Starting phenix.real_space_refine on Tue Sep 15 18:36:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nfy_49377/09_2026/9nfy_49377.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nfy_49377/09_2026/9nfy_49377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nfy_49377/09_2026/9nfy_49377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nfy_49377/09_2026/9nfy_49377.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nfy_49377/09_2026/9nfy_49377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nfy_49377/09_2026/9nfy_49377.map" } resolution = 3.4 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 181 5.16 5 C 25956 2.51 5 N 7529 2.21 5 O 8473 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s 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: 42380 Number of models: 1 Model: "" Number of chains: 30 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: 1531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1531 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 13, 'TRANS': 177} Chain breaks: 4 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: "Q" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 740 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "R" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 718 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} 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: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} 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: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} 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 10889 SG CYS D 128 75.266 116.945 64.530 1.00 85.80 S ATOM 10908 SG CYS D 131 71.972 118.358 63.330 1.00 80.74 S ATOM 11048 SG CYS D 149 75.315 119.985 62.250 1.00 97.33 S ATOM 10811 SG CYS D 117 72.711 109.148 56.598 1.00 76.71 S ATOM 10829 SG CYS D 120 73.018 106.837 53.639 1.00 88.37 S ATOM 10946 SG CYS D 136 75.038 106.134 56.686 1.00 72.16 S ATOM 10977 SG CYS D 140 75.903 109.244 54.590 1.00 90.35 S Time building chain proxies: 10.19, per 1000 atoms: 0.24 Number of scatterers: 42380 At special positions: 0 Unit cell: (173.225, 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 181 16.00 P 234 15.00 Mg 5 11.99 O 8473 8.00 N 7529 7.00 C 25956 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: 3.97 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 120 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 136 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 140 " Number of angles added : 9 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8906 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 42 sheets defined 52.6% alpha, 10.4% beta 108 base pairs and 196 stacking pairs defined. Time for finding SS restraints: 6.11 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: 4.062A 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: 3.914A pdb=" N ARG A 737 " --> pdb=" O GLN A 733 " (cutoff:3.500A) removed outlier: 4.082A 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: 4.391A pdb=" N ASN A 764 " --> pdb=" O GLN A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 793 removed outlier: 4.076A pdb=" N LEU A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 807 removed outlier: 3.740A 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: 3.984A 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: 3.861A pdb=" N ARG A 945 " --> pdb=" O ASP A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 952 removed outlier: 3.543A 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: 3.823A 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: 3.532A pdb=" N GLY A1912 " --> pdb=" O SER A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1918 through 1927 removed outlier: 4.278A 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: 3.606A 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 2059 Processing helix chain 'A' and resid 2068 through 2083 removed outlier: 3.890A pdb=" N LEU A2072 " --> pdb=" O MET A2068 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP A2073 " --> pdb=" O THR A2069 " (cutoff:3.500A) removed outlier: 3.732A 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: 3.724A pdb=" N ASP A2145 " --> pdb=" O ASN A2141 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N CYS A2152 " --> pdb=" O ALA A2148 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS A2153 " --> pdb=" O GLN A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2171 through 2191 removed outlier: 3.835A pdb=" N ASN A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET A2185 " --> pdb=" O ASN A2181 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU A2186 " --> pdb=" O GLN A2182 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A2187 " --> pdb=" O LYS A2183 " (cutoff:3.500A) Processing helix chain 'A' and resid 2198 through 2203 removed outlier: 3.684A pdb=" N LYS A2202 " --> pdb=" O THR A2198 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 16 through 23 Processing helix chain 'B' and resid 27 through 33 removed outlier: 4.200A pdb=" N GLN B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 36 No H-bonds generated for 'chain 'B' and resid 34 through 36' 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: 3.832A 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 283 removed outlier: 3.757A pdb=" N VAL C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 4.562A pdb=" N LEU C 281 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 4.214A 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: 3.629A 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 removed outlier: 3.500A pdb=" N PHE C 326 " --> pdb=" O ASN C 323 " (cutoff:3.500A) 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: 3.567A pdb=" N MET C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 394 removed outlier: 4.153A pdb=" N GLU C 384 " --> pdb=" O GLU C 380 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N HIS C 387 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.868A 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: 3.781A 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: 3.602A pdb=" N VAL E 101 " --> pdb=" O GLY E 98 " (cutoff:3.500A) removed outlier: 3.775A 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: 3.573A 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: 3.862A 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: 3.560A 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: 3.603A 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: 4.131A pdb=" N ARG F 253 " --> pdb=" O VAL F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 263 removed outlier: 3.539A pdb=" N ALA F 259 " --> pdb=" O GLN F 255 " (cutoff:3.500A) removed outlier: 4.322A 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: 3.760A 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: 3.890A 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: 3.679A 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: 4.272A 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: 4.136A 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: 3.537A pdb=" N LYS G 400 " --> pdb=" O GLU G 396 " (cutoff:3.500A) Processing helix chain 'G' and resid 402 through 409 removed outlier: 3.629A 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: 3.882A pdb=" N ASP H 214 " --> pdb=" O ARG H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 253 removed outlier: 4.213A pdb=" N ARG H 253 " --> pdb=" O VAL H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 269 through 287 Processing helix chain 'H' and resid 301 through 304 Processing helix chain 'H' and resid 305 through 316 removed outlier: 3.745A 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: 3.784A 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: 4.052A 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: 3.623A pdb=" N GLN I 262 " --> pdb=" O SER I 258 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU I 263 " --> pdb=" O MET I 259 " (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: 3.593A pdb=" N ARG I 317 " --> pdb=" O THR I 313 " (cutoff:3.500A) removed outlier: 3.718A 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: 4.155A 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: 3.709A 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: 4.135A pdb=" N THR J 407 " --> pdb=" O ILE J 403 " (cutoff:3.500A) removed outlier: 3.608A 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 'Q' and resid 18 through 24 Processing helix chain 'Q' and resid 28 through 39 removed outlier: 3.741A pdb=" N ARG Q 39 " --> pdb=" O HIS Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 76 Processing helix chain 'Q' and resid 82 through 92 Processing helix chain 'Q' and resid 93 through 108 removed outlier: 4.058A pdb=" N GLY Q 108 " --> pdb=" O ILE Q 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 49 Processing helix chain 'R' and resid 55 through 84 Processing helix chain 'R' and resid 90 through 102 Processing helix chain 'R' and resid 103 through 124 removed outlier: 3.604A pdb=" N ALA R 107 " --> pdb=" O PRO R 103 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS R 108 " --> pdb=" O GLY R 104 " (cutoff:3.500A) 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: 4.386A 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: 3.676A pdb=" N ALA T 107 " --> pdb=" O PRO T 103 " (cutoff:3.500A) removed outlier: 3.611A 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: 4.044A pdb=" N ASP U 77 " --> pdb=" O GLU U 73 " (cutoff:3.500A) removed outlier: 4.198A 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: 3.527A pdb=" N ILE U 124 " --> pdb=" O MET U 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 24 through 29 removed outlier: 3.890A 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: 3.785A pdb=" N GLU V 53 " --> pdb=" O LEU V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 94 Processing helix chain 'W' and resid 44 through 57 Processing helix chain 'W' and resid 63 through 79 removed outlier: 4.245A pdb=" N ASP W 77 " --> pdb=" O GLU W 73 " (cutoff:3.500A) removed outlier: 3.995A 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: 3.811A 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: 3.712A pdb=" N GLU X 53 " --> pdb=" O LEU X 49 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA X 76 " --> pdb=" O TYR X 72 " (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: 7.940A 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: 6.537A pdb=" N ARG A 741 " --> pdb=" O ARG A 769 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N LEU A 771 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 743 " --> pdb=" O LEU A 771 " (cutoff:3.500A) removed outlier: 7.638A 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: 4.014A pdb=" N GLY A 639 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 4.078A 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: 6.346A pdb=" N TYR A 853 " --> pdb=" O ILE A2163 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ARG A2165 " --> pdb=" O TYR A 853 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N HIS A 855 " --> pdb=" O ARG A2165 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A2167 " --> pdb=" O HIS A 855 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE A 857 " --> pdb=" O ILE A2167 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A2063 " --> pdb=" O VAL A2134 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A2062 " --> pdb=" O PHE A2114 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU A2116 " --> pdb=" O VAL A2062 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ILE A2064 " --> pdb=" O LEU A2116 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU A2087 " --> pdb=" O ILE A2115 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N SER A2117 " --> pdb=" O LEU A2087 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU A2089 " --> pdb=" O SER A2117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 916 through 917 removed outlier: 5.945A 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: 4.395A 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: 3.799A 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: 5.338A pdb=" N VAL G 221 " --> pdb=" O GLN G 203 " (cutoff:3.500A) removed outlier: 5.854A 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: 4.480A pdb=" N ASN C 8 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.859A 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: 6.402A pdb=" N ILE C 146 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR C 320 " --> pdb=" O ILE C 146 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N VAL C 148 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 6.665A 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: 3.519A 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: 6.239A pdb=" N VAL E 66 " --> pdb=" O PHE E 329 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER E 331 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU E 68 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA E 65 " --> pdb=" O MET E 359 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE E 361 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.361A 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: 5.812A pdb=" N VAL E 135 " --> pdb=" O LYS E 162 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS E 162 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU E 137 " --> pdb=" O GLY E 160 " (cutoff:3.500A) removed outlier: 3.527A 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: 5.453A pdb=" N VAL E 221 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 5.888A 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: 6.589A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU F 296 " --> pdb=" O ILE F 325 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ALA F 327 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE F 298 " --> pdb=" O ALA F 327 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY F 77 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N THR F 359 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.185A 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: 6.419A pdb=" N CYS G 94 " --> pdb=" O PHE G 300 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASP G 302 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N MET G 96 " --> pdb=" O ASP G 302 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL G 66 " --> pdb=" O PHE G 329 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N SER G 331 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU G 68 " --> pdb=" O SER G 331 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA G 65 " --> pdb=" O MET G 359 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ILE G 361 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.446A 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: 3.610A pdb=" N GLY H 77 " --> pdb=" O THR H 328 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA H 72 " --> pdb=" O LEU H 355 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL H 357 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU H 74 " --> pdb=" O VAL H 357 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR H 359 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 7.074A 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: 6.764A pdb=" N THR H 162 " --> pdb=" O VAL H 143 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE H 145 " --> pdb=" O LYS H 160 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS H 160 " --> pdb=" O ILE H 145 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE H 147 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL H 158 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.859A 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: 6.159A pdb=" N CYS I 94 " --> pdb=" O PHE I 300 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP I 302 " --> pdb=" O CYS I 94 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N MET I 96 " --> pdb=" O ASP I 302 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL I 66 " --> pdb=" O PHE I 329 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER I 331 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU I 68 " --> pdb=" O SER I 331 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ALA I 65 " --> pdb=" O MET I 359 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE I 361 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.329A 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: 6.314A pdb=" N GLY I 160 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU I 138 " --> pdb=" O ILE I 158 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE I 158 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 6.858A 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: 5.165A pdb=" N VAL I 221 " --> pdb=" O GLN I 203 " (cutoff:3.500A) removed outlier: 5.664A 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: 6.457A pdb=" N THR J 101 " --> pdb=" O PHE J 297 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASP J 299 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE J 103 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU J 296 " --> pdb=" O ILE J 325 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA J 327 " --> pdb=" O LEU J 296 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE J 298 " --> pdb=" O ALA J 327 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA J 72 " --> pdb=" O LEU J 355 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N VAL J 357 " --> pdb=" O ALA J 72 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU J 74 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR J 359 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 7.194A 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: 6.725A pdb=" N THR J 162 " --> pdb=" O VAL J 143 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE J 145 " --> pdb=" O LYS J 160 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS J 160 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ILE J 147 " --> pdb=" O VAL J 158 " (cutoff:3.500A) removed outlier: 7.128A 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 'Q' and resid 45 through 46 removed outlier: 7.084A pdb=" N ARG Q 45 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'Q' and resid 80 through 81 Processing sheet with id=AD9, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.487A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'S' and resid 77 through 78 Processing sheet with id=AE2, first strand: chain 'S' and resid 101 through 102 removed outlier: 6.997A pdb=" N THR S 101 " --> pdb=" O TYR X 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'U' and resid 83 through 84 removed outlier: 7.184A pdb=" N ARG U 83 " --> pdb=" O VAL V 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'U' and resid 118 through 119 Processing sheet with id=AE5, first strand: chain 'W' and resid 83 through 84 removed outlier: 7.054A pdb=" N ARG W 83 " --> pdb=" O VAL X 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'W' and resid 118 through 119 1802 hydrogen bonds defined for protein. 5196 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 562 hydrogen bond angles 0 basepair planarities 108 basepair parallelities 196 stacking parallelities Total time for adding SS restraints: 15.08 Time building geometry restraints manager: 5.27 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: 13963 1.36 - 1.51: 12114 1.51 - 1.65: 17150 1.65 - 1.80: 163 1.80 - 1.95: 136 Bond restraints: 43526 Sorted by residual: bond pdb=" O3B AGS A3301 " pdb=" PB AGS A3301 " ideal model delta sigma weight residual 1.673 1.572 0.101 2.00e-02 2.50e+03 2.53e+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 2.07e+01 bond pdb=" O3A AGS A3301 " pdb=" PA AGS A3301 " ideal model delta sigma weight residual 1.664 1.573 0.091 2.00e-02 2.50e+03 2.05e+01 bond pdb=" O3A AGS C 401 " pdb=" PA AGS C 401 " ideal model delta sigma weight residual 1.664 1.581 0.083 2.00e-02 2.50e+03 1.72e+01 ... (remaining 43521 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 59334 3.05 - 6.09: 304 6.09 - 9.14: 24 9.14 - 12.19: 25 12.19 - 15.23: 4 Bond angle restraints: 59691 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 106.00 102.51 3.49 6.00e-01 2.78e+00 3.38e+01 angle pdb=" O5' DG Z -18 " pdb=" C5' DG Z -18 " pdb=" C4' DG Z -18 " ideal model delta sigma weight residual 109.40 114.01 -4.61 8.00e-01 1.56e+00 3.32e+01 angle pdb=" O4' DA Y -35 " pdb=" C1' DA Y -35 " pdb=" N9 DA Y -35 " ideal model delta sigma weight residual 108.00 104.24 3.76 7.00e-01 2.04e+00 2.89e+01 angle pdb=" O5' DG Z -19 " pdb=" C5' DG Z -19 " pdb=" C4' DG Z -19 " ideal model delta sigma weight residual 109.40 113.67 -4.27 8.00e-01 1.56e+00 2.85e+01 angle pdb=" O4' DC Z -20 " pdb=" C1' DC Z -20 " pdb=" N1 DC Z -20 " ideal model delta sigma weight residual 108.00 111.56 -3.56 7.00e-01 2.04e+00 2.59e+01 ... (remaining 59686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.04: 24696 35.04 - 70.07: 1305 70.07 - 105.11: 62 105.11 - 140.14: 4 140.14 - 175.18: 10 Dihedral angle restraints: 26077 sinusoidal: 12280 harmonic: 13797 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 -60.00 109.45 -169.46 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 300.00 157.73 142.27 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 300.00 161.91 138.09 1 2.00e+01 2.50e-03 4.19e+01 ... (remaining 26074 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 6561 0.110 - 0.219: 206 0.219 - 0.329: 6 0.329 - 0.438: 12 0.438 - 0.548: 4 Chirality restraints: 6789 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 -2.88 -0.55 2.00e-01 2.50e+01 7.50e+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 -0.53 2.00e-01 2.50e+01 6.99e+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 -2.85 -0.52 2.00e-01 2.50e+01 6.75e+00 ... (remaining 6786 not shown) Planarity restraints: 6883 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC Y -64 " -0.043 2.00e-02 2.50e+03 2.32e-02 1.21e+01 pdb=" N1 DC Y -64 " 0.051 2.00e-02 2.50e+03 pdb=" C2 DC Y -64 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DC Y -64 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC Y -64 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC Y -64 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC Y -64 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC Y -64 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DC Y -64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC Z -20 " 0.034 2.00e-02 2.50e+03 2.17e-02 1.06e+01 pdb=" N1 DC Z -20 " -0.053 2.00e-02 2.50e+03 pdb=" C2 DC Z -20 " 0.013 2.00e-02 2.50e+03 pdb=" O2 DC Z -20 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DC Z -20 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DC Z -20 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC Z -20 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC Z -20 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DC Z -20 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT Y 31 " -0.040 2.00e-02 2.50e+03 1.91e-02 9.17e+00 pdb=" N1 DT Y 31 " 0.042 2.00e-02 2.50e+03 pdb=" C2 DT Y 31 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT Y 31 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DT Y 31 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT Y 31 " -0.006 2.00e-02 2.50e+03 pdb=" O4 DT Y 31 " -0.013 2.00e-02 2.50e+03 pdb=" C5 DT Y 31 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT Y 31 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT Y 31 " 0.008 2.00e-02 2.50e+03 ... (remaining 6880 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 182 2.55 - 3.14: 32245 3.14 - 3.73: 68799 3.73 - 4.31: 97151 4.31 - 4.90: 156871 Nonbonded interactions: 355248 Sorted by model distance: nonbonded pdb=" O2G AGS C 401 " pdb="MG MG C 402 " model vdw 1.964 2.170 nonbonded pdb=" O1B ADP J 501 " pdb="MG MG J 502 " model vdw 1.967 2.170 nonbonded pdb=" O2B ADP F 501 " pdb="MG MG F 502 " model vdw 1.986 2.170 nonbonded pdb=" O2G AGS A3301 " pdb="MG MG A3302 " model vdw 1.986 2.170 nonbonded pdb=" OG1 THR F 84 " pdb="MG MG F 502 " model vdw 2.005 2.170 ... (remaining 355243 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 'R' and (resid 34 through 37 or resid 40 through 59 or resid 61 through 6 \ 8 or resid 70 through 123 or resid 125)) selection = (chain 'T' and (resid 34 through 37 or resid 40 through 59 or resid 61 through 6 \ 8 or resid 70 through 123 or resid 125)) } ncs_group { reference = (chain 'U' and resid 39 through 134) selection = chain 'W' } ncs_group { reference = chain 'V' selection = (chain 'X' and resid 24 through 102) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.050 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 58.060 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 0.101 43534 Z= 0.295 Angle : 0.656 15.232 59700 Z= 0.426 Chirality : 0.050 0.548 6789 Planarity : 0.007 0.087 6883 Dihedral : 18.356 175.181 17171 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 1.47 (0.12), residues: 4719 helix: 1.53 (0.11), residues: 2308 sheet: 0.75 (0.19), residues: 697 loop : 0.49 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG A2154 TYR 0.029 0.002 TYR B 30 PHE 0.017 0.001 PHE R 65 TRP 0.038 0.001 TRP A 712 HIS 0.006 0.001 HIS X 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.30 (43526) covalent geometry : angle 0.65554 / 0.43 (59691) hydrogen bonds : bond 0.14071 / 9.50 ( 2083) hydrogen bonds : angle 4.83749 / 3.48 ( 5758) metal coordination : bond 0.00586 / 0.24 ( 8) metal coordination : angle 2.05446 / 1.06 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1631 time to evaluate : 1.447 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 628 TRP cc_start: 0.8578 (t60) cc_final: 0.7937 (t60) REVERT: A 632 MET cc_start: 0.8141 (mmm) cc_final: 0.7700 (mmm) REVERT: A 636 LYS cc_start: 0.8346 (mttt) cc_final: 0.8119 (mttt) REVERT: A 640 ILE cc_start: 0.8371 (mt) cc_final: 0.8072 (mp) REVERT: A 643 ASP cc_start: 0.7779 (m-30) cc_final: 0.7547 (m-30) REVERT: A 644 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7641 (mp0) REVERT: A 684 MET cc_start: 0.8426 (tpt) cc_final: 0.8196 (tpt) REVERT: A 694 LYS cc_start: 0.8444 (mttt) cc_final: 0.7985 (mttt) REVERT: A 703 LYS cc_start: 0.8507 (mtpp) cc_final: 0.8241 (mtpp) REVERT: A 704 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6932 (mt-10) REVERT: A 719 HIS cc_start: 0.7973 (m170) cc_final: 0.7427 (m90) REVERT: A 721 CYS cc_start: 0.8097 (t) cc_final: 0.7888 (t) REVERT: A 722 ILE cc_start: 0.8182 (mt) cc_final: 0.7931 (mp) REVERT: A 745 LEU cc_start: 0.8124 (mp) cc_final: 0.7905 (mp) REVERT: A 764 ASN cc_start: 0.8716 (m-40) cc_final: 0.8120 (t0) REVERT: A 783 MET cc_start: 0.8189 (mmp) cc_final: 0.7952 (mmp) REVERT: A 789 MET cc_start: 0.7578 (mmp) cc_final: 0.7168 (mmp) REVERT: A 792 LEU cc_start: 0.8064 (mt) cc_final: 0.7820 (mt) REVERT: A 826 VAL cc_start: 0.8350 (t) cc_final: 0.8077 (t) REVERT: A 830 HIS cc_start: 0.6969 (m90) cc_final: 0.6761 (m90) REVERT: A 851 LYS cc_start: 0.8917 (mmtp) cc_final: 0.8678 (mmtp) REVERT: A 958 TYR cc_start: 0.8232 (t80) cc_final: 0.7776 (t80) REVERT: A 964 LEU cc_start: 0.8546 (mt) cc_final: 0.8320 (mm) REVERT: A 966 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7755 (mtp-110) REVERT: A 975 LEU cc_start: 0.8186 (mt) cc_final: 0.7938 (mt) REVERT: A 976 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7201 (mt-10) REVERT: A 992 MET cc_start: 0.2632 (ttm) cc_final: 0.1921 (ttm) REVERT: A 1891 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 1893 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7805 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8367 (ptpp) cc_final: 0.7971 (ptpp) REVERT: A 1895 ARG cc_start: 0.7817 (ttp-170) cc_final: 0.7566 (ttp-170) REVERT: A 1896 GLN cc_start: 0.8191 (mt0) cc_final: 0.7967 (mt0) REVERT: A 1897 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7808 (ttp-170) REVERT: A 1899 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 1903 ARG cc_start: 0.8076 (ttm110) cc_final: 0.7837 (ttp-170) REVERT: A 1934 SER cc_start: 0.8331 (m) cc_final: 0.7942 (p) REVERT: A 1936 ILE cc_start: 0.8852 (mm) cc_final: 0.8203 (mt) REVERT: A 1948 PHE cc_start: 0.8693 (t80) cc_final: 0.8386 (t80) REVERT: A 1957 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7919 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7723 (tp30) cc_final: 0.6958 (tp30) REVERT: A 2025 VAL cc_start: 0.8076 (t) cc_final: 0.7792 (m) REVERT: A 2026 CYS cc_start: 0.8205 (m) cc_final: 0.7717 (m) REVERT: A 2028 MET cc_start: 0.8388 (mtt) cc_final: 0.8147 (mtp) REVERT: A 2058 GLU cc_start: 0.7421 (pt0) cc_final: 0.7118 (pt0) REVERT: A 2094 ARG cc_start: 0.7650 (mtp85) cc_final: 0.7305 (mtm-85) REVERT: A 2096 GLU cc_start: 0.7995 (mp0) cc_final: 0.7756 (pm20) REVERT: A 2150 ASP cc_start: 0.7997 (m-30) cc_final: 0.7601 (m-30) REVERT: A 2169 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 2179 LYS cc_start: 0.8533 (tppp) cc_final: 0.8152 (ttmm) REVERT: A 2185 MET cc_start: 0.6798 (ttm) cc_final: 0.6502 (ttm) REVERT: A 2196 PHE cc_start: 0.7890 (m-80) cc_final: 0.7621 (m-80) REVERT: C 7 ASP cc_start: 0.8404 (t0) cc_final: 0.8115 (t0) REVERT: C 12 ASN cc_start: 0.8615 (m-40) cc_final: 0.8339 (m110) REVERT: C 14 LYS cc_start: 0.8607 (mppt) cc_final: 0.8111 (mppt) REVERT: C 55 PHE cc_start: 0.7400 (t80) cc_final: 0.6950 (t80) REVERT: C 56 TYR cc_start: 0.8480 (m-80) cc_final: 0.8241 (m-10) REVERT: C 67 ASN cc_start: 0.8929 (t0) cc_final: 0.8670 (t0) REVERT: C 71 GLN cc_start: 0.8033 (tp40) cc_final: 0.7597 (tp-100) REVERT: C 72 ARG cc_start: 0.8728 (tpp80) cc_final: 0.8473 (tpp80) REVERT: C 86 VAL cc_start: 0.8787 (t) cc_final: 0.8324 (m) REVERT: C 87 ASP cc_start: 0.7992 (t0) cc_final: 0.7772 (t0) REVERT: C 90 ASP cc_start: 0.8478 (t0) cc_final: 0.7614 (t0) REVERT: C 92 ASN cc_start: 0.8401 (m-40) cc_final: 0.8113 (m-40) REVERT: C 103 THR cc_start: 0.8842 (m) cc_final: 0.8523 (p) REVERT: C 116 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8075 (mm-30) REVERT: C 149 ASP cc_start: 0.8432 (t0) cc_final: 0.8180 (t0) REVERT: C 164 LYS cc_start: 0.7798 (tptm) cc_final: 0.7559 (tptm) REVERT: C 196 MET cc_start: 0.8430 (mmm) cc_final: 0.7646 (mmm) REVERT: C 204 GLN cc_start: 0.8762 (tp40) cc_final: 0.8194 (tp40) REVERT: C 208 ASP cc_start: 0.8131 (m-30) cc_final: 0.7636 (m-30) REVERT: C 218 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7500 (ttp80) REVERT: C 229 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8405 (pt0) REVERT: C 230 ASN cc_start: 0.8581 (t0) cc_final: 0.8234 (t0) REVERT: C 250 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8648 (mtpp) REVERT: C 366 ILE cc_start: 0.8932 (tt) cc_final: 0.8692 (tt) REVERT: C 374 ASP cc_start: 0.8049 (m-30) cc_final: 0.7714 (m-30) REVERT: C 379 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7804 (ttp-110) REVERT: E 15 ILE cc_start: 0.8660 (mm) cc_final: 0.8401 (mm) REVERT: E 22 LYS cc_start: 0.8260 (mmtp) cc_final: 0.7890 (mmtp) REVERT: E 28 GLU cc_start: 0.7717 (mp0) cc_final: 0.7183 (mp0) REVERT: E 43 GLU cc_start: 0.8133 (mp0) cc_final: 0.7909 (mp0) REVERT: E 81 LEU cc_start: 0.8345 (mt) cc_final: 0.8133 (mp) REVERT: E 85 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8227 (mm-40) REVERT: E 134 GLU cc_start: 0.7538 (tt0) cc_final: 0.7244 (tt0) REVERT: E 165 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7553 (mmtt) REVERT: E 167 THR cc_start: 0.8190 (m) cc_final: 0.7793 (p) REVERT: E 168 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7952 (ttmt) REVERT: E 178 GLU cc_start: 0.8066 (tt0) cc_final: 0.7762 (tt0) REVERT: E 181 GLN cc_start: 0.7953 (mt0) cc_final: 0.7729 (mt0) REVERT: E 182 LYS cc_start: 0.7977 (mtmt) cc_final: 0.7668 (mtmt) REVERT: E 183 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7800 (mm-30) REVERT: E 214 ASP cc_start: 0.7987 (m-30) cc_final: 0.7754 (m-30) REVERT: E 230 LYS cc_start: 0.8304 (mttt) cc_final: 0.8074 (mttt) REVERT: E 262 GLN cc_start: 0.7352 (mt0) cc_final: 0.7099 (mm-40) REVERT: E 285 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7902 (ttmm) REVERT: E 286 TYR cc_start: 0.8320 (m-10) cc_final: 0.7858 (m-80) REVERT: E 314 TYR cc_start: 0.8109 (t80) cc_final: 0.7784 (t80) REVERT: E 356 ASP cc_start: 0.7727 (t0) cc_final: 0.7346 (t0) REVERT: E 370 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7888 (mt-10) REVERT: E 389 GLU cc_start: 0.7619 (tt0) cc_final: 0.7371 (tt0) REVERT: E 397 ILE cc_start: 0.8131 (mt) cc_final: 0.7893 (tt) REVERT: E 400 LYS cc_start: 0.7972 (ptpt) cc_final: 0.7676 (mtmm) REVERT: E 408 GLN cc_start: 0.7743 (mt0) cc_final: 0.7384 (mt0) REVERT: E 418 LYS cc_start: 0.8002 (ttmm) cc_final: 0.7793 (ttmm) REVERT: E 441 LYS cc_start: 0.8434 (mttt) cc_final: 0.8092 (mttt) REVERT: E 445 LYS cc_start: 0.7666 (mmtp) cc_final: 0.7440 (mmtp) REVERT: F 18 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7897 (mmm-85) REVERT: F 40 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7766 (mtt90) REVERT: F 112 GLU cc_start: 0.7584 (tp30) cc_final: 0.7285 (tp30) REVERT: F 142 VAL cc_start: 0.8196 (t) cc_final: 0.7767 (m) REVERT: F 160 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7898 (mtpt) REVERT: F 177 LYS cc_start: 0.8035 (mttt) cc_final: 0.7749 (mttt) REVERT: F 182 LEU cc_start: 0.8835 (mt) cc_final: 0.8540 (mm) REVERT: F 192 VAL cc_start: 0.8378 (t) cc_final: 0.7944 (p) REVERT: F 201 LYS cc_start: 0.8491 (tttp) cc_final: 0.8274 (tttp) REVERT: F 233 GLN cc_start: 0.7815 (tt0) cc_final: 0.7610 (tt0) REVERT: F 246 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7168 (mt-10) REVERT: F 248 ASP cc_start: 0.7575 (m-30) cc_final: 0.7256 (m-30) REVERT: F 269 LYS cc_start: 0.8522 (mmtp) cc_final: 0.8258 (mmtp) REVERT: F 271 GLU cc_start: 0.7735 (mp0) cc_final: 0.7513 (mp0) REVERT: F 274 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7533 (mm-30) REVERT: F 303 MET cc_start: 0.8553 (mmm) cc_final: 0.8199 (mmp) REVERT: F 317 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7070 (mt-10) REVERT: F 326 MET cc_start: 0.8134 (mtt) cc_final: 0.7928 (mtm) REVERT: F 341 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8107 (mt0) REVERT: F 376 GLU cc_start: 0.7845 (tt0) cc_final: 0.7507 (tt0) REVERT: F 392 ARG cc_start: 0.8071 (ttp-110) cc_final: 0.7808 (ttp-170) REVERT: F 436 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7093 (tm-30) REVERT: F 441 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7268 (mm-40) REVERT: F 446 TYR cc_start: 0.7931 (m-80) cc_final: 0.7569 (m-80) REVERT: G 15 ILE cc_start: 0.8838 (mt) cc_final: 0.8621 (mm) REVERT: G 34 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7982 (tm-30) REVERT: G 61 MET cc_start: 0.8563 (mmt) cc_final: 0.8073 (mmm) REVERT: G 79 LEU cc_start: 0.8572 (mt) cc_final: 0.8369 (mm) REVERT: G 86 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7665 (mm-30) REVERT: G 89 SER cc_start: 0.8284 (m) cc_final: 0.7943 (t) REVERT: G 90 LYS cc_start: 0.8549 (tptm) cc_final: 0.7203 (tptm) REVERT: G 96 MET cc_start: 0.7954 (ttp) cc_final: 0.7597 (ttm) REVERT: G 102 TYR cc_start: 0.8277 (m-80) cc_final: 0.7994 (m-80) REVERT: G 105 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7738 (mt-10) REVERT: G 110 GLU cc_start: 0.8105 (tp30) cc_final: 0.7819 (tp30) REVERT: G 115 ASN cc_start: 0.8429 (m110) cc_final: 0.8207 (m-40) REVERT: G 123 ARG cc_start: 0.8088 (ttm170) cc_final: 0.7272 (ttt180) REVERT: G 125 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7761 (mtmt) REVERT: G 126 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7469 (mt-10) REVERT: G 128 LYS cc_start: 0.8253 (tttt) cc_final: 0.7929 (tttt) REVERT: G 147 MET cc_start: 0.6354 (mtp) cc_final: 0.5948 (mtp) REVERT: G 158 ILE cc_start: 0.8625 (mt) cc_final: 0.8421 (mm) REVERT: G 162 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8176 (ttmm) REVERT: G 169 GLN cc_start: 0.8476 (mt0) cc_final: 0.8236 (mt0) REVERT: G 170 LEU cc_start: 0.8863 (mt) cc_final: 0.8652 (mp) REVERT: G 171 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7472 (tttm) REVERT: G 178 GLU cc_start: 0.7920 (tt0) cc_final: 0.7248 (tt0) REVERT: G 186 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7570 (mt-10) REVERT: G 189 ASP cc_start: 0.8094 (m-30) cc_final: 0.7866 (m-30) REVERT: G 193 ILE cc_start: 0.8563 (mt) cc_final: 0.8240 (mm) REVERT: G 209 TYR cc_start: 0.8349 (m-80) cc_final: 0.8062 (m-10) REVERT: G 227 ASP cc_start: 0.7623 (t0) cc_final: 0.7413 (t0) REVERT: G 233 GLU cc_start: 0.7951 (tt0) cc_final: 0.7366 (tt0) REVERT: G 244 ASP cc_start: 0.7333 (m-30) cc_final: 0.7032 (m-30) REVERT: G 268 LYS cc_start: 0.7998 (mttt) cc_final: 0.7762 (mttt) REVERT: G 280 ASN cc_start: 0.7906 (m-40) cc_final: 0.7648 (m-40) REVERT: G 326 ILE cc_start: 0.8473 (mt) cc_final: 0.8217 (mm) REVERT: G 362 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7981 (ttt-90) REVERT: G 370 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7840 (mt-10) REVERT: G 385 ASN cc_start: 0.8091 (m-40) cc_final: 0.7879 (m-40) REVERT: G 420 ASN cc_start: 0.7780 (t0) cc_final: 0.7576 (t0) REVERT: G 428 GLU cc_start: 0.7955 (mp0) cc_final: 0.7681 (mp0) REVERT: G 438 TYR cc_start: 0.8435 (m-80) cc_final: 0.8050 (m-80) REVERT: G 455 MET cc_start: 0.7004 (mmm) cc_final: 0.6735 (mmm) REVERT: H 18 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7395 (mtp85) REVERT: H 26 SER cc_start: 0.8758 (m) cc_final: 0.8382 (p) REVERT: H 33 LEU cc_start: 0.8291 (mt) cc_final: 0.8082 (mt) REVERT: H 38 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7657 (mm-30) REVERT: H 83 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8228 (mtmm) REVERT: H 113 MET cc_start: 0.8209 (ptt) cc_final: 0.7996 (ptt) REVERT: H 132 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8104 (ttmm) REVERT: H 144 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7372 (mm-30) REVERT: H 145 ILE cc_start: 0.8347 (mt) cc_final: 0.8021 (tp) REVERT: H 160 LYS cc_start: 0.8237 (mttt) cc_final: 0.7947 (mttt) REVERT: H 168 MET cc_start: 0.7047 (ttm) cc_final: 0.5508 (ttm) REVERT: H 186 LYS cc_start: 0.8274 (ttpt) cc_final: 0.8016 (ttpt) REVERT: H 201 LYS cc_start: 0.8482 (ptmt) cc_final: 0.8281 (ptmt) REVERT: H 204 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8537 (mtmm) REVERT: H 211 ARG cc_start: 0.8232 (ttt180) cc_final: 0.7974 (ttt180) REVERT: H 214 ASP cc_start: 0.7500 (p0) cc_final: 0.7267 (p0) REVERT: H 231 GLU cc_start: 0.7337 (tt0) cc_final: 0.6777 (tp30) REVERT: H 232 LEU cc_start: 0.8627 (mt) cc_final: 0.8007 (mt) REVERT: H 238 VAL cc_start: 0.8110 (t) cc_final: 0.7821 (p) REVERT: H 246 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7369 (mt-10) REVERT: H 253 ARG cc_start: 0.7923 (ptm160) cc_final: 0.7691 (ptm-80) REVERT: H 264 ASP cc_start: 0.7881 (t0) cc_final: 0.7627 (t0) REVERT: H 267 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7850 (mt-10) REVERT: H 270 SER cc_start: 0.8190 (p) cc_final: 0.7944 (t) REVERT: H 274 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7628 (mt-10) REVERT: H 275 GLN cc_start: 0.8231 (mm110) cc_final: 0.7966 (mm110) REVERT: H 277 ASN cc_start: 0.8529 (m-40) cc_final: 0.8151 (m110) REVERT: H 279 LYS cc_start: 0.8304 (tppt) cc_final: 0.8075 (tptp) REVERT: H 305 ASP cc_start: 0.7529 (m-30) cc_final: 0.7306 (m-30) REVERT: H 307 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7533 (mm-30) REVERT: H 314 ARG cc_start: 0.7303 (mmt180) cc_final: 0.6737 (mmt180) REVERT: H 317 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7330 (mt-10) REVERT: H 339 SER cc_start: 0.8730 (p) cc_final: 0.8482 (m) REVERT: H 348 ILE cc_start: 0.8631 (tp) cc_final: 0.8352 (mt) REVERT: H 369 GLN cc_start: 0.8354 (tp-100) cc_final: 0.8092 (mt0) REVERT: H 417 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8223 (mtmt) REVERT: H 443 MET cc_start: 0.8435 (ttm) cc_final: 0.8231 (ttp) REVERT: H 445 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7319 (mt-10) REVERT: H 452 PHE cc_start: 0.8631 (m-80) cc_final: 0.8416 (m-80) REVERT: I 17 SER cc_start: 0.8653 (m) cc_final: 0.8323 (t) REVERT: I 43 GLU cc_start: 0.8017 (mp0) cc_final: 0.7761 (mp0) REVERT: I 61 MET cc_start: 0.8313 (mmm) cc_final: 0.7627 (mmm) REVERT: I 64 ARG cc_start: 0.8215 (mmt-90) cc_final: 0.7790 (mmt-90) REVERT: I 105 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7614 (mt-10) REVERT: I 139 THR cc_start: 0.8749 (m) cc_final: 0.8318 (p) REVERT: I 141 CYS cc_start: 0.8505 (m) cc_final: 0.8244 (m) REVERT: I 162 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8531 (ttpp) REVERT: I 171 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8203 (tttm) REVERT: I 196 ASN cc_start: 0.8451 (p0) cc_final: 0.8232 (p0) REVERT: I 218 GLU cc_start: 0.7719 (tp30) cc_final: 0.7510 (tp30) REVERT: I 225 LYS cc_start: 0.7990 (mtpt) cc_final: 0.7755 (mtpp) REVERT: I 233 GLU cc_start: 0.7890 (tt0) cc_final: 0.7666 (tt0) REVERT: I 236 GLN cc_start: 0.8501 (tt0) cc_final: 0.8232 (tt0) REVERT: I 249 ARG cc_start: 0.7977 (mtp85) cc_final: 0.7775 (mtp85) REVERT: I 259 MET cc_start: 0.8528 (mtp) cc_final: 0.8023 (mtp) REVERT: I 269 THR cc_start: 0.8462 (p) cc_final: 0.8197 (p) REVERT: I 288 ASP cc_start: 0.7350 (m-30) cc_final: 0.6868 (m-30) REVERT: I 302 ASP cc_start: 0.8306 (t0) cc_final: 0.7828 (t0) REVERT: I 308 ASP cc_start: 0.8142 (p0) cc_final: 0.7860 (p0) REVERT: I 310 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7674 (mt-10) REVERT: I 322 SER cc_start: 0.8533 (p) cc_final: 0.8076 (t) REVERT: I 376 LYS cc_start: 0.8511 (tptp) cc_final: 0.8267 (tptp) REVERT: I 380 GLN cc_start: 0.8025 (mt0) cc_final: 0.7821 (mt0) REVERT: I 414 ASN cc_start: 0.8603 (t0) cc_final: 0.8347 (t0) REVERT: I 415 LEU cc_start: 0.8077 (mt) cc_final: 0.7822 (mt) REVERT: I 416 LEU cc_start: 0.8413 (mt) cc_final: 0.8211 (mt) REVERT: I 426 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7564 (mm-30) REVERT: I 438 TYR cc_start: 0.8313 (m-80) cc_final: 0.7824 (m-80) REVERT: I 439 ASP cc_start: 0.8060 (p0) cc_final: 0.7815 (p0) REVERT: I 441 LYS cc_start: 0.8364 (mttm) cc_final: 0.8075 (mttm) REVERT: I 445 LYS cc_start: 0.8210 (tppt) cc_final: 0.7242 (tppt) REVERT: J 38 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7458 (tp30) REVERT: J 78 GLN cc_start: 0.8464 (mt0) cc_final: 0.8263 (mt0) REVERT: J 86 ILE cc_start: 0.8568 (mm) cc_final: 0.8270 (mp) REVERT: J 90 MET cc_start: 0.8349 (mtm) cc_final: 0.8131 (mtm) REVERT: J 133 GLU cc_start: 0.8026 (pt0) cc_final: 0.7751 (pt0) REVERT: J 136 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7467 (mt-10) REVERT: J 144 GLU cc_start: 0.8013 (tt0) cc_final: 0.7784 (tt0) REVERT: J 164 LYS cc_start: 0.8356 (pttt) cc_final: 0.7887 (ptmm) REVERT: J 180 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7065 (mt-10) REVERT: J 183 THR cc_start: 0.8146 (m) cc_final: 0.7829 (p) REVERT: J 184 LYS cc_start: 0.8023 (mttp) cc_final: 0.7769 (mttp) REVERT: J 185 ASP cc_start: 0.7456 (t0) cc_final: 0.7169 (t0) REVERT: J 192 VAL cc_start: 0.8579 (t) cc_final: 0.8101 (p) REVERT: J 201 LYS cc_start: 0.8300 (tptm) cc_final: 0.7934 (tttt) REVERT: J 225 VAL cc_start: 0.8448 (t) cc_final: 0.8138 (p) REVERT: J 231 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7299 (mm-30) REVERT: J 234 LYS cc_start: 0.8525 (mtpt) cc_final: 0.8281 (ttmm) REVERT: J 236 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8037 (mmmm) REVERT: J 255 GLN cc_start: 0.8330 (mm110) cc_final: 0.8078 (mm-40) REVERT: J 267 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7202 (mt-10) REVERT: J 270 SER cc_start: 0.8362 (p) cc_final: 0.8062 (t) REVERT: J 288 LYS cc_start: 0.8763 (mttm) cc_final: 0.8555 (mttp) REVERT: J 314 ARG cc_start: 0.8095 (mmt180) cc_final: 0.7845 (mmt180) REVERT: J 326 MET cc_start: 0.8369 (mtm) cc_final: 0.8057 (mtp) REVERT: J 353 ARG cc_start: 0.7846 (mtt-85) cc_final: 0.7516 (mtm-85) REVERT: J 368 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8230 (ttmm) REVERT: J 376 GLU cc_start: 0.7912 (tt0) cc_final: 0.7705 (tt0) REVERT: J 377 GLU cc_start: 0.7896 (tp30) cc_final: 0.7463 (tp30) REVERT: J 382 MET cc_start: 0.8420 (mtt) cc_final: 0.8097 (mtt) REVERT: J 430 TYR cc_start: 0.8618 (t80) cc_final: 0.8371 (t80) REVERT: J 436 GLU cc_start: 0.7082 (tm-30) cc_final: 0.6587 (tm-30) REVERT: J 444 LYS cc_start: 0.8310 (mttm) cc_final: 0.8063 (mttm) REVERT: J 445 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7513 (mt-10) REVERT: J 447 GLN cc_start: 0.8220 (pt0) cc_final: 0.8009 (pt0) REVERT: P 250 SER cc_start: 0.8781 (m) cc_final: 0.8059 (p) REVERT: P 254 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7201 (mt-10) REVERT: P 273 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7693 (mm-30) REVERT: S 39 TYR cc_start: 0.9034 (m-80) cc_final: 0.8553 (m-80) REVERT: S 87 VAL cc_start: 0.8907 (t) cc_final: 0.8670 (p) REVERT: S 99 ARG cc_start: 0.8298 (mtt90) cc_final: 0.8078 (mtt90) REVERT: T 43 LYS cc_start: 0.8802 (mttt) cc_final: 0.8599 (mtmm) REVERT: T 44 VAL cc_start: 0.9192 (t) cc_final: 0.8954 (p) REVERT: T 68 ASP cc_start: 0.8348 (t0) cc_final: 0.7862 (t0) REVERT: T 70 PHE cc_start: 0.8982 (t80) cc_final: 0.8758 (t80) REVERT: T 79 ARG cc_start: 0.8331 (mtm110) cc_final: 0.7845 (mtm110) REVERT: T 111 VAL cc_start: 0.8957 (t) cc_final: 0.8677 (m) REVERT: T 115 THR cc_start: 0.8613 (t) cc_final: 0.8300 (p) REVERT: U 83 ARG cc_start: 0.8386 (mtt90) cc_final: 0.8050 (mtt90) REVERT: U 93 GLN cc_start: 0.8893 (tt0) cc_final: 0.8646 (tt0) REVERT: U 106 ASP cc_start: 0.8099 (m-30) cc_final: 0.7603 (m-30) REVERT: V 58 LEU cc_start: 0.9279 (tp) cc_final: 0.9076 (tp) REVERT: V 64 ASN cc_start: 0.8760 (m-40) cc_final: 0.8405 (m-40) REVERT: V 68 ASP cc_start: 0.8761 (m-30) cc_final: 0.7951 (m-30) REVERT: W 41 TYR cc_start: 0.8864 (m-80) cc_final: 0.8587 (m-80) REVERT: W 52 ARG cc_start: 0.8624 (mtm-85) cc_final: 0.8297 (mtt-85) REVERT: W 54 TYR cc_start: 0.8573 (m-80) cc_final: 0.8315 (m-10) REVERT: W 56 LYS cc_start: 0.8715 (mttp) cc_final: 0.8491 (tppp) REVERT: W 78 PHE cc_start: 0.7958 (m-80) cc_final: 0.7715 (m-10) REVERT: W 90 MET cc_start: 0.8589 (mmm) cc_final: 0.8347 (mmp) REVERT: W 120 MET cc_start: 0.8248 (mtt) cc_final: 0.7611 (mmm) REVERT: W 123 ASP cc_start: 0.8186 (m-30) cc_final: 0.7745 (m-30) REVERT: W 128 ARG cc_start: 0.8750 (mtp180) cc_final: 0.8537 (mtp-110) REVERT: X 39 ARG cc_start: 0.8859 (mmt-90) cc_final: 0.8455 (mmt-90) REVERT: X 84 MET cc_start: 0.8524 (tpt) cc_final: 0.8220 (mmm) outliers start: 0 outliers final: 0 residues processed: 1631 average time/residue: 0.3028 time to fit residues: 765.5111 Evaluate side-chains 1454 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1454 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.8980 chunk 455 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 194 HIS D 91 GLN E 115 ASN E 169 GLN 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 247 ASN I 335 ASN I 385 ASN I 408 GLN J 341 GLN R 84 ASN T 63 ASN U 108 ASN X 27 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.129927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104713 restraints weight = 68644.055| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.98 r_work: 0.3093 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43534 Z= 0.167 Angle : 0.602 7.423 59700 Z= 0.322 Chirality : 0.045 0.339 6789 Planarity : 0.005 0.079 6883 Dihedral : 20.457 177.001 7705 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.17 % Allowed : 8.99 % Favored : 89.84 % 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: 1.71 (0.12), residues: 4719 helix: 1.80 (0.11), residues: 2348 sheet: 0.74 (0.20), residues: 669 loop : 0.51 (0.15), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 185 TYR 0.021 0.001 TYR B 30 PHE 0.020 0.001 PHE A 836 TRP 0.030 0.002 TRP A 712 HIS 0.006 0.001 HIS A 659 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (43526) covalent geometry : angle 0.60183 / 0.32 (59691) hydrogen bonds : bond 0.04643 / 3.13 ( 2083) hydrogen bonds : angle 4.00693 / 2.89 ( 5758) metal coordination : bond 0.00716 / 0.29 ( 8) metal coordination : angle 0.97723 / 0.46 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1516 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1468 time to evaluate : 1.641 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 628 TRP cc_start: 0.8613 (t60) cc_final: 0.8069 (t60) REVERT: A 629 LEU cc_start: 0.8796 (mt) cc_final: 0.8461 (mt) REVERT: A 632 MET cc_start: 0.8097 (mmm) cc_final: 0.7872 (mmm) REVERT: A 660 LEU cc_start: 0.8963 (mp) cc_final: 0.8696 (mp) REVERT: A 663 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7164 (mt-10) REVERT: A 684 MET cc_start: 0.8736 (tpt) cc_final: 0.8521 (tpt) REVERT: A 687 LYS cc_start: 0.8749 (mttt) cc_final: 0.8448 (mttm) REVERT: A 694 LYS cc_start: 0.8623 (mttt) cc_final: 0.8137 (mmtp) REVERT: A 703 LYS cc_start: 0.8341 (mtpp) cc_final: 0.8081 (mtpp) REVERT: A 704 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6866 (mt-10) REVERT: A 719 HIS cc_start: 0.8026 (m170) cc_final: 0.7367 (m90) REVERT: A 727 LEU cc_start: 0.9008 (mt) cc_final: 0.8755 (mm) REVERT: A 745 LEU cc_start: 0.8359 (mp) cc_final: 0.8135 (mm) REVERT: A 764 ASN cc_start: 0.8529 (m-40) cc_final: 0.8326 (t0) REVERT: A 789 MET cc_start: 0.7362 (mmp) cc_final: 0.7136 (mmp) REVERT: A 792 LEU cc_start: 0.8113 (mt) cc_final: 0.7872 (mt) REVERT: A 863 LYS cc_start: 0.8569 (tptp) cc_final: 0.8356 (tttm) REVERT: A 888 MET cc_start: 0.7154 (mtm) cc_final: 0.6905 (ptm) REVERT: A 966 ARG cc_start: 0.7965 (mtp85) cc_final: 0.7716 (mtp-110) REVERT: A 973 VAL cc_start: 0.8730 (t) cc_final: 0.8504 (p) REVERT: A 975 LEU cc_start: 0.8412 (mt) cc_final: 0.8139 (mt) REVERT: A 992 MET cc_start: 0.2581 (ttm) cc_final: 0.1808 (ttm) REVERT: A 1891 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7703 (tm-30) REVERT: A 1893 ARG cc_start: 0.8444 (mtt180) cc_final: 0.8012 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8519 (ptpp) cc_final: 0.8148 (ptpp) REVERT: A 1895 ARG cc_start: 0.8079 (ttp-170) cc_final: 0.7818 (ttp-170) REVERT: A 1896 GLN cc_start: 0.8260 (mt0) cc_final: 0.7983 (mt0) REVERT: A 1897 ARG cc_start: 0.8175 (ttp-170) cc_final: 0.7833 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8442 (ttm110) cc_final: 0.8179 (ttp-170) REVERT: A 1934 SER cc_start: 0.8404 (m) cc_final: 0.8170 (p) REVERT: A 1936 ILE cc_start: 0.8968 (mm) cc_final: 0.8354 (mt) REVERT: A 1948 PHE cc_start: 0.8778 (t80) cc_final: 0.8321 (t80) REVERT: A 1953 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7770 (mm-30) REVERT: A 1957 ARG cc_start: 0.8350 (mtp180) cc_final: 0.8109 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7884 (tp30) cc_final: 0.7055 (tp30) REVERT: A 2026 CYS cc_start: 0.8416 (m) cc_final: 0.8040 (m) REVERT: A 2028 MET cc_start: 0.8598 (mtt) cc_final: 0.8344 (mtp) REVERT: A 2058 GLU cc_start: 0.7498 (pt0) cc_final: 0.7295 (pt0) REVERT: A 2102 MET cc_start: 0.8613 (mmm) cc_final: 0.8017 (mmm) REVERT: A 2150 ASP cc_start: 0.7997 (m-30) cc_final: 0.7630 (m-30) REVERT: A 2185 MET cc_start: 0.6840 (ttm) cc_final: 0.6590 (ttm) REVERT: A 2196 PHE cc_start: 0.7969 (m-80) cc_final: 0.7718 (m-80) REVERT: B 133 MET cc_start: 0.5929 (mmt) cc_final: 0.5479 (mmt) REVERT: C 2 THR cc_start: 0.7691 (t) cc_final: 0.7211 (m) REVERT: C 7 ASP cc_start: 0.8140 (t0) cc_final: 0.7923 (t0) REVERT: C 12 ASN cc_start: 0.8540 (m-40) cc_final: 0.8225 (m110) REVERT: C 14 LYS cc_start: 0.8730 (mppt) cc_final: 0.8162 (mppt) REVERT: C 72 ARG cc_start: 0.8590 (tpp80) cc_final: 0.8271 (tpp80) REVERT: C 83 MET cc_start: 0.8292 (mmm) cc_final: 0.8028 (mmm) REVERT: C 86 VAL cc_start: 0.8792 (t) cc_final: 0.8518 (m) REVERT: C 90 ASP cc_start: 0.8066 (t0) cc_final: 0.7341 (t0) REVERT: C 103 THR cc_start: 0.8805 (m) cc_final: 0.8458 (p) REVERT: C 107 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7969 (mm-30) REVERT: C 115 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7910 (mt-10) REVERT: C 116 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7989 (mm-30) REVERT: C 124 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8110 (mtp180) REVERT: C 149 ASP cc_start: 0.8383 (t0) cc_final: 0.8145 (t0) REVERT: C 204 GLN cc_start: 0.8680 (tp40) cc_final: 0.7986 (tp40) REVERT: C 208 ASP cc_start: 0.8064 (m-30) cc_final: 0.7652 (m-30) REVERT: C 220 MET cc_start: 0.8135 (tpp) cc_final: 0.7933 (mmt) REVERT: C 230 ASN cc_start: 0.8609 (t0) cc_final: 0.7986 (t0) REVERT: C 250 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8605 (mtpp) REVERT: C 252 ARG cc_start: 0.8635 (mmm-85) cc_final: 0.8412 (mmm160) REVERT: C 269 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7910 (tpp80) REVERT: C 308 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8237 (mt-10) REVERT: C 366 ILE cc_start: 0.8976 (tt) cc_final: 0.8755 (tt) REVERT: C 371 ASP cc_start: 0.7877 (t0) cc_final: 0.7408 (t0) REVERT: C 373 GLU cc_start: 0.7840 (pm20) cc_final: 0.7520 (pm20) REVERT: C 374 ASP cc_start: 0.8011 (m-30) cc_final: 0.7749 (m-30) REVERT: D 92 ASN cc_start: 0.8733 (t0) cc_final: 0.8182 (t0) REVERT: E 15 ILE cc_start: 0.8681 (mm) cc_final: 0.8404 (mm) REVERT: E 22 LYS cc_start: 0.8437 (mmtp) cc_final: 0.8030 (mmtp) REVERT: E 28 GLU cc_start: 0.7822 (mp0) cc_final: 0.7291 (mp0) REVERT: E 64 ARG cc_start: 0.8328 (mtp85) cc_final: 0.7913 (mmt-90) REVERT: E 81 LEU cc_start: 0.8440 (mt) cc_final: 0.8228 (mp) REVERT: E 85 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8363 (mm-40) REVERT: E 134 GLU cc_start: 0.7718 (tt0) cc_final: 0.7455 (tt0) REVERT: E 162 LYS cc_start: 0.8404 (ptmt) cc_final: 0.7869 (ptmm) REVERT: E 165 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7584 (mmtt) REVERT: E 167 THR cc_start: 0.8160 (m) cc_final: 0.7797 (p) REVERT: E 168 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8094 (ttmt) REVERT: E 178 GLU cc_start: 0.8037 (tt0) cc_final: 0.7730 (tt0) REVERT: E 182 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7797 (mtmt) REVERT: E 183 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7882 (mm-30) REVERT: E 194 GLU cc_start: 0.7955 (tt0) cc_final: 0.7690 (tt0) REVERT: E 212 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7436 (mm-30) REVERT: E 214 ASP cc_start: 0.8050 (m-30) cc_final: 0.7801 (m-30) REVERT: E 227 ASP cc_start: 0.7697 (t0) cc_final: 0.7432 (t0) REVERT: E 230 LYS cc_start: 0.8315 (mttt) cc_final: 0.8087 (mttt) REVERT: E 236 GLN cc_start: 0.8607 (mm110) cc_final: 0.8228 (mm-40) REVERT: E 255 ASP cc_start: 0.7542 (p0) cc_final: 0.7342 (p0) REVERT: E 285 LYS cc_start: 0.8011 (ttmm) cc_final: 0.7778 (ttmm) REVERT: E 286 TYR cc_start: 0.8334 (m-10) cc_final: 0.7917 (m-80) REVERT: E 356 ASP cc_start: 0.8007 (t0) cc_final: 0.7641 (t70) REVERT: E 370 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8140 (mt-10) REVERT: E 389 GLU cc_start: 0.7832 (tt0) cc_final: 0.7586 (tt0) REVERT: E 397 ILE cc_start: 0.8192 (mt) cc_final: 0.7918 (tt) REVERT: E 408 GLN cc_start: 0.7774 (mt0) cc_final: 0.7488 (mt0) REVERT: E 418 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7860 (ttmm) REVERT: E 441 LYS cc_start: 0.8394 (mttt) cc_final: 0.8176 (mttt) REVERT: E 445 LYS cc_start: 0.7756 (mmtp) cc_final: 0.7540 (mmtp) REVERT: E 446 ILE cc_start: 0.8317 (mm) cc_final: 0.7998 (mt) REVERT: F 19 ILE cc_start: 0.8639 (tt) cc_final: 0.8292 (tt) REVERT: F 40 ARG cc_start: 0.8170 (mtt90) cc_final: 0.7846 (mtt90) REVERT: F 83 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7713 (mtmt) REVERT: F 112 GLU cc_start: 0.7764 (tp30) cc_final: 0.7481 (tp30) REVERT: F 117 GLU cc_start: 0.8210 (tp30) cc_final: 0.7620 (mm-30) REVERT: F 142 VAL cc_start: 0.8252 (t) cc_final: 0.7835 (m) REVERT: F 160 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7833 (mtpt) REVERT: F 168 MET cc_start: 0.7386 (mtp) cc_final: 0.7039 (mtp) REVERT: F 177 LYS cc_start: 0.8294 (mttt) cc_final: 0.7911 (mttt) REVERT: F 192 VAL cc_start: 0.8362 (t) cc_final: 0.7883 (p) REVERT: F 218 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.7037 (tpp) REVERT: F 246 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7288 (mt-10) REVERT: F 248 ASP cc_start: 0.7719 (m-30) cc_final: 0.7397 (m-30) REVERT: F 267 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7212 (mt-10) REVERT: F 269 LYS cc_start: 0.8265 (mmtp) cc_final: 0.8011 (mmtp) REVERT: F 271 GLU cc_start: 0.7893 (mp0) cc_final: 0.7555 (mp0) REVERT: F 274 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7652 (mm-30) REVERT: F 303 MET cc_start: 0.8611 (mmm) cc_final: 0.8280 (mmp) REVERT: F 317 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7425 (mt-10) REVERT: F 329 ASN cc_start: 0.8017 (p0) cc_final: 0.7650 (p0) REVERT: F 341 GLN cc_start: 0.8395 (mm-40) cc_final: 0.8165 (mt0) REVERT: F 376 GLU cc_start: 0.8058 (tt0) cc_final: 0.7692 (tt0) REVERT: F 392 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7911 (ttp-170) REVERT: F 436 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7197 (tm-30) REVERT: F 441 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7567 (mm-40) REVERT: F 445 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7588 (mm-30) REVERT: G 15 ILE cc_start: 0.8834 (mt) cc_final: 0.8618 (mm) REVERT: G 79 LEU cc_start: 0.8548 (mt) cc_final: 0.8321 (mm) REVERT: G 86 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7650 (mm-30) REVERT: G 89 SER cc_start: 0.8241 (m) cc_final: 0.7899 (t) REVERT: G 90 LYS cc_start: 0.8579 (tptm) cc_final: 0.7333 (tptm) REVERT: G 96 MET cc_start: 0.7982 (ttp) cc_final: 0.7674 (ttt) REVERT: G 102 TYR cc_start: 0.8298 (m-80) cc_final: 0.8018 (m-10) REVERT: G 105 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7594 (mt-10) REVERT: G 110 GLU cc_start: 0.8207 (tp30) cc_final: 0.7891 (mm-30) REVERT: G 123 ARG cc_start: 0.8240 (ttm170) cc_final: 0.7379 (ttt90) REVERT: G 125 LYS cc_start: 0.8304 (mtmt) cc_final: 0.7861 (mtmt) REVERT: G 126 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7441 (mt-10) REVERT: G 129 GLU cc_start: 0.7367 (tt0) cc_final: 0.6841 (tt0) REVERT: G 137 GLU cc_start: 0.7761 (tt0) cc_final: 0.7421 (tp30) REVERT: G 147 MET cc_start: 0.6264 (mtp) cc_final: 0.5641 (mtp) REVERT: G 158 ILE cc_start: 0.8559 (mt) cc_final: 0.8236 (mm) REVERT: G 162 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8007 (ttmm) REVERT: G 169 GLN cc_start: 0.8533 (mt0) cc_final: 0.8324 (mt0) REVERT: G 170 LEU cc_start: 0.8618 (mt) cc_final: 0.8379 (mp) REVERT: G 171 LYS cc_start: 0.8579 (mtpt) cc_final: 0.7934 (tttp) REVERT: G 178 GLU cc_start: 0.8144 (tt0) cc_final: 0.7388 (tt0) REVERT: G 193 ILE cc_start: 0.8593 (mt) cc_final: 0.8215 (mm) REVERT: G 209 TYR cc_start: 0.8553 (m-80) cc_final: 0.8167 (m-10) REVERT: G 225 LYS cc_start: 0.8271 (mmpt) cc_final: 0.7854 (mmpt) REVERT: G 227 ASP cc_start: 0.7677 (t0) cc_final: 0.7455 (t0) REVERT: G 233 GLU cc_start: 0.7904 (tt0) cc_final: 0.7228 (tt0) REVERT: G 244 ASP cc_start: 0.7360 (m-30) cc_final: 0.7061 (m-30) REVERT: G 247 ASN cc_start: 0.8304 (m-40) cc_final: 0.8056 (m110) REVERT: G 249 ARG cc_start: 0.7812 (ttt-90) cc_final: 0.7537 (ttt-90) REVERT: G 267 LYS cc_start: 0.7783 (tttp) cc_final: 0.7553 (tttp) REVERT: G 268 LYS cc_start: 0.7966 (mttt) cc_final: 0.7719 (mttt) REVERT: G 280 ASN cc_start: 0.7919 (m-40) cc_final: 0.7708 (m-40) REVERT: G 302 ASP cc_start: 0.8173 (t0) cc_final: 0.7942 (t0) REVERT: G 370 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7877 (mt-10) REVERT: G 376 LYS cc_start: 0.8753 (tptt) cc_final: 0.8482 (tptm) REVERT: G 422 LYS cc_start: 0.8265 (mttp) cc_final: 0.7885 (mtpp) REVERT: G 428 GLU cc_start: 0.8209 (mp0) cc_final: 0.7877 (mp0) REVERT: G 438 TYR cc_start: 0.8393 (m-80) cc_final: 0.8018 (m-80) REVERT: G 446 ILE cc_start: 0.8557 (mt) cc_final: 0.8172 (mm) REVERT: G 455 MET cc_start: 0.7114 (mmm) cc_final: 0.6765 (mmm) REVERT: H 26 SER cc_start: 0.8755 (m) cc_final: 0.8370 (p) REVERT: H 33 LEU cc_start: 0.8229 (mt) cc_final: 0.8018 (mt) REVERT: H 38 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7859 (mm-30) REVERT: H 83 LYS cc_start: 0.8764 (mtmm) cc_final: 0.8411 (mtmm) REVERT: H 113 MET cc_start: 0.8287 (ptt) cc_final: 0.7678 (ptp) REVERT: H 132 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8095 (ttmm) REVERT: H 144 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7458 (mm-30) REVERT: H 145 ILE cc_start: 0.8333 (mt) cc_final: 0.8106 (tp) REVERT: H 160 LYS cc_start: 0.8321 (mttt) cc_final: 0.8097 (mttt) REVERT: H 174 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8225 (mp) REVERT: H 186 LYS cc_start: 0.8321 (ttpt) cc_final: 0.7875 (ttpt) REVERT: H 201 LYS cc_start: 0.8372 (ptmt) cc_final: 0.8110 (ptmt) REVERT: H 204 LYS cc_start: 0.8887 (mtpt) cc_final: 0.8500 (mtpt) REVERT: H 214 ASP cc_start: 0.7447 (p0) cc_final: 0.7193 (p0) REVERT: H 238 VAL cc_start: 0.8184 (t) cc_final: 0.7907 (p) REVERT: H 253 ARG cc_start: 0.8196 (ptm160) cc_final: 0.7844 (ptm-80) REVERT: H 267 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7786 (mt-10) REVERT: H 274 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7703 (mt-10) REVERT: H 275 GLN cc_start: 0.8331 (mm110) cc_final: 0.8016 (mm-40) REVERT: H 277 ASN cc_start: 0.8507 (m-40) cc_final: 0.8152 (m110) REVERT: H 279 LYS cc_start: 0.8313 (tppt) cc_final: 0.8106 (tptp) REVERT: H 313 ASN cc_start: 0.8077 (m-40) cc_final: 0.7808 (m-40) REVERT: H 314 ARG cc_start: 0.7423 (mmt180) cc_final: 0.7038 (mmt180) REVERT: H 339 SER cc_start: 0.8712 (p) cc_final: 0.8455 (m) REVERT: H 348 ILE cc_start: 0.8430 (tp) cc_final: 0.8210 (mt) REVERT: H 369 GLN cc_start: 0.8436 (tp-100) cc_final: 0.8211 (mt0) REVERT: H 384 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8046 (mm-30) REVERT: H 452 PHE cc_start: 0.8569 (m-80) cc_final: 0.8366 (m-80) REVERT: I 17 SER cc_start: 0.8665 (m) cc_final: 0.8408 (t) REVERT: I 60 LYS cc_start: 0.8407 (ptpt) cc_final: 0.8100 (ptmm) REVERT: I 61 MET cc_start: 0.8319 (mmm) cc_final: 0.7848 (mmm) REVERT: I 64 ARG cc_start: 0.8176 (mmt-90) cc_final: 0.7823 (tpp80) REVERT: I 125 LYS cc_start: 0.8575 (ttpp) cc_final: 0.8238 (ttmm) REVERT: I 134 GLU cc_start: 0.7661 (tt0) cc_final: 0.7387 (tt0) REVERT: I 139 THR cc_start: 0.8676 (m) cc_final: 0.8354 (p) REVERT: I 141 CYS cc_start: 0.8548 (m) cc_final: 0.8309 (m) REVERT: I 171 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8289 (tttm) REVERT: I 218 GLU cc_start: 0.7881 (tp30) cc_final: 0.7646 (tp30) REVERT: I 227 ASP cc_start: 0.7545 (t0) cc_final: 0.7313 (t0) REVERT: I 231 LYS cc_start: 0.8212 (mttt) cc_final: 0.7991 (mtpp) REVERT: I 244 ASP cc_start: 0.7656 (m-30) cc_final: 0.7365 (t0) REVERT: I 249 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7825 (mtp85) REVERT: I 259 MET cc_start: 0.8120 (mtp) cc_final: 0.7780 (mtp) REVERT: I 269 THR cc_start: 0.8512 (p) cc_final: 0.8274 (p) REVERT: I 281 LYS cc_start: 0.8641 (mttt) cc_final: 0.8393 (mtmt) REVERT: I 302 ASP cc_start: 0.8419 (t0) cc_final: 0.7995 (t0) REVERT: I 322 SER cc_start: 0.8585 (p) cc_final: 0.8248 (t) REVERT: I 376 LYS cc_start: 0.8529 (tptp) cc_final: 0.8310 (tptp) REVERT: I 380 GLN cc_start: 0.8118 (mt0) cc_final: 0.7863 (mt0) REVERT: I 438 TYR cc_start: 0.8252 (m-80) cc_final: 0.7690 (m-80) REVERT: I 439 ASP cc_start: 0.8117 (p0) cc_final: 0.7860 (p0) REVERT: I 441 LYS cc_start: 0.8493 (mttm) cc_final: 0.8023 (mtmm) REVERT: I 445 LYS cc_start: 0.8177 (tppt) cc_final: 0.7182 (tppt) REVERT: J 61 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7689 (mm-30) REVERT: J 90 MET cc_start: 0.8414 (mtm) cc_final: 0.8177 (mtm) REVERT: J 133 GLU cc_start: 0.7715 (pt0) cc_final: 0.7384 (pt0) REVERT: J 136 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7444 (mt-10) REVERT: J 144 GLU cc_start: 0.8152 (tt0) cc_final: 0.7915 (tt0) REVERT: J 146 GLN cc_start: 0.7752 (tt0) cc_final: 0.7153 (tm-30) REVERT: J 164 LYS cc_start: 0.8437 (pttt) cc_final: 0.7951 (ptmm) REVERT: J 180 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7037 (mt-10) REVERT: J 183 THR cc_start: 0.8224 (m) cc_final: 0.7894 (p) REVERT: J 184 LYS cc_start: 0.8227 (mttp) cc_final: 0.8023 (mttp) REVERT: J 185 ASP cc_start: 0.7571 (t0) cc_final: 0.7277 (t0) REVERT: J 192 VAL cc_start: 0.8603 (t) cc_final: 0.8289 (p) REVERT: J 201 LYS cc_start: 0.8248 (tptm) cc_final: 0.8046 (tttt) REVERT: J 225 VAL cc_start: 0.8413 (t) cc_final: 0.8105 (p) REVERT: J 234 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8423 (ttmm) REVERT: J 236 LYS cc_start: 0.8460 (mtpt) cc_final: 0.8166 (mtpt) REVERT: J 267 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7188 (mt-10) REVERT: J 270 SER cc_start: 0.8458 (p) cc_final: 0.8053 (t) REVERT: J 286 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7855 (mt-10) REVERT: J 314 ARG cc_start: 0.8105 (mmt180) cc_final: 0.7835 (mmt180) REVERT: J 326 MET cc_start: 0.8264 (mtm) cc_final: 0.8023 (mtp) REVERT: J 352 ASP cc_start: 0.7766 (m-30) cc_final: 0.7391 (t0) REVERT: J 353 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7241 (mtm-85) REVERT: J 368 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8116 (ttmm) REVERT: J 376 GLU cc_start: 0.7856 (tt0) cc_final: 0.7622 (tt0) REVERT: J 377 GLU cc_start: 0.7919 (tp30) cc_final: 0.7502 (tp30) REVERT: J 430 TYR cc_start: 0.8647 (t80) cc_final: 0.8314 (t80) REVERT: J 436 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6566 (tm-30) REVERT: J 444 LYS cc_start: 0.8223 (mttm) cc_final: 0.7960 (mttm) REVERT: J 445 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7757 (mt-10) REVERT: P 250 SER cc_start: 0.9073 (m) cc_final: 0.8855 (p) REVERT: P 273 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7959 (mm-30) REVERT: P 280 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8298 (mtm110) REVERT: S 39 TYR cc_start: 0.9007 (m-80) cc_final: 0.8528 (m-80) REVERT: S 87 VAL cc_start: 0.8989 (t) cc_final: 0.8752 (p) REVERT: T 43 LYS cc_start: 0.8880 (mttt) cc_final: 0.8664 (mtmm) REVERT: T 44 VAL cc_start: 0.9207 (t) cc_final: 0.9004 (p) REVERT: T 68 ASP cc_start: 0.8141 (t0) cc_final: 0.7644 (t0) REVERT: T 79 ARG cc_start: 0.8302 (mtm110) cc_final: 0.7869 (mtm110) REVERT: T 93 GLU cc_start: 0.7895 (mp0) cc_final: 0.7602 (mp0) REVERT: T 115 THR cc_start: 0.8707 (t) cc_final: 0.8480 (p) REVERT: U 93 GLN cc_start: 0.8815 (tt0) cc_final: 0.8526 (tt0) REVERT: U 106 ASP cc_start: 0.8271 (m-30) cc_final: 0.7808 (m-30) REVERT: U 112 ILE cc_start: 0.9135 (mm) cc_final: 0.8867 (mm) REVERT: V 64 ASN cc_start: 0.8788 (m-40) cc_final: 0.8040 (m-40) REVERT: V 67 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8151 (ttp80) REVERT: W 52 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8550 (mtt90) REVERT: W 56 LYS cc_start: 0.8811 (mttp) cc_final: 0.8555 (ttmm) REVERT: W 78 PHE cc_start: 0.7908 (m-80) cc_final: 0.7692 (m-10) REVERT: W 94 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8115 (mm-30) REVERT: W 106 ASP cc_start: 0.8366 (m-30) cc_final: 0.8018 (m-30) REVERT: W 123 ASP cc_start: 0.8388 (m-30) cc_final: 0.8143 (m-30) REVERT: X 39 ARG cc_start: 0.8890 (mmt-90) cc_final: 0.8690 (mmt-90) REVERT: X 75 HIS cc_start: 0.8468 (t70) cc_final: 0.7784 (t70) REVERT: X 84 MET cc_start: 0.8865 (tpt) cc_final: 0.8597 (mmm) REVERT: X 91 LYS cc_start: 0.9066 (tttt) cc_final: 0.8844 (tttt) outliers start: 48 outliers final: 30 residues processed: 1479 average time/residue: 0.3154 time to fit residues: 720.3798 Evaluate side-chains 1445 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1413 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 768 GLN 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 C residue 255 MET Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 129 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 268 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 257 LEU Chi-restraints excluded: chain G residue 397 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 360 THR Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 226 GLN Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain W residue 124 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 291 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 144 optimal weight: 0.0030 chunk 94 optimal weight: 0.0670 chunk 13 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 479 optimal weight: 6.9990 chunk 322 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 overall best weight: 0.5530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 GLN C 92 ASN D 91 GLN E 380 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN F 277 ASN I 262 GLN I 385 ASN I 408 GLN T 63 ASN W 39 HIS X 27 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104747 restraints weight = 68488.751| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.03 r_work: 0.3098 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43534 Z= 0.134 Angle : 0.564 8.689 59700 Z= 0.301 Chirality : 0.044 0.355 6789 Planarity : 0.004 0.052 6883 Dihedral : 20.473 179.586 7705 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.92 % Allowed : 11.53 % Favored : 86.55 % 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: 1.78 (0.12), residues: 4719 helix: 1.89 (0.11), residues: 2352 sheet: 0.66 (0.19), residues: 682 loop : 0.51 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 619 TYR 0.024 0.001 TYR C 382 PHE 0.018 0.001 PHE A1884 TRP 0.043 0.002 TRP C 360 HIS 0.005 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (43526) covalent geometry : angle 0.56391 / 0.30 (59691) hydrogen bonds : bond 0.04136 / 2.78 ( 2083) hydrogen bonds : angle 3.81844 / 2.76 ( 5758) metal coordination : bond 0.00622 / 0.26 ( 8) metal coordination : angle 1.71856 / 0.74 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1497 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 1418 time to evaluate : 1.439 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 621 TYR cc_start: 0.7154 (p90) cc_final: 0.6852 (p90) REVERT: A 628 TRP cc_start: 0.8583 (t60) cc_final: 0.8048 (t60) REVERT: A 660 LEU cc_start: 0.8943 (mp) cc_final: 0.8671 (mp) REVERT: A 678 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8451 (m) REVERT: A 684 MET cc_start: 0.8816 (tpt) cc_final: 0.8612 (tpt) REVERT: A 687 LYS cc_start: 0.8753 (mttt) cc_final: 0.8418 (mttp) REVERT: A 694 LYS cc_start: 0.8627 (mttt) cc_final: 0.8150 (mmtp) REVERT: A 704 GLU cc_start: 0.7324 (mt-10) cc_final: 0.7030 (mt-10) REVERT: A 719 HIS cc_start: 0.8057 (m170) cc_final: 0.7369 (m90) REVERT: A 727 LEU cc_start: 0.8970 (mt) cc_final: 0.8768 (mm) REVERT: A 789 MET cc_start: 0.7479 (mmt) cc_final: 0.7090 (mmt) REVERT: A 851 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8781 (mmmm) REVERT: A 863 LYS cc_start: 0.8543 (tptp) cc_final: 0.8326 (tttm) REVERT: A 892 ASN cc_start: 0.8809 (m110) cc_final: 0.8376 (m110) REVERT: A 966 ARG cc_start: 0.8033 (mtp85) cc_final: 0.7775 (mtp-110) REVERT: A 973 VAL cc_start: 0.8648 (t) cc_final: 0.8436 (p) REVERT: A 975 LEU cc_start: 0.8406 (mt) cc_final: 0.8135 (mt) REVERT: A 992 MET cc_start: 0.2585 (ttm) cc_final: 0.1799 (ttm) REVERT: A 1893 ARG cc_start: 0.8440 (mtt180) cc_final: 0.8020 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8538 (ptpp) cc_final: 0.8129 (ptpp) REVERT: A 1895 ARG cc_start: 0.8107 (ttp-170) cc_final: 0.7836 (ttp-170) REVERT: A 1896 GLN cc_start: 0.8266 (mt0) cc_final: 0.7998 (mt0) REVERT: A 1897 ARG cc_start: 0.8239 (ttp-170) cc_final: 0.7904 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8445 (ttm110) cc_final: 0.8187 (ttp-170) REVERT: A 1934 SER cc_start: 0.8406 (m) cc_final: 0.8163 (p) REVERT: A 1936 ILE cc_start: 0.8962 (mm) cc_final: 0.8333 (mt) REVERT: A 1948 PHE cc_start: 0.8717 (t80) cc_final: 0.8346 (t80) REVERT: A 1953 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7744 (mm-30) REVERT: A 1957 ARG cc_start: 0.8340 (mtp180) cc_final: 0.8099 (mtm-85) REVERT: A 2013 GLU cc_start: 0.7918 (tp30) cc_final: 0.7130 (tp30) REVERT: A 2026 CYS cc_start: 0.8380 (m) cc_final: 0.8041 (m) REVERT: A 2028 MET cc_start: 0.8589 (mtt) cc_final: 0.8362 (mtp) REVERT: A 2094 ARG cc_start: 0.8053 (ptp90) cc_final: 0.7842 (mtm-85) REVERT: A 2096 GLU cc_start: 0.8193 (mp0) cc_final: 0.7943 (pm20) REVERT: A 2097 GLN cc_start: 0.8699 (mm-40) cc_final: 0.8455 (mm-40) REVERT: A 2102 MET cc_start: 0.8600 (mmm) cc_final: 0.8277 (mpp) REVERT: A 2150 ASP cc_start: 0.7989 (m-30) cc_final: 0.7647 (m-30) REVERT: A 2185 MET cc_start: 0.6844 (ttm) cc_final: 0.6573 (ttm) REVERT: A 2196 PHE cc_start: 0.8038 (m-80) cc_final: 0.7712 (m-80) REVERT: B 133 MET cc_start: 0.5965 (mmt) cc_final: 0.5513 (mmt) REVERT: C 1 MET cc_start: 0.4432 (tmm) cc_final: 0.4144 (tmm) REVERT: C 2 THR cc_start: 0.7777 (t) cc_final: 0.7319 (m) REVERT: C 14 LYS cc_start: 0.8763 (mppt) cc_final: 0.8321 (mppt) REVERT: C 23 SER cc_start: 0.7868 (m) cc_final: 0.7397 (p) REVERT: C 71 GLN cc_start: 0.8132 (tp-100) cc_final: 0.7619 (tp-100) REVERT: C 72 ARG cc_start: 0.8610 (tpp80) cc_final: 0.7943 (tpp80) REVERT: C 75 TRP cc_start: 0.9009 (m-10) cc_final: 0.8637 (m-10) REVERT: C 76 ASP cc_start: 0.8076 (m-30) cc_final: 0.7584 (m-30) REVERT: C 83 MET cc_start: 0.8239 (mmm) cc_final: 0.7996 (mmm) REVERT: C 90 ASP cc_start: 0.8090 (t0) cc_final: 0.7345 (t0) REVERT: C 103 THR cc_start: 0.8792 (m) cc_final: 0.8449 (p) REVERT: C 107 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7957 (mm-30) REVERT: C 111 GLU cc_start: 0.8030 (tm-30) cc_final: 0.6938 (tm-30) REVERT: C 115 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7776 (mt-10) REVERT: C 149 ASP cc_start: 0.8381 (t0) cc_final: 0.8123 (t0) REVERT: C 196 MET cc_start: 0.8120 (tpp) cc_final: 0.7774 (mmm) REVERT: C 204 GLN cc_start: 0.8674 (tp40) cc_final: 0.7974 (tp40) REVERT: C 208 ASP cc_start: 0.8043 (m-30) cc_final: 0.7628 (m-30) REVERT: C 229 GLU cc_start: 0.8167 (pt0) cc_final: 0.7829 (pt0) REVERT: C 230 ASN cc_start: 0.8546 (t0) cc_final: 0.8082 (t0) REVERT: C 250 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8584 (mtpp) REVERT: C 269 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7882 (tpp80) REVERT: C 308 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8369 (mt-10) REVERT: C 366 ILE cc_start: 0.8957 (tt) cc_final: 0.8726 (tt) REVERT: C 371 ASP cc_start: 0.7859 (t0) cc_final: 0.7271 (t0) REVERT: C 373 GLU cc_start: 0.7941 (pm20) cc_final: 0.7637 (pm20) REVERT: C 374 ASP cc_start: 0.8084 (m-30) cc_final: 0.7787 (m-30) REVERT: D 92 ASN cc_start: 0.8733 (t0) cc_final: 0.8197 (t0) REVERT: D 148 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8221 (mtt180) REVERT: E 15 ILE cc_start: 0.8670 (mm) cc_final: 0.8447 (mt) REVERT: E 22 LYS cc_start: 0.8445 (mmtp) cc_final: 0.8193 (mmtp) REVERT: E 28 GLU cc_start: 0.7806 (mp0) cc_final: 0.7249 (mp0) REVERT: E 64 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7899 (mmt-90) REVERT: E 81 LEU cc_start: 0.8438 (mt) cc_final: 0.8194 (mp) REVERT: E 162 LYS cc_start: 0.8339 (ptmt) cc_final: 0.8088 (ptmm) REVERT: E 165 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7597 (mmtt) REVERT: E 167 THR cc_start: 0.8164 (m) cc_final: 0.7805 (p) REVERT: E 168 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8147 (ttmt) REVERT: E 173 ASP cc_start: 0.7986 (m-30) cc_final: 0.7766 (m-30) REVERT: E 178 GLU cc_start: 0.8025 (tt0) cc_final: 0.7748 (tt0) REVERT: E 182 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7709 (mtmt) REVERT: E 183 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7844 (mm-30) REVERT: E 194 GLU cc_start: 0.7858 (tt0) cc_final: 0.7565 (tt0) REVERT: E 212 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7408 (mm-30) REVERT: E 214 ASP cc_start: 0.8036 (m-30) cc_final: 0.7801 (m-30) REVERT: E 255 ASP cc_start: 0.7529 (p0) cc_final: 0.7298 (p0) REVERT: E 285 LYS cc_start: 0.7998 (ttmm) cc_final: 0.7751 (ttmm) REVERT: E 286 TYR cc_start: 0.8345 (m-10) cc_final: 0.7930 (m-80) REVERT: E 356 ASP cc_start: 0.8031 (t0) cc_final: 0.7767 (t70) REVERT: E 370 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8144 (mt-10) REVERT: E 389 GLU cc_start: 0.7823 (tt0) cc_final: 0.7582 (tt0) REVERT: E 418 LYS cc_start: 0.8034 (ttmm) cc_final: 0.7813 (ttmm) REVERT: E 441 LYS cc_start: 0.8352 (mttt) cc_final: 0.8123 (mttt) REVERT: E 445 LYS cc_start: 0.7681 (mmtp) cc_final: 0.7472 (mmtp) REVERT: E 446 ILE cc_start: 0.8243 (mm) cc_final: 0.7920 (mt) REVERT: F 19 ILE cc_start: 0.8623 (tt) cc_final: 0.8390 (tt) REVERT: F 40 ARG cc_start: 0.8157 (mtt90) cc_final: 0.7825 (mtt90) REVERT: F 112 GLU cc_start: 0.7726 (tp30) cc_final: 0.7432 (tp30) REVERT: F 117 GLU cc_start: 0.8199 (tp30) cc_final: 0.7576 (mm-30) REVERT: F 142 VAL cc_start: 0.8227 (t) cc_final: 0.7819 (m) REVERT: F 160 LYS cc_start: 0.8284 (ttpt) cc_final: 0.7904 (mtpt) REVERT: F 168 MET cc_start: 0.7457 (mtp) cc_final: 0.7055 (mtp) REVERT: F 170 THR cc_start: 0.8178 (m) cc_final: 0.7887 (t) REVERT: F 177 LYS cc_start: 0.8297 (mttt) cc_final: 0.7948 (mttt) REVERT: F 181 SER cc_start: 0.8649 (m) cc_final: 0.8307 (p) REVERT: F 182 LEU cc_start: 0.8921 (mt) cc_final: 0.8690 (mm) REVERT: F 192 VAL cc_start: 0.8325 (t) cc_final: 0.7825 (p) REVERT: F 235 ARG cc_start: 0.7764 (ttm-80) cc_final: 0.7437 (mtp85) REVERT: F 246 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7253 (mt-10) REVERT: F 248 ASP cc_start: 0.7753 (m-30) cc_final: 0.7475 (m-30) REVERT: F 269 LYS cc_start: 0.8208 (mmtp) cc_final: 0.7993 (mmtp) REVERT: F 271 GLU cc_start: 0.7913 (mp0) cc_final: 0.7641 (mp0) REVERT: F 274 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7681 (mm-30) REVERT: F 279 LYS cc_start: 0.8434 (tppp) cc_final: 0.8080 (tptm) REVERT: F 286 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7959 (mt-10) REVERT: F 303 MET cc_start: 0.8596 (mmm) cc_final: 0.8283 (mmp) REVERT: F 317 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7411 (mt-10) REVERT: F 376 GLU cc_start: 0.8058 (tt0) cc_final: 0.7695 (tt0) REVERT: F 392 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7923 (ttp-170) REVERT: F 436 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7159 (tm-30) REVERT: F 441 GLN cc_start: 0.7766 (mm-40) cc_final: 0.7530 (mm-40) REVERT: F 445 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7538 (mm-30) REVERT: G 15 ILE cc_start: 0.8855 (mt) cc_final: 0.8625 (mm) REVERT: G 89 SER cc_start: 0.8248 (m) cc_final: 0.7929 (t) REVERT: G 90 LYS cc_start: 0.8586 (tptm) cc_final: 0.7482 (tptm) REVERT: G 102 TYR cc_start: 0.8215 (m-80) cc_final: 0.7961 (m-10) REVERT: G 105 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7235 (mt-10) REVERT: G 123 ARG cc_start: 0.8229 (ttm170) cc_final: 0.7078 (ttt90) REVERT: G 126 GLU cc_start: 0.7742 (mt-10) cc_final: 0.6722 (mt-10) REVERT: G 129 GLU cc_start: 0.7280 (tt0) cc_final: 0.6981 (tt0) REVERT: G 134 GLU cc_start: 0.7495 (tt0) cc_final: 0.7014 (tm-30) REVERT: G 137 GLU cc_start: 0.7774 (tt0) cc_final: 0.7415 (tp30) REVERT: G 147 MET cc_start: 0.6116 (mtp) cc_final: 0.5530 (mtp) REVERT: G 158 ILE cc_start: 0.8552 (mt) cc_final: 0.8232 (mm) REVERT: G 162 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8002 (ttmm) REVERT: G 171 LYS cc_start: 0.8655 (mtpt) cc_final: 0.8024 (ttmm) REVERT: G 178 GLU cc_start: 0.8162 (tt0) cc_final: 0.7495 (tt0) REVERT: G 186 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7682 (mm-30) REVERT: G 193 ILE cc_start: 0.8629 (mt) cc_final: 0.8253 (mm) REVERT: G 209 TYR cc_start: 0.8495 (m-80) cc_final: 0.8084 (m-10) REVERT: G 225 LYS cc_start: 0.8316 (mmpt) cc_final: 0.7882 (mmpt) REVERT: G 227 ASP cc_start: 0.7666 (t0) cc_final: 0.7436 (t0) REVERT: G 244 ASP cc_start: 0.7351 (m-30) cc_final: 0.7085 (m-30) REVERT: G 247 ASN cc_start: 0.8330 (m-40) cc_final: 0.8097 (m-40) REVERT: G 249 ARG cc_start: 0.7812 (ttt-90) cc_final: 0.7522 (ttt-90) REVERT: G 267 LYS cc_start: 0.7804 (tttp) cc_final: 0.7589 (tttp) REVERT: G 302 ASP cc_start: 0.8189 (t0) cc_final: 0.7935 (t0) REVERT: G 428 GLU cc_start: 0.8228 (mp0) cc_final: 0.7821 (mp0) REVERT: G 438 TYR cc_start: 0.8386 (m-80) cc_final: 0.8041 (m-80) REVERT: G 447 LEU cc_start: 0.8406 (mt) cc_final: 0.8199 (mt) REVERT: G 455 MET cc_start: 0.6998 (mmm) cc_final: 0.6591 (mmm) REVERT: H 18 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7492 (mtp85) REVERT: H 26 SER cc_start: 0.8724 (m) cc_final: 0.8370 (p) REVERT: H 38 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7890 (mm-30) REVERT: H 83 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8445 (mtmm) REVERT: H 88 MET cc_start: 0.7965 (mmp) cc_final: 0.7588 (mmm) REVERT: H 113 MET cc_start: 0.8282 (ptt) cc_final: 0.7677 (ptp) REVERT: H 132 LYS cc_start: 0.8355 (ttmm) cc_final: 0.8065 (ttmm) REVERT: H 144 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7505 (mm-30) REVERT: H 145 ILE cc_start: 0.8317 (mt) cc_final: 0.8083 (tp) REVERT: H 186 LYS cc_start: 0.8350 (ttpt) cc_final: 0.7952 (ttpt) REVERT: H 201 LYS cc_start: 0.8368 (ptmt) cc_final: 0.8091 (ptmt) REVERT: H 211 ARG cc_start: 0.8456 (ttt180) cc_final: 0.8246 (ttt180) REVERT: H 214 ASP cc_start: 0.7515 (p0) cc_final: 0.7233 (p0) REVERT: H 238 VAL cc_start: 0.8183 (t) cc_final: 0.7888 (p) REVERT: H 253 ARG cc_start: 0.8180 (ptm160) cc_final: 0.7812 (ptm-80) REVERT: H 267 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7434 (mt-10) REVERT: H 274 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7654 (mt-10) REVERT: H 275 GLN cc_start: 0.8271 (mm110) cc_final: 0.7939 (mm-40) REVERT: H 277 ASN cc_start: 0.8507 (m-40) cc_final: 0.8138 (m110) REVERT: H 279 LYS cc_start: 0.8299 (tppt) cc_final: 0.8077 (tptp) REVERT: H 303 MET cc_start: 0.8121 (mmm) cc_final: 0.7920 (mmm) REVERT: H 307 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7521 (mm-30) REVERT: H 313 ASN cc_start: 0.8054 (m-40) cc_final: 0.7776 (m-40) REVERT: H 314 ARG cc_start: 0.7393 (mmt180) cc_final: 0.7146 (mmt180) REVERT: H 339 SER cc_start: 0.8719 (p) cc_final: 0.8479 (m) REVERT: I 17 SER cc_start: 0.8669 (m) cc_final: 0.8358 (t) REVERT: I 61 MET cc_start: 0.8184 (mmm) cc_final: 0.7784 (mmm) REVERT: I 64 ARG cc_start: 0.8117 (mmt-90) cc_final: 0.7861 (tpp80) REVERT: I 125 LYS cc_start: 0.8452 (ttpp) cc_final: 0.8209 (ttmm) REVERT: I 134 GLU cc_start: 0.7719 (tt0) cc_final: 0.7518 (tt0) REVERT: I 139 THR cc_start: 0.8718 (m) cc_final: 0.8367 (p) REVERT: I 141 CYS cc_start: 0.8608 (m) cc_final: 0.8364 (m) REVERT: I 171 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8648 (ttmm) REVERT: I 216 GLU cc_start: 0.7883 (tp30) cc_final: 0.7619 (tp30) REVERT: I 227 ASP cc_start: 0.7592 (t0) cc_final: 0.7334 (t0) REVERT: I 249 ARG cc_start: 0.8138 (mtp85) cc_final: 0.7845 (mtp85) REVERT: I 259 MET cc_start: 0.8144 (mtp) cc_final: 0.7765 (mtp) REVERT: I 269 THR cc_start: 0.8502 (p) cc_final: 0.8286 (p) REVERT: I 281 LYS cc_start: 0.8643 (mttt) cc_final: 0.8386 (mtmt) REVERT: I 302 ASP cc_start: 0.8286 (t0) cc_final: 0.7772 (t0) REVERT: I 322 SER cc_start: 0.8591 (p) cc_final: 0.8277 (t) REVERT: I 376 LYS cc_start: 0.8535 (tptp) cc_final: 0.8290 (tptp) REVERT: I 380 GLN cc_start: 0.8101 (mt0) cc_final: 0.7800 (mt0) REVERT: I 416 LEU cc_start: 0.8446 (mt) cc_final: 0.8191 (mp) REVERT: I 438 TYR cc_start: 0.8252 (m-80) cc_final: 0.7709 (m-80) REVERT: I 439 ASP cc_start: 0.8118 (p0) cc_final: 0.7823 (p0) REVERT: I 441 LYS cc_start: 0.8494 (mttm) cc_final: 0.8015 (mtmm) REVERT: I 445 LYS cc_start: 0.8170 (tppt) cc_final: 0.7143 (tppt) REVERT: J 38 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7836 (mm-30) REVERT: J 71 ARG cc_start: 0.8389 (tpp80) cc_final: 0.8137 (tpp-160) REVERT: J 90 MET cc_start: 0.8435 (mtm) cc_final: 0.8073 (mtp) REVERT: J 92 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7893 (mm-40) REVERT: J 117 GLU cc_start: 0.7694 (tp30) cc_final: 0.7444 (tp30) REVERT: J 133 GLU cc_start: 0.7715 (pt0) cc_final: 0.7369 (pt0) REVERT: J 136 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7416 (mt-10) REVERT: J 142 VAL cc_start: 0.8723 (t) cc_final: 0.8313 (m) REVERT: J 144 GLU cc_start: 0.8129 (tt0) cc_final: 0.7893 (tt0) REVERT: J 164 LYS cc_start: 0.8438 (pttt) cc_final: 0.8156 (ptmm) REVERT: J 168 MET cc_start: 0.8691 (ptm) cc_final: 0.8348 (ptm) REVERT: J 172 TYR cc_start: 0.8487 (m-80) cc_final: 0.7805 (m-80) REVERT: J 180 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7041 (mt-10) REVERT: J 183 THR cc_start: 0.8181 (m) cc_final: 0.7858 (p) REVERT: J 184 LYS cc_start: 0.8243 (mttp) cc_final: 0.8026 (mttp) REVERT: J 185 ASP cc_start: 0.7564 (t0) cc_final: 0.7266 (t0) REVERT: J 192 VAL cc_start: 0.8595 (t) cc_final: 0.8291 (p) REVERT: J 225 VAL cc_start: 0.8402 (t) cc_final: 0.8090 (p) REVERT: J 231 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7321 (mm-30) REVERT: J 234 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8373 (ttmm) REVERT: J 267 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7275 (mt-10) REVERT: J 270 SER cc_start: 0.8465 (p) cc_final: 0.8021 (t) REVERT: J 314 ARG cc_start: 0.8042 (mmt180) cc_final: 0.7742 (mmt180) REVERT: J 326 MET cc_start: 0.8275 (mtm) cc_final: 0.8016 (mtp) REVERT: J 352 ASP cc_start: 0.7731 (m-30) cc_final: 0.7401 (t0) REVERT: J 368 LYS cc_start: 0.8531 (ttmt) cc_final: 0.8252 (ttmm) REVERT: J 376 GLU cc_start: 0.7889 (tt0) cc_final: 0.7667 (tt0) REVERT: J 377 GLU cc_start: 0.7834 (tp30) cc_final: 0.7431 (tp30) REVERT: J 430 TYR cc_start: 0.8647 (t80) cc_final: 0.8353 (t80) REVERT: J 436 GLU cc_start: 0.7053 (tm-30) cc_final: 0.6551 (tm-30) REVERT: P 250 SER cc_start: 0.8948 (m) cc_final: 0.8722 (p) REVERT: P 273 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8017 (mm-30) REVERT: P 289 GLU cc_start: 0.7676 (tp30) cc_final: 0.7429 (tp30) REVERT: S 39 TYR cc_start: 0.9004 (m-80) cc_final: 0.8567 (m-80) REVERT: S 42 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7571 (mtm110) REVERT: S 87 VAL cc_start: 0.8955 (t) cc_final: 0.8741 (p) REVERT: T 43 LYS cc_start: 0.8877 (mttt) cc_final: 0.8651 (mtmm) REVERT: T 68 ASP cc_start: 0.8148 (t0) cc_final: 0.7711 (t0) REVERT: T 79 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7495 (mtm110) REVERT: T 115 THR cc_start: 0.8720 (t) cc_final: 0.8492 (p) REVERT: U 93 GLN cc_start: 0.8707 (tt0) cc_final: 0.8492 (tt0) REVERT: U 106 ASP cc_start: 0.8272 (m-30) cc_final: 0.7789 (m-30) REVERT: U 112 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8844 (mm) REVERT: V 67 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8255 (ttp80) REVERT: W 52 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8564 (mtt180) REVERT: W 56 LYS cc_start: 0.8808 (mttp) cc_final: 0.8544 (ttmm) REVERT: W 94 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8100 (mm-30) REVERT: W 123 ASP cc_start: 0.8478 (m-30) cc_final: 0.8209 (m-30) REVERT: X 35 ARG cc_start: 0.8591 (mtp85) cc_final: 0.8320 (mmm160) REVERT: X 55 ARG cc_start: 0.8704 (mtt90) cc_final: 0.8469 (mtt90) REVERT: X 75 HIS cc_start: 0.8433 (t70) cc_final: 0.7893 (t70) REVERT: X 84 MET cc_start: 0.8859 (tpt) cc_final: 0.8615 (mmm) outliers start: 79 outliers final: 51 residues processed: 1436 average time/residue: 0.3211 time to fit residues: 709.5620 Evaluate side-chains 1442 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 1389 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 768 GLN 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 2019 ARG Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2176 ILE Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 368 GLU Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 268 ILE 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 257 LEU 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 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 360 THR Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 414 ARG Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 86 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 J residue 158 VAL Chi-restraints excluded: chain J residue 226 GLN Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 379 ASP Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 65 LEU Chi-restraints excluded: chain U residue 112 ILE Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 48 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 168 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 426 optimal weight: 4.9990 chunk 43 optimal weight: 0.0980 chunk 217 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 282 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 251 optimal weight: 1.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 659 HIS C 12 ASN C 110 ASN D 91 GLN E 420 ASN F 277 ASN H 41 GLN H 240 HIS I 262 GLN I 348 HIS I 408 GLN J 78 GLN T 49 HIS T 63 ASN T 84 ASN V 75 HIS X 27 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.126239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.100928 restraints weight = 69215.619| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.04 r_work: 0.3029 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 43534 Z= 0.299 Angle : 0.652 10.023 59700 Z= 0.344 Chirality : 0.048 0.359 6789 Planarity : 0.005 0.067 6883 Dihedral : 20.671 179.822 7705 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.44 % Allowed : 12.72 % Favored : 84.84 % 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: 1.44 (0.12), residues: 4719 helix: 1.64 (0.11), residues: 2363 sheet: 0.48 (0.19), residues: 673 loop : 0.33 (0.15), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 202 TYR 0.027 0.002 TYR C 382 PHE 0.022 0.002 PHE H 452 TRP 0.056 0.002 TRP C 360 HIS 0.007 0.001 HIS E 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00646 / 0.30 (43526) covalent geometry : angle 0.65161 / 0.34 (59691) hydrogen bonds : bond 0.04964 / 3.34 ( 2083) hydrogen bonds : angle 3.95554 / 2.86 ( 5758) metal coordination : bond 0.02033 / 0.88 ( 8) metal coordination : angle 2.55598 / 1.23 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1467 time to evaluate : 1.623 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 621 TYR cc_start: 0.7311 (p90) cc_final: 0.7034 (p90) REVERT: A 628 TRP cc_start: 0.8566 (t60) cc_final: 0.8282 (t60) REVERT: A 660 LEU cc_start: 0.8963 (mp) cc_final: 0.8731 (mp) REVERT: A 678 VAL cc_start: 0.8804 (OUTLIER) cc_final: 0.8545 (m) REVERT: A 687 LYS cc_start: 0.8813 (mttt) cc_final: 0.8487 (mttm) REVERT: A 694 LYS cc_start: 0.8711 (mttt) cc_final: 0.8441 (mmtm) REVERT: A 704 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 719 HIS cc_start: 0.8113 (m170) cc_final: 0.7618 (m-70) REVERT: A 747 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8227 (mm-30) REVERT: A 749 GLN cc_start: 0.8524 (pm20) cc_final: 0.8307 (pm20) REVERT: A 789 MET cc_start: 0.7695 (mmt) cc_final: 0.7218 (mmm) REVERT: A 851 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8656 (mmmm) REVERT: A 854 GLU cc_start: 0.8115 (pm20) cc_final: 0.7802 (pm20) REVERT: A 870 ASP cc_start: 0.8797 (t0) cc_final: 0.8548 (t0) REVERT: A 871 ASP cc_start: 0.8379 (t0) cc_final: 0.7998 (t70) REVERT: A 966 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7924 (mtp-110) REVERT: A 973 VAL cc_start: 0.8709 (t) cc_final: 0.8474 (p) REVERT: A 992 MET cc_start: 0.2516 (ttm) cc_final: 0.1733 (ttm) REVERT: A 1893 ARG cc_start: 0.8471 (mtt180) cc_final: 0.8164 (tpp80) REVERT: A 1894 LYS cc_start: 0.8561 (ptpp) cc_final: 0.8168 (ptpp) REVERT: A 1895 ARG cc_start: 0.8145 (ttp-170) cc_final: 0.7850 (ttp-170) REVERT: A 1896 GLN cc_start: 0.8242 (mt0) cc_final: 0.7951 (mt0) REVERT: A 1897 ARG cc_start: 0.8227 (ttp-170) cc_final: 0.7881 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8458 (ttm110) cc_final: 0.8181 (ttp-170) REVERT: A 1936 ILE cc_start: 0.9008 (mm) cc_final: 0.8397 (mt) REVERT: A 1953 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7790 (mm-30) REVERT: A 2013 GLU cc_start: 0.7939 (tp30) cc_final: 0.7232 (tp30) REVERT: A 2026 CYS cc_start: 0.8414 (m) cc_final: 0.8080 (m) REVERT: A 2038 ILE cc_start: 0.8766 (tt) cc_final: 0.8565 (tp) REVERT: A 2094 ARG cc_start: 0.8236 (ptp90) cc_final: 0.7990 (ptp90) REVERT: A 2097 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8597 (mm-40) REVERT: A 2150 ASP cc_start: 0.8016 (m-30) cc_final: 0.7744 (m-30) REVERT: A 2185 MET cc_start: 0.6887 (ttm) cc_final: 0.6298 (ppp) REVERT: A 2189 MET cc_start: 0.7818 (mtt) cc_final: 0.7185 (mtt) REVERT: A 2196 PHE cc_start: 0.8093 (m-80) cc_final: 0.7831 (m-80) REVERT: B 133 MET cc_start: 0.5936 (mmt) cc_final: 0.5472 (mmt) REVERT: B 174 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.8179 (mtm-85) REVERT: C 1 MET cc_start: 0.4541 (tmm) cc_final: 0.4222 (tmm) REVERT: C 2 THR cc_start: 0.7940 (t) cc_final: 0.7325 (m) REVERT: C 14 LYS cc_start: 0.8831 (mppt) cc_final: 0.8284 (mptp) REVERT: C 23 SER cc_start: 0.8029 (m) cc_final: 0.7608 (p) REVERT: C 72 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8141 (tpp80) REVERT: C 76 ASP cc_start: 0.8175 (m-30) cc_final: 0.7658 (m-30) REVERT: C 90 ASP cc_start: 0.8435 (t0) cc_final: 0.7800 (t0) REVERT: C 103 THR cc_start: 0.8784 (m) cc_final: 0.8542 (p) REVERT: C 107 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7952 (mm-30) REVERT: C 111 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7174 (tm-30) REVERT: C 115 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7915 (mt-10) REVERT: C 135 TYR cc_start: 0.8898 (t80) cc_final: 0.8554 (t80) REVERT: C 149 ASP cc_start: 0.8420 (t0) cc_final: 0.8160 (t0) REVERT: C 196 MET cc_start: 0.8192 (tpp) cc_final: 0.7865 (mmm) REVERT: C 204 GLN cc_start: 0.8716 (tp40) cc_final: 0.8111 (tp-100) REVERT: C 208 ASP cc_start: 0.8067 (m-30) cc_final: 0.7647 (m-30) REVERT: C 228 GLU cc_start: 0.7868 (pm20) cc_final: 0.7530 (pm20) REVERT: C 229 GLU cc_start: 0.8214 (pt0) cc_final: 0.7858 (pm20) REVERT: C 230 ASN cc_start: 0.8586 (t0) cc_final: 0.8202 (t0) REVERT: C 248 PHE cc_start: 0.8503 (p90) cc_final: 0.8291 (p90) REVERT: C 250 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8630 (mtpp) REVERT: C 252 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8439 (mmm160) REVERT: C 373 GLU cc_start: 0.8015 (pm20) cc_final: 0.7700 (pm20) REVERT: C 382 TYR cc_start: 0.8234 (t80) cc_final: 0.7649 (t80) REVERT: D 92 ASN cc_start: 0.8727 (t0) cc_final: 0.8446 (t0) REVERT: E 15 ILE cc_start: 0.8596 (mm) cc_final: 0.8372 (mt) REVERT: E 22 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8284 (mmtp) REVERT: E 28 GLU cc_start: 0.7828 (mp0) cc_final: 0.7354 (mp0) REVERT: E 81 LEU cc_start: 0.8458 (mt) cc_final: 0.8224 (mp) REVERT: E 165 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7674 (mmtt) REVERT: E 167 THR cc_start: 0.8095 (m) cc_final: 0.7818 (p) REVERT: E 168 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8197 (ttmt) REVERT: E 178 GLU cc_start: 0.7973 (tt0) cc_final: 0.7693 (tt0) REVERT: E 182 LYS cc_start: 0.8100 (mtmt) cc_final: 0.7783 (mtmt) REVERT: E 183 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7820 (mm-30) REVERT: E 185 VAL cc_start: 0.8358 (t) cc_final: 0.8062 (m) REVERT: E 194 GLU cc_start: 0.7837 (tt0) cc_final: 0.7544 (tt0) REVERT: E 212 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7487 (mm-30) REVERT: E 214 ASP cc_start: 0.8078 (m-30) cc_final: 0.7798 (m-30) REVERT: E 227 ASP cc_start: 0.7795 (t0) cc_final: 0.7509 (t0) REVERT: E 274 LYS cc_start: 0.8249 (tttt) cc_final: 0.7991 (tttm) REVERT: E 285 LYS cc_start: 0.8068 (ttmm) cc_final: 0.7844 (ttmm) REVERT: E 286 TYR cc_start: 0.8336 (m-10) cc_final: 0.7957 (m-80) REVERT: E 295 VAL cc_start: 0.8673 (t) cc_final: 0.8393 (m) REVERT: E 352 LEU cc_start: 0.8385 (mt) cc_final: 0.8106 (mm) REVERT: E 356 ASP cc_start: 0.8168 (t0) cc_final: 0.7906 (t70) REVERT: E 370 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8127 (mt-10) REVERT: E 389 GLU cc_start: 0.8011 (tt0) cc_final: 0.7722 (tt0) REVERT: E 415 LEU cc_start: 0.8824 (mt) cc_final: 0.8596 (mm) REVERT: E 418 LYS cc_start: 0.8164 (ttmm) cc_final: 0.7929 (ttmm) REVERT: E 420 ASN cc_start: 0.8394 (m-40) cc_final: 0.8118 (m-40) REVERT: E 441 LYS cc_start: 0.8369 (mttt) cc_final: 0.8143 (mttt) REVERT: E 445 LYS cc_start: 0.7780 (mmtp) cc_final: 0.7542 (mmtp) REVERT: E 446 ILE cc_start: 0.8298 (mm) cc_final: 0.7951 (mt) REVERT: F 40 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7827 (mtt90) REVERT: F 71 ARG cc_start: 0.7851 (mmt90) cc_final: 0.7587 (mmt-90) REVERT: F 117 GLU cc_start: 0.8218 (tp30) cc_final: 0.7633 (mm-30) REVERT: F 142 VAL cc_start: 0.8250 (t) cc_final: 0.7943 (m) REVERT: F 160 LYS cc_start: 0.8333 (ttpt) cc_final: 0.7925 (mtpt) REVERT: F 168 MET cc_start: 0.7443 (mtp) cc_final: 0.7011 (mtp) REVERT: F 170 THR cc_start: 0.8148 (m) cc_final: 0.7872 (t) REVERT: F 181 SER cc_start: 0.8724 (m) cc_final: 0.8341 (p) REVERT: F 182 LEU cc_start: 0.8934 (mt) cc_final: 0.8640 (mm) REVERT: F 183 THR cc_start: 0.8622 (m) cc_final: 0.8328 (p) REVERT: F 192 VAL cc_start: 0.8252 (t) cc_final: 0.7712 (p) REVERT: F 197 LYS cc_start: 0.7631 (mtpt) cc_final: 0.7118 (mtpt) REVERT: F 233 GLN cc_start: 0.7749 (tp40) cc_final: 0.6993 (tp40) REVERT: F 246 GLU cc_start: 0.7556 (mt-10) cc_final: 0.7317 (mt-10) REVERT: F 248 ASP cc_start: 0.7727 (m-30) cc_final: 0.7417 (m-30) REVERT: F 252 SER cc_start: 0.8762 (t) cc_final: 0.8393 (p) REVERT: F 269 LYS cc_start: 0.8331 (mmtp) cc_final: 0.7974 (mmtp) REVERT: F 271 GLU cc_start: 0.7906 (mp0) cc_final: 0.7638 (mp0) REVERT: F 274 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7714 (mm-30) REVERT: F 286 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7995 (mt-10) REVERT: F 303 MET cc_start: 0.8664 (mmm) cc_final: 0.8363 (mmp) REVERT: F 392 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7943 (ttp-170) REVERT: F 441 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7530 (mm-40) REVERT: F 445 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7595 (mm-30) REVERT: G 15 ILE cc_start: 0.8823 (mt) cc_final: 0.8617 (mm) REVERT: G 34 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7951 (tm-30) REVERT: G 54 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7527 (mm-30) REVERT: G 89 SER cc_start: 0.8533 (m) cc_final: 0.8185 (t) REVERT: G 90 LYS cc_start: 0.8591 (tptm) cc_final: 0.7653 (tptm) REVERT: G 105 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7289 (mt-10) REVERT: G 123 ARG cc_start: 0.8195 (ttm170) cc_final: 0.7489 (ttt180) REVERT: G 125 LYS cc_start: 0.8295 (mtmt) cc_final: 0.7846 (mmmt) REVERT: G 126 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7120 (mt-10) REVERT: G 134 GLU cc_start: 0.7569 (tt0) cc_final: 0.7046 (tm-30) REVERT: G 137 GLU cc_start: 0.7787 (tt0) cc_final: 0.7442 (tp30) REVERT: G 147 MET cc_start: 0.6172 (mtp) cc_final: 0.5589 (mtp) REVERT: G 158 ILE cc_start: 0.8543 (mt) cc_final: 0.8239 (mm) REVERT: G 162 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8084 (ttmm) REVERT: G 171 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8408 (mtpt) REVERT: G 178 GLU cc_start: 0.8233 (tt0) cc_final: 0.7596 (tt0) REVERT: G 183 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8246 (mm-30) REVERT: G 186 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7428 (mm-30) REVERT: G 189 ASP cc_start: 0.8042 (m-30) cc_final: 0.7808 (m-30) REVERT: G 193 ILE cc_start: 0.8658 (mt) cc_final: 0.8325 (mm) REVERT: G 209 TYR cc_start: 0.8527 (m-80) cc_final: 0.8093 (m-10) REVERT: G 225 LYS cc_start: 0.8356 (mmpt) cc_final: 0.7870 (mmpt) REVERT: G 233 GLU cc_start: 0.7336 (tp30) cc_final: 0.6732 (tp30) REVERT: G 244 ASP cc_start: 0.7480 (m-30) cc_final: 0.7226 (m-30) REVERT: G 247 ASN cc_start: 0.8363 (m-40) cc_final: 0.8149 (m110) REVERT: G 249 ARG cc_start: 0.7930 (ttt-90) cc_final: 0.7574 (ttt-90) REVERT: G 264 MET cc_start: 0.8151 (mmt) cc_final: 0.7919 (mmt) REVERT: G 302 ASP cc_start: 0.8070 (t0) cc_final: 0.7804 (t0) REVERT: G 323 ILE cc_start: 0.8726 (mm) cc_final: 0.8362 (mt) REVERT: G 376 LYS cc_start: 0.8716 (tptt) cc_final: 0.8468 (tptm) REVERT: G 428 GLU cc_start: 0.8333 (mp0) cc_final: 0.7904 (mp0) REVERT: G 447 LEU cc_start: 0.8377 (mt) cc_final: 0.8176 (mt) REVERT: G 455 MET cc_start: 0.7136 (mmm) cc_final: 0.6803 (mmm) REVERT: H 18 ARG cc_start: 0.7887 (mtp85) cc_final: 0.7489 (mtp85) REVERT: H 20 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7738 (mt-10) REVERT: H 38 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7887 (mm-30) REVERT: H 83 LYS cc_start: 0.8797 (mtmm) cc_final: 0.8426 (mtmm) REVERT: H 88 MET cc_start: 0.7946 (mmp) cc_final: 0.7598 (mmm) REVERT: H 117 GLU cc_start: 0.8194 (tp30) cc_final: 0.7845 (tp30) REVERT: H 132 LYS cc_start: 0.8432 (ttmm) cc_final: 0.8129 (ttmm) REVERT: H 139 GLU cc_start: 0.7505 (tt0) cc_final: 0.7093 (tm-30) REVERT: H 144 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7513 (mm-30) REVERT: H 164 LYS cc_start: 0.8397 (pttt) cc_final: 0.7899 (pttm) REVERT: H 201 LYS cc_start: 0.8415 (ptmt) cc_final: 0.8174 (ptmt) REVERT: H 204 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8570 (mtpt) REVERT: H 214 ASP cc_start: 0.7675 (p0) cc_final: 0.7380 (p0) REVERT: H 238 VAL cc_start: 0.8098 (t) cc_final: 0.7791 (p) REVERT: H 253 ARG cc_start: 0.8239 (ptm160) cc_final: 0.7847 (ptm-80) REVERT: H 267 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7553 (mt-10) REVERT: H 273 ARG cc_start: 0.8406 (mtt90) cc_final: 0.7894 (mtt90) REVERT: H 274 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7630 (mt-10) REVERT: H 275 GLN cc_start: 0.8243 (mm110) cc_final: 0.7867 (mm-40) REVERT: H 277 ASN cc_start: 0.8545 (m-40) cc_final: 0.8183 (m110) REVERT: H 279 LYS cc_start: 0.8368 (tppt) cc_final: 0.8063 (tptp) REVERT: H 284 ARG cc_start: 0.8192 (ttt90) cc_final: 0.7992 (ptm160) REVERT: H 307 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7559 (mm-30) REVERT: H 313 ASN cc_start: 0.8074 (m-40) cc_final: 0.7737 (m-40) REVERT: H 314 ARG cc_start: 0.7427 (mmt180) cc_final: 0.7059 (mmt180) REVERT: H 339 SER cc_start: 0.8752 (p) cc_final: 0.8512 (m) REVERT: H 358 SER cc_start: 0.8170 (m) cc_final: 0.7836 (t) REVERT: I 61 MET cc_start: 0.8261 (mmm) cc_final: 0.8026 (mmm) REVERT: I 125 LYS cc_start: 0.8500 (ttpp) cc_final: 0.8259 (ttmm) REVERT: I 137 GLU cc_start: 0.7938 (tt0) cc_final: 0.7675 (tt0) REVERT: I 139 THR cc_start: 0.8747 (m) cc_final: 0.8325 (p) REVERT: I 171 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8484 (tttt) REVERT: I 216 GLU cc_start: 0.7963 (tp30) cc_final: 0.7688 (tp30) REVERT: I 244 ASP cc_start: 0.7553 (m-30) cc_final: 0.7224 (t0) REVERT: I 249 ARG cc_start: 0.8082 (mtp85) cc_final: 0.7795 (mtp85) REVERT: I 259 MET cc_start: 0.8129 (mtp) cc_final: 0.7773 (mtp) REVERT: I 267 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7982 (tttp) REVERT: I 281 LYS cc_start: 0.8645 (mttt) cc_final: 0.8389 (mtmt) REVERT: I 302 ASP cc_start: 0.8433 (t0) cc_final: 0.8031 (t0) REVERT: I 322 SER cc_start: 0.8528 (p) cc_final: 0.8225 (t) REVERT: I 426 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7297 (mm-30) REVERT: I 438 TYR cc_start: 0.8391 (m-80) cc_final: 0.7891 (m-80) REVERT: I 439 ASP cc_start: 0.8186 (p0) cc_final: 0.7876 (p0) REVERT: I 441 LYS cc_start: 0.8517 (mttm) cc_final: 0.8041 (mtmm) REVERT: I 445 LYS cc_start: 0.8229 (tppt) cc_final: 0.7188 (tppt) REVERT: J 61 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7633 (mm-30) REVERT: J 71 ARG cc_start: 0.8374 (tpp80) cc_final: 0.8158 (tpp-160) REVERT: J 90 MET cc_start: 0.8501 (mtm) cc_final: 0.8300 (mtm) REVERT: J 117 GLU cc_start: 0.7617 (tp30) cc_final: 0.7384 (tp30) REVERT: J 133 GLU cc_start: 0.7730 (pt0) cc_final: 0.7432 (pt0) REVERT: J 136 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7402 (mt-10) REVERT: J 142 VAL cc_start: 0.8632 (t) cc_final: 0.8333 (m) REVERT: J 144 GLU cc_start: 0.8174 (tt0) cc_final: 0.7908 (tt0) REVERT: J 164 LYS cc_start: 0.8419 (pttt) cc_final: 0.8107 (ptmm) REVERT: J 183 THR cc_start: 0.8211 (m) cc_final: 0.7916 (p) REVERT: J 192 VAL cc_start: 0.8613 (t) cc_final: 0.8257 (p) REVERT: J 225 VAL cc_start: 0.8460 (t) cc_final: 0.8198 (p) REVERT: J 234 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8327 (ttmm) REVERT: J 264 ASP cc_start: 0.7532 (m-30) cc_final: 0.7311 (m-30) REVERT: J 267 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7319 (mt-10) REVERT: J 270 SER cc_start: 0.8447 (p) cc_final: 0.8087 (t) REVERT: J 314 ARG cc_start: 0.8057 (mmt180) cc_final: 0.7795 (mmt180) REVERT: J 352 ASP cc_start: 0.7840 (m-30) cc_final: 0.7486 (t0) REVERT: J 376 GLU cc_start: 0.7818 (tt0) cc_final: 0.7593 (tt0) REVERT: J 377 GLU cc_start: 0.7791 (tp30) cc_final: 0.7396 (tp30) REVERT: J 430 TYR cc_start: 0.8771 (t80) cc_final: 0.8526 (t80) REVERT: J 436 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6657 (tm-30) REVERT: P 247 ASP cc_start: 0.8561 (t0) cc_final: 0.8317 (t0) REVERT: P 249 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8119 (mm-30) REVERT: P 250 SER cc_start: 0.9005 (m) cc_final: 0.8317 (p) REVERT: P 253 GLU cc_start: 0.8494 (tp30) cc_final: 0.8128 (tp30) REVERT: P 254 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7897 (mp0) REVERT: P 273 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8065 (mm-30) REVERT: S 31 HIS cc_start: 0.8683 (t-170) cc_final: 0.8438 (t-170) REVERT: S 42 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7426 (mtm110) REVERT: S 61 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8099 (mm-30) REVERT: S 73 ASN cc_start: 0.8839 (m110) cc_final: 0.8452 (t0) REVERT: S 87 VAL cc_start: 0.8963 (t) cc_final: 0.8758 (p) REVERT: T 43 LYS cc_start: 0.8895 (mttt) cc_final: 0.8685 (mtmm) REVERT: T 68 ASP cc_start: 0.8173 (t0) cc_final: 0.7716 (t0) REVERT: T 76 GLU cc_start: 0.8345 (tp30) cc_final: 0.7840 (tp30) REVERT: T 93 GLU cc_start: 0.7964 (mp0) cc_final: 0.7678 (mp0) REVERT: T 115 THR cc_start: 0.8773 (t) cc_final: 0.8570 (p) REVERT: T 120 LYS cc_start: 0.8720 (tttp) cc_final: 0.8182 (ttpp) REVERT: U 63 ARG cc_start: 0.8500 (mmp80) cc_final: 0.8178 (mmp80) REVERT: U 106 ASP cc_start: 0.8331 (m-30) cc_final: 0.7859 (m-30) REVERT: U 112 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8885 (tp) REVERT: V 67 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8363 (ttp80) REVERT: V 70 VAL cc_start: 0.9064 (p) cc_final: 0.8859 (m) REVERT: V 82 THR cc_start: 0.9163 (t) cc_final: 0.8848 (p) REVERT: W 56 LYS cc_start: 0.8882 (mttp) cc_final: 0.8679 (ttmm) REVERT: W 94 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8181 (mm-30) REVERT: W 123 ASP cc_start: 0.8562 (m-30) cc_final: 0.8249 (m-30) REVERT: X 71 THR cc_start: 0.9269 (m) cc_final: 0.8936 (t) REVERT: X 75 HIS cc_start: 0.8536 (t70) cc_final: 0.7919 (t70) REVERT: X 84 MET cc_start: 0.8838 (tpt) cc_final: 0.8630 (mmm) outliers start: 100 outliers final: 70 residues processed: 1492 average time/residue: 0.3068 time to fit residues: 709.0637 Evaluate side-chains 1493 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1421 time to evaluate : 1.432 ------------------------------------------------------------------------------- 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 768 GLN 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 A residue 2143 THR Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 40 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 189 ASP Chi-restraints excluded: chain E residue 233 GLU Chi-restraints excluded: chain E residue 251 GLN Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 291 ILE 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 257 LEU 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 389 GLU Chi-restraints excluded: chain G residue 397 ILE 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 199 THR Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 360 THR 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 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 350 ILE Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain J residue 379 ASP Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain U residue 40 ARG 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 42 ARG Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 76 GLN Chi-restraints excluded: chain W residue 83 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 310 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 170 optimal weight: 0.0670 chunk 361 optimal weight: 0.5980 chunk 453 optimal weight: 0.9980 chunk 326 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 332 optimal weight: 0.5980 chunk 292 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 110 ASN D 91 GLN ** E 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN G 169 GLN G 262 GLN ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 408 GLN T 49 HIS X 27 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103316 restraints weight = 68859.186| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.07 r_work: 0.3066 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 43534 Z= 0.140 Angle : 0.575 9.386 59700 Z= 0.303 Chirality : 0.044 0.365 6789 Planarity : 0.004 0.066 6883 Dihedral : 20.601 179.412 7705 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.10 % Allowed : 14.50 % Favored : 83.41 % 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 (0.12), residues: 4719 helix: 1.84 (0.11), residues: 2354 sheet: 0.54 (0.20), residues: 642 loop : 0.42 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 615 TYR 0.017 0.001 TYR I 192 PHE 0.021 0.001 PHE A1948 TRP 0.070 0.002 TRP C 360 HIS 0.006 0.001 HIS V 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (43526) covalent geometry : angle 0.57430 / 0.30 (59691) hydrogen bonds : bond 0.03984 / 2.68 ( 2083) hydrogen bonds : angle 3.75700 / 2.71 ( 5758) metal coordination : bond 0.01029 / 0.35 ( 8) metal coordination : angle 1.75745 / 0.81 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 1437 time to evaluate : 1.656 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 621 TYR cc_start: 0.7256 (p90) cc_final: 0.6946 (p90) REVERT: A 628 TRP cc_start: 0.8472 (t60) cc_final: 0.8086 (t60) REVERT: A 660 LEU cc_start: 0.8967 (mp) cc_final: 0.8698 (mp) REVERT: A 678 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8511 (m) REVERT: A 694 LYS cc_start: 0.8649 (mttt) cc_final: 0.8383 (mmtm) REVERT: A 704 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6882 (mt-10) REVERT: A 719 HIS cc_start: 0.8137 (m170) cc_final: 0.7613 (m-70) REVERT: A 774 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8536 (m) REVERT: A 789 MET cc_start: 0.7640 (mmt) cc_final: 0.7330 (mmm) REVERT: A 851 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8612 (mmmm) REVERT: A 854 GLU cc_start: 0.8137 (pm20) cc_final: 0.7594 (pm20) REVERT: A 863 LYS cc_start: 0.8541 (tptp) cc_final: 0.8304 (tttm) REVERT: A 870 ASP cc_start: 0.8720 (t0) cc_final: 0.8505 (t0) REVERT: A 871 ASP cc_start: 0.8350 (t0) cc_final: 0.7999 (t70) REVERT: A 892 ASN cc_start: 0.8664 (m110) cc_final: 0.8333 (m110) REVERT: A 966 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7788 (mtp-110) REVERT: A 975 LEU cc_start: 0.8434 (mt) cc_final: 0.8164 (mt) REVERT: A 992 MET cc_start: 0.2420 (ttm) cc_final: 0.1665 (ttm) REVERT: A 1891 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7791 (tm-30) REVERT: A 1893 ARG cc_start: 0.8352 (mtt180) cc_final: 0.7935 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8536 (ptpp) cc_final: 0.8192 (ptpp) REVERT: A 1895 ARG cc_start: 0.8065 (ttp-170) cc_final: 0.7784 (ttp-170) REVERT: A 1896 GLN cc_start: 0.8211 (mt0) cc_final: 0.7937 (mt0) REVERT: A 1897 ARG cc_start: 0.8164 (ttp-170) cc_final: 0.7816 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8183 (ttp-170) REVERT: A 1936 ILE cc_start: 0.8873 (mm) cc_final: 0.8433 (mt) REVERT: A 1953 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7717 (mm-30) REVERT: A 2013 GLU cc_start: 0.7886 (tp30) cc_final: 0.7194 (tp30) REVERT: A 2026 CYS cc_start: 0.8416 (m) cc_final: 0.8067 (m) REVERT: A 2038 ILE cc_start: 0.8693 (tt) cc_final: 0.8456 (tp) REVERT: A 2094 ARG cc_start: 0.8132 (ptp90) cc_final: 0.7931 (ptp90) REVERT: A 2097 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8583 (mm-40) REVERT: A 2150 ASP cc_start: 0.8035 (m-30) cc_final: 0.7687 (m-30) REVERT: A 2185 MET cc_start: 0.6707 (ttm) cc_final: 0.6182 (ppp) REVERT: A 2189 MET cc_start: 0.7760 (mtt) cc_final: 0.7152 (mtt) REVERT: A 2196 PHE cc_start: 0.8074 (m-80) cc_final: 0.7820 (m-80) REVERT: B 133 MET cc_start: 0.6004 (mmt) cc_final: 0.5530 (mmt) REVERT: B 174 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8124 (mtm-85) REVERT: C 1 MET cc_start: 0.4442 (tmm) cc_final: 0.4204 (tmm) REVERT: C 2 THR cc_start: 0.7861 (t) cc_final: 0.7306 (m) REVERT: C 14 LYS cc_start: 0.8814 (mppt) cc_final: 0.8156 (mttp) REVERT: C 55 PHE cc_start: 0.7452 (t80) cc_final: 0.7121 (t80) REVERT: C 71 GLN cc_start: 0.8318 (tp-100) cc_final: 0.7692 (tp-100) REVERT: C 72 ARG cc_start: 0.8663 (tpp80) cc_final: 0.8113 (tpp80) REVERT: C 75 TRP cc_start: 0.9029 (m-10) cc_final: 0.8719 (m-10) REVERT: C 76 ASP cc_start: 0.8159 (m-30) cc_final: 0.7627 (m-30) REVERT: C 83 MET cc_start: 0.8361 (mmp) cc_final: 0.8049 (mmm) REVERT: C 90 ASP cc_start: 0.8301 (t0) cc_final: 0.7653 (t0) REVERT: C 97 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7853 (mm-30) REVERT: C 103 THR cc_start: 0.8709 (m) cc_final: 0.8452 (p) REVERT: C 107 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7950 (mm-30) REVERT: C 111 GLU cc_start: 0.8114 (tm-30) cc_final: 0.6985 (tm-30) REVERT: C 115 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 116 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 135 TYR cc_start: 0.8898 (t80) cc_final: 0.8550 (t80) REVERT: C 149 ASP cc_start: 0.8433 (t0) cc_final: 0.8170 (t0) REVERT: C 196 MET cc_start: 0.8131 (tpp) cc_final: 0.7931 (mmm) REVERT: C 204 GLN cc_start: 0.8738 (tp40) cc_final: 0.8151 (tp-100) REVERT: C 208 ASP cc_start: 0.8074 (m-30) cc_final: 0.7654 (m-30) REVERT: C 230 ASN cc_start: 0.8565 (t0) cc_final: 0.8206 (t0) REVERT: C 248 PHE cc_start: 0.8531 (p90) cc_final: 0.8154 (p90) REVERT: C 250 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8611 (mtpp) REVERT: C 252 ARG cc_start: 0.8636 (mmm-85) cc_final: 0.8429 (mmm160) REVERT: C 372 PHE cc_start: 0.8553 (t80) cc_final: 0.8311 (t80) REVERT: C 382 TYR cc_start: 0.8136 (t80) cc_final: 0.7557 (t80) REVERT: D 92 ASN cc_start: 0.8651 (t0) cc_final: 0.8405 (t0) REVERT: E 15 ILE cc_start: 0.8670 (mm) cc_final: 0.8444 (mt) REVERT: E 22 LYS cc_start: 0.8468 (mmtp) cc_final: 0.8221 (mmtp) REVERT: E 28 GLU cc_start: 0.7751 (mp0) cc_final: 0.7314 (mp0) REVERT: E 64 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7918 (mmt-90) REVERT: E 81 LEU cc_start: 0.8442 (mt) cc_final: 0.8179 (mp) REVERT: E 85 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8497 (mm-40) REVERT: E 135 VAL cc_start: 0.8361 (t) cc_final: 0.8135 (p) REVERT: E 165 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7570 (mmtt) REVERT: E 167 THR cc_start: 0.8013 (m) cc_final: 0.7780 (p) REVERT: E 168 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8134 (ttmt) REVERT: E 178 GLU cc_start: 0.7915 (tt0) cc_final: 0.7610 (tt0) REVERT: E 182 LYS cc_start: 0.8066 (mtmt) cc_final: 0.7733 (mtmt) REVERT: E 183 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7826 (mm-30) REVERT: E 185 VAL cc_start: 0.8315 (t) cc_final: 0.8071 (m) REVERT: E 194 GLU cc_start: 0.7801 (tt0) cc_final: 0.7496 (tt0) REVERT: E 212 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7420 (mm-30) REVERT: E 214 ASP cc_start: 0.8091 (m-30) cc_final: 0.7808 (m-30) REVERT: E 227 ASP cc_start: 0.7831 (t0) cc_final: 0.7558 (t0) REVERT: E 285 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7779 (ttmm) REVERT: E 286 TYR cc_start: 0.8345 (m-10) cc_final: 0.8045 (m-80) REVERT: E 352 LEU cc_start: 0.8383 (mt) cc_final: 0.8099 (mm) REVERT: E 370 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8126 (mt-10) REVERT: E 389 GLU cc_start: 0.7920 (tt0) cc_final: 0.7666 (tt0) REVERT: E 415 LEU cc_start: 0.8793 (mt) cc_final: 0.8570 (mm) REVERT: E 418 LYS cc_start: 0.8228 (ttmm) cc_final: 0.8006 (ttmm) REVERT: E 439 ASP cc_start: 0.7503 (p0) cc_final: 0.7045 (p0) REVERT: E 441 LYS cc_start: 0.8276 (mttt) cc_final: 0.8009 (mttt) REVERT: E 445 LYS cc_start: 0.7746 (mmtp) cc_final: 0.7541 (mmtp) REVERT: E 446 ILE cc_start: 0.8325 (mm) cc_final: 0.7994 (mt) REVERT: F 40 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7798 (mtt90) REVERT: F 71 ARG cc_start: 0.7797 (mmt90) cc_final: 0.7559 (mmm-85) REVERT: F 112 GLU cc_start: 0.7756 (tp30) cc_final: 0.7445 (tp30) REVERT: F 117 GLU cc_start: 0.8188 (tp30) cc_final: 0.7604 (mm-30) REVERT: F 142 VAL cc_start: 0.8244 (t) cc_final: 0.7949 (m) REVERT: F 160 LYS cc_start: 0.8314 (ttpt) cc_final: 0.7890 (mtpt) REVERT: F 168 MET cc_start: 0.7456 (mtp) cc_final: 0.7059 (mtp) REVERT: F 170 THR cc_start: 0.8154 (m) cc_final: 0.7886 (t) REVERT: F 181 SER cc_start: 0.8691 (m) cc_final: 0.8287 (p) REVERT: F 182 LEU cc_start: 0.8915 (mt) cc_final: 0.8628 (mm) REVERT: F 192 VAL cc_start: 0.8229 (t) cc_final: 0.7715 (p) REVERT: F 197 LYS cc_start: 0.7584 (mtpt) cc_final: 0.7091 (mtpt) REVERT: F 233 GLN cc_start: 0.7745 (tp40) cc_final: 0.6903 (tp40) REVERT: F 246 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7274 (mt-10) REVERT: F 248 ASP cc_start: 0.7744 (m-30) cc_final: 0.7460 (m-30) REVERT: F 267 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7224 (mt-10) REVERT: F 269 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7880 (mmtp) REVERT: F 271 GLU cc_start: 0.7862 (mp0) cc_final: 0.7660 (mp0) REVERT: F 274 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7691 (mm-30) REVERT: F 286 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7885 (mt-10) REVERT: F 303 MET cc_start: 0.8661 (mmm) cc_final: 0.8340 (mmp) REVERT: F 317 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7406 (mt-10) REVERT: F 392 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7876 (ttp-170) REVERT: F 441 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7563 (mm-40) REVERT: F 445 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7551 (mm-30) REVERT: G 15 ILE cc_start: 0.8826 (mt) cc_final: 0.8594 (mm) REVERT: G 19 SER cc_start: 0.8593 (m) cc_final: 0.8388 (m) REVERT: G 34 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7986 (tm-30) REVERT: G 54 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7427 (mm-30) REVERT: G 61 MET cc_start: 0.8706 (mmm) cc_final: 0.8102 (mmm) REVERT: G 90 LYS cc_start: 0.8580 (tptm) cc_final: 0.8016 (tptm) REVERT: G 125 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7835 (mmmt) REVERT: G 126 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7159 (mt-10) REVERT: G 128 LYS cc_start: 0.8333 (tttt) cc_final: 0.7784 (tttt) REVERT: G 134 GLU cc_start: 0.7518 (tt0) cc_final: 0.6997 (tm-30) REVERT: G 137 GLU cc_start: 0.7766 (tt0) cc_final: 0.7400 (tp30) REVERT: G 147 MET cc_start: 0.6246 (mtp) cc_final: 0.5655 (mtp) REVERT: G 158 ILE cc_start: 0.8546 (mt) cc_final: 0.8263 (mm) REVERT: G 162 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8044 (ttmm) REVERT: G 171 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8353 (mtpt) REVERT: G 178 GLU cc_start: 0.8155 (tt0) cc_final: 0.7498 (tt0) REVERT: G 186 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7413 (mm-30) REVERT: G 189 ASP cc_start: 0.8024 (m-30) cc_final: 0.7822 (m-30) REVERT: G 193 ILE cc_start: 0.8656 (mt) cc_final: 0.8318 (mm) REVERT: G 209 TYR cc_start: 0.8521 (m-80) cc_final: 0.8131 (m-10) REVERT: G 212 GLU cc_start: 0.7806 (pm20) cc_final: 0.7576 (pm20) REVERT: G 225 LYS cc_start: 0.8332 (mmpt) cc_final: 0.7890 (mmpt) REVERT: G 233 GLU cc_start: 0.7419 (tp30) cc_final: 0.6829 (tp30) REVERT: G 244 ASP cc_start: 0.7444 (m-30) cc_final: 0.7193 (m-30) REVERT: G 247 ASN cc_start: 0.8371 (m-40) cc_final: 0.8116 (m110) REVERT: G 249 ARG cc_start: 0.7867 (ttt-90) cc_final: 0.7548 (ttt-90) REVERT: G 302 ASP cc_start: 0.8061 (t0) cc_final: 0.7218 (t0) REVERT: G 303 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7298 (mp0) REVERT: G 376 LYS cc_start: 0.8745 (tptt) cc_final: 0.8515 (tptm) REVERT: G 422 LYS cc_start: 0.8248 (mttp) cc_final: 0.7985 (mptt) REVERT: G 428 GLU cc_start: 0.8278 (mp0) cc_final: 0.7837 (mp0) REVERT: G 447 LEU cc_start: 0.8366 (mt) cc_final: 0.8144 (mt) REVERT: H 18 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7516 (mtp85) REVERT: H 38 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7891 (mm-30) REVERT: H 46 MET cc_start: 0.8429 (mtp) cc_final: 0.8222 (mtt) REVERT: H 64 ARG cc_start: 0.8375 (mtt180) cc_final: 0.8164 (mtt-85) REVERT: H 83 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8426 (mtmm) REVERT: H 88 MET cc_start: 0.7962 (mmp) cc_final: 0.7640 (mmm) REVERT: H 117 GLU cc_start: 0.8215 (tp30) cc_final: 0.7613 (tp30) REVERT: H 132 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8107 (ttmm) REVERT: H 139 GLU cc_start: 0.7527 (tt0) cc_final: 0.7168 (tm-30) REVERT: H 144 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7457 (mm-30) REVERT: H 145 ILE cc_start: 0.8344 (mt) cc_final: 0.8139 (tp) REVERT: H 164 LYS cc_start: 0.8398 (pttt) cc_final: 0.7967 (pttm) REVERT: H 201 LYS cc_start: 0.8396 (ptmt) cc_final: 0.8186 (ptmt) REVERT: H 204 LYS cc_start: 0.8865 (mtpt) cc_final: 0.8545 (mtpt) REVERT: H 214 ASP cc_start: 0.7653 (p0) cc_final: 0.7328 (p0) REVERT: H 238 VAL cc_start: 0.8072 (t) cc_final: 0.7775 (p) REVERT: H 246 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7654 (mt-10) REVERT: H 253 ARG cc_start: 0.8215 (ptm160) cc_final: 0.7958 (ptm-80) REVERT: H 267 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7555 (tt0) REVERT: H 273 ARG cc_start: 0.8371 (mtt90) cc_final: 0.7742 (mtt90) REVERT: H 274 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7654 (mt-10) REVERT: H 275 GLN cc_start: 0.8235 (mm110) cc_final: 0.7876 (mm-40) REVERT: H 277 ASN cc_start: 0.8494 (m-40) cc_final: 0.8113 (m110) REVERT: H 279 LYS cc_start: 0.8330 (tppt) cc_final: 0.8000 (tptp) REVERT: H 313 ASN cc_start: 0.8079 (m-40) cc_final: 0.7748 (m-40) REVERT: H 314 ARG cc_start: 0.7459 (mmt180) cc_final: 0.6907 (mmt180) REVERT: H 317 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7419 (mt-10) REVERT: H 339 SER cc_start: 0.8721 (p) cc_final: 0.8503 (m) REVERT: H 404 GLN cc_start: 0.8318 (mt0) cc_final: 0.8079 (mt0) REVERT: I 13 GLN cc_start: 0.8041 (tp40) cc_final: 0.7791 (mm-40) REVERT: I 64 ARG cc_start: 0.8284 (mmm-85) cc_final: 0.7964 (mmt-90) REVERT: I 129 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7898 (mt-10) REVERT: I 137 GLU cc_start: 0.7853 (tt0) cc_final: 0.7572 (tt0) REVERT: I 139 THR cc_start: 0.8727 (m) cc_final: 0.8320 (p) REVERT: I 171 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8498 (tttt) REVERT: I 216 GLU cc_start: 0.7989 (tp30) cc_final: 0.7714 (tp30) REVERT: I 244 ASP cc_start: 0.7609 (m-30) cc_final: 0.7271 (t0) REVERT: I 249 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7754 (mtp85) REVERT: I 259 MET cc_start: 0.8112 (mtp) cc_final: 0.7879 (mtp) REVERT: I 267 LYS cc_start: 0.8270 (ttpp) cc_final: 0.7975 (tttp) REVERT: I 281 LYS cc_start: 0.8639 (mttt) cc_final: 0.8342 (mtmt) REVERT: I 302 ASP cc_start: 0.8310 (t0) cc_final: 0.7789 (t0) REVERT: I 310 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7698 (mt-10) REVERT: I 322 SER cc_start: 0.8533 (p) cc_final: 0.8278 (t) REVERT: I 438 TYR cc_start: 0.8330 (m-80) cc_final: 0.7860 (m-80) REVERT: I 439 ASP cc_start: 0.8137 (p0) cc_final: 0.7793 (p0) REVERT: I 441 LYS cc_start: 0.8482 (mttm) cc_final: 0.8023 (mtmm) REVERT: I 445 LYS cc_start: 0.8177 (tppt) cc_final: 0.7198 (tppt) REVERT: I 446 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8099 (mp) REVERT: J 90 MET cc_start: 0.8475 (mtm) cc_final: 0.8218 (mtp) REVERT: J 92 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7913 (mm-40) REVERT: J 117 GLU cc_start: 0.7684 (tp30) cc_final: 0.7429 (tp30) REVERT: J 133 GLU cc_start: 0.7704 (pt0) cc_final: 0.7474 (pt0) REVERT: J 142 VAL cc_start: 0.8646 (t) cc_final: 0.8368 (m) REVERT: J 144 GLU cc_start: 0.8127 (tt0) cc_final: 0.7871 (tt0) REVERT: J 164 LYS cc_start: 0.8415 (pttt) cc_final: 0.8125 (ptmm) REVERT: J 172 TYR cc_start: 0.8459 (m-80) cc_final: 0.8258 (m-80) REVERT: J 179 ILE cc_start: 0.8391 (mt) cc_final: 0.8143 (mt) REVERT: J 183 THR cc_start: 0.8192 (m) cc_final: 0.7911 (p) REVERT: J 192 VAL cc_start: 0.8611 (t) cc_final: 0.8265 (p) REVERT: J 225 VAL cc_start: 0.8449 (t) cc_final: 0.8170 (p) REVERT: J 234 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8290 (mtpp) REVERT: J 267 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7534 (mt-10) REVERT: J 270 SER cc_start: 0.8421 (p) cc_final: 0.8048 (t) REVERT: J 314 ARG cc_start: 0.8069 (mmt180) cc_final: 0.7770 (mmt180) REVERT: J 352 ASP cc_start: 0.7774 (m-30) cc_final: 0.7428 (t0) REVERT: J 376 GLU cc_start: 0.7807 (tt0) cc_final: 0.7588 (tt0) REVERT: J 377 GLU cc_start: 0.7774 (tp30) cc_final: 0.7381 (tp30) REVERT: J 430 TYR cc_start: 0.8719 (t80) cc_final: 0.8402 (t80) REVERT: P 247 ASP cc_start: 0.8508 (t0) cc_final: 0.8241 (t0) REVERT: P 249 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7820 (mm-30) REVERT: P 250 SER cc_start: 0.8888 (m) cc_final: 0.8261 (p) REVERT: P 252 LYS cc_start: 0.9079 (mtmm) cc_final: 0.8447 (mtmm) REVERT: P 253 GLU cc_start: 0.8454 (tp30) cc_final: 0.8059 (tp30) REVERT: P 254 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: P 273 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7975 (mm-30) REVERT: P 289 GLU cc_start: 0.7607 (tp30) cc_final: 0.7350 (tp30) REVERT: P 293 ARG cc_start: 0.7877 (ttp-110) cc_final: 0.7407 (ttp-170) REVERT: S 31 HIS cc_start: 0.8616 (t-170) cc_final: 0.8385 (t-170) REVERT: S 39 TYR cc_start: 0.8972 (m-80) cc_final: 0.8655 (m-80) REVERT: S 42 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7512 (mtm110) REVERT: S 59 THR cc_start: 0.9214 (m) cc_final: 0.8919 (p) REVERT: S 61 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7976 (mm-30) REVERT: S 73 ASN cc_start: 0.8878 (m110) cc_final: 0.8456 (t0) REVERT: S 87 VAL cc_start: 0.8972 (t) cc_final: 0.8755 (p) REVERT: T 68 ASP cc_start: 0.8191 (t0) cc_final: 0.7761 (t0) REVERT: T 79 ARG cc_start: 0.8253 (mtm110) cc_final: 0.7535 (mtm110) REVERT: T 93 GLU cc_start: 0.7819 (mp0) cc_final: 0.7573 (mp0) REVERT: T 120 LYS cc_start: 0.8759 (tttp) cc_final: 0.8286 (ttpp) REVERT: U 106 ASP cc_start: 0.8312 (m-30) cc_final: 0.7837 (m-30) REVERT: V 82 THR cc_start: 0.9117 (t) cc_final: 0.8864 (p) REVERT: V 87 VAL cc_start: 0.9239 (t) cc_final: 0.9019 (m) REVERT: W 94 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8178 (mm-30) REVERT: W 123 ASP cc_start: 0.8536 (m-30) cc_final: 0.8256 (m-30) REVERT: X 35 ARG cc_start: 0.8612 (mtp85) cc_final: 0.8353 (mmm160) REVERT: X 71 THR cc_start: 0.9277 (m) cc_final: 0.8953 (t) REVERT: X 75 HIS cc_start: 0.8467 (t70) cc_final: 0.7857 (t70) REVERT: X 84 MET cc_start: 0.8819 (tpt) cc_final: 0.8603 (mmm) outliers start: 86 outliers final: 60 residues processed: 1455 average time/residue: 0.3078 time to fit residues: 692.8662 Evaluate side-chains 1466 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1401 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 761 SER Chi-restraints excluded: chain A residue 768 GLN 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 833 LEU Chi-restraints excluded: chain A residue 2019 ARG Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 129 VAL 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 107 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR 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 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 420 ASN Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 264 ASP 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 258 SER Chi-restraints excluded: chain I residue 264 MET Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 364 MET Chi-restraints excluded: chain I residue 446 ILE Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 369 GLN Chi-restraints excluded: chain J residue 373 ILE Chi-restraints excluded: chain J residue 379 ASP Chi-restraints excluded: chain P residue 254 GLU Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 466 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 320 optimal weight: 0.7980 chunk 100 optimal weight: 0.0060 chunk 482 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 197 optimal weight: 4.9990 chunk 114 optimal weight: 0.0170 chunk 233 optimal weight: 0.9980 chunk 486 optimal weight: 7.9990 overall best weight: 1.1636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 892 ASN A1991 HIS C 12 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 110 ASN D 91 GLN E 380 GLN E 408 GLN E 420 ASN F 277 ASN G 169 GLN G 262 GLN ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 HIS X 27 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.127536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.102326 restraints weight = 69261.991| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.03 r_work: 0.3052 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 43534 Z= 0.196 Angle : 0.593 9.550 59700 Z= 0.313 Chirality : 0.045 0.362 6789 Planarity : 0.004 0.059 6883 Dihedral : 20.617 179.142 7705 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.41 % Allowed : 14.99 % Favored : 82.60 % 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: 1.56 (0.12), residues: 4719 helix: 1.77 (0.11), residues: 2358 sheet: 0.43 (0.20), residues: 644 loop : 0.38 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 858 TYR 0.019 0.001 TYR W 54 PHE 0.018 0.001 PHE R 65 TRP 0.040 0.002 TRP C 360 HIS 0.009 0.001 HIS V 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (43526) covalent geometry : angle 0.59302 / 0.31 (59691) hydrogen bonds : bond 0.04207 / 2.83 ( 2083) hydrogen bonds : angle 3.77437 / 2.73 ( 5758) metal coordination : bond 0.01351 / 0.53 ( 8) metal coordination : angle 1.92868 / 0.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1551 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1452 time to evaluate : 1.552 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 621 TYR cc_start: 0.7313 (p90) cc_final: 0.6998 (p90) REVERT: A 628 TRP cc_start: 0.8555 (t60) cc_final: 0.8305 (t60) REVERT: A 660 LEU cc_start: 0.8985 (mp) cc_final: 0.8720 (mp) REVERT: A 678 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8544 (m) REVERT: A 694 LYS cc_start: 0.8667 (mttt) cc_final: 0.8443 (mmtm) REVERT: A 704 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6969 (mt-10) REVERT: A 719 HIS cc_start: 0.8125 (m170) cc_final: 0.7633 (m-70) REVERT: A 747 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8138 (mm-30) REVERT: A 749 GLN cc_start: 0.8464 (pm20) cc_final: 0.8252 (pm20) REVERT: A 774 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8575 (m) REVERT: A 789 MET cc_start: 0.7709 (mmt) cc_final: 0.7334 (mmt) REVERT: A 833 LEU cc_start: 0.8300 (mt) cc_final: 0.8069 (mm) REVERT: A 854 GLU cc_start: 0.8204 (pm20) cc_final: 0.7879 (pm20) REVERT: A 870 ASP cc_start: 0.8777 (t0) cc_final: 0.8505 (t0) REVERT: A 871 ASP cc_start: 0.8270 (t0) cc_final: 0.7948 (t70) REVERT: A 892 ASN cc_start: 0.8670 (m-40) cc_final: 0.8372 (m110) REVERT: A 918 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8380 (m) REVERT: A 966 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7864 (mtp-110) REVERT: A 976 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7636 (mt-10) REVERT: A 992 MET cc_start: 0.2608 (ttm) cc_final: 0.1828 (ttm) REVERT: A 1891 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7813 (tm-30) REVERT: A 1893 ARG cc_start: 0.8419 (mtt180) cc_final: 0.7993 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8539 (ptpp) cc_final: 0.8202 (ptpp) REVERT: A 1895 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7849 (ttp-170) REVERT: A 1896 GLN cc_start: 0.8221 (mt0) cc_final: 0.7942 (mt0) REVERT: A 1897 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7865 (ttp-170) REVERT: A 1903 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8163 (ttp-170) REVERT: A 1936 ILE cc_start: 0.8877 (mm) cc_final: 0.8439 (mt) REVERT: A 1953 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7781 (mm-30) REVERT: A 2013 GLU cc_start: 0.7916 (tp30) cc_final: 0.7210 (tp30) REVERT: A 2026 CYS cc_start: 0.8419 (m) cc_final: 0.8079 (m) REVERT: A 2094 ARG cc_start: 0.8211 (ptp90) cc_final: 0.7735 (mtm-85) REVERT: A 2096 GLU cc_start: 0.8214 (mp0) cc_final: 0.7835 (pm20) REVERT: A 2097 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8666 (mm-40) REVERT: A 2150 ASP cc_start: 0.8084 (m-30) cc_final: 0.7754 (m-30) REVERT: A 2169 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7493 (mm-30) REVERT: A 2185 MET cc_start: 0.6743 (ttm) cc_final: 0.6478 (ttm) REVERT: A 2196 PHE cc_start: 0.8055 (m-80) cc_final: 0.7789 (m-80) REVERT: B 133 MET cc_start: 0.5986 (mmt) cc_final: 0.5515 (mmt) REVERT: B 174 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8148 (mtm-85) REVERT: C 14 LYS cc_start: 0.8791 (mppt) cc_final: 0.8199 (mttp) REVERT: C 55 PHE cc_start: 0.7512 (t80) cc_final: 0.7169 (t80) REVERT: C 65 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8509 (tp) REVERT: C 71 GLN cc_start: 0.8287 (tp-100) cc_final: 0.8064 (tp-100) REVERT: C 72 ARG cc_start: 0.8709 (tpp80) cc_final: 0.8126 (tpp80) REVERT: C 76 ASP cc_start: 0.8178 (m-30) cc_final: 0.7638 (m-30) REVERT: C 83 MET cc_start: 0.8409 (mmp) cc_final: 0.8122 (mmm) REVERT: C 90 ASP cc_start: 0.8240 (t0) cc_final: 0.7575 (t0) REVERT: C 97 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7881 (mp0) REVERT: C 103 THR cc_start: 0.8777 (m) cc_final: 0.8527 (p) REVERT: C 107 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7992 (mm-30) REVERT: C 111 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7019 (tm-30) REVERT: C 115 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7891 (mt-10) REVERT: C 116 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8021 (mm-30) REVERT: C 135 TYR cc_start: 0.8875 (t80) cc_final: 0.8586 (t80) REVERT: C 142 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7675 (mp0) REVERT: C 149 ASP cc_start: 0.8440 (t0) cc_final: 0.8168 (t0) REVERT: C 196 MET cc_start: 0.8139 (tpp) cc_final: 0.7864 (mmm) REVERT: C 204 GLN cc_start: 0.8779 (tp40) cc_final: 0.8180 (tp-100) REVERT: C 208 ASP cc_start: 0.8073 (m-30) cc_final: 0.7653 (m-30) REVERT: C 230 ASN cc_start: 0.8536 (t0) cc_final: 0.8206 (t0) REVERT: C 248 PHE cc_start: 0.8570 (p90) cc_final: 0.8202 (p90) REVERT: C 250 LYS cc_start: 0.8931 (mtpp) cc_final: 0.8598 (mtpp) REVERT: C 372 PHE cc_start: 0.8542 (t80) cc_final: 0.8236 (t80) REVERT: C 382 TYR cc_start: 0.8165 (t80) cc_final: 0.7680 (t80) REVERT: D 92 ASN cc_start: 0.8815 (t0) cc_final: 0.8468 (t0) REVERT: E 15 ILE cc_start: 0.8666 (mm) cc_final: 0.8444 (mt) REVERT: E 22 LYS cc_start: 0.8503 (mmtp) cc_final: 0.8242 (mmtp) REVERT: E 28 GLU cc_start: 0.7841 (mp0) cc_final: 0.7386 (mp0) REVERT: E 81 LEU cc_start: 0.8446 (mt) cc_final: 0.8188 (mp) REVERT: E 135 VAL cc_start: 0.8350 (t) cc_final: 0.8144 (p) REVERT: E 138 LEU cc_start: 0.8381 (mp) cc_final: 0.8138 (mp) REVERT: E 165 LYS cc_start: 0.7908 (mmtt) cc_final: 0.7653 (mmtt) REVERT: E 167 THR cc_start: 0.8028 (m) cc_final: 0.7828 (p) REVERT: E 168 LYS cc_start: 0.8474 (ttmt) cc_final: 0.8182 (ttmt) REVERT: E 178 GLU cc_start: 0.7939 (tt0) cc_final: 0.7643 (tt0) REVERT: E 182 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7756 (mtmt) REVERT: E 183 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7827 (mm-30) REVERT: E 185 VAL cc_start: 0.8302 (t) cc_final: 0.8084 (m) REVERT: E 194 GLU cc_start: 0.7722 (tt0) cc_final: 0.7475 (tt0) REVERT: E 212 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7451 (mm-30) REVERT: E 214 ASP cc_start: 0.8077 (m-30) cc_final: 0.7778 (m-30) REVERT: E 285 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7811 (ttmm) REVERT: E 286 TYR cc_start: 0.8361 (m-10) cc_final: 0.8024 (m-80) REVERT: E 295 VAL cc_start: 0.8632 (t) cc_final: 0.8336 (m) REVERT: E 352 LEU cc_start: 0.8379 (mt) cc_final: 0.8113 (mm) REVERT: E 356 ASP cc_start: 0.8151 (t70) cc_final: 0.7859 (t0) REVERT: E 370 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8178 (mt-10) REVERT: E 389 GLU cc_start: 0.7993 (tt0) cc_final: 0.7721 (tt0) REVERT: E 415 LEU cc_start: 0.8831 (mt) cc_final: 0.8617 (mm) REVERT: E 418 LYS cc_start: 0.8262 (ttmm) cc_final: 0.8038 (ttmm) REVERT: E 445 LYS cc_start: 0.7750 (mmtp) cc_final: 0.7542 (mmtp) REVERT: E 446 ILE cc_start: 0.8320 (mm) cc_final: 0.7985 (mt) REVERT: F 40 ARG cc_start: 0.8172 (mtt90) cc_final: 0.7815 (mtt90) REVERT: F 71 ARG cc_start: 0.7833 (mmt90) cc_final: 0.7571 (mmm-85) REVERT: F 112 GLU cc_start: 0.7806 (tp30) cc_final: 0.7513 (tp30) REVERT: F 117 GLU cc_start: 0.8210 (tp30) cc_final: 0.7598 (mm-30) REVERT: F 142 VAL cc_start: 0.8323 (t) cc_final: 0.7985 (m) REVERT: F 160 LYS cc_start: 0.8317 (ttpt) cc_final: 0.7897 (mtpt) REVERT: F 168 MET cc_start: 0.7498 (mtp) cc_final: 0.7100 (mtp) REVERT: F 170 THR cc_start: 0.8148 (m) cc_final: 0.7905 (t) REVERT: F 181 SER cc_start: 0.8721 (m) cc_final: 0.8320 (p) REVERT: F 182 LEU cc_start: 0.8924 (mt) cc_final: 0.8642 (mm) REVERT: F 183 THR cc_start: 0.8591 (m) cc_final: 0.8292 (p) REVERT: F 192 VAL cc_start: 0.8214 (t) cc_final: 0.7693 (p) REVERT: F 197 LYS cc_start: 0.7622 (mtpt) cc_final: 0.7123 (mtpt) REVERT: F 233 GLN cc_start: 0.7798 (tp40) cc_final: 0.7029 (tp40) REVERT: F 238 VAL cc_start: 0.8582 (t) cc_final: 0.8227 (m) REVERT: F 246 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7297 (mt-10) REVERT: F 248 ASP cc_start: 0.7732 (m-30) cc_final: 0.7470 (m-30) REVERT: F 269 LYS cc_start: 0.8246 (mmtp) cc_final: 0.7948 (mmtp) REVERT: F 271 GLU cc_start: 0.7912 (mp0) cc_final: 0.7700 (mp0) REVERT: F 274 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7719 (mm-30) REVERT: F 286 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7894 (mt-10) REVERT: F 303 MET cc_start: 0.8658 (mmm) cc_final: 0.8334 (mmp) REVERT: F 317 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7412 (mt-10) REVERT: F 392 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7882 (ttp-170) REVERT: F 441 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7566 (mm-40) REVERT: F 445 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7616 (mm-30) REVERT: G 15 ILE cc_start: 0.8808 (mt) cc_final: 0.8584 (mm) REVERT: G 19 SER cc_start: 0.8608 (m) cc_final: 0.8400 (m) REVERT: G 34 GLN cc_start: 0.8272 (tm-30) cc_final: 0.7983 (tm-30) REVERT: G 54 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7474 (mm-30) REVERT: G 61 MET cc_start: 0.8745 (mmm) cc_final: 0.8105 (mmm) REVERT: G 90 LYS cc_start: 0.8597 (tptm) cc_final: 0.8007 (tptm) REVERT: G 125 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7882 (mmmt) REVERT: G 126 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7143 (mt-10) REVERT: G 128 LYS cc_start: 0.8348 (tttt) cc_final: 0.7842 (tttt) REVERT: G 134 GLU cc_start: 0.7534 (tt0) cc_final: 0.7038 (tm-30) REVERT: G 137 GLU cc_start: 0.7793 (tt0) cc_final: 0.7443 (tp30) REVERT: G 147 MET cc_start: 0.6194 (mtp) cc_final: 0.5598 (mtp) REVERT: G 158 ILE cc_start: 0.8486 (mt) cc_final: 0.8210 (mm) REVERT: G 162 LYS cc_start: 0.8467 (ttmt) cc_final: 0.8137 (ttmm) REVERT: G 171 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8331 (mtpt) REVERT: G 178 GLU cc_start: 0.8177 (tt0) cc_final: 0.7549 (tt0) REVERT: G 186 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7432 (mm-30) REVERT: G 189 ASP cc_start: 0.8029 (m-30) cc_final: 0.7823 (m-30) REVERT: G 193 ILE cc_start: 0.8684 (mt) cc_final: 0.8334 (mm) REVERT: G 209 TYR cc_start: 0.8546 (m-80) cc_final: 0.8147 (m-10) REVERT: G 225 LYS cc_start: 0.8334 (mmpt) cc_final: 0.7866 (mmpt) REVERT: G 244 ASP cc_start: 0.7468 (m-30) cc_final: 0.7223 (m-30) REVERT: G 247 ASN cc_start: 0.8395 (m-40) cc_final: 0.8149 (m110) REVERT: G 249 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7549 (ttt-90) REVERT: G 281 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8178 (mtmm) REVERT: G 302 ASP cc_start: 0.8027 (t0) cc_final: 0.7217 (t0) REVERT: G 303 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7283 (mp0) REVERT: G 323 ILE cc_start: 0.8736 (mm) cc_final: 0.8371 (mt) REVERT: G 376 LYS cc_start: 0.8754 (tptt) cc_final: 0.8513 (tptm) REVERT: G 422 LYS cc_start: 0.8294 (mttp) cc_final: 0.8004 (mptt) REVERT: G 428 GLU cc_start: 0.8328 (mp0) cc_final: 0.7895 (mp0) REVERT: G 447 LEU cc_start: 0.8368 (mt) cc_final: 0.8157 (mt) REVERT: H 18 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7539 (mtp85) REVERT: H 20 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7734 (mt-10) REVERT: H 38 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7943 (mm-30) REVERT: H 46 MET cc_start: 0.8431 (mtp) cc_final: 0.8222 (mtt) REVERT: H 83 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8391 (mtmm) REVERT: H 88 MET cc_start: 0.7983 (mmp) cc_final: 0.7660 (mmm) REVERT: H 117 GLU cc_start: 0.8221 (tp30) cc_final: 0.7851 (tp30) REVERT: H 132 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8108 (ttmm) REVERT: H 135 THR cc_start: 0.7931 (m) cc_final: 0.7709 (p) REVERT: H 139 GLU cc_start: 0.7558 (tt0) cc_final: 0.7196 (tm-30) REVERT: H 144 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7510 (mm-30) REVERT: H 164 LYS cc_start: 0.8410 (pttt) cc_final: 0.7912 (pttm) REVERT: H 201 LYS cc_start: 0.8423 (ptmt) cc_final: 0.8214 (ptmt) REVERT: H 204 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8564 (mtpt) REVERT: H 214 ASP cc_start: 0.7663 (p0) cc_final: 0.7330 (p0) REVERT: H 238 VAL cc_start: 0.8060 (t) cc_final: 0.7753 (p) REVERT: H 246 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7625 (mt-10) REVERT: H 253 ARG cc_start: 0.8206 (ptm160) cc_final: 0.7937 (ptm-80) REVERT: H 273 ARG cc_start: 0.8383 (mtt90) cc_final: 0.7870 (mtt90) REVERT: H 274 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7663 (mt-10) REVERT: H 275 GLN cc_start: 0.8257 (mm110) cc_final: 0.7965 (mm-40) REVERT: H 277 ASN cc_start: 0.8519 (m-40) cc_final: 0.8134 (m110) REVERT: H 279 LYS cc_start: 0.8360 (tppt) cc_final: 0.8001 (tptp) REVERT: H 284 ARG cc_start: 0.8156 (ttt90) cc_final: 0.7911 (ptm-80) REVERT: H 307 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7384 (mm-30) REVERT: H 313 ASN cc_start: 0.8069 (m-40) cc_final: 0.7742 (m-40) REVERT: H 314 ARG cc_start: 0.7462 (mmt180) cc_final: 0.6874 (mmt180) REVERT: H 339 SER cc_start: 0.8736 (p) cc_final: 0.8494 (m) REVERT: H 404 GLN cc_start: 0.8324 (mt0) cc_final: 0.8006 (mt0) REVERT: I 13 GLN cc_start: 0.8061 (tp40) cc_final: 0.7809 (mm-40) REVERT: I 64 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8046 (mmt-90) REVERT: I 137 GLU cc_start: 0.7858 (tt0) cc_final: 0.7600 (tt0) REVERT: I 139 THR cc_start: 0.8712 (m) cc_final: 0.8301 (p) REVERT: I 169 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7731 (mt0) REVERT: I 171 LYS cc_start: 0.8916 (ttmt) cc_final: 0.8533 (tttt) REVERT: I 216 GLU cc_start: 0.7968 (tp30) cc_final: 0.7686 (tp30) REVERT: I 219 GLU cc_start: 0.7864 (tp30) cc_final: 0.7651 (tp30) REVERT: I 244 ASP cc_start: 0.7591 (m-30) cc_final: 0.7281 (t0) REVERT: I 249 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7799 (mtp85) REVERT: I 259 MET cc_start: 0.8122 (mtp) cc_final: 0.7809 (mtp) REVERT: I 267 LYS cc_start: 0.8286 (ttpp) cc_final: 0.7994 (tttp) REVERT: I 281 LYS cc_start: 0.8649 (mttt) cc_final: 0.8405 (mtmt) REVERT: I 302 ASP cc_start: 0.8379 (t0) cc_final: 0.7910 (t0) REVERT: I 322 SER cc_start: 0.8541 (p) cc_final: 0.8267 (t) REVERT: I 438 TYR cc_start: 0.8378 (m-80) cc_final: 0.7890 (m-80) REVERT: I 439 ASP cc_start: 0.8158 (p0) cc_final: 0.7817 (p0) REVERT: I 441 LYS cc_start: 0.8501 (mttm) cc_final: 0.8067 (mtmm) REVERT: I 445 LYS cc_start: 0.8172 (tppt) cc_final: 0.7209 (tppt) REVERT: J 90 MET cc_start: 0.8500 (mtm) cc_final: 0.8255 (mtp) REVERT: J 92 GLN cc_start: 0.8457 (mm-40) cc_final: 0.7907 (mm-40) REVERT: J 117 GLU cc_start: 0.7696 (tp30) cc_final: 0.7442 (tp30) REVERT: J 142 VAL cc_start: 0.8691 (t) cc_final: 0.8406 (m) REVERT: J 144 GLU cc_start: 0.8162 (tt0) cc_final: 0.7889 (tt0) REVERT: J 164 LYS cc_start: 0.8436 (pttt) cc_final: 0.8092 (ptmm) REVERT: J 179 ILE cc_start: 0.8397 (mt) cc_final: 0.8144 (mt) REVERT: J 180 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7301 (mt-10) REVERT: J 183 THR cc_start: 0.8193 (m) cc_final: 0.7908 (p) REVERT: J 192 VAL cc_start: 0.8618 (t) cc_final: 0.8247 (p) REVERT: J 225 VAL cc_start: 0.8435 (t) cc_final: 0.8165 (p) REVERT: J 267 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7547 (mt-10) REVERT: J 270 SER cc_start: 0.8428 (p) cc_final: 0.8072 (t) REVERT: J 314 ARG cc_start: 0.8103 (mmt180) cc_final: 0.7814 (mmt180) REVERT: J 352 ASP cc_start: 0.7720 (m-30) cc_final: 0.7386 (t0) REVERT: J 376 GLU cc_start: 0.7844 (tt0) cc_final: 0.7620 (tt0) REVERT: J 377 GLU cc_start: 0.7792 (tp30) cc_final: 0.7387 (tp30) REVERT: J 430 TYR cc_start: 0.8716 (t80) cc_final: 0.8465 (t80) REVERT: J 436 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6667 (tm-30) REVERT: P 247 ASP cc_start: 0.8537 (t0) cc_final: 0.8268 (t0) REVERT: P 250 SER cc_start: 0.8894 (m) cc_final: 0.8252 (p) REVERT: P 252 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8915 (mtpp) REVERT: P 253 GLU cc_start: 0.8516 (tp30) cc_final: 0.8129 (tp30) REVERT: P 254 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: P 273 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8039 (mm-30) REVERT: P 293 ARG cc_start: 0.7876 (ttp-110) cc_final: 0.7069 (mtm-85) REVERT: S 31 HIS cc_start: 0.8653 (t-170) cc_final: 0.8418 (t-170) REVERT: S 39 TYR cc_start: 0.8988 (m-80) cc_final: 0.8744 (m-80) REVERT: S 42 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7527 (mtm110) REVERT: S 59 THR cc_start: 0.9221 (m) cc_final: 0.8896 (p) REVERT: S 61 GLU cc_start: 0.8213 (mm-30) cc_final: 0.8008 (mm-30) REVERT: S 73 ASN cc_start: 0.8862 (m110) cc_final: 0.8449 (t0) REVERT: T 68 ASP cc_start: 0.8164 (t0) cc_final: 0.7731 (t0) REVERT: T 120 LYS cc_start: 0.8805 (tttp) cc_final: 0.8342 (ttpp) REVERT: U 106 ASP cc_start: 0.8328 (m-30) cc_final: 0.7831 (m-30) REVERT: V 35 ARG cc_start: 0.8772 (mtp-110) cc_final: 0.8550 (mtp85) REVERT: V 82 THR cc_start: 0.9123 (t) cc_final: 0.8867 (p) REVERT: W 94 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8211 (mm-30) REVERT: W 123 ASP cc_start: 0.8523 (m-30) cc_final: 0.8244 (m-30) REVERT: X 35 ARG cc_start: 0.8630 (mtp85) cc_final: 0.8369 (mmm160) REVERT: X 71 THR cc_start: 0.9265 (m) cc_final: 0.8942 (t) REVERT: X 75 HIS cc_start: 0.8500 (t70) cc_final: 0.7848 (t70) REVERT: X 84 MET cc_start: 0.8859 (tpt) cc_final: 0.8647 (mmm) outliers start: 99 outliers final: 71 residues processed: 1473 average time/residue: 0.3127 time to fit residues: 712.5822 Evaluate side-chains 1503 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 1425 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 761 SER Chi-restraints excluded: chain A residue 768 GLN 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 918 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 65 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 255 MET Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 138 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 107 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 268 ILE 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 125 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 313 THR Chi-restraints excluded: chain G residue 377 ILE Chi-restraints excluded: chain G residue 397 ILE 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 108 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 264 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 258 SER Chi-restraints excluded: chain I residue 264 MET Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 236 LYS Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 272 VAL 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 J residue 379 ASP Chi-restraints excluded: chain P residue 254 GLU Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 76 GLN Chi-restraints excluded: chain W residue 83 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 263 optimal weight: 2.9990 chunk 419 optimal weight: 2.9990 chunk 473 optimal weight: 8.9990 chunk 482 optimal weight: 7.9990 chunk 245 optimal weight: 0.8980 chunk 147 optimal weight: 6.9990 chunk 143 optimal weight: 0.5980 chunk 270 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 69 optimal weight: 0.0770 chunk 92 optimal weight: 3.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 GLN C 92 ASN C 110 ASN C 385 ASN E 369 GLN E 420 ASN F 277 ASN G 169 GLN G 262 GLN ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 HIS X 27 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.101602 restraints weight = 69218.599| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.04 r_work: 0.3038 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 43534 Z= 0.237 Angle : 0.618 8.593 59700 Z= 0.326 Chirality : 0.046 0.362 6789 Planarity : 0.004 0.059 6883 Dihedral : 20.674 178.827 7705 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.29 % Allowed : 15.64 % Favored : 82.07 % 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: 1.44 (0.12), residues: 4719 helix: 1.70 (0.11), residues: 2350 sheet: 0.31 (0.20), residues: 657 loop : 0.32 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 414 TYR 0.020 0.002 TYR W 54 PHE 0.018 0.001 PHE R 65 TRP 0.083 0.002 TRP C 360 HIS 0.008 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.24 (43526) covalent geometry : angle 0.61757 / 0.33 (59691) hydrogen bonds : bond 0.04399 / 2.96 ( 2083) hydrogen bonds : angle 3.81634 / 2.76 ( 5758) metal coordination : bond 0.01666 / 0.67 ( 8) metal coordination : angle 2.17471 / 1.03 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1538 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1444 time to evaluate : 1.627 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: A 621 TYR cc_start: 0.7299 (p90) cc_final: 0.6945 (p90) REVERT: A 628 TRP cc_start: 0.8546 (t60) cc_final: 0.8236 (t60) REVERT: A 660 LEU cc_start: 0.8986 (mp) cc_final: 0.8724 (mp) REVERT: A 678 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8548 (m) REVERT: A 694 LYS cc_start: 0.8631 (mttt) cc_final: 0.8400 (mmtm) REVERT: A 704 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6985 (mt-10) REVERT: A 719 HIS cc_start: 0.8128 (m170) cc_final: 0.7664 (m-70) REVERT: A 747 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8119 (mm-30) REVERT: A 774 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8643 (m) REVERT: A 789 MET cc_start: 0.7724 (mmt) cc_final: 0.7338 (mmt) REVERT: A 833 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8102 (mm) REVERT: A 851 LYS cc_start: 0.8838 (mmmm) cc_final: 0.8615 (mmmm) REVERT: A 854 GLU cc_start: 0.8237 (pm20) cc_final: 0.7922 (pm20) REVERT: A 870 ASP cc_start: 0.8791 (t0) cc_final: 0.8549 (t0) REVERT: A 871 ASP cc_start: 0.8290 (t0) cc_final: 0.7960 (t70) REVERT: A 966 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7865 (mtp-110) REVERT: A 975 LEU cc_start: 0.8405 (mt) cc_final: 0.8159 (mt) REVERT: A 976 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 992 MET cc_start: 0.3185 (ttm) cc_final: 0.2449 (ttm) REVERT: A 1891 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7612 (tm-30) REVERT: A 1893 ARG cc_start: 0.8442 (mtt180) cc_final: 0.8025 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8534 (ptpp) cc_final: 0.8152 (ptpp) REVERT: A 1895 ARG cc_start: 0.8138 (ttp-170) cc_final: 0.7857 (ttp-170) REVERT: A 1896 GLN cc_start: 0.8216 (mt0) cc_final: 0.7940 (mt0) REVERT: A 1897 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7867 (ttp-170) REVERT: A 1936 ILE cc_start: 0.8887 (mm) cc_final: 0.8461 (mt) REVERT: A 1953 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 2013 GLU cc_start: 0.7889 (tp30) cc_final: 0.7179 (tp30) REVERT: A 2026 CYS cc_start: 0.8446 (m) cc_final: 0.8098 (m) REVERT: A 2094 ARG cc_start: 0.8258 (ptp90) cc_final: 0.8027 (ptp90) REVERT: A 2097 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8601 (mm-40) REVERT: A 2150 ASP cc_start: 0.8123 (m-30) cc_final: 0.7788 (m-30) REVERT: A 2169 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 2185 MET cc_start: 0.6727 (ttm) cc_final: 0.6466 (ttm) REVERT: A 2196 PHE cc_start: 0.8069 (m-80) cc_final: 0.7797 (m-80) REVERT: B 133 MET cc_start: 0.5989 (mmt) cc_final: 0.5522 (mmt) REVERT: B 174 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.8108 (mtm-85) REVERT: C 14 LYS cc_start: 0.8793 (mppt) cc_final: 0.8204 (mttp) REVERT: C 55 PHE cc_start: 0.7539 (t80) cc_final: 0.7156 (t80) REVERT: C 65 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8539 (tp) REVERT: C 71 GLN cc_start: 0.8259 (tp40) cc_final: 0.7731 (tp-100) REVERT: C 72 ARG cc_start: 0.8731 (tpp80) cc_final: 0.7990 (tpp80) REVERT: C 76 ASP cc_start: 0.8188 (m-30) cc_final: 0.7625 (m-30) REVERT: C 83 MET cc_start: 0.8434 (mmp) cc_final: 0.8181 (mmm) REVERT: C 97 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7687 (mp0) REVERT: C 103 THR cc_start: 0.8794 (m) cc_final: 0.8559 (p) REVERT: C 107 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7982 (mm-30) REVERT: C 111 GLU cc_start: 0.8125 (tm-30) cc_final: 0.6956 (tm-30) REVERT: C 115 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7846 (mt-10) REVERT: C 135 TYR cc_start: 0.8866 (t80) cc_final: 0.8573 (t80) REVERT: C 142 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7800 (mp0) REVERT: C 149 ASP cc_start: 0.8434 (t0) cc_final: 0.8165 (t0) REVERT: C 196 MET cc_start: 0.8163 (tpp) cc_final: 0.7860 (mmm) REVERT: C 204 GLN cc_start: 0.8782 (tp40) cc_final: 0.8170 (tp-100) REVERT: C 208 ASP cc_start: 0.8072 (m-30) cc_final: 0.7643 (m-30) REVERT: C 229 GLU cc_start: 0.7905 (pm20) cc_final: 0.7413 (pm20) REVERT: C 230 ASN cc_start: 0.8579 (t0) cc_final: 0.8239 (t0) REVERT: C 248 PHE cc_start: 0.8614 (p90) cc_final: 0.8263 (p90) REVERT: C 250 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8577 (mtpp) REVERT: C 372 PHE cc_start: 0.8514 (t80) cc_final: 0.8255 (t80) REVERT: D 92 ASN cc_start: 0.8775 (t0) cc_final: 0.8442 (t0) REVERT: E 15 ILE cc_start: 0.8599 (mm) cc_final: 0.8385 (mt) REVERT: E 22 LYS cc_start: 0.8511 (mmtp) cc_final: 0.8272 (mmtp) REVERT: E 28 GLU cc_start: 0.7838 (mp0) cc_final: 0.7392 (mp0) REVERT: E 81 LEU cc_start: 0.8442 (mt) cc_final: 0.8179 (mp) REVERT: E 85 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8517 (mm-40) REVERT: E 128 LYS cc_start: 0.8010 (mmtm) cc_final: 0.7795 (mmtm) REVERT: E 135 VAL cc_start: 0.8326 (t) cc_final: 0.8122 (p) REVERT: E 165 LYS cc_start: 0.7886 (mmtt) cc_final: 0.7657 (mmtt) REVERT: E 168 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8206 (ttmt) REVERT: E 178 GLU cc_start: 0.7939 (tt0) cc_final: 0.7637 (tt0) REVERT: E 182 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7707 (mtmt) REVERT: E 183 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7744 (mm-30) REVERT: E 184 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7442 (mtm-85) REVERT: E 185 VAL cc_start: 0.8326 (t) cc_final: 0.8116 (m) REVERT: E 194 GLU cc_start: 0.7775 (tt0) cc_final: 0.7487 (tt0) REVERT: E 212 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7478 (mm-30) REVERT: E 214 ASP cc_start: 0.8078 (m-30) cc_final: 0.7780 (m-30) REVERT: E 236 GLN cc_start: 0.8594 (mm110) cc_final: 0.8318 (mm110) REVERT: E 285 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7850 (ttmm) REVERT: E 286 TYR cc_start: 0.8365 (m-10) cc_final: 0.8051 (m-80) REVERT: E 295 VAL cc_start: 0.8652 (t) cc_final: 0.8354 (m) REVERT: E 352 LEU cc_start: 0.8371 (mt) cc_final: 0.8113 (mm) REVERT: E 370 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8165 (mt-10) REVERT: E 389 GLU cc_start: 0.7962 (tt0) cc_final: 0.7689 (tt0) REVERT: E 415 LEU cc_start: 0.8854 (mt) cc_final: 0.8631 (mm) REVERT: E 418 LYS cc_start: 0.8271 (ttmm) cc_final: 0.8065 (ttmm) REVERT: E 439 ASP cc_start: 0.7603 (p0) cc_final: 0.7210 (p0) REVERT: E 445 LYS cc_start: 0.7763 (mmtp) cc_final: 0.7525 (mmtp) REVERT: E 446 ILE cc_start: 0.8325 (mm) cc_final: 0.7981 (mt) REVERT: F 40 ARG cc_start: 0.8202 (mtt90) cc_final: 0.7859 (mtt90) REVERT: F 71 ARG cc_start: 0.7836 (mmt90) cc_final: 0.7559 (mmm-85) REVERT: F 112 GLU cc_start: 0.7769 (tp30) cc_final: 0.7493 (tp30) REVERT: F 117 GLU cc_start: 0.8210 (tp30) cc_final: 0.7606 (mm-30) REVERT: F 142 VAL cc_start: 0.8228 (t) cc_final: 0.8014 (m) REVERT: F 145 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8023 (pt) REVERT: F 160 LYS cc_start: 0.8317 (ttpt) cc_final: 0.7906 (mtpt) REVERT: F 168 MET cc_start: 0.7480 (mtp) cc_final: 0.7090 (mtp) REVERT: F 170 THR cc_start: 0.8180 (m) cc_final: 0.7938 (t) REVERT: F 176 THR cc_start: 0.8136 (m) cc_final: 0.7914 (t) REVERT: F 181 SER cc_start: 0.8721 (m) cc_final: 0.8316 (p) REVERT: F 183 THR cc_start: 0.8637 (m) cc_final: 0.8332 (p) REVERT: F 192 VAL cc_start: 0.8195 (t) cc_final: 0.7665 (p) REVERT: F 197 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7189 (mtpt) REVERT: F 233 GLN cc_start: 0.7842 (tp40) cc_final: 0.7038 (tp40) REVERT: F 238 VAL cc_start: 0.8592 (t) cc_final: 0.8233 (m) REVERT: F 246 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7295 (mt-10) REVERT: F 248 ASP cc_start: 0.7731 (m-30) cc_final: 0.7478 (m-30) REVERT: F 267 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7285 (mt-10) REVERT: F 269 LYS cc_start: 0.8288 (mmtp) cc_final: 0.7987 (mmtp) REVERT: F 271 GLU cc_start: 0.7912 (mp0) cc_final: 0.7706 (mp0) REVERT: F 274 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7689 (mm-30) REVERT: F 286 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7926 (mt-10) REVERT: F 303 MET cc_start: 0.8698 (mmm) cc_final: 0.8400 (mmp) REVERT: F 317 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7384 (mt-10) REVERT: F 392 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7878 (ttp-170) REVERT: F 441 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7549 (mm-40) REVERT: F 445 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7612 (mm-30) REVERT: G 15 ILE cc_start: 0.8807 (mt) cc_final: 0.8569 (mm) REVERT: G 61 MET cc_start: 0.8729 (mmm) cc_final: 0.8083 (mmm) REVERT: G 90 LYS cc_start: 0.8613 (tptm) cc_final: 0.8017 (tptm) REVERT: G 125 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7902 (mmmt) REVERT: G 126 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7076 (mt-10) REVERT: G 128 LYS cc_start: 0.8392 (tttt) cc_final: 0.7936 (tttt) REVERT: G 134 GLU cc_start: 0.7546 (tt0) cc_final: 0.7064 (tm-30) REVERT: G 137 GLU cc_start: 0.7784 (tt0) cc_final: 0.7413 (tp30) REVERT: G 147 MET cc_start: 0.6170 (mtp) cc_final: 0.5586 (mtp) REVERT: G 158 ILE cc_start: 0.8500 (mt) cc_final: 0.8248 (mm) REVERT: G 162 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8175 (ttmm) REVERT: G 171 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8301 (mtpt) REVERT: G 178 GLU cc_start: 0.8201 (tt0) cc_final: 0.7584 (tt0) REVERT: G 186 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7445 (mm-30) REVERT: G 189 ASP cc_start: 0.8030 (m-30) cc_final: 0.7814 (m-30) REVERT: G 193 ILE cc_start: 0.8702 (mt) cc_final: 0.8357 (mm) REVERT: G 209 TYR cc_start: 0.8533 (m-80) cc_final: 0.8155 (m-10) REVERT: G 212 GLU cc_start: 0.7879 (pm20) cc_final: 0.7666 (pm20) REVERT: G 225 LYS cc_start: 0.8306 (mmpt) cc_final: 0.7809 (mmpt) REVERT: G 227 ASP cc_start: 0.7749 (t0) cc_final: 0.7434 (t0) REVERT: G 233 GLU cc_start: 0.7396 (tp30) cc_final: 0.6766 (tp30) REVERT: G 244 ASP cc_start: 0.7490 (m-30) cc_final: 0.7267 (m-30) REVERT: G 247 ASN cc_start: 0.8392 (m-40) cc_final: 0.8147 (m110) REVERT: G 249 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7548 (ttt-90) REVERT: G 281 LYS cc_start: 0.8383 (mtmm) cc_final: 0.8081 (mtmm) REVERT: G 302 ASP cc_start: 0.8047 (t0) cc_final: 0.7210 (t0) REVERT: G 303 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7298 (mp0) REVERT: G 323 ILE cc_start: 0.8734 (mm) cc_final: 0.8384 (mt) REVERT: G 422 LYS cc_start: 0.8303 (mttp) cc_final: 0.8007 (mptt) REVERT: G 428 GLU cc_start: 0.8347 (mp0) cc_final: 0.7895 (mp0) REVERT: G 438 TYR cc_start: 0.8466 (m-80) cc_final: 0.8248 (m-10) REVERT: H 18 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7478 (mtp85) REVERT: H 20 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7739 (mt-10) REVERT: H 38 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7920 (mm-30) REVERT: H 83 LYS cc_start: 0.8800 (mtmm) cc_final: 0.8454 (mtmm) REVERT: H 88 MET cc_start: 0.7934 (mmp) cc_final: 0.7616 (mmm) REVERT: H 113 MET cc_start: 0.8275 (ptp) cc_final: 0.7738 (ptp) REVERT: H 132 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8101 (ttmm) REVERT: H 135 THR cc_start: 0.7939 (m) cc_final: 0.7710 (p) REVERT: H 139 GLU cc_start: 0.7549 (tt0) cc_final: 0.7202 (tm-30) REVERT: H 144 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7553 (mm-30) REVERT: H 164 LYS cc_start: 0.8416 (pttt) cc_final: 0.7937 (pttm) REVERT: H 201 LYS cc_start: 0.8410 (ptmt) cc_final: 0.8185 (ptmt) REVERT: H 204 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8590 (mtpt) REVERT: H 211 ARG cc_start: 0.8468 (ttt180) cc_final: 0.8188 (ttt180) REVERT: H 214 ASP cc_start: 0.7651 (p0) cc_final: 0.7314 (p0) REVERT: H 238 VAL cc_start: 0.8070 (t) cc_final: 0.7762 (p) REVERT: H 253 ARG cc_start: 0.8223 (ptm160) cc_final: 0.7955 (ptm-80) REVERT: H 267 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7644 (tt0) REVERT: H 273 ARG cc_start: 0.8353 (mtt90) cc_final: 0.7843 (mtt90) REVERT: H 274 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7658 (mt-10) REVERT: H 275 GLN cc_start: 0.8258 (mm110) cc_final: 0.7941 (mm-40) REVERT: H 277 ASN cc_start: 0.8505 (m-40) cc_final: 0.8136 (m110) REVERT: H 279 LYS cc_start: 0.8374 (tppt) cc_final: 0.8005 (tptp) REVERT: H 284 ARG cc_start: 0.8159 (ttt90) cc_final: 0.7946 (ptm-80) REVERT: H 307 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7597 (mm-30) REVERT: H 313 ASN cc_start: 0.8055 (m-40) cc_final: 0.7708 (m-40) REVERT: H 314 ARG cc_start: 0.7460 (mmt180) cc_final: 0.7001 (mmt180) REVERT: H 317 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7687 (mt-10) REVERT: H 339 SER cc_start: 0.8744 (p) cc_final: 0.8490 (m) REVERT: H 404 GLN cc_start: 0.8313 (mt0) cc_final: 0.8015 (mt0) REVERT: I 61 MET cc_start: 0.8199 (mmm) cc_final: 0.7822 (mmm) REVERT: I 137 GLU cc_start: 0.7854 (tt0) cc_final: 0.7585 (tt0) REVERT: I 139 THR cc_start: 0.8742 (m) cc_final: 0.8340 (p) REVERT: I 171 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8509 (tttt) REVERT: I 216 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7784 (tp30) REVERT: I 244 ASP cc_start: 0.7610 (m-30) cc_final: 0.7291 (t0) REVERT: I 259 MET cc_start: 0.8107 (mtp) cc_final: 0.7768 (mtp) REVERT: I 263 LEU cc_start: 0.8538 (mt) cc_final: 0.8336 (mp) REVERT: I 267 LYS cc_start: 0.8303 (ttpp) cc_final: 0.8009 (tttp) REVERT: I 281 LYS cc_start: 0.8648 (mttt) cc_final: 0.8409 (mtmt) REVERT: I 302 ASP cc_start: 0.8390 (t0) cc_final: 0.7920 (t0) REVERT: I 322 SER cc_start: 0.8510 (p) cc_final: 0.8241 (t) REVERT: I 404 ARG cc_start: 0.7782 (mtt90) cc_final: 0.7322 (mtt180) REVERT: I 438 TYR cc_start: 0.8443 (m-80) cc_final: 0.7927 (m-80) REVERT: I 439 ASP cc_start: 0.8184 (p0) cc_final: 0.7841 (p0) REVERT: I 441 LYS cc_start: 0.8524 (mttm) cc_final: 0.8050 (mtmm) REVERT: I 445 LYS cc_start: 0.8222 (tppt) cc_final: 0.7259 (tppt) REVERT: J 38 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7741 (tp30) REVERT: J 90 MET cc_start: 0.8561 (mtm) cc_final: 0.8314 (mtp) REVERT: J 117 GLU cc_start: 0.7689 (tp30) cc_final: 0.7431 (tp30) REVERT: J 133 GLU cc_start: 0.7714 (pt0) cc_final: 0.7466 (pt0) REVERT: J 142 VAL cc_start: 0.8732 (t) cc_final: 0.8454 (m) REVERT: J 144 GLU cc_start: 0.8159 (tt0) cc_final: 0.7904 (tt0) REVERT: J 164 LYS cc_start: 0.8456 (pttt) cc_final: 0.8119 (ptmm) REVERT: J 179 ILE cc_start: 0.8403 (mt) cc_final: 0.8156 (mt) REVERT: J 180 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7310 (mt-10) REVERT: J 183 THR cc_start: 0.8221 (m) cc_final: 0.7942 (p) REVERT: J 192 VAL cc_start: 0.8613 (t) cc_final: 0.8212 (p) REVERT: J 225 VAL cc_start: 0.8437 (t) cc_final: 0.8181 (p) REVERT: J 267 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7588 (mt-10) REVERT: J 270 SER cc_start: 0.8454 (p) cc_final: 0.8105 (t) REVERT: J 314 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7806 (mmt180) REVERT: J 352 ASP cc_start: 0.7748 (m-30) cc_final: 0.7411 (t0) REVERT: J 377 GLU cc_start: 0.7774 (tp30) cc_final: 0.7356 (tp30) REVERT: J 378 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7633 (mt-10) REVERT: J 430 TYR cc_start: 0.8717 (t80) cc_final: 0.8469 (t80) REVERT: J 436 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6681 (tm-30) REVERT: P 247 ASP cc_start: 0.8551 (t0) cc_final: 0.8286 (t0) REVERT: P 250 SER cc_start: 0.8992 (m) cc_final: 0.8341 (p) REVERT: P 253 GLU cc_start: 0.8520 (tp30) cc_final: 0.8144 (tp30) REVERT: P 254 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7965 (mp0) REVERT: P 273 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8029 (mm-30) REVERT: S 31 HIS cc_start: 0.8658 (t-170) cc_final: 0.8410 (t-170) REVERT: S 39 TYR cc_start: 0.9009 (m-80) cc_final: 0.8776 (m-80) REVERT: S 42 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7545 (mtm110) REVERT: S 59 THR cc_start: 0.9244 (m) cc_final: 0.8911 (p) REVERT: S 61 GLU cc_start: 0.8257 (mm-30) cc_final: 0.8055 (mm-30) REVERT: S 115 LEU cc_start: 0.8838 (mt) cc_final: 0.8581 (mp) REVERT: T 68 ASP cc_start: 0.8177 (t0) cc_final: 0.7748 (t0) REVERT: T 76 GLU cc_start: 0.8416 (tp30) cc_final: 0.7965 (tp30) REVERT: T 120 LYS cc_start: 0.8828 (tttp) cc_final: 0.8367 (ttpp) REVERT: U 106 ASP cc_start: 0.8318 (m-30) cc_final: 0.7823 (m-30) REVERT: V 35 ARG cc_start: 0.8761 (mtp-110) cc_final: 0.8233 (mtp85) REVERT: V 88 TYR cc_start: 0.8239 (m-10) cc_final: 0.8028 (m-80) REVERT: W 94 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8182 (mm-30) REVERT: W 123 ASP cc_start: 0.8527 (m-30) cc_final: 0.8288 (m-30) REVERT: X 71 THR cc_start: 0.9252 (m) cc_final: 0.8948 (t) REVERT: X 75 HIS cc_start: 0.8547 (t70) cc_final: 0.8061 (t70) outliers start: 94 outliers final: 67 residues processed: 1464 average time/residue: 0.3098 time to fit residues: 703.9636 Evaluate side-chains 1503 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1427 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL 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 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 833 LEU Chi-restraints excluded: chain A residue 2019 ARG Chi-restraints excluded: chain A residue 2062 VAL Chi-restraints excluded: chain A residue 2143 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 268 LYS Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 107 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 348 ILE 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 125 LYS Chi-restraints excluded: chain G residue 211 THR Chi-restraints excluded: chain G residue 257 LEU Chi-restraints excluded: chain G residue 353 ASP Chi-restraints excluded: chain G residue 377 ILE Chi-restraints excluded: chain G residue 397 ILE 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 108 ILE Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 264 ASP Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 246 GLU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 299 ASP Chi-restraints excluded: chain J residue 313 ASN 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 272 ILE Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 122 THR Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 76 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 455 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 393 optimal weight: 1.9990 chunk 293 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 252 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 233 optimal weight: 3.9990 chunk 366 optimal weight: 0.9990 chunk 294 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 GLN ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN E 380 GLN E 420 ASN F 277 ASN ** I 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 262 GLN J 78 GLN T 49 HIS X 27 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.127856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.102601 restraints weight = 68993.060| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.05 r_work: 0.3052 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43534 Z= 0.161 Angle : 0.599 10.769 59700 Z= 0.314 Chirality : 0.044 0.360 6789 Planarity : 0.004 0.058 6883 Dihedral : 20.662 178.621 7705 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.12 % Allowed : 16.64 % Favored : 81.24 % 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: 1.50 (0.12), residues: 4719 helix: 1.76 (0.11), residues: 2349 sheet: 0.31 (0.20), residues: 645 loop : 0.35 (0.15), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 78 TYR 0.037 0.001 TYR C 382 PHE 0.018 0.001 PHE R 65 TRP 0.110 0.002 TRP C 360 HIS 0.008 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (43526) covalent geometry : angle 0.59869 / 0.31 (59691) hydrogen bonds : bond 0.04019 / 2.70 ( 2083) hydrogen bonds : angle 3.73465 / 2.70 ( 5758) metal coordination : bond 0.01201 / 0.43 ( 8) metal coordination : angle 1.86299 / 0.87 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1516 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 1429 time to evaluate : 1.375 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 628 TRP cc_start: 0.8504 (t60) cc_final: 0.8237 (t60) REVERT: A 660 LEU cc_start: 0.8979 (mp) cc_final: 0.8727 (mp) REVERT: A 678 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8554 (m) REVERT: A 704 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6906 (mt-10) REVERT: A 719 HIS cc_start: 0.8143 (m170) cc_final: 0.7687 (m-70) REVERT: A 747 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 789 MET cc_start: 0.7690 (mmt) cc_final: 0.7340 (mmm) REVERT: A 833 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7991 (mm) REVERT: A 854 GLU cc_start: 0.8261 (pm20) cc_final: 0.7951 (pm20) REVERT: A 864 ARG cc_start: 0.8528 (mtp85) cc_final: 0.8283 (mtp85) REVERT: A 870 ASP cc_start: 0.8690 (t0) cc_final: 0.8444 (t0) REVERT: A 871 ASP cc_start: 0.8323 (t0) cc_final: 0.7968 (t70) REVERT: A 918 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8363 (m) REVERT: A 966 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7850 (mtp-110) REVERT: A 975 LEU cc_start: 0.8409 (mt) cc_final: 0.8162 (mt) REVERT: A 976 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7626 (mt-10) REVERT: A 992 MET cc_start: 0.3213 (ttm) cc_final: 0.2472 (ttm) REVERT: A 1893 ARG cc_start: 0.8387 (mtt180) cc_final: 0.7969 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8520 (ptpp) cc_final: 0.8155 (ptpp) REVERT: A 1895 ARG cc_start: 0.8107 (ttp-170) cc_final: 0.7846 (ttp-170) REVERT: A 1896 GLN cc_start: 0.8219 (mt0) cc_final: 0.7934 (mt0) REVERT: A 1897 ARG cc_start: 0.8254 (ttp-170) cc_final: 0.7907 (ttp-170) REVERT: A 1936 ILE cc_start: 0.8890 (mm) cc_final: 0.8471 (mt) REVERT: A 1953 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 2013 GLU cc_start: 0.7947 (tp30) cc_final: 0.7233 (tp30) REVERT: A 2026 CYS cc_start: 0.8457 (m) cc_final: 0.8111 (m) REVERT: A 2094 ARG cc_start: 0.8220 (ptp90) cc_final: 0.7702 (mtm-85) REVERT: A 2096 GLU cc_start: 0.8182 (mp0) cc_final: 0.7802 (pm20) REVERT: A 2102 MET cc_start: 0.8595 (tpp) cc_final: 0.8354 (mmm) REVERT: A 2150 ASP cc_start: 0.8070 (m-30) cc_final: 0.7734 (m-30) REVERT: A 2185 MET cc_start: 0.6723 (ttm) cc_final: 0.6459 (ttm) REVERT: B 133 MET cc_start: 0.5994 (mmt) cc_final: 0.5518 (mmt) REVERT: B 174 ARG cc_start: 0.8285 (mtm-85) cc_final: 0.8055 (mtm-85) REVERT: C 2 THR cc_start: 0.7869 (t) cc_final: 0.7554 (m) REVERT: C 14 LYS cc_start: 0.8781 (mppt) cc_final: 0.8164 (mttp) REVERT: C 19 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8318 (p90) REVERT: C 55 PHE cc_start: 0.7489 (t80) cc_final: 0.7115 (t80) REVERT: C 65 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8541 (tp) REVERT: C 72 ARG cc_start: 0.8687 (tpp80) cc_final: 0.8100 (tpp80) REVERT: C 76 ASP cc_start: 0.8190 (m-30) cc_final: 0.7613 (m-30) REVERT: C 83 MET cc_start: 0.8395 (mmp) cc_final: 0.8131 (mmm) REVERT: C 90 ASP cc_start: 0.8278 (t0) cc_final: 0.7555 (t0) REVERT: C 97 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7819 (mm-30) REVERT: C 103 THR cc_start: 0.8792 (m) cc_final: 0.8530 (p) REVERT: C 107 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7965 (mm-30) REVERT: C 111 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7800 (tm-30) REVERT: C 135 TYR cc_start: 0.8877 (t80) cc_final: 0.8571 (t80) REVERT: C 142 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7694 (mp0) REVERT: C 149 ASP cc_start: 0.8431 (t0) cc_final: 0.8137 (t0) REVERT: C 196 MET cc_start: 0.8134 (tpp) cc_final: 0.7821 (mmm) REVERT: C 204 GLN cc_start: 0.8763 (tp40) cc_final: 0.8150 (tp-100) REVERT: C 208 ASP cc_start: 0.8055 (m-30) cc_final: 0.7617 (m-30) REVERT: C 226 LYS cc_start: 0.7707 (mptt) cc_final: 0.7492 (mptt) REVERT: C 230 ASN cc_start: 0.8571 (t0) cc_final: 0.8234 (t0) REVERT: C 248 PHE cc_start: 0.8616 (p90) cc_final: 0.8285 (p90) REVERT: C 250 LYS cc_start: 0.8872 (mtpp) cc_final: 0.8568 (mtpp) REVERT: C 382 TYR cc_start: 0.8073 (t80) cc_final: 0.7809 (t80) REVERT: D 91 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8334 (tp40) REVERT: D 92 ASN cc_start: 0.8652 (t0) cc_final: 0.8288 (t0) REVERT: E 15 ILE cc_start: 0.8672 (mm) cc_final: 0.8457 (mt) REVERT: E 22 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8249 (mmtp) REVERT: E 28 GLU cc_start: 0.7853 (mp0) cc_final: 0.7362 (mp0) REVERT: E 64 ARG cc_start: 0.8345 (mtp85) cc_final: 0.7953 (mmt-90) REVERT: E 81 LEU cc_start: 0.8463 (mt) cc_final: 0.8193 (mp) REVERT: E 105 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8182 (mt-10) REVERT: E 128 LYS cc_start: 0.8040 (mmtm) cc_final: 0.7833 (mmtt) REVERT: E 138 LEU cc_start: 0.8434 (mp) cc_final: 0.8230 (mp) REVERT: E 165 LYS cc_start: 0.7840 (mmtt) cc_final: 0.7621 (mmtt) REVERT: E 168 LYS cc_start: 0.8421 (ttmt) cc_final: 0.8140 (ttmt) REVERT: E 178 GLU cc_start: 0.7912 (tt0) cc_final: 0.7617 (tt0) REVERT: E 182 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7707 (mtmt) REVERT: E 183 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7804 (mm-30) REVERT: E 184 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7400 (mtm-85) REVERT: E 194 GLU cc_start: 0.7810 (tt0) cc_final: 0.7577 (tt0) REVERT: E 212 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7448 (mm-30) REVERT: E 214 ASP cc_start: 0.8064 (m-30) cc_final: 0.7784 (m-30) REVERT: E 236 GLN cc_start: 0.8566 (mm110) cc_final: 0.8311 (mm110) REVERT: E 285 LYS cc_start: 0.8068 (ttmm) cc_final: 0.7826 (ttmm) REVERT: E 286 TYR cc_start: 0.8403 (m-10) cc_final: 0.8075 (m-80) REVERT: E 295 VAL cc_start: 0.8650 (t) cc_final: 0.8395 (m) REVERT: E 352 LEU cc_start: 0.8390 (mt) cc_final: 0.8140 (mm) REVERT: E 356 ASP cc_start: 0.8159 (t0) cc_final: 0.7924 (t0) REVERT: E 370 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8170 (mt-10) REVERT: E 389 GLU cc_start: 0.7939 (tt0) cc_final: 0.7674 (tt0) REVERT: E 415 LEU cc_start: 0.8824 (mt) cc_final: 0.8614 (mm) REVERT: E 418 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8089 (ttmm) REVERT: E 445 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7518 (mmtp) REVERT: E 446 ILE cc_start: 0.8321 (mm) cc_final: 0.7976 (mt) REVERT: F 40 ARG cc_start: 0.8134 (mtt90) cc_final: 0.7766 (mtt90) REVERT: F 71 ARG cc_start: 0.7799 (mmt90) cc_final: 0.7529 (mmm-85) REVERT: F 112 GLU cc_start: 0.7790 (tp30) cc_final: 0.7514 (tp30) REVERT: F 117 GLU cc_start: 0.8211 (tp30) cc_final: 0.7605 (mm-30) REVERT: F 142 VAL cc_start: 0.8228 (t) cc_final: 0.7935 (m) REVERT: F 160 LYS cc_start: 0.8309 (ttpt) cc_final: 0.7889 (mtpt) REVERT: F 168 MET cc_start: 0.7459 (mtp) cc_final: 0.7110 (mtp) REVERT: F 170 THR cc_start: 0.8181 (m) cc_final: 0.7937 (t) REVERT: F 176 THR cc_start: 0.8137 (m) cc_final: 0.7921 (t) REVERT: F 181 SER cc_start: 0.8728 (m) cc_final: 0.8297 (p) REVERT: F 182 LEU cc_start: 0.8930 (mt) cc_final: 0.8664 (mm) REVERT: F 183 THR cc_start: 0.8633 (m) cc_final: 0.8330 (p) REVERT: F 192 VAL cc_start: 0.8196 (t) cc_final: 0.7667 (p) REVERT: F 197 LYS cc_start: 0.7674 (mtpt) cc_final: 0.7167 (mtpt) REVERT: F 233 GLN cc_start: 0.7828 (tp40) cc_final: 0.7184 (tp40) REVERT: F 238 VAL cc_start: 0.8616 (t) cc_final: 0.8267 (m) REVERT: F 246 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7303 (mt-10) REVERT: F 248 ASP cc_start: 0.7752 (m-30) cc_final: 0.7483 (m-30) REVERT: F 267 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7184 (mt-10) REVERT: F 269 LYS cc_start: 0.8237 (mmtp) cc_final: 0.7919 (mmtp) REVERT: F 274 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7715 (mm-30) REVERT: F 285 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7385 (mp0) REVERT: F 286 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7889 (mt-10) REVERT: F 303 MET cc_start: 0.8700 (mmm) cc_final: 0.8382 (mmp) REVERT: F 317 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7384 (mt-10) REVERT: F 392 ARG cc_start: 0.8121 (ttp-110) cc_final: 0.7856 (ttp-170) REVERT: F 441 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7539 (mm-40) REVERT: F 445 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7648 (mm-30) REVERT: G 15 ILE cc_start: 0.8789 (mt) cc_final: 0.8579 (mm) REVERT: G 61 MET cc_start: 0.8705 (mmm) cc_final: 0.8068 (mmm) REVERT: G 90 LYS cc_start: 0.8608 (tptm) cc_final: 0.8022 (tptm) REVERT: G 125 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7906 (mmmt) REVERT: G 126 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7129 (mt-10) REVERT: G 128 LYS cc_start: 0.8378 (tttt) cc_final: 0.7908 (tttt) REVERT: G 134 GLU cc_start: 0.7532 (tt0) cc_final: 0.7088 (tm-30) REVERT: G 137 GLU cc_start: 0.7753 (tt0) cc_final: 0.7384 (tp30) REVERT: G 147 MET cc_start: 0.6436 (mtp) cc_final: 0.5934 (mtp) REVERT: G 158 ILE cc_start: 0.8518 (mt) cc_final: 0.8248 (mm) REVERT: G 162 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8156 (ttmm) REVERT: G 171 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8269 (mtpt) REVERT: G 178 GLU cc_start: 0.8168 (tt0) cc_final: 0.7543 (tt0) REVERT: G 186 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7454 (mm-30) REVERT: G 189 ASP cc_start: 0.8040 (m-30) cc_final: 0.7838 (m-30) REVERT: G 193 ILE cc_start: 0.8679 (mt) cc_final: 0.8333 (mm) REVERT: G 209 TYR cc_start: 0.8507 (m-80) cc_final: 0.8195 (m-10) REVERT: G 225 LYS cc_start: 0.8298 (mmpt) cc_final: 0.7811 (mmpt) REVERT: G 227 ASP cc_start: 0.7736 (t0) cc_final: 0.7436 (t0) REVERT: G 233 GLU cc_start: 0.7475 (tp30) cc_final: 0.6895 (tp30) REVERT: G 247 ASN cc_start: 0.8389 (m-40) cc_final: 0.8145 (m110) REVERT: G 249 ARG cc_start: 0.7851 (ttt-90) cc_final: 0.7541 (ttt-90) REVERT: G 281 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8122 (mtmm) REVERT: G 303 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7608 (mp0) REVERT: G 323 ILE cc_start: 0.8759 (mm) cc_final: 0.8425 (mt) REVERT: G 376 LYS cc_start: 0.8751 (tptt) cc_final: 0.8517 (tptm) REVERT: G 422 LYS cc_start: 0.8253 (mttp) cc_final: 0.8000 (mptt) REVERT: G 428 GLU cc_start: 0.8307 (mp0) cc_final: 0.7865 (mp0) REVERT: H 18 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7487 (mtp85) REVERT: H 20 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7689 (mt-10) REVERT: H 38 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7897 (mm-30) REVERT: H 83 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8449 (mtmm) REVERT: H 88 MET cc_start: 0.8005 (mmp) cc_final: 0.7663 (mmm) REVERT: H 111 LEU cc_start: 0.8844 (mp) cc_final: 0.8632 (mt) REVERT: H 113 MET cc_start: 0.8213 (ptp) cc_final: 0.7657 (ptp) REVERT: H 132 LYS cc_start: 0.8390 (ttmm) cc_final: 0.8078 (ttmm) REVERT: H 135 THR cc_start: 0.7896 (m) cc_final: 0.7685 (p) REVERT: H 144 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7506 (mm-30) REVERT: H 164 LYS cc_start: 0.8408 (pttt) cc_final: 0.7926 (pttm) REVERT: H 201 LYS cc_start: 0.8390 (ptmt) cc_final: 0.8166 (ptmt) REVERT: H 204 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8590 (mtpt) REVERT: H 211 ARG cc_start: 0.8459 (ttt180) cc_final: 0.8176 (ttt180) REVERT: H 214 ASP cc_start: 0.7658 (p0) cc_final: 0.7313 (p0) REVERT: H 238 VAL cc_start: 0.8089 (t) cc_final: 0.7781 (p) REVERT: H 246 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7629 (mt-10) REVERT: H 253 ARG cc_start: 0.8248 (ptm160) cc_final: 0.7985 (ptm-80) REVERT: H 267 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7652 (tt0) REVERT: H 273 ARG cc_start: 0.8315 (mtt90) cc_final: 0.7810 (mtt90) REVERT: H 274 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7658 (mt-10) REVERT: H 275 GLN cc_start: 0.8261 (mm110) cc_final: 0.7959 (mm-40) REVERT: H 277 ASN cc_start: 0.8482 (m-40) cc_final: 0.8112 (m110) REVERT: H 279 LYS cc_start: 0.8368 (tppt) cc_final: 0.7993 (tptp) REVERT: H 284 ARG cc_start: 0.8147 (ttt90) cc_final: 0.7922 (ptm-80) REVERT: H 313 ASN cc_start: 0.8056 (m-40) cc_final: 0.7716 (m-40) REVERT: H 314 ARG cc_start: 0.7472 (mmt180) cc_final: 0.7148 (mmt180) REVERT: H 317 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7657 (mt-10) REVERT: H 339 SER cc_start: 0.8726 (p) cc_final: 0.8476 (m) REVERT: H 404 GLN cc_start: 0.8300 (mt0) cc_final: 0.8063 (mt0) REVERT: I 61 MET cc_start: 0.8174 (mmm) cc_final: 0.7777 (mmm) REVERT: I 137 GLU cc_start: 0.7849 (tt0) cc_final: 0.7587 (tt0) REVERT: I 139 THR cc_start: 0.8690 (m) cc_final: 0.8301 (p) REVERT: I 171 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8511 (tttt) REVERT: I 216 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7757 (tp30) REVERT: I 244 ASP cc_start: 0.7577 (m-30) cc_final: 0.7205 (t0) REVERT: I 249 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7893 (mtp85) REVERT: I 259 MET cc_start: 0.8109 (mtp) cc_final: 0.7783 (mtp) REVERT: I 264 MET cc_start: 0.8057 (mtp) cc_final: 0.7664 (mtp) REVERT: I 267 LYS cc_start: 0.8289 (ttpp) cc_final: 0.8008 (tttp) REVERT: I 281 LYS cc_start: 0.8651 (mttt) cc_final: 0.8361 (mtmt) REVERT: I 302 ASP cc_start: 0.8371 (t0) cc_final: 0.7869 (t0) REVERT: I 322 SER cc_start: 0.8505 (p) cc_final: 0.8214 (t) REVERT: I 404 ARG cc_start: 0.7768 (mtt90) cc_final: 0.7260 (mtt180) REVERT: I 438 TYR cc_start: 0.8421 (m-80) cc_final: 0.7917 (m-80) REVERT: I 439 ASP cc_start: 0.8171 (p0) cc_final: 0.7827 (p0) REVERT: I 441 LYS cc_start: 0.8474 (mttm) cc_final: 0.8003 (mtmm) REVERT: J 71 ARG cc_start: 0.8296 (tpp80) cc_final: 0.8089 (tpp-160) REVERT: J 90 MET cc_start: 0.8504 (mtm) cc_final: 0.8258 (mtp) REVERT: J 92 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7909 (mm-40) REVERT: J 117 GLU cc_start: 0.7709 (tp30) cc_final: 0.7348 (tp30) REVERT: J 133 GLU cc_start: 0.7728 (pt0) cc_final: 0.7486 (pt0) REVERT: J 142 VAL cc_start: 0.8737 (t) cc_final: 0.8482 (m) REVERT: J 144 GLU cc_start: 0.8131 (tt0) cc_final: 0.7881 (tt0) REVERT: J 164 LYS cc_start: 0.8444 (pttt) cc_final: 0.8115 (ptmm) REVERT: J 179 ILE cc_start: 0.8420 (mt) cc_final: 0.8155 (mt) REVERT: J 180 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7355 (mt-10) REVERT: J 183 THR cc_start: 0.8202 (m) cc_final: 0.7927 (p) REVERT: J 192 VAL cc_start: 0.8618 (t) cc_final: 0.8206 (p) REVERT: J 225 VAL cc_start: 0.8447 (t) cc_final: 0.8189 (p) REVERT: J 267 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7382 (mt-10) REVERT: J 270 SER cc_start: 0.8461 (p) cc_final: 0.8112 (t) REVERT: J 314 ARG cc_start: 0.8083 (mmt180) cc_final: 0.7766 (mmt180) REVERT: J 334 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7721 (ttp80) REVERT: J 352 ASP cc_start: 0.7727 (m-30) cc_final: 0.7399 (t0) REVERT: J 377 GLU cc_start: 0.7747 (tp30) cc_final: 0.7322 (tp30) REVERT: J 430 TYR cc_start: 0.8692 (t80) cc_final: 0.8376 (t80) REVERT: J 436 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6699 (tm-30) REVERT: P 250 SER cc_start: 0.8905 (m) cc_final: 0.8220 (p) REVERT: P 253 GLU cc_start: 0.8520 (tp30) cc_final: 0.8113 (tp30) REVERT: P 254 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: P 273 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7989 (mm-30) REVERT: S 31 HIS cc_start: 0.8630 (t-170) cc_final: 0.8389 (t-170) REVERT: S 39 TYR cc_start: 0.9006 (m-80) cc_final: 0.8726 (m-80) REVERT: S 42 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7566 (mtm110) REVERT: S 59 THR cc_start: 0.9216 (m) cc_final: 0.8892 (p) REVERT: S 61 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7922 (mm-30) REVERT: S 112 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7972 (mt0) REVERT: S 115 LEU cc_start: 0.8831 (mt) cc_final: 0.8603 (mp) REVERT: T 63 ASN cc_start: 0.9067 (t0) cc_final: 0.8835 (t0) REVERT: T 68 ASP cc_start: 0.8224 (t0) cc_final: 0.7788 (t0) REVERT: T 120 LYS cc_start: 0.8806 (tttp) cc_final: 0.8419 (ttpp) REVERT: U 106 ASP cc_start: 0.8308 (m-30) cc_final: 0.7821 (m-30) REVERT: V 35 ARG cc_start: 0.8798 (mtp-110) cc_final: 0.8466 (mtp85) REVERT: W 73 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8130 (tm-30) REVERT: W 94 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8219 (mm-30) REVERT: W 123 ASP cc_start: 0.8519 (m-30) cc_final: 0.8265 (m-30) REVERT: X 71 THR cc_start: 0.9254 (m) cc_final: 0.8957 (t) REVERT: X 75 HIS cc_start: 0.8525 (t70) cc_final: 0.8052 (t70) outliers start: 87 outliers final: 63 residues processed: 1452 average time/residue: 0.3043 time to fit residues: 685.4434 Evaluate side-chains 1479 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 1405 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL 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 761 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 918 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 19 HIS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 154 PHE 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 D residue 138 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 F residue 107 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 348 ILE 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 125 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 281 LYS Chi-restraints excluded: chain G residue 377 ILE Chi-restraints excluded: chain G residue 397 ILE Chi-restraints excluded: chain G residue 420 ASN Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 264 ASP 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 28 GLU Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 246 GLU 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 252 LYS Chi-restraints excluded: chain P residue 254 GLU Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 76 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 79 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 268 optimal weight: 0.9990 chunk 280 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 451 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 413 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 GLN A 739 ASN A 779 GLN ** A2147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN E 380 GLN E 420 ASN F 277 ASN H 240 HIS I 196 ASN ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 262 GLN X 27 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101811 restraints weight = 68830.181| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.01 r_work: 0.3042 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 43534 Z= 0.223 Angle : 0.636 10.574 59700 Z= 0.332 Chirality : 0.046 0.358 6789 Planarity : 0.005 0.058 6883 Dihedral : 20.693 178.397 7705 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.97 % Allowed : 17.47 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.41 (0.12), residues: 4719 helix: 1.70 (0.11), residues: 2336 sheet: 0.27 (0.20), residues: 645 loop : 0.28 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG W 63 TYR 0.036 0.002 TYR C 382 PHE 0.061 0.002 PHE C 372 TRP 0.124 0.003 TRP C 360 HIS 0.008 0.001 HIS A 830 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (43526) covalent geometry : angle 0.63554 / 0.33 (59691) hydrogen bonds : bond 0.04328 / 2.91 ( 2083) hydrogen bonds : angle 3.79653 / 2.74 ( 5758) metal coordination : bond 0.01594 / 0.63 ( 8) metal coordination : angle 2.18564 / 1.03 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1499 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1418 time to evaluate : 1.463 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 621 TYR cc_start: 0.7287 (p90) cc_final: 0.7002 (p90) REVERT: A 628 TRP cc_start: 0.8492 (t60) cc_final: 0.8176 (t60) REVERT: A 660 LEU cc_start: 0.8997 (mp) cc_final: 0.8726 (mp) REVERT: A 678 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8589 (m) REVERT: A 694 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8081 (mmtp) REVERT: A 704 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6951 (mt-10) REVERT: A 719 HIS cc_start: 0.8202 (m170) cc_final: 0.7746 (m-70) REVERT: A 789 MET cc_start: 0.7690 (mmt) cc_final: 0.7336 (mmm) REVERT: A 833 LEU cc_start: 0.8289 (mt) cc_final: 0.8018 (mm) REVERT: A 854 GLU cc_start: 0.8271 (pm20) cc_final: 0.7960 (pm20) REVERT: A 864 ARG cc_start: 0.8548 (mtp85) cc_final: 0.8222 (mtp85) REVERT: A 867 CYS cc_start: 0.8550 (m) cc_final: 0.8129 (m) REVERT: A 870 ASP cc_start: 0.8705 (t0) cc_final: 0.8497 (t0) REVERT: A 871 ASP cc_start: 0.8250 (t0) cc_final: 0.7956 (t70) REVERT: A 934 ASP cc_start: 0.7639 (m-30) cc_final: 0.7438 (m-30) REVERT: A 966 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7907 (mtp-110) REVERT: A 975 LEU cc_start: 0.8414 (mt) cc_final: 0.8163 (mt) REVERT: A 976 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 992 MET cc_start: 0.3173 (ttm) cc_final: 0.2409 (ttm) REVERT: A 1893 ARG cc_start: 0.8415 (mtt180) cc_final: 0.8093 (tpp80) REVERT: A 1894 LYS cc_start: 0.8561 (ptpp) cc_final: 0.8154 (ptpp) REVERT: A 1895 ARG cc_start: 0.8118 (ttp-170) cc_final: 0.7823 (ttp-170) REVERT: A 1896 GLN cc_start: 0.8224 (mt0) cc_final: 0.7938 (mt0) REVERT: A 1897 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.7887 (ttp-170) REVERT: A 1921 GLU cc_start: 0.8193 (mp0) cc_final: 0.7715 (mp0) REVERT: A 1936 ILE cc_start: 0.8883 (mm) cc_final: 0.8462 (mt) REVERT: A 1953 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7751 (mm-30) REVERT: A 2013 GLU cc_start: 0.7870 (tp30) cc_final: 0.7178 (tp30) REVERT: A 2026 CYS cc_start: 0.8449 (m) cc_final: 0.8101 (m) REVERT: A 2094 ARG cc_start: 0.8228 (ptp90) cc_final: 0.7637 (mtm-85) REVERT: A 2096 GLU cc_start: 0.8167 (mp0) cc_final: 0.7803 (pm20) REVERT: A 2102 MET cc_start: 0.8551 (tpp) cc_final: 0.8291 (mmm) REVERT: A 2150 ASP cc_start: 0.8044 (m-30) cc_final: 0.7703 (m-30) REVERT: A 2185 MET cc_start: 0.6730 (ttm) cc_final: 0.6468 (ttm) REVERT: B 133 MET cc_start: 0.6005 (mmt) cc_final: 0.5527 (mmt) REVERT: B 174 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.8060 (mtm-85) REVERT: C 14 LYS cc_start: 0.8783 (mppt) cc_final: 0.8229 (mttp) REVERT: C 19 HIS cc_start: 0.8915 (OUTLIER) cc_final: 0.8534 (p90) REVERT: C 55 PHE cc_start: 0.7528 (t80) cc_final: 0.7133 (t80) REVERT: C 65 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8547 (tp) REVERT: C 71 GLN cc_start: 0.8125 (tp-100) cc_final: 0.7742 (tp-100) REVERT: C 72 ARG cc_start: 0.8705 (tpp80) cc_final: 0.8139 (tpp80) REVERT: C 75 TRP cc_start: 0.9042 (m-10) cc_final: 0.8765 (m-10) REVERT: C 76 ASP cc_start: 0.8195 (m-30) cc_final: 0.7625 (m-30) REVERT: C 83 MET cc_start: 0.8415 (mmp) cc_final: 0.8155 (mmm) REVERT: C 88 PHE cc_start: 0.8970 (m-10) cc_final: 0.8766 (m-10) REVERT: C 90 ASP cc_start: 0.8309 (t0) cc_final: 0.7573 (t0) REVERT: C 97 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7833 (mm-30) REVERT: C 103 THR cc_start: 0.8793 (m) cc_final: 0.8566 (p) REVERT: C 107 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7987 (mm-30) REVERT: C 111 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7873 (tm-30) REVERT: C 149 ASP cc_start: 0.8434 (t0) cc_final: 0.8146 (t0) REVERT: C 196 MET cc_start: 0.8155 (tpp) cc_final: 0.7854 (mmm) REVERT: C 204 GLN cc_start: 0.8786 (tp40) cc_final: 0.8179 (tp-100) REVERT: C 208 ASP cc_start: 0.8071 (m-30) cc_final: 0.7603 (m-30) REVERT: C 226 LYS cc_start: 0.7891 (mptt) cc_final: 0.7677 (mptt) REVERT: C 229 GLU cc_start: 0.7963 (pm20) cc_final: 0.7731 (pm20) REVERT: C 230 ASN cc_start: 0.8580 (t0) cc_final: 0.8229 (t0) REVERT: C 250 LYS cc_start: 0.8896 (mtpp) cc_final: 0.8582 (mtpp) REVERT: D 92 ASN cc_start: 0.8683 (t0) cc_final: 0.8393 (t0) REVERT: E 15 ILE cc_start: 0.8621 (mm) cc_final: 0.8400 (mt) REVERT: E 22 LYS cc_start: 0.8533 (mmtp) cc_final: 0.8279 (mmtp) REVERT: E 28 GLU cc_start: 0.7863 (mp0) cc_final: 0.7407 (mp0) REVERT: E 81 LEU cc_start: 0.8466 (mt) cc_final: 0.8206 (mp) REVERT: E 138 LEU cc_start: 0.8449 (mp) cc_final: 0.8226 (mp) REVERT: E 165 LYS cc_start: 0.7872 (mmtt) cc_final: 0.7655 (mmtt) REVERT: E 168 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8175 (ttmt) REVERT: E 178 GLU cc_start: 0.7896 (tt0) cc_final: 0.7604 (tt0) REVERT: E 182 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7766 (mtmt) REVERT: E 183 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7824 (mm-30) REVERT: E 184 ARG cc_start: 0.7797 (mtm-85) cc_final: 0.7556 (mtm-85) REVERT: E 194 GLU cc_start: 0.7788 (tt0) cc_final: 0.7533 (tt0) REVERT: E 212 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7492 (mm-30) REVERT: E 214 ASP cc_start: 0.8058 (m-30) cc_final: 0.7776 (m-30) REVERT: E 262 GLN cc_start: 0.7314 (mm-40) cc_final: 0.7113 (mm110) REVERT: E 285 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7805 (ttmm) REVERT: E 286 TYR cc_start: 0.8370 (m-10) cc_final: 0.8062 (m-80) REVERT: E 352 LEU cc_start: 0.8380 (mt) cc_final: 0.8125 (mm) REVERT: E 370 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8163 (mt-10) REVERT: E 389 GLU cc_start: 0.7977 (tt0) cc_final: 0.7709 (tt0) REVERT: E 415 LEU cc_start: 0.8840 (mt) cc_final: 0.8638 (mm) REVERT: E 439 ASP cc_start: 0.7622 (p0) cc_final: 0.7188 (p0) REVERT: E 445 LYS cc_start: 0.7766 (mmtp) cc_final: 0.7521 (mmtp) REVERT: E 446 ILE cc_start: 0.8323 (mm) cc_final: 0.7972 (mt) REVERT: F 40 ARG cc_start: 0.8176 (mtt90) cc_final: 0.7864 (mtt90) REVERT: F 71 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7533 (mmm-85) REVERT: F 112 GLU cc_start: 0.7759 (tp30) cc_final: 0.7494 (tp30) REVERT: F 117 GLU cc_start: 0.8184 (tp30) cc_final: 0.7583 (mm-30) REVERT: F 142 VAL cc_start: 0.8215 (t) cc_final: 0.8013 (m) REVERT: F 145 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8016 (pt) REVERT: F 160 LYS cc_start: 0.8303 (ttpt) cc_final: 0.7884 (mtpt) REVERT: F 168 MET cc_start: 0.7447 (mtp) cc_final: 0.7086 (mtp) REVERT: F 170 THR cc_start: 0.8164 (m) cc_final: 0.7925 (t) REVERT: F 176 THR cc_start: 0.8157 (m) cc_final: 0.7936 (t) REVERT: F 181 SER cc_start: 0.8734 (m) cc_final: 0.8321 (p) REVERT: F 183 THR cc_start: 0.8637 (m) cc_final: 0.8333 (p) REVERT: F 192 VAL cc_start: 0.8186 (t) cc_final: 0.7655 (p) REVERT: F 197 LYS cc_start: 0.7706 (mtpt) cc_final: 0.7190 (mtpt) REVERT: F 233 GLN cc_start: 0.7867 (tp40) cc_final: 0.7221 (tp40) REVERT: F 238 VAL cc_start: 0.8626 (t) cc_final: 0.8272 (m) REVERT: F 246 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7304 (mt-10) REVERT: F 248 ASP cc_start: 0.7737 (m-30) cc_final: 0.7500 (m-30) REVERT: F 267 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7289 (mt-10) REVERT: F 274 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7717 (mm-30) REVERT: F 286 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7927 (mt-10) REVERT: F 303 MET cc_start: 0.8661 (mmm) cc_final: 0.8358 (mmp) REVERT: F 317 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7388 (mt-10) REVERT: F 392 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7866 (ttp-170) REVERT: F 415 LYS cc_start: 0.8484 (tptp) cc_final: 0.8079 (tppt) REVERT: F 441 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7524 (mm-40) REVERT: F 445 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7668 (mm-30) REVERT: G 15 ILE cc_start: 0.8778 (mt) cc_final: 0.8565 (mm) REVERT: G 61 MET cc_start: 0.8706 (mmm) cc_final: 0.8070 (mmm) REVERT: G 90 LYS cc_start: 0.8609 (tptm) cc_final: 0.8037 (tptm) REVERT: G 125 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7889 (mmmt) REVERT: G 126 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7137 (mt-10) REVERT: G 128 LYS cc_start: 0.8391 (tttt) cc_final: 0.7957 (tttt) REVERT: G 134 GLU cc_start: 0.7510 (tt0) cc_final: 0.7066 (tm-30) REVERT: G 137 GLU cc_start: 0.7801 (tt0) cc_final: 0.7432 (tp30) REVERT: G 147 MET cc_start: 0.6414 (mtp) cc_final: 0.5918 (mtp) REVERT: G 158 ILE cc_start: 0.8508 (mt) cc_final: 0.8232 (mm) REVERT: G 162 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8145 (ttmm) REVERT: G 171 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8238 (mtpt) REVERT: G 178 GLU cc_start: 0.8169 (tt0) cc_final: 0.7549 (tt0) REVERT: G 186 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7652 (mm-30) REVERT: G 193 ILE cc_start: 0.8687 (mt) cc_final: 0.8351 (mm) REVERT: G 194 GLU cc_start: 0.7798 (tp30) cc_final: 0.7414 (tp30) REVERT: G 209 TYR cc_start: 0.8502 (m-80) cc_final: 0.8195 (m-10) REVERT: G 225 LYS cc_start: 0.8300 (mmpt) cc_final: 0.7799 (mmpt) REVERT: G 227 ASP cc_start: 0.7731 (t0) cc_final: 0.7445 (t0) REVERT: G 233 GLU cc_start: 0.7468 (tp30) cc_final: 0.6812 (tp30) REVERT: G 247 ASN cc_start: 0.8414 (m-40) cc_final: 0.8163 (m110) REVERT: G 249 ARG cc_start: 0.7863 (ttt-90) cc_final: 0.7553 (ttt-90) REVERT: G 281 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8134 (mtmm) REVERT: G 303 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7629 (mp0) REVERT: G 323 ILE cc_start: 0.8747 (mm) cc_final: 0.8419 (mt) REVERT: G 376 LYS cc_start: 0.8748 (tptt) cc_final: 0.8508 (tptm) REVERT: G 422 LYS cc_start: 0.8273 (mttp) cc_final: 0.8015 (mptt) REVERT: G 428 GLU cc_start: 0.8333 (mp0) cc_final: 0.7875 (mp0) REVERT: H 18 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7494 (mtp85) REVERT: H 20 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7739 (mt-10) REVERT: H 38 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7909 (mm-30) REVERT: H 83 LYS cc_start: 0.8780 (mtmm) cc_final: 0.8454 (mtmm) REVERT: H 88 MET cc_start: 0.7947 (mmp) cc_final: 0.7628 (mmm) REVERT: H 113 MET cc_start: 0.8198 (ptp) cc_final: 0.7662 (ptp) REVERT: H 117 GLU cc_start: 0.8276 (tp30) cc_final: 0.7971 (tp30) REVERT: H 132 LYS cc_start: 0.8392 (ttmm) cc_final: 0.8091 (ttmm) REVERT: H 135 THR cc_start: 0.7865 (m) cc_final: 0.7649 (p) REVERT: H 201 LYS cc_start: 0.8406 (ptmt) cc_final: 0.8196 (ptmt) REVERT: H 204 LYS cc_start: 0.8863 (mtpt) cc_final: 0.8578 (mtpt) REVERT: H 214 ASP cc_start: 0.7682 (p0) cc_final: 0.7331 (p0) REVERT: H 238 VAL cc_start: 0.8066 (t) cc_final: 0.7762 (p) REVERT: H 246 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7649 (mt-10) REVERT: H 253 ARG cc_start: 0.8254 (ptm160) cc_final: 0.7991 (ptm-80) REVERT: H 267 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7675 (tt0) REVERT: H 273 ARG cc_start: 0.8324 (mtt90) cc_final: 0.7784 (mtt90) REVERT: H 274 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7659 (mt-10) REVERT: H 275 GLN cc_start: 0.8251 (mm110) cc_final: 0.7933 (mm-40) REVERT: H 277 ASN cc_start: 0.8476 (m-40) cc_final: 0.8069 (m110) REVERT: H 279 LYS cc_start: 0.8392 (tppt) cc_final: 0.8030 (tptp) REVERT: H 284 ARG cc_start: 0.8168 (ttt90) cc_final: 0.7954 (ptm-80) REVERT: H 313 ASN cc_start: 0.8057 (m-40) cc_final: 0.7713 (m-40) REVERT: H 314 ARG cc_start: 0.7449 (mmt180) cc_final: 0.7126 (mmt180) REVERT: H 317 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7664 (mt-10) REVERT: H 330 ARG cc_start: 0.8191 (mmt90) cc_final: 0.7986 (mmt90) REVERT: H 339 SER cc_start: 0.8742 (p) cc_final: 0.8502 (m) REVERT: H 404 GLN cc_start: 0.8315 (mt0) cc_final: 0.8061 (mt0) REVERT: I 61 MET cc_start: 0.8192 (mmm) cc_final: 0.7809 (mmm) REVERT: I 137 GLU cc_start: 0.7894 (tt0) cc_final: 0.7660 (tt0) REVERT: I 139 THR cc_start: 0.8708 (m) cc_final: 0.8312 (p) REVERT: I 171 LYS cc_start: 0.8943 (ttmt) cc_final: 0.8547 (tttt) REVERT: I 216 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7783 (tp30) REVERT: I 244 ASP cc_start: 0.7596 (m-30) cc_final: 0.7211 (t0) REVERT: I 249 ARG cc_start: 0.8191 (mtp85) cc_final: 0.7898 (mtp85) REVERT: I 259 MET cc_start: 0.8164 (mtp) cc_final: 0.7836 (mtp) REVERT: I 264 MET cc_start: 0.8092 (mtp) cc_final: 0.7714 (mtp) REVERT: I 267 LYS cc_start: 0.8288 (ttpp) cc_final: 0.7994 (tttp) REVERT: I 281 LYS cc_start: 0.8662 (mttt) cc_final: 0.8423 (mtmt) REVERT: I 302 ASP cc_start: 0.8370 (t0) cc_final: 0.7860 (t0) REVERT: I 322 SER cc_start: 0.8493 (p) cc_final: 0.8213 (t) REVERT: I 404 ARG cc_start: 0.7788 (mtt90) cc_final: 0.7289 (mtt180) REVERT: I 438 TYR cc_start: 0.8420 (m-80) cc_final: 0.7946 (m-80) REVERT: I 439 ASP cc_start: 0.8191 (p0) cc_final: 0.7836 (p0) REVERT: I 441 LYS cc_start: 0.8483 (mttm) cc_final: 0.8044 (mtmm) REVERT: J 71 ARG cc_start: 0.8320 (tpp80) cc_final: 0.8090 (tpp-160) REVERT: J 90 MET cc_start: 0.8513 (mtm) cc_final: 0.8266 (mtp) REVERT: J 117 GLU cc_start: 0.7708 (tp30) cc_final: 0.7463 (tp30) REVERT: J 133 GLU cc_start: 0.7689 (pt0) cc_final: 0.7428 (pt0) REVERT: J 142 VAL cc_start: 0.8715 (t) cc_final: 0.8470 (m) REVERT: J 144 GLU cc_start: 0.8167 (tt0) cc_final: 0.7902 (tt0) REVERT: J 164 LYS cc_start: 0.8468 (pttt) cc_final: 0.8146 (ptmm) REVERT: J 179 ILE cc_start: 0.8405 (mt) cc_final: 0.8147 (mt) REVERT: J 180 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7357 (mt-10) REVERT: J 183 THR cc_start: 0.8215 (m) cc_final: 0.7935 (p) REVERT: J 192 VAL cc_start: 0.8604 (t) cc_final: 0.8171 (p) REVERT: J 267 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7338 (mt-10) REVERT: J 270 SER cc_start: 0.8463 (p) cc_final: 0.8117 (t) REVERT: J 314 ARG cc_start: 0.8117 (mmt180) cc_final: 0.7796 (mmt180) REVERT: J 334 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7753 (ttp80) REVERT: J 352 ASP cc_start: 0.7798 (m-30) cc_final: 0.7529 (t0) REVERT: J 377 GLU cc_start: 0.7733 (tp30) cc_final: 0.7323 (tp30) REVERT: J 430 TYR cc_start: 0.8722 (t80) cc_final: 0.8452 (t80) REVERT: J 435 ASP cc_start: 0.7362 (p0) cc_final: 0.7116 (p0) REVERT: J 436 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6678 (tm-30) REVERT: P 250 SER cc_start: 0.8926 (m) cc_final: 0.8238 (p) REVERT: P 253 GLU cc_start: 0.8516 (tp30) cc_final: 0.8134 (tp30) REVERT: P 254 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7958 (mp0) REVERT: P 273 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8004 (mm-30) REVERT: S 31 HIS cc_start: 0.8674 (t-170) cc_final: 0.8419 (t-170) REVERT: S 39 TYR cc_start: 0.9015 (m-80) cc_final: 0.8735 (m-80) REVERT: S 42 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7585 (mtm110) REVERT: S 59 THR cc_start: 0.9237 (m) cc_final: 0.8896 (p) REVERT: S 61 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7979 (mm-30) REVERT: S 112 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7994 (mt0) REVERT: S 115 LEU cc_start: 0.8817 (mt) cc_final: 0.8592 (mp) REVERT: T 68 ASP cc_start: 0.8160 (t0) cc_final: 0.7732 (t0) REVERT: T 76 GLU cc_start: 0.8412 (tp30) cc_final: 0.7658 (tp30) REVERT: T 79 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7495 (mtm110) REVERT: T 120 LYS cc_start: 0.8798 (tttp) cc_final: 0.8426 (ttpp) REVERT: U 106 ASP cc_start: 0.8303 (m-30) cc_final: 0.7833 (m-30) REVERT: V 35 ARG cc_start: 0.8776 (mtp-110) cc_final: 0.8480 (mtp85) REVERT: V 85 ASP cc_start: 0.8010 (m-30) cc_final: 0.7634 (m-30) REVERT: V 88 TYR cc_start: 0.8235 (m-80) cc_final: 0.7756 (m-80) REVERT: W 73 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8120 (tm-30) REVERT: W 94 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8225 (mm-30) REVERT: W 123 ASP cc_start: 0.8513 (m-30) cc_final: 0.8274 (m-30) REVERT: X 71 THR cc_start: 0.9252 (m) cc_final: 0.8953 (t) REVERT: X 75 HIS cc_start: 0.8561 (t70) cc_final: 0.7999 (t-90) outliers start: 81 outliers final: 67 residues processed: 1441 average time/residue: 0.3110 time to fit residues: 694.8734 Evaluate side-chains 1479 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 1403 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 694 LYS 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 761 SER Chi-restraints excluded: chain A residue 772 LEU 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 C residue 19 HIS Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 154 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 60 LYS 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 107 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 365 LYS 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 125 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 281 LYS Chi-restraints excluded: chain G residue 377 ILE Chi-restraints excluded: chain G residue 397 ILE Chi-restraints excluded: chain G residue 420 ASN Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 205 LEU Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 264 ASP Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 126 GLU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 258 SER Chi-restraints excluded: chain I residue 285 LYS Chi-restraints excluded: chain I residue 323 ILE Chi-restraints excluded: chain I residue 346 SER Chi-restraints excluded: chain I residue 364 MET Chi-restraints excluded: chain I residue 402 THR Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 246 GLU 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 268 LYS Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain U residue 115 LYS Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 76 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 451 optimal weight: 0.9980 chunk 427 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 381 optimal weight: 0.9990 chunk 387 optimal weight: 0.6980 chunk 378 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 404 optimal weight: 50.0000 chunk 52 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 GLN ** A2147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 91 GLN E 420 ASN F 277 ASN ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 HIS X 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.127665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.102724 restraints weight = 68801.751| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.01 r_work: 0.3057 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 43534 Z= 0.171 Angle : 0.618 12.085 59700 Z= 0.322 Chirality : 0.045 0.390 6789 Planarity : 0.004 0.056 6883 Dihedral : 20.648 178.238 7705 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.88 % Allowed : 18.06 % Favored : 80.07 % 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: 1.46 (0.12), residues: 4719 helix: 1.75 (0.11), residues: 2333 sheet: 0.28 (0.20), residues: 666 loop : 0.31 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 32 TYR 0.020 0.001 TYR T 83 PHE 0.035 0.001 PHE C 372 TRP 0.104 0.002 TRP C 360 HIS 0.009 0.001 HIS I 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (43526) covalent geometry : angle 0.61802 / 0.32 (59691) hydrogen bonds : bond 0.04033 / 2.71 ( 2083) hydrogen bonds : angle 3.77518 / 2.73 ( 5758) metal coordination : bond 0.01291 / 0.47 ( 8) metal coordination : angle 1.74307 / 0.84 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9438 Ramachandran restraints generated. 4719 Oldfield, 0 Emsley, 4719 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1482 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1405 time to evaluate : 1.685 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 628 TRP cc_start: 0.8495 (t60) cc_final: 0.8222 (t60) REVERT: A 660 LEU cc_start: 0.8983 (mp) cc_final: 0.8709 (mp) REVERT: A 678 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8586 (m) REVERT: A 704 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6968 (mt-10) REVERT: A 719 HIS cc_start: 0.8179 (m170) cc_final: 0.7891 (m-70) REVERT: A 747 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8229 (mm-30) REVERT: A 789 MET cc_start: 0.7634 (mmt) cc_final: 0.7310 (mmm) REVERT: A 833 LEU cc_start: 0.8245 (mt) cc_final: 0.7985 (mm) REVERT: A 846 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8558 (mm-30) REVERT: A 854 GLU cc_start: 0.8282 (pm20) cc_final: 0.7966 (pm20) REVERT: A 864 ARG cc_start: 0.8515 (mtp85) cc_final: 0.8193 (mtp85) REVERT: A 867 CYS cc_start: 0.8556 (m) cc_final: 0.8152 (m) REVERT: A 870 ASP cc_start: 0.8688 (t0) cc_final: 0.8463 (t0) REVERT: A 918 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8366 (m) REVERT: A 966 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7948 (mtp-110) REVERT: A 975 LEU cc_start: 0.8381 (mt) cc_final: 0.8143 (mt) REVERT: A 976 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7577 (mt-10) REVERT: A 992 MET cc_start: 0.3165 (ttm) cc_final: 0.2389 (ttm) REVERT: A 1893 ARG cc_start: 0.8414 (mtt180) cc_final: 0.7975 (ttm-80) REVERT: A 1894 LYS cc_start: 0.8535 (ptpp) cc_final: 0.8153 (ptpp) REVERT: A 1895 ARG cc_start: 0.8120 (ttp-170) cc_final: 0.7838 (ttp-170) REVERT: A 1896 GLN cc_start: 0.8201 (mt0) cc_final: 0.7931 (mt0) REVERT: A 1897 ARG cc_start: 0.8280 (ttp-170) cc_final: 0.7933 (ttp-170) REVERT: A 1921 GLU cc_start: 0.8190 (mp0) cc_final: 0.7749 (mp0) REVERT: A 1936 ILE cc_start: 0.8887 (mm) cc_final: 0.8466 (mt) REVERT: A 1948 PHE cc_start: 0.8819 (t80) cc_final: 0.8397 (t80) REVERT: A 2013 GLU cc_start: 0.7968 (tp30) cc_final: 0.7260 (tp30) REVERT: A 2026 CYS cc_start: 0.8443 (m) cc_final: 0.8097 (m) REVERT: A 2094 ARG cc_start: 0.8182 (ptp90) cc_final: 0.7591 (mtm-85) REVERT: A 2096 GLU cc_start: 0.8218 (mp0) cc_final: 0.7840 (pm20) REVERT: A 2102 MET cc_start: 0.8528 (tpp) cc_final: 0.8254 (mmm) REVERT: A 2150 ASP cc_start: 0.8037 (m-30) cc_final: 0.7702 (m-30) REVERT: A 2185 MET cc_start: 0.6703 (ttm) cc_final: 0.6441 (ttm) REVERT: B 133 MET cc_start: 0.5996 (mmt) cc_final: 0.5515 (mmt) REVERT: C 14 LYS cc_start: 0.8731 (mppt) cc_final: 0.8207 (mttp) REVERT: C 43 ASN cc_start: 0.8760 (p0) cc_final: 0.8542 (p0) REVERT: C 55 PHE cc_start: 0.7484 (t80) cc_final: 0.7142 (t80) REVERT: C 71 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7721 (tp-100) REVERT: C 72 ARG cc_start: 0.8689 (tpp80) cc_final: 0.8172 (tpp80) REVERT: C 75 TRP cc_start: 0.9042 (m-10) cc_final: 0.8757 (m-10) REVERT: C 76 ASP cc_start: 0.8158 (m-30) cc_final: 0.7599 (m-30) REVERT: C 83 MET cc_start: 0.8384 (mmp) cc_final: 0.8102 (mmm) REVERT: C 90 ASP cc_start: 0.8295 (t0) cc_final: 0.7598 (t0) REVERT: C 97 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7817 (mm-30) REVERT: C 103 THR cc_start: 0.8775 (m) cc_final: 0.8572 (p) REVERT: C 107 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7996 (mm-30) REVERT: C 111 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7850 (tm-30) REVERT: C 149 ASP cc_start: 0.8444 (t0) cc_final: 0.8132 (t0) REVERT: C 196 MET cc_start: 0.8143 (tpp) cc_final: 0.7904 (mmm) REVERT: C 198 GLU cc_start: 0.8294 (mp0) cc_final: 0.8047 (mp0) REVERT: C 204 GLN cc_start: 0.8775 (tp40) cc_final: 0.8156 (tp-100) REVERT: C 208 ASP cc_start: 0.8036 (m-30) cc_final: 0.7567 (m-30) REVERT: C 226 LYS cc_start: 0.7825 (mptt) cc_final: 0.7610 (mptt) REVERT: C 230 ASN cc_start: 0.8593 (t0) cc_final: 0.8231 (t0) REVERT: C 237 VAL cc_start: 0.8794 (t) cc_final: 0.8583 (p) REVERT: C 250 LYS cc_start: 0.8852 (mtpp) cc_final: 0.8575 (mtpp) REVERT: C 393 LYS cc_start: 0.8864 (tttp) cc_final: 0.8258 (tttp) REVERT: D 92 ASN cc_start: 0.8611 (t0) cc_final: 0.8268 (t0) REVERT: E 15 ILE cc_start: 0.8656 (mm) cc_final: 0.8435 (mt) REVERT: E 22 LYS cc_start: 0.8509 (mmtp) cc_final: 0.8255 (mmtp) REVERT: E 28 GLU cc_start: 0.7862 (mp0) cc_final: 0.7388 (mp0) REVERT: E 64 ARG cc_start: 0.8318 (mtp85) cc_final: 0.7933 (mmt-90) REVERT: E 81 LEU cc_start: 0.8468 (mt) cc_final: 0.8202 (mp) REVERT: E 127 THR cc_start: 0.8720 (m) cc_final: 0.8316 (p) REVERT: E 138 LEU cc_start: 0.8465 (mp) cc_final: 0.8243 (mp) REVERT: E 165 LYS cc_start: 0.7859 (mmtt) cc_final: 0.7639 (mmtt) REVERT: E 168 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8146 (ttmt) REVERT: E 178 GLU cc_start: 0.7867 (tt0) cc_final: 0.7568 (tt0) REVERT: E 182 LYS cc_start: 0.8150 (mtmt) cc_final: 0.7757 (mtmt) REVERT: E 183 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7822 (mm-30) REVERT: E 184 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7477 (mtm-85) REVERT: E 194 GLU cc_start: 0.7766 (tt0) cc_final: 0.7517 (tt0) REVERT: E 214 ASP cc_start: 0.8049 (m-30) cc_final: 0.7770 (m-30) REVERT: E 262 GLN cc_start: 0.7310 (mm-40) cc_final: 0.7086 (mm110) REVERT: E 285 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7797 (ttmm) REVERT: E 286 TYR cc_start: 0.8364 (m-10) cc_final: 0.8105 (m-80) REVERT: E 352 LEU cc_start: 0.8390 (mt) cc_final: 0.8142 (mm) REVERT: E 370 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8151 (mt-10) REVERT: E 389 GLU cc_start: 0.7941 (tt0) cc_final: 0.7672 (tt0) REVERT: E 439 ASP cc_start: 0.7614 (p0) cc_final: 0.7161 (p0) REVERT: E 445 LYS cc_start: 0.7741 (mmtp) cc_final: 0.7506 (mmtp) REVERT: E 446 ILE cc_start: 0.8322 (mm) cc_final: 0.7971 (mt) REVERT: F 40 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7798 (mtt90) REVERT: F 71 ARG cc_start: 0.7774 (mmt90) cc_final: 0.7508 (mmm-85) REVERT: F 112 GLU cc_start: 0.7763 (tp30) cc_final: 0.7491 (tp30) REVERT: F 117 GLU cc_start: 0.8180 (tp30) cc_final: 0.7567 (mm-30) REVERT: F 142 VAL cc_start: 0.8210 (t) cc_final: 0.7924 (m) REVERT: F 160 LYS cc_start: 0.8295 (ttpt) cc_final: 0.7880 (mtpt) REVERT: F 168 MET cc_start: 0.7449 (mtp) cc_final: 0.7095 (mtp) REVERT: F 170 THR cc_start: 0.8155 (m) cc_final: 0.7909 (t) REVERT: F 176 THR cc_start: 0.8161 (m) cc_final: 0.7946 (t) REVERT: F 181 SER cc_start: 0.8723 (m) cc_final: 0.8309 (p) REVERT: F 183 THR cc_start: 0.8636 (m) cc_final: 0.8324 (p) REVERT: F 192 VAL cc_start: 0.8183 (t) cc_final: 0.7652 (p) REVERT: F 197 LYS cc_start: 0.7732 (mtpt) cc_final: 0.7219 (mtpt) REVERT: F 233 GLN cc_start: 0.7876 (tp40) cc_final: 0.7254 (tp40) REVERT: F 238 VAL cc_start: 0.8631 (t) cc_final: 0.8281 (m) REVERT: F 246 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7285 (mt-10) REVERT: F 248 ASP cc_start: 0.7767 (m-30) cc_final: 0.7518 (m-30) REVERT: F 274 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7689 (mm-30) REVERT: F 286 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8007 (mt-10) REVERT: F 303 MET cc_start: 0.8668 (mmm) cc_final: 0.8346 (mmp) REVERT: F 317 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7394 (mt-10) REVERT: F 392 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7855 (ttp-170) REVERT: F 415 LYS cc_start: 0.8471 (tptp) cc_final: 0.8107 (tppt) REVERT: F 441 GLN cc_start: 0.7758 (mm-40) cc_final: 0.7508 (mm-40) REVERT: F 445 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7677 (mm-30) REVERT: G 15 ILE cc_start: 0.8762 (mt) cc_final: 0.8550 (mm) REVERT: G 61 MET cc_start: 0.8696 (mmm) cc_final: 0.8052 (mmm) REVERT: G 89 SER cc_start: 0.8435 (m) cc_final: 0.8107 (t) REVERT: G 90 LYS cc_start: 0.8626 (tptm) cc_final: 0.8128 (tptm) REVERT: G 125 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7892 (mmmt) REVERT: G 126 GLU cc_start: 0.7470 (mt-10) cc_final: 0.7119 (mt-10) REVERT: G 128 LYS cc_start: 0.8390 (tttt) cc_final: 0.7884 (tttt) REVERT: G 134 GLU cc_start: 0.7502 (tt0) cc_final: 0.7080 (tm-30) REVERT: G 137 GLU cc_start: 0.7807 (tt0) cc_final: 0.7433 (tp30) REVERT: G 147 MET cc_start: 0.6277 (mtp) cc_final: 0.5831 (mtp) REVERT: G 158 ILE cc_start: 0.8516 (mt) cc_final: 0.8234 (mm) REVERT: G 162 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8151 (ttmm) REVERT: G 171 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8207 (mtpt) REVERT: G 178 GLU cc_start: 0.8158 (tt0) cc_final: 0.7575 (tt0) REVERT: G 186 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7662 (mm-30) REVERT: G 193 ILE cc_start: 0.8662 (mt) cc_final: 0.8311 (mm) REVERT: G 209 TYR cc_start: 0.8497 (m-80) cc_final: 0.8174 (m-10) REVERT: G 212 GLU cc_start: 0.7860 (pm20) cc_final: 0.7642 (pm20) REVERT: G 225 LYS cc_start: 0.8288 (mmpt) cc_final: 0.7793 (mmpt) REVERT: G 227 ASP cc_start: 0.7698 (t0) cc_final: 0.7420 (t0) REVERT: G 233 GLU cc_start: 0.7507 (tp30) cc_final: 0.6912 (tp30) REVERT: G 234 ILE cc_start: 0.8417 (mt) cc_final: 0.8206 (mt) REVERT: G 247 ASN cc_start: 0.8395 (m-40) cc_final: 0.8151 (m110) REVERT: G 249 ARG cc_start: 0.7846 (ttt-90) cc_final: 0.7536 (ttt-90) REVERT: G 281 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8155 (mtmm) REVERT: G 303 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7656 (mp0) REVERT: G 323 ILE cc_start: 0.8736 (mm) cc_final: 0.8411 (mt) REVERT: G 376 LYS cc_start: 0.8742 (tptt) cc_final: 0.8502 (tptm) REVERT: G 422 LYS cc_start: 0.8247 (mttp) cc_final: 0.7995 (mptt) REVERT: G 428 GLU cc_start: 0.8323 (mp0) cc_final: 0.7863 (mp0) REVERT: H 18 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7472 (mtp85) REVERT: H 20 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7724 (mt-10) REVERT: H 38 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7886 (mm-30) REVERT: H 46 MET cc_start: 0.8421 (mtp) cc_final: 0.8208 (mtt) REVERT: H 83 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8472 (mtmm) REVERT: H 88 MET cc_start: 0.7938 (mmp) cc_final: 0.7736 (mmp) REVERT: H 111 LEU cc_start: 0.8835 (mp) cc_final: 0.8605 (mt) REVERT: H 113 MET cc_start: 0.8215 (ptp) cc_final: 0.7633 (ptp) REVERT: H 132 LYS cc_start: 0.8365 (ttmm) cc_final: 0.8049 (ttmm) REVERT: H 201 LYS cc_start: 0.8409 (ptmt) cc_final: 0.8135 (ptmt) REVERT: H 204 LYS cc_start: 0.8857 (mtpt) cc_final: 0.8550 (mtpt) REVERT: H 211 ARG cc_start: 0.8458 (ttt180) cc_final: 0.8163 (ttt180) REVERT: H 214 ASP cc_start: 0.7683 (p0) cc_final: 0.7323 (p0) REVERT: H 238 VAL cc_start: 0.8083 (t) cc_final: 0.7784 (p) REVERT: H 246 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7625 (mt-10) REVERT: H 253 ARG cc_start: 0.8255 (ptm160) cc_final: 0.7988 (ptm-80) REVERT: H 267 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7616 (tt0) REVERT: H 273 ARG cc_start: 0.8329 (mtt90) cc_final: 0.7814 (mtt90) REVERT: H 274 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7668 (mt-10) REVERT: H 275 GLN cc_start: 0.8235 (mm110) cc_final: 0.7919 (mm-40) REVERT: H 277 ASN cc_start: 0.8441 (m-40) cc_final: 0.8041 (m110) REVERT: H 279 LYS cc_start: 0.8386 (tppt) cc_final: 0.8033 (tptp) REVERT: H 284 ARG cc_start: 0.8203 (ttt90) cc_final: 0.7983 (ptm-80) REVERT: H 313 ASN cc_start: 0.8063 (m-40) cc_final: 0.7731 (m-40) REVERT: H 314 ARG cc_start: 0.7446 (mmt180) cc_final: 0.7132 (mmt180) REVERT: H 317 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7646 (mt-10) REVERT: H 339 SER cc_start: 0.8740 (p) cc_final: 0.8501 (m) REVERT: H 404 GLN cc_start: 0.8292 (mt0) cc_final: 0.8056 (mt0) REVERT: I 134 GLU cc_start: 0.7542 (tt0) cc_final: 0.7268 (tt0) REVERT: I 137 GLU cc_start: 0.7908 (tt0) cc_final: 0.7664 (tt0) REVERT: I 139 THR cc_start: 0.8662 (m) cc_final: 0.8272 (p) REVERT: I 142 GLU cc_start: 0.8078 (mp0) cc_final: 0.7752 (mp0) REVERT: I 171 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8539 (tttt) REVERT: I 216 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7753 (tp30) REVERT: I 244 ASP cc_start: 0.7590 (m-30) cc_final: 0.7201 (t0) REVERT: I 249 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7906 (mtp85) REVERT: I 259 MET cc_start: 0.8170 (mtp) cc_final: 0.7813 (mtp) REVERT: I 264 MET cc_start: 0.8034 (mtp) cc_final: 0.7656 (mtp) REVERT: I 267 LYS cc_start: 0.8305 (ttpp) cc_final: 0.8017 (tttp) REVERT: I 281 LYS cc_start: 0.8636 (mttt) cc_final: 0.8354 (mtmt) REVERT: I 302 ASP cc_start: 0.8355 (t0) cc_final: 0.8091 (t0) REVERT: I 310 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7719 (mt-10) REVERT: I 322 SER cc_start: 0.8460 (p) cc_final: 0.8176 (t) REVERT: I 404 ARG cc_start: 0.7775 (mtt90) cc_final: 0.7280 (mtt180) REVERT: I 438 TYR cc_start: 0.8386 (m-80) cc_final: 0.7911 (m-80) REVERT: I 439 ASP cc_start: 0.8183 (p0) cc_final: 0.7804 (p0) REVERT: I 441 LYS cc_start: 0.8489 (mttm) cc_final: 0.8043 (mtmm) REVERT: J 90 MET cc_start: 0.8506 (mtm) cc_final: 0.8250 (mtp) REVERT: J 92 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7919 (mm110) REVERT: J 117 GLU cc_start: 0.7693 (tp30) cc_final: 0.7337 (tp30) REVERT: J 133 GLU cc_start: 0.7653 (pt0) cc_final: 0.7387 (pt0) REVERT: J 142 VAL cc_start: 0.8699 (t) cc_final: 0.8450 (m) REVERT: J 144 GLU cc_start: 0.8146 (tt0) cc_final: 0.7877 (tt0) REVERT: J 164 LYS cc_start: 0.8467 (pttt) cc_final: 0.8155 (ptmm) REVERT: J 179 ILE cc_start: 0.8399 (mt) cc_final: 0.8145 (mt) REVERT: J 180 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7367 (mt-10) REVERT: J 183 THR cc_start: 0.8197 (m) cc_final: 0.7917 (p) REVERT: J 192 VAL cc_start: 0.8606 (t) cc_final: 0.8174 (p) REVERT: J 225 VAL cc_start: 0.8543 (t) cc_final: 0.8293 (p) REVERT: J 267 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7384 (mt-10) REVERT: J 270 SER cc_start: 0.8459 (p) cc_final: 0.8114 (t) REVERT: J 314 ARG cc_start: 0.8074 (mmt180) cc_final: 0.7839 (mmt180) REVERT: J 334 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7763 (ttp80) REVERT: J 352 ASP cc_start: 0.7801 (m-30) cc_final: 0.7534 (t0) REVERT: J 377 GLU cc_start: 0.7655 (tp30) cc_final: 0.7439 (tp30) REVERT: J 430 TYR cc_start: 0.8698 (t80) cc_final: 0.8402 (t80) REVERT: J 435 ASP cc_start: 0.7365 (p0) cc_final: 0.7105 (p0) REVERT: J 436 GLU cc_start: 0.7248 (tm-30) cc_final: 0.6654 (tm-30) REVERT: P 250 SER cc_start: 0.8922 (m) cc_final: 0.8192 (p) REVERT: P 253 GLU cc_start: 0.8511 (tp30) cc_final: 0.8118 (tp30) REVERT: P 254 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7932 (mp0) REVERT: P 272 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8254 (mm) REVERT: P 273 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8006 (mm-30) REVERT: S 31 HIS cc_start: 0.8679 (t-170) cc_final: 0.8435 (t-170) REVERT: S 39 TYR cc_start: 0.9015 (m-80) cc_final: 0.8748 (m-80) REVERT: S 42 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7586 (mtm110) REVERT: S 59 THR cc_start: 0.9230 (m) cc_final: 0.8886 (p) REVERT: S 112 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7951 (mt0) REVERT: S 115 LEU cc_start: 0.8809 (mt) cc_final: 0.8584 (mp) REVERT: T 63 ASN cc_start: 0.9046 (t0) cc_final: 0.8819 (t0) REVERT: T 68 ASP cc_start: 0.8171 (t0) cc_final: 0.7724 (t0) REVERT: T 76 GLU cc_start: 0.8364 (tp30) cc_final: 0.7640 (tp30) REVERT: T 79 ARG cc_start: 0.8219 (mtm110) cc_final: 0.7542 (mtm110) REVERT: T 120 LYS cc_start: 0.8794 (tttp) cc_final: 0.8403 (ttpp) REVERT: U 103 LEU cc_start: 0.9211 (tp) cc_final: 0.9002 (tp) REVERT: U 106 ASP cc_start: 0.8280 (m-30) cc_final: 0.7788 (m-30) REVERT: V 35 ARG cc_start: 0.8773 (mtp-110) cc_final: 0.8437 (mtp85) REVERT: V 85 ASP cc_start: 0.8024 (m-30) cc_final: 0.7662 (m-30) REVERT: V 88 TYR cc_start: 0.8251 (m-80) cc_final: 0.7836 (m-80) REVERT: W 73 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8103 (tm-30) REVERT: W 94 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8212 (mm-30) REVERT: W 123 ASP cc_start: 0.8496 (m-30) cc_final: 0.8263 (m-30) REVERT: X 71 THR cc_start: 0.9243 (m) cc_final: 0.8959 (t) REVERT: X 75 HIS cc_start: 0.8549 (t70) cc_final: 0.7998 (t-90) outliers start: 77 outliers final: 63 residues processed: 1427 average time/residue: 0.3075 time to fit residues: 681.0448 Evaluate side-chains 1473 residues out of total 4104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1403 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 VAL 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 761 SER Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 918 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 154 PHE Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 60 LYS 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 107 GLU Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 348 ILE Chi-restraints excluded: chain F residue 365 LYS 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 125 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 281 LYS Chi-restraints excluded: chain G residue 377 ILE Chi-restraints excluded: chain G residue 397 ILE Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 141 GLU Chi-restraints excluded: chain H residue 188 GLN Chi-restraints excluded: chain H residue 264 ASP Chi-restraints excluded: chain H residue 398 SER Chi-restraints excluded: chain H residue 445 GLU Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 86 GLU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 258 SER 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 402 THR Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain J residue 158 VAL Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 194 THR 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 J residue 382 MET Chi-restraints excluded: chain P residue 268 LYS Chi-restraints excluded: chain P residue 272 ILE Chi-restraints excluded: chain S residue 42 ARG Chi-restraints excluded: chain T residue 71 GLU Chi-restraints excluded: chain T residue 113 GLU Chi-restraints excluded: chain U residue 40 ARG Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain W residue 42 ARG Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 51 ILE Chi-restraints excluded: chain W residue 60 LEU Chi-restraints excluded: chain W residue 76 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 152 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 451 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 320 optimal weight: 0.3980 chunk 374 optimal weight: 0.7980 chunk 80 optimal weight: 0.0570 chunk 326 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 343 optimal weight: 1.9990 chunk 275 optimal weight: 0.8980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 GLN ** A2147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN E 420 ASN F 277 ASN G 305 HIS G 348 HIS H 240 HIS ** I 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 262 GLN U 93 GLN X 27 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.128557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103466 restraints weight = 69289.784| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.04 r_work: 0.3073 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 43534 Z= 0.136 Angle : 0.600 10.009 59700 Z= 0.313 Chirality : 0.043 0.354 6789 Planarity : 0.004 0.057 6883 Dihedral : 20.585 179.147 7705 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.58 % Allowed : 18.37 % Favored : 80.04 % 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: 1.54 (0.12), residues: 4719 helix: 1.81 (0.11), residues: 2335 sheet: 0.35 (0.20), residues: 644 loop : 0.33 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG W 63 TYR 0.020 0.001 TYR W 54 PHE 0.023 0.001 PHE C 248 TRP 0.089 0.002 TRP C 360 HIS 0.009 0.001 HIS I 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (43526) covalent geometry : angle 0.59998 / 0.31 (59691) hydrogen bonds : bond 0.03788 / 2.54 ( 2083) hydrogen bonds : angle 3.70208 / 2.68 ( 5758) metal coordination : bond 0.00796 / 0.28 ( 8) metal coordination : angle 1.68455 / 0.83 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16525.88 seconds wall clock time: 281 minutes 47.79 seconds (16907.79 seconds total)