0.8134 (mttm) REVERT: P 252 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8343 (mtmt) REVERT: P 254 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7783 (mp0) REVERT: S 31 HIS cc_start: 0.8594 (t-90) cc_final: 0.8356 (t70) REVERT: S 59 THR cc_start: 0.9156 (m) cc_final: 0.8853 (p) REVERT: T 43 LYS cc_start: 0.8932 (mtmm) cc_final: 0.8649 (mtmm) REVERT: T 44 VAL cc_start: 0.9256 (t) cc_final: 0.9022 (p) REVERT: T 68 ASP cc_start: 0.8215 (t0) cc_final: 0.7744 (t0) REVERT: T 76 GLU cc_start: 0.8394 (tp30) cc_final: 0.7678 (tp30) REVERT: T 79 ARG cc_start: 0.8224 (mtm110) cc_final: 0.7495 (mtm110) REVERT: T 101 LEU cc_start: 0.8785 (mm) cc_final: 0.8504 (mt) REVERT: T 120 LYS cc_start: 0.8730 (tttp) cc_final: 0.8188 (ttpp) REVERT: U 106 ASP cc_start: 0.8389 (m-30) cc_final: 0.7908 (m-30) REVERT: V 35 ARG cc_start: 0.8837 (mtp-110) cc_final: 0.8580 (mtp85) REVERT: V 88 TYR cc_start: 0.8395 (m-80) cc_final: 0.7875 (m-80) REVERT: W 73 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8131 (tm-30) REVERT: W 94 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8348 (tm-30) outliers start: 77 outliers final: 55 residues processed: 1419 average time/residue: 0.2943 time to fit residues: 645.0844 Evaluate side-chains 1436 residues out of total 3891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1372 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 732 HIS Chi-restraints excluded: chain A residue 751 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 774 THR Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 918 THR Chi-restraints excluded: chain A residue 2019 ARG Chi-restraints excluded: chain A residue 2068 MET Chi-restraints excluded: chain A residue 2117 SER Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 379 ARG Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 189 ASP Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 385 ASP Chi-restraints excluded: chain F residue 415 LYS Chi-restraints excluded: chain F residue 444 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 269 THR Chi-restraints excluded: chain G residue 281 LYS Chi-restraints excluded: chain G residue 353 ASP Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 379 ASP Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 364 MET Chi-restraints excluded: chain I residue 371 MET Chi-restraints excluded: chain I residue 446 ILE Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain X residue 66 ILE Chi-restraints excluded: chain X residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 463 random chunks: chunk 340 optimal weight: 0.9990 chunk 384 optimal weight: 1.9990 chunk 191 optimal weight: 0.8980 chunk 341 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 chunk 445 optimal weight: 10.0000 chunk 35 optimal weight: 0.0170 chunk 180 optimal weight: 2.9990 chunk 343 optimal weight: 0.0570 chunk 148 optimal weight: 0.0170 chunk 58 optimal weight: 0.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 719 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN E 241 HIS E 420 ASN F 277 ASN G 203 GLN G 262 GLN G 380 GLN ** G 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 112 GLN T 63 ASN ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.119269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100255 restraints weight = 66073.562| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.86 r_work: 0.3117 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41479 Z= 0.129 Angle : 0.611 13.603 56931 Z= 0.318 Chirality : 0.043 0.353 6479 Planarity : 0.004 0.076 6519 Dihedral : 20.913 179.548 7413 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.82 % Allowed : 18.94 % Favored : 79.23 % 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 are not related in a simple way. whole: 1.64 (0.13), residues: 4461 helix: 1.86 (0.11), residues: 2178 sheet: 0.53 (0.20), residues: 673 loop : 0.41 (0.16), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 64 TYR 0.036 0.001 TYR C 382 PHE 0.030 0.001 PHE A 718 TRP 0.067 0.002 TRP C 360 HIS 0.009 0.001 HIS I 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (41471) covalent geometry : angle 0.61073 / 0.32 (56922) hydrogen bonds : bond 0.03749 / 2.54 ( 1954) hydrogen bonds : angle 3.66087 / 2.66 ( 5374) metal coordination : bond 0.00723 / 0.27 ( 8) metal coordination : angle 2.13857 / 1.06 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15709.22 seconds wall clock time: 267 minutes 52.89 seconds (16072.89 seconds total)