Starting phenix.real_space_refine on Thu Jan 23 08:39:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8n_47725/01_2025/9e8n_47725.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8n_47725/01_2025/9e8n_47725.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e8n_47725/01_2025/9e8n_47725.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8n_47725/01_2025/9e8n_47725.map" model { file = "/net/cci-nas-00/data/ceres_data/9e8n_47725/01_2025/9e8n_47725.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8n_47725/01_2025/9e8n_47725.cif" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.036 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 1 6.06 5 P 14 5.49 5 Mg 2 5.21 5 S 383 5.16 5 C 44839 2.51 5 N 12205 2.21 5 O 13468 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 472 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 70912 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3168 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 23, 'TRANS': 380} Chain: "C" Number of atoms: 2926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2926 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 351} Chain breaks: 2 Chain: "D" Number of atoms: 2904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2904 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 1 Chain: "G" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1820 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1704 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 217} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "I" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1699 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 6, 'TRANS': 231} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 78 Chain: "L" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1845 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 226} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 355 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "W" Number of atoms: 3570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3570 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 8, 'TRANS': 429} Chain: "X" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2994 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 10, 'TRANS': 367} Chain: "Y" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3127 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 371} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1458 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 9, 'TRANS': 181} Chain: "d" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2188 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain: "g" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 771 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "u" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1376 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "v" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2962 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 357} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain: "E" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2980 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 356} Chain: "F" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2911 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 352} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2201 Classifications: {'peptide': 279} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 268} Chain breaks: 1 Chain: "K" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1720 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 349 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 1 Chain: "U" Number of atoms: 6536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 838, 6536 Classifications: {'peptide': 838} Link IDs: {'PTRANS': 28, 'TRANS': 809} Chain breaks: 4 Chain: "f" Number of atoms: 6512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 842, 6512 Classifications: {'peptide': 842} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 811} Chain breaks: 1 Chain: "V" Number of atoms: 3586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3586 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 15, 'TRANS': 424} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY Z 30 " occ=0.66 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.66 Time building chain proxies: 28.20, per 1000 atoms: 0.40 Number of scatterers: 70912 At special positions: 0 Unit cell: (208.552, 221.128, 199.12, 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 1 29.99 S 383 16.00 P 14 15.00 Mg 2 11.99 O 13468 8.00 N 12205 7.00 C 44839 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.05 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " distance=1.99 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.51 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 113 " 17770 Ramachandran restraints generated. 8885 Oldfield, 0 Emsley, 8885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MET J 71 " Number of C-beta restraints generated: 16962 Finding SS restraints... Secondary structure from input PDB file: 405 helices and 47 sheets defined 61.4% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.81 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 removed outlier: 4.440A pdb=" N ALA A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.584A pdb=" N ASP A 83 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 158 through 164 removed outlier: 3.598A pdb=" N MET A 164 " --> pdb=" O THR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 205 removed outlier: 4.416A pdb=" N PHE A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 242 through 246 removed outlier: 4.036A pdb=" N VAL A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 242 through 246' Processing helix chain 'A' and resid 251 through 267 removed outlier: 3.892A pdb=" N LYS A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.040A pdb=" N GLY A 282 " --> pdb=" O ASP A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 307 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 362 removed outlier: 4.127A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 Processing helix chain 'A' and resid 381 through 399 Processing helix chain 'A' and resid 405 through 422 Processing helix chain 'C' and resid 22 through 67 Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.668A pdb=" N ILE C 151 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 165 Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 195 through 208 removed outlier: 3.990A pdb=" N ALA C 200 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C 202 " --> pdb=" O LEU C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 220 Processing helix chain 'C' and resid 226 through 231 Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.992A pdb=" N ALA C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 299 through 306 removed outlier: 4.124A pdb=" N SER C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 304 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 334 removed outlier: 3.641A pdb=" N HIS C 332 " --> pdb=" O ILE C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 349 removed outlier: 3.667A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 373 removed outlier: 4.155A pdb=" N CYS C 363 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 394 removed outlier: 3.632A pdb=" N ALA C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 406 Processing helix chain 'D' and resid 40 through 83 removed outlier: 3.588A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 170 through 187 removed outlier: 3.505A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 188 through 192 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 231 through 236 removed outlier: 3.713A pdb=" N PHE D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 231 through 236' Processing helix chain 'D' and resid 242 through 257 removed outlier: 3.810A pdb=" N ARG D 248 " --> pdb=" O PRO D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 298 Processing helix chain 'D' and resid 318 through 323 Processing helix chain 'D' and resid 339 through 352 removed outlier: 3.680A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 4.362A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 389 removed outlier: 4.539A pdb=" N SER D 382 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY D 383 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'G' and resid 8 through 12 removed outlier: 4.269A pdb=" N HIS G 12 " --> pdb=" O PHE G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.546A pdb=" N VAL G 66 " --> pdb=" O SER G 63 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR G 67 " --> pdb=" O SER G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 171 through 184 removed outlier: 3.776A pdb=" N SER G 175 " --> pdb=" O LYS G 171 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 231 through 244 removed outlier: 4.006A pdb=" N GLU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 32 removed outlier: 3.712A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 3.645A pdb=" N TYR H 83 " --> pdb=" O MET H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 121 removed outlier: 3.614A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 removed outlier: 3.766A pdb=" N GLY H 170 " --> pdb=" O ASN H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 199 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'I' and resid 18 through 30 removed outlier: 3.520A pdb=" N HIS I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 Processing helix chain 'I' and resid 106 through 124 Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'I' and resid 229 through 250 removed outlier: 3.508A pdb=" N VAL I 233 " --> pdb=" O LYS I 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 29 Processing helix chain 'J' and resid 56 through 60 removed outlier: 3.707A pdb=" N ARG J 60 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 98 Processing helix chain 'J' and resid 103 through 120 removed outlier: 3.806A pdb=" N ILE J 107 " --> pdb=" O THR J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 176 removed outlier: 4.040A pdb=" N SER J 167 " --> pdb=" O ARG J 163 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU J 170 " --> pdb=" O LYS J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 198 removed outlier: 3.888A pdb=" N LEU J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 239 Processing helix chain 'L' and resid 19 through 31 Processing helix chain 'L' and resid 77 through 99 removed outlier: 4.031A pdb=" N ALA L 81 " --> pdb=" O LEU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 122 Proline residue: L 119 - end of helix Processing helix chain 'L' and resid 164 through 180 removed outlier: 4.663A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 Processing helix chain 'L' and resid 225 through 233 Proline residue: L 231 - end of helix Processing helix chain 'M' and resid 20 through 32 Processing helix chain 'M' and resid 80 through 103 Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.941A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 178 Processing helix chain 'M' and resid 186 through 200 removed outlier: 3.537A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 219 through 221 No H-bonds generated for 'chain 'M' and resid 219 through 221' Processing helix chain 'M' and resid 233 through 243 removed outlier: 3.531A pdb=" N LEU M 243 " --> pdb=" O ALA M 239 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 71 Processing helix chain 'O' and resid 75 through 90 removed outlier: 4.300A pdb=" N ALA O 79 " --> pdb=" O ARG O 75 " (cutoff:3.500A) Processing helix chain 'W' and resid 20 through 25 removed outlier: 3.782A pdb=" N ASP W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 37 removed outlier: 4.195A pdb=" N GLU W 30 " --> pdb=" O GLN W 26 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 58 Processing helix chain 'W' and resid 59 through 77 Processing helix chain 'W' and resid 79 through 93 Processing helix chain 'W' and resid 97 through 115 Processing helix chain 'W' and resid 117 through 132 Processing helix chain 'W' and resid 135 through 157 removed outlier: 3.855A pdb=" N ILE W 140 " --> pdb=" O ILE W 136 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU W 141 " --> pdb=" O TYR W 137 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG W 144 " --> pdb=" O ILE W 140 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 169 Processing helix chain 'W' and resid 170 through 174 Processing helix chain 'W' and resid 178 through 196 Processing helix chain 'W' and resid 198 through 209 Processing helix chain 'W' and resid 210 through 214 removed outlier: 3.748A pdb=" N PHE W 213 " --> pdb=" O ASN W 210 " (cutoff:3.500A) Processing helix chain 'W' and resid 216 through 218 No H-bonds generated for 'chain 'W' and resid 216 through 218' Processing helix chain 'W' and resid 219 through 238 Processing helix chain 'W' and resid 239 through 252 Processing helix chain 'W' and resid 253 through 259 removed outlier: 3.535A pdb=" N GLU W 259 " --> pdb=" O CYS W 255 " (cutoff:3.500A) Processing helix chain 'W' and resid 259 through 277 Processing helix chain 'W' and resid 280 through 292 Processing helix chain 'W' and resid 293 through 299 removed outlier: 4.069A pdb=" N GLU W 297 " --> pdb=" O ASP W 293 " (cutoff:3.500A) Processing helix chain 'W' and resid 299 through 311 removed outlier: 3.612A pdb=" N LYS W 303 " --> pdb=" O ILE W 299 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 330 removed outlier: 3.526A pdb=" N LEU W 320 " --> pdb=" O ARG W 316 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) Processing helix chain 'W' and resid 344 through 369 Processing helix chain 'W' and resid 375 through 383 Processing helix chain 'W' and resid 385 through 399 Processing helix chain 'W' and resid 420 through 454 Processing helix chain 'X' and resid 45 through 60 removed outlier: 4.231A pdb=" N SER X 49 " --> pdb=" O VAL X 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 80 Proline residue: X 75 - end of helix Processing helix chain 'X' and resid 81 through 98 Processing helix chain 'X' and resid 105 through 120 Processing helix chain 'X' and resid 122 through 140 Processing helix chain 'X' and resid 142 through 160 Processing helix chain 'X' and resid 162 through 180 Processing helix chain 'X' and resid 182 through 200 removed outlier: 3.714A pdb=" N ILE X 200 " --> pdb=" O THR X 196 " (cutoff:3.500A) Processing helix chain 'X' and resid 203 through 221 Processing helix chain 'X' and resid 225 through 243 Processing helix chain 'X' and resid 245 through 261 Processing helix chain 'X' and resid 263 through 272 removed outlier: 3.828A pdb=" N VAL X 267 " --> pdb=" O THR X 263 " (cutoff:3.500A) Processing helix chain 'X' and resid 275 through 279 removed outlier: 4.230A pdb=" N ARG X 278 " --> pdb=" O LEU X 275 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 Processing helix chain 'X' and resid 298 through 309 Processing helix chain 'X' and resid 309 through 314 Processing helix chain 'X' and resid 316 through 340 removed outlier: 3.706A pdb=" N GLU X 340 " --> pdb=" O ILE X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 347 through 355 Processing helix chain 'X' and resid 357 through 371 Processing helix chain 'X' and resid 394 through 417 removed outlier: 3.516A pdb=" N GLU X 398 " --> pdb=" O ASP X 394 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 28 Processing helix chain 'Y' and resid 28 through 33 Processing helix chain 'Y' and resid 35 through 49 removed outlier: 4.258A pdb=" N ASP Y 39 " --> pdb=" O ALA Y 35 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU Y 40 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 62 removed outlier: 3.550A pdb=" N SER Y 60 " --> pdb=" O ALA Y 56 " (cutoff:3.500A) Processing helix chain 'Y' and resid 66 through 95 Processing helix chain 'Y' and resid 96 through 114 removed outlier: 3.807A pdb=" N ILE Y 100 " --> pdb=" O GLY Y 96 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 130 Processing helix chain 'Y' and resid 133 through 152 removed outlier: 3.604A pdb=" N ARG Y 137 " --> pdb=" O ALA Y 133 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 170 removed outlier: 3.548A pdb=" N ILE Y 157 " --> pdb=" O ASP Y 153 " (cutoff:3.500A) Processing helix chain 'Y' and resid 173 through 191 Processing helix chain 'Y' and resid 193 through 204 Processing helix chain 'Y' and resid 215 through 231 Processing helix chain 'Y' and resid 232 through 240 Processing helix chain 'Y' and resid 243 through 253 removed outlier: 3.781A pdb=" N SER Y 252 " --> pdb=" O GLU Y 248 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 265 Processing helix chain 'Y' and resid 267 through 285 Processing helix chain 'Y' and resid 288 through 309 removed outlier: 3.715A pdb=" N ARG Y 293 " --> pdb=" O ALA Y 289 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR Y 294 " --> pdb=" O PRO Y 290 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 324 Processing helix chain 'Y' and resid 326 through 340 removed outlier: 3.797A pdb=" N ILE Y 330 " --> pdb=" O GLY Y 326 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 384 Processing helix chain 'a' and resid 4 through 6 No H-bonds generated for 'chain 'a' and resid 4 through 6' Processing helix chain 'a' and resid 7 through 12 Processing helix chain 'a' and resid 17 through 31 Processing helix chain 'a' and resid 33 through 46 Processing helix chain 'a' and resid 52 through 65 removed outlier: 3.748A pdb=" N LEU a 56 " --> pdb=" O GLN a 52 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER a 65 " --> pdb=" O GLU a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 88 removed outlier: 3.562A pdb=" N THR a 88 " --> pdb=" O VAL a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 105 removed outlier: 5.129A pdb=" N LYS a 103 " --> pdb=" O LYS a 99 " (cutoff:3.500A) Processing helix chain 'a' and resid 109 through 125 removed outlier: 4.188A pdb=" N LEU a 113 " --> pdb=" O GLU a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 143 removed outlier: 3.558A pdb=" N THR a 134 " --> pdb=" O VAL a 130 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET a 141 " --> pdb=" O ASP a 137 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 145 through 148 removed outlier: 4.278A pdb=" N VAL a 148 " --> pdb=" O LEU a 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 145 through 148' Processing helix chain 'a' and resid 149 through 164 removed outlier: 3.912A pdb=" N GLN a 164 " --> pdb=" O SER a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 183 Processing helix chain 'a' and resid 189 through 207 removed outlier: 3.697A pdb=" N GLN a 193 " --> pdb=" O PRO a 189 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 243 Processing helix chain 'a' and resid 246 through 257 removed outlier: 3.638A pdb=" N GLN a 257 " --> pdb=" O THR a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 257 through 284 removed outlier: 3.660A pdb=" N ALA a 263 " --> pdb=" O PRO a 259 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA a 266 " --> pdb=" O ALA a 262 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN a 267 " --> pdb=" O ALA a 263 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG a 284 " --> pdb=" O MET a 280 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 300 Processing helix chain 'a' and resid 303 through 318 removed outlier: 4.312A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY a 318 " --> pdb=" O ALA a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 371 Processing helix chain 'a' and resid 371 through 376 removed outlier: 4.374A pdb=" N THR a 376 " --> pdb=" O HIS a 372 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 18 Processing helix chain 'b' and resid 24 through 44 removed outlier: 4.065A pdb=" N ASN b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 76 removed outlier: 4.140A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 98 Processing helix chain 'b' and resid 120 through 134 removed outlier: 4.661A pdb=" N LYS b 126 " --> pdb=" O LYS b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 162 Processing helix chain 'b' and resid 180 through 185 removed outlier: 3.626A pdb=" N ILE b 184 " --> pdb=" O ALA b 180 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER b 185 " --> pdb=" O ASP b 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 180 through 185' Processing helix chain 'd' and resid 83 through 104 Processing helix chain 'd' and resid 108 through 124 removed outlier: 3.609A pdb=" N LEU d 121 " --> pdb=" O GLY d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 159 removed outlier: 3.924A pdb=" N LEU d 141 " --> pdb=" O THR d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 177 Processing helix chain 'd' and resid 185 through 202 removed outlier: 3.984A pdb=" N HIS d 189 " --> pdb=" O SER d 185 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN d 190 " --> pdb=" O ALA d 186 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 215 Processing helix chain 'd' and resid 216 through 223 Processing helix chain 'd' and resid 223 through 239 Proline residue: d 229 - end of helix Processing helix chain 'd' and resid 240 through 245 removed outlier: 3.525A pdb=" N PHE d 245 " --> pdb=" O TYR d 241 " (cutoff:3.500A) Processing helix chain 'd' and resid 246 through 251 removed outlier: 3.938A pdb=" N GLY d 249 " --> pdb=" O LEU d 246 " (cutoff:3.500A) Processing helix chain 'd' and resid 253 through 279 removed outlier: 3.597A pdb=" N LYS d 277 " --> pdb=" O GLY d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 284 through 291 Processing helix chain 'd' and resid 295 through 307 removed outlier: 3.699A pdb=" N MET d 299 " --> pdb=" O THR d 295 " (cutoff:3.500A) Processing helix chain 'd' and resid 318 through 323 Processing helix chain 'd' and resid 332 through 348 Processing helix chain 'g' and resid 108 through 121 Processing helix chain 'g' and resid 123 through 125 No H-bonds generated for 'chain 'g' and resid 123 through 125' Processing helix chain 'g' and resid 161 through 172 Processing helix chain 'u' and resid 131 through 135 Processing helix chain 'u' and resid 141 through 145 removed outlier: 4.121A pdb=" N GLY u 145 " --> pdb=" O ASP u 142 " (cutoff:3.500A) Processing helix chain 'u' and resid 146 through 151 removed outlier: 3.502A pdb=" N LEU u 150 " --> pdb=" O PHE u 146 " (cutoff:3.500A) Processing helix chain 'u' and resid 205 through 212 Processing helix chain 'u' and resid 274 through 278 Processing helix chain 'B' and resid 58 through 85 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 208 through 215 Processing helix chain 'B' and resid 231 through 243 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.622A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 256' Processing helix chain 'B' and resid 261 through 278 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.502A pdb=" N LEU B 337 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 357 through 370 Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.810A pdb=" N MET B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 415 through 429 Processing helix chain 'Z' and resid 12 through 28 removed outlier: 3.805A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 104 through 116 removed outlier: 3.560A pdb=" N TYR Z 115 " --> pdb=" O LEU Z 111 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 178 removed outlier: 4.378A pdb=" N ASP Z 178 " --> pdb=" O HIS Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 217 Processing helix chain 'Z' and resid 226 through 237 Processing helix chain 'Z' and resid 242 through 289 Processing helix chain 'E' and resid 16 through 51 Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 116 through 125 Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 138 through 146 Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 156 through 163 Processing helix chain 'E' and resid 179 through 191 Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'E' and resid 209 through 225 removed outlier: 3.561A pdb=" N ARG E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 240 Processing helix chain 'E' and resid 247 through 266 removed outlier: 3.832A pdb=" N GLY E 266 " --> pdb=" O ASN E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.587A pdb=" N LEU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 318 Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.655A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 358 removed outlier: 3.603A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 381 removed outlier: 3.679A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 84 removed outlier: 3.734A pdb=" N LYS F 56 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL F 59 " --> pdb=" O MET F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 169 through 176 removed outlier: 3.688A pdb=" N GLU F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 191 through 208 removed outlier: 3.751A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 232 through 245 removed outlier: 4.605A pdb=" N LYS F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 258 removed outlier: 4.406A pdb=" N GLN F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 288 through 293 Processing helix chain 'F' and resid 304 through 319 Processing helix chain 'F' and resid 334 through 339 removed outlier: 4.016A pdb=" N LEU F 338 " --> pdb=" O ARG F 334 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP F 339 " --> pdb=" O VAL F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 339' Processing helix chain 'F' and resid 358 through 374 removed outlier: 4.228A pdb=" N LYS F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET F 373 " --> pdb=" O HIS F 369 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 411 Processing helix chain 'F' and resid 416 through 428 Processing helix chain 'c' and resid 34 through 49 Processing helix chain 'c' and resid 83 through 87 Processing helix chain 'c' and resid 88 through 101 removed outlier: 3.623A pdb=" N GLN c 101 " --> pdb=" O ASP c 97 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 164 through 170 removed outlier: 3.855A pdb=" N MET c 168 " --> pdb=" O ASN c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 195 removed outlier: 3.543A pdb=" N HIS c 194 " --> pdb=" O GLN c 190 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 219 removed outlier: 3.981A pdb=" N ASN c 219 " --> pdb=" O LYS c 215 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 230 Processing helix chain 'c' and resid 233 through 261 Processing helix chain 'c' and resid 279 through 309 removed outlier: 4.285A pdb=" N HIS c 283 " --> pdb=" O ASP c 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 33 removed outlier: 3.726A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 64 removed outlier: 3.630A pdb=" N ILE K 64 " --> pdb=" O PRO K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 104 Processing helix chain 'K' and resid 108 through 121 removed outlier: 3.504A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 185 Processing helix chain 'K' and resid 190 through 207 removed outlier: 4.430A pdb=" N GLU K 207 " --> pdb=" O LYS K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 241 removed outlier: 4.211A pdb=" N VAL K 237 " --> pdb=" O GLU K 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 64 Processing helix chain 'U' and resid 6 through 14 removed outlier: 3.837A pdb=" N SER U 10 " --> pdb=" O ALA U 6 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU U 11 " --> pdb=" O GLY U 7 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 31 Processing helix chain 'U' and resid 34 through 51 removed outlier: 3.680A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP U 43 " --> pdb=" O SER U 39 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS U 44 " --> pdb=" O GLU U 40 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL U 47 " --> pdb=" O ASP U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 84 removed outlier: 3.500A pdb=" N SER U 77 " --> pdb=" O ALA U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 94 through 116 removed outlier: 3.605A pdb=" N ASP U 106 " --> pdb=" O ALA U 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 145 removed outlier: 3.540A pdb=" N ASP U 144 " --> pdb=" O ARG U 140 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 157 removed outlier: 6.237A pdb=" N GLY U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE U 153 " --> pdb=" O GLN U 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 169 Processing helix chain 'U' and resid 173 through 188 removed outlier: 4.234A pdb=" N LEU U 177 " --> pdb=" O VAL U 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 208 Processing helix chain 'U' and resid 212 through 224 Processing helix chain 'U' and resid 225 through 239 Processing helix chain 'U' and resid 242 through 254 Processing helix chain 'U' and resid 257 through 270 Processing helix chain 'U' and resid 321 through 330 Processing helix chain 'U' and resid 331 through 345 Processing helix chain 'U' and resid 350 through 355 Processing helix chain 'U' and resid 364 through 377 removed outlier: 3.536A pdb=" N ALA U 368 " --> pdb=" O VAL U 364 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 389 removed outlier: 3.722A pdb=" N ASN U 389 " --> pdb=" O PHE U 385 " (cutoff:3.500A) Processing helix chain 'U' and resid 389 through 395 removed outlier: 3.635A pdb=" N LEU U 393 " --> pdb=" O ASN U 389 " (cutoff:3.500A) Processing helix chain 'U' and resid 397 through 412 Processing helix chain 'U' and resid 418 through 427 Processing helix chain 'U' and resid 436 through 450 Processing helix chain 'U' and resid 454 through 468 Processing helix chain 'U' and resid 471 through 485 Processing helix chain 'U' and resid 490 through 503 Processing helix chain 'U' and resid 505 through 521 removed outlier: 3.515A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 537 Processing helix chain 'U' and resid 541 through 557 removed outlier: 3.619A pdb=" N LEU U 545 " --> pdb=" O HIS U 541 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA U 553 " --> pdb=" O ALA U 549 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR U 557 " --> pdb=" O ALA U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 559 through 571 removed outlier: 3.517A pdb=" N ASP U 564 " --> pdb=" O MET U 560 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA U 565 " --> pdb=" O GLU U 561 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU U 566 " --> pdb=" O GLU U 562 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 590 Processing helix chain 'U' and resid 595 through 609 Processing helix chain 'U' and resid 611 through 627 removed outlier: 3.792A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) Processing helix chain 'U' and resid 631 through 642 removed outlier: 3.532A pdb=" N SER U 635 " --> pdb=" O GLU U 631 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU U 642 " --> pdb=" O SER U 638 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 661 Processing helix chain 'U' and resid 666 through 678 Proline residue: U 674 - end of helix removed outlier: 3.539A pdb=" N ASN U 677 " --> pdb=" O GLU U 673 " (cutoff:3.500A) Processing helix chain 'U' and resid 680 through 696 removed outlier: 3.518A pdb=" N ARG U 684 " --> pdb=" O VAL U 680 " (cutoff:3.500A) Processing helix chain 'U' and resid 705 through 719 Processing helix chain 'U' and resid 723 through 738 Processing helix chain 'U' and resid 739 through 742 Processing helix chain 'U' and resid 756 through 769 Processing helix chain 'U' and resid 770 through 773 removed outlier: 5.975A pdb=" N PHE U 773 " --> pdb=" O TRP U 770 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 770 through 773' Processing helix chain 'U' and resid 774 through 780 removed outlier: 4.081A pdb=" N PHE U 778 " --> pdb=" O PRO U 774 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU U 779 " --> pdb=" O LEU U 775 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER U 780 " --> pdb=" O SER U 776 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 774 through 780' Processing helix chain 'U' and resid 781 through 783 No H-bonds generated for 'chain 'U' and resid 781 through 783' Processing helix chain 'U' and resid 835 through 846 Processing helix chain 'U' and resid 885 through 890 Processing helix chain 'f' and resid 46 through 63 removed outlier: 3.541A pdb=" N LEU f 52 " --> pdb=" O GLU f 48 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 88 Proline residue: f 73 - end of helix Processing helix chain 'f' and resid 93 through 99 Processing helix chain 'f' and resid 102 through 105 removed outlier: 3.775A pdb=" N LYS f 105 " --> pdb=" O HIS f 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 102 through 105' Processing helix chain 'f' and resid 106 through 113 Processing helix chain 'f' and resid 116 through 131 removed outlier: 3.541A pdb=" N MET f 131 " --> pdb=" O SER f 127 " (cutoff:3.500A) Processing helix chain 'f' and resid 135 through 146 removed outlier: 4.096A pdb=" N CYS f 139 " --> pdb=" O GLY f 135 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU f 140 " --> pdb=" O GLU f 136 " (cutoff:3.500A) Processing helix chain 'f' and resid 150 through 154 Processing helix chain 'f' and resid 155 through 173 Processing helix chain 'f' and resid 180 through 198 Proline residue: f 193 - end of helix Processing helix chain 'f' and resid 200 through 211 Processing helix chain 'f' and resid 214 through 218 Processing helix chain 'f' and resid 225 through 238 removed outlier: 3.655A pdb=" N ASN f 238 " --> pdb=" O THR f 234 " (cutoff:3.500A) Processing helix chain 'f' and resid 243 through 260 removed outlier: 3.619A pdb=" N ALA f 247 " --> pdb=" O PRO f 243 " (cutoff:3.500A) Processing helix chain 'f' and resid 261 through 273 Processing helix chain 'f' and resid 274 through 285 Processing helix chain 'f' and resid 287 through 302 Processing helix chain 'f' and resid 313 through 323 Processing helix chain 'f' and resid 323 through 337 Processing helix chain 'f' and resid 344 through 350 Processing helix chain 'f' and resid 351 through 354 Processing helix chain 'f' and resid 361 through 365 removed outlier: 3.957A pdb=" N VAL f 365 " --> pdb=" O GLY f 362 " (cutoff:3.500A) Processing helix chain 'f' and resid 367 through 382 Processing helix chain 'f' and resid 389 through 394 Processing helix chain 'f' and resid 394 through 402 removed outlier: 3.602A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 403 through 418 Processing helix chain 'f' and resid 421 through 430 Processing helix chain 'f' and resid 431 through 435 removed outlier: 4.047A pdb=" N TYR f 434 " --> pdb=" O LYS f 431 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER f 435 " --> pdb=" O TYR f 432 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 431 through 435' Processing helix chain 'f' and resid 438 through 453 removed outlier: 4.251A pdb=" N SER f 442 " --> pdb=" O ASP f 438 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY f 443 " --> pdb=" O TYR f 439 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 468 removed outlier: 3.603A pdb=" N ALA f 464 " --> pdb=" O ASP f 460 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP f 468 " --> pdb=" O ALA f 464 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 489 Processing helix chain 'f' and resid 494 through 506 Proline residue: f 503 - end of helix removed outlier: 4.122A pdb=" N GLY f 506 " --> pdb=" O LEU f 502 " (cutoff:3.500A) Processing helix chain 'f' and resid 511 through 526 removed outlier: 3.650A pdb=" N ALA f 515 " --> pdb=" O SER f 511 " (cutoff:3.500A) Processing helix chain 'f' and resid 531 through 544 Processing helix chain 'f' and resid 546 through 551 Processing helix chain 'f' and resid 556 through 567 Processing helix chain 'f' and resid 569 through 582 removed outlier: 3.587A pdb=" N ILE f 573 " --> pdb=" O LYS f 569 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA f 578 " --> pdb=" O GLU f 574 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) Processing helix chain 'f' and resid 586 through 601 Processing helix chain 'f' and resid 605 through 616 Processing helix chain 'f' and resid 645 through 663 removed outlier: 4.294A pdb=" N GLY f 663 " --> pdb=" O LEU f 659 " (cutoff:3.500A) Processing helix chain 'f' and resid 664 through 682 removed outlier: 3.575A pdb=" N ARG f 673 " --> pdb=" O GLU f 669 " (cutoff:3.500A) Processing helix chain 'f' and resid 683 through 699 Proline residue: f 691 - end of helix Processing helix chain 'f' and resid 703 through 715 Processing helix chain 'f' and resid 718 through 733 Processing helix chain 'f' and resid 738 through 752 Processing helix chain 'f' and resid 755 through 772 removed outlier: 4.458A pdb=" N GLY f 772 " --> pdb=" O LEU f 768 " (cutoff:3.500A) Processing helix chain 'f' and resid 789 through 806 removed outlier: 3.595A pdb=" N VAL f 799 " --> pdb=" O GLY f 795 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP f 805 " --> pdb=" O VAL f 801 " (cutoff:3.500A) Processing helix chain 'f' and resid 814 through 825 removed outlier: 4.109A pdb=" N LEU f 818 " --> pdb=" O SER f 814 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL f 822 " --> pdb=" O LEU f 818 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA f 824 " --> pdb=" O GLY f 820 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 67 Processing helix chain 'V' and resid 69 through 89 Processing helix chain 'V' and resid 91 through 106 Proline residue: V 102 - end of helix removed outlier: 4.346A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 120 removed outlier: 4.077A pdb=" N LEU V 113 " --> pdb=" O ASN V 109 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR V 114 " --> pdb=" O HIS V 110 " (cutoff:3.500A) Processing helix chain 'V' and resid 125 through 132 removed outlier: 3.771A pdb=" N ASP V 129 " --> pdb=" O ASN V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 157 Processing helix chain 'V' and resid 160 through 174 Processing helix chain 'V' and resid 176 through 177 No H-bonds generated for 'chain 'V' and resid 176 through 177' Processing helix chain 'V' and resid 180 through 196 removed outlier: 3.573A pdb=" N ALA V 184 " --> pdb=" O ARG V 180 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS V 186 " --> pdb=" O LYS V 182 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE V 187 " --> pdb=" O GLU V 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 221 removed outlier: 4.098A pdb=" N CYS V 210 " --> pdb=" O VAL V 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR V 211 " --> pdb=" O ALA V 207 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TYR V 212 " --> pdb=" O ALA V 208 " (cutoff:3.500A) Processing helix chain 'V' and resid 224 through 240 Processing helix chain 'V' and resid 245 through 262 removed outlier: 3.527A pdb=" N THR V 249 " --> pdb=" O ASP V 245 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 271 Processing helix chain 'V' and resid 282 through 299 Processing helix chain 'V' and resid 301 through 316 Processing helix chain 'V' and resid 321 through 339 Processing helix chain 'V' and resid 344 through 349 removed outlier: 3.711A pdb=" N ARG V 349 " --> pdb=" O LEU V 346 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 367 Proline residue: V 359 - end of helix Processing helix chain 'V' and resid 371 through 389 removed outlier: 5.141A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) Processing helix chain 'V' and resid 392 through 413 removed outlier: 3.597A pdb=" N ILE V 396 " --> pdb=" O TYR V 392 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE V 403 " --> pdb=" O ARG V 399 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LYS V 404 " --> pdb=" O HIS V 400 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR V 405 " --> pdb=" O ASN V 401 " (cutoff:3.500A) Processing helix chain 'V' and resid 419 through 427 removed outlier: 3.762A pdb=" N ALA V 423 " --> pdb=" O LEU V 419 " (cutoff:3.500A) Processing helix chain 'V' and resid 430 through 445 Processing helix chain 'V' and resid 470 through 493 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 123 removed outlier: 6.554A pdb=" N CYS A 98 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N MET A 138 " --> pdb=" O CYS A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 241 removed outlier: 6.326A pdb=" N CYS A 236 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE A 273 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE A 238 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASP A 275 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 240 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLY A 211 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE A 341 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 213 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 74 through 78 removed outlier: 6.709A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS C 94 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE B 122 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ILE B 115 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS B 120 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 74 through 78 removed outlier: 6.709A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS C 94 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 161 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN B 153 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 159 " --> pdb=" O ASN B 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=AA6, first strand: chain 'C' and resid 140 through 141 removed outlier: 3.630A pdb=" N PHE C 211 " --> pdb=" O GLU C 141 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N MET C 248 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL C 186 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N THR C 295 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU C 188 " --> pdb=" O THR C 295 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 110 through 114 removed outlier: 7.526A pdb=" N THR D 100 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ALA D 95 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE D 102 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 201 through 204 removed outlier: 6.390A pdb=" N ILE D 262 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ALA D 310 " --> pdb=" O ILE D 262 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 165 through 169 removed outlier: 4.798A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N THR G 221 " --> pdb=" O LYS G 226 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS G 226 " --> pdb=" O THR G 221 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 69 through 73 removed outlier: 5.685A pdb=" N ILE G 76 " --> pdb=" O ILE G 72 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY G 148 " --> pdb=" O ASP G 144 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL G 151 " --> pdb=" O PHE G 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AB3, first strand: chain 'H' and resid 66 through 69 removed outlier: 3.805A pdb=" N ILE H 68 " --> pdb=" O ILE H 72 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE H 136 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 162 through 163 Processing sheet with id=AB5, first strand: chain 'I' and resid 65 through 67 Processing sheet with id=AB6, first strand: chain 'J' and resid 158 through 159 Processing sheet with id=AB7, first strand: chain 'J' and resid 63 through 66 removed outlier: 6.015A pdb=" N ALA J 64 " --> pdb=" O MET J 71 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N MET J 71 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP J 137 " --> pdb=" O THR J 141 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N THR J 141 " --> pdb=" O ASP J 137 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 158 through 159 removed outlier: 5.196A pdb=" N GLY L 216 " --> pdb=" O GLU L 220 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLU L 220 " --> pdb=" O GLY L 216 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.510A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 162 through 165 Processing sheet with id=AC2, first strand: chain 'M' and resid 66 through 67 Processing sheet with id=AC3, first strand: chain 'W' and resid 331 through 332 Processing sheet with id=AC4, first strand: chain 'a' and resid 290 through 292 removed outlier: 3.541A pdb=" N ARG a 330 " --> pdb=" O ASP a 325 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N GLU a 326 " --> pdb=" O THR W 371 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE W 373 " --> pdb=" O GLU a 326 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL W 406 " --> pdb=" O SER X 343 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N VAL X 345 " --> pdb=" O VAL W 406 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N SER X 343 " --> pdb=" O ILE X 387 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ARG Y 312 " --> pdb=" O GLY X 376 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU X 378 " --> pdb=" O ARG Y 312 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LEU Y 314 " --> pdb=" O LEU X 378 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ARG Y 312 " --> pdb=" O THR Y 356 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N CYS Y 345 " --> pdb=" O TYR V 414 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N ARG V 416 " --> pdb=" O CYS Y 345 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE Y 347 " --> pdb=" O ARG V 416 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N SER V 418 " --> pdb=" O ILE Y 347 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N SER V 415 " --> pdb=" O SER V 460 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'b' and resid 62 through 65 removed outlier: 5.111A pdb=" N THR b 63 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LEU b 51 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU b 4 " --> pdb=" O ASN b 48 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY b 50 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR b 6 " --> pdb=" O GLY b 50 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N ILE b 52 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL b 8 " --> pdb=" O ILE b 52 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER b 5 " --> pdb=" O ARG b 108 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ILE b 110 " --> pdb=" O SER b 5 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N MET b 7 " --> pdb=" O ILE b 110 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N PHE b 112 " --> pdb=" O MET b 7 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N CYS b 9 " --> pdb=" O PHE b 112 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 281 through 283 Processing sheet with id=AC7, first strand: chain 'g' and resid 99 through 102 removed outlier: 4.335A pdb=" N VAL g 151 " --> pdb=" O THR g 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'u' and resid 124 through 125 Processing sheet with id=AC9, first strand: chain 'u' and resid 124 through 125 removed outlier: 3.599A pdb=" N LEU u 165 " --> pdb=" O VAL u 248 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN u 242 " --> pdb=" O PHE u 171 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR u 193 " --> pdb=" O GLN u 249 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ASN u 251 " --> pdb=" O PRO u 191 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN u 216 " --> pdb=" O ILE u 196 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'u' and resid 157 through 158 Processing sheet with id=AD2, first strand: chain 'u' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'B' and resid 246 through 251 removed outlier: 6.278A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 250 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER B 280 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE B 328 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 282 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ALA B 330 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE B 284 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 152 through 157 removed outlier: 3.930A pdb=" N SER Z 152 " --> pdb=" O GLU Z 143 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU Z 143 " --> pdb=" O SER Z 152 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N VAL Z 120 " --> pdb=" O ARG Z 90 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL Z 92 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL Z 122 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP Z 94 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ILE Z 91 " --> pdb=" O GLY Z 41 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLY Z 41 " --> pdb=" O ILE Z 91 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY Z 93 " --> pdb=" O LEU Z 39 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N SER Z 42 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N VAL Z 50 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLN Z 44 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LEU Z 48 " --> pdb=" O GLN Z 44 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 58 through 59 Processing sheet with id=AD6, first strand: chain 'E' and resid 107 through 110 removed outlier: 6.892A pdb=" N ILE E 107 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP E 101 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG E 109 " --> pdb=" O ALA E 99 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N THR F 131 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 123 " --> pdb=" O ILE F 94 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 63 through 65 Processing sheet with id=AD8, first strand: chain 'E' and resid 194 through 199 removed outlier: 6.305A pdb=" N ASN E 194 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N PHE E 231 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU E 196 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ASP E 233 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL E 198 " --> pdb=" O ASP E 233 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS E 228 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE E 276 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE E 230 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA E 278 " --> pdb=" O ILE E 230 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N MET E 232 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLY E 169 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE E 299 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU E 171 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 247 through 252 removed outlier: 6.146A pdb=" N THR F 247 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N PHE F 284 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU F 249 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP F 286 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU F 251 " --> pdb=" O ASP F 286 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER F 281 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE F 329 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE F 283 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N ALA F 331 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 285 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLY F 222 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ILE F 352 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU F 224 " --> pdb=" O ILE F 352 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 31 through 33 removed outlier: 6.116A pdb=" N VAL c 31 " --> pdb=" O ASN c 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'c' and resid 68 through 74 removed outlier: 5.043A pdb=" N VAL c 69 " --> pdb=" O GLU c 60 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU c 60 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY c 110 " --> pdb=" O MET c 57 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 167 through 170 Processing sheet with id=AE4, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.611A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU K 153 " --> pdb=" O CYS K 165 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 744 through 745 Processing sheet with id=AE6, first strand: chain 'U' and resid 881 through 882 Processing sheet with id=AE7, first strand: chain 'f' and resid 776 through 777 Processing sheet with id=AE8, first strand: chain 'f' and resid 781 through 782 Processing sheet with id=AE9, first strand: chain 'f' and resid 838 through 839 Processing sheet with id=AF1, first strand: chain 'f' and resid 838 through 839 removed outlier: 7.617A pdb=" N VAL f 898 " --> pdb=" O MET f 829 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL f 831 " --> pdb=" O VAL f 898 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU f 900 " --> pdb=" O VAL f 831 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N PHE f 833 " --> pdb=" O LEU f 900 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LYS f 902 " --> pdb=" O PHE f 833 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'f' and resid 866 through 869 4169 hydrogen bonds defined for protein. 12126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 31.31 Time building geometry restraints manager: 15.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.26: 12167 1.26 - 1.69: 59277 1.69 - 2.13: 643 2.13 - 2.56: 2 2.56 - 2.99: 3 Bond restraints: 72092 Sorted by residual: bond pdb=" CA MET J 71 " pdb=" C MET J 71 " ideal model delta sigma weight residual 1.522 2.993 -1.471 1.24e-02 6.50e+03 1.41e+04 bond pdb=" C LEU V 67 " pdb=" N ASP V 68 " ideal model delta sigma weight residual 1.335 2.749 -1.415 1.31e-02 5.83e+03 1.17e+04 bond pdb=" C PHE V 174 " pdb=" N MET V 175 " ideal model delta sigma weight residual 1.335 2.587 -1.252 1.31e-02 5.83e+03 9.14e+03 bond pdb=" C HIS V 110 " pdb=" N TYR V 111 " ideal model delta sigma weight residual 1.332 2.219 -0.887 1.36e-02 5.41e+03 4.26e+03 bond pdb=" C PRO V 138 " pdb=" N MET V 139 " ideal model delta sigma weight residual 1.329 2.351 -1.022 1.71e-02 3.42e+03 3.57e+03 ... (remaining 72087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.31: 97392 11.31 - 22.62: 36 22.62 - 33.93: 2 33.93 - 45.24: 0 45.24 - 56.55: 4 Bond angle restraints: 97434 Sorted by residual: angle pdb=" O PHE V 174 " pdb=" C PHE V 174 " pdb=" N MET V 175 " ideal model delta sigma weight residual 122.12 168.74 -46.62 1.06e+00 8.90e-01 1.93e+03 angle pdb=" O PRO V 158 " pdb=" C PRO V 158 " pdb=" N LEU V 159 " ideal model delta sigma weight residual 122.64 66.09 56.55 1.35e+00 5.49e-01 1.75e+03 angle pdb=" CA PHE V 174 " pdb=" C PHE V 174 " pdb=" N MET V 175 " ideal model delta sigma weight residual 117.30 69.99 47.31 1.16e+00 7.43e-01 1.66e+03 angle pdb=" C PHE V 174 " pdb=" N MET V 175 " pdb=" CA MET V 175 " ideal model delta sigma weight residual 120.28 73.53 46.75 1.34e+00 5.57e-01 1.22e+03 angle pdb=" O SER V 105 " pdb=" C SER V 105 " pdb=" N ARG V 106 " ideal model delta sigma weight residual 122.59 90.56 32.03 1.33e+00 5.65e-01 5.80e+02 ... (remaining 97429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 41483 24.98 - 49.96: 2333 49.96 - 74.93: 339 74.93 - 99.91: 93 99.91 - 124.89: 7 Dihedral angle restraints: 44255 sinusoidal: 18045 harmonic: 26210 Sorted by residual: dihedral pdb=" CA ALA C 242 " pdb=" C ALA C 242 " pdb=" N PRO C 243 " pdb=" CA PRO C 243 " ideal model delta harmonic sigma weight residual -180.00 -65.26 -114.74 0 5.00e+00 4.00e-02 5.27e+02 dihedral pdb=" CA LEU F 86 " pdb=" C LEU F 86 " pdb=" N PRO F 87 " pdb=" CA PRO F 87 " ideal model delta harmonic sigma weight residual 180.00 65.84 114.16 0 5.00e+00 4.00e-02 5.21e+02 dihedral pdb=" C LEU V 224 " pdb=" N LEU V 224 " pdb=" CA LEU V 224 " pdb=" CB LEU V 224 " ideal model delta harmonic sigma weight residual -122.60 -144.05 21.45 0 2.50e+00 1.60e-01 7.36e+01 ... (remaining 44252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.313: 10975 0.313 - 0.626: 163 0.626 - 0.939: 6 0.939 - 1.251: 1 1.251 - 1.564: 1 Chirality restraints: 11146 Sorted by residual: chirality pdb=" CA MET J 71 " pdb=" N MET J 71 " pdb=" C MET J 71 " pdb=" CB MET J 71 " both_signs ideal model delta sigma weight residual False 2.51 4.07 -1.56 2.00e-01 2.50e+01 6.12e+01 chirality pdb=" CB ILE A 403 " pdb=" CA ILE A 403 " pdb=" CG1 ILE A 403 " pdb=" CG2 ILE A 403 " both_signs ideal model delta sigma weight residual False 2.64 1.49 1.16 2.00e-01 2.50e+01 3.34e+01 chirality pdb=" CA LEU V 224 " pdb=" N LEU V 224 " pdb=" C LEU V 224 " pdb=" CB LEU V 224 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.88e+01 ... (remaining 11143 not shown) Planarity restraints: 12551 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO V 158 " 0.178 2.00e-02 2.50e+03 2.26e-01 5.11e+02 pdb=" C PRO V 158 " -0.387 2.00e-02 2.50e+03 pdb=" O PRO V 158 " 0.130 2.00e-02 2.50e+03 pdb=" N LEU V 159 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP A 501 " -0.260 2.00e-02 2.50e+03 1.04e-01 2.99e+02 pdb=" C2 ADP A 501 " 0.029 2.00e-02 2.50e+03 pdb=" C4 ADP A 501 " 0.098 2.00e-02 2.50e+03 pdb=" C5 ADP A 501 " 0.036 2.00e-02 2.50e+03 pdb=" C6 ADP A 501 " -0.039 2.00e-02 2.50e+03 pdb=" C8 ADP A 501 " 0.078 2.00e-02 2.50e+03 pdb=" N1 ADP A 501 " -0.030 2.00e-02 2.50e+03 pdb=" N3 ADP A 501 " 0.087 2.00e-02 2.50e+03 pdb=" N6 ADP A 501 " -0.123 2.00e-02 2.50e+03 pdb=" N7 ADP A 501 " 0.034 2.00e-02 2.50e+03 pdb=" N9 ADP A 501 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 78 " -0.220 2.00e-02 2.50e+03 1.09e-01 2.98e+02 pdb=" CG TRP A 78 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 78 " 0.118 2.00e-02 2.50e+03 pdb=" CD2 TRP A 78 " 0.061 2.00e-02 2.50e+03 pdb=" NE1 TRP A 78 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP A 78 " -0.031 2.00e-02 2.50e+03 pdb=" CE3 TRP A 78 " 0.133 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 78 " -0.119 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 78 " 0.065 2.00e-02 2.50e+03 pdb=" CH2 TRP A 78 " -0.106 2.00e-02 2.50e+03 ... (remaining 12548 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.84: 22 1.84 - 2.60: 783 2.60 - 3.37: 100319 3.37 - 4.13: 176958 4.13 - 4.90: 313387 Nonbonded interactions: 591469 Sorted by model distance: nonbonded pdb=" O ILE V 173 " pdb=" N ASN V 177 " model vdw 1.070 3.120 nonbonded pdb=" O VAL V 172 " pdb=" N MET V 176 " model vdw 1.155 3.120 nonbonded pdb=" SD MET V 192 " pdb=" CE2 TYR V 211 " model vdw 1.162 3.700 nonbonded pdb=" OE2 GLU B 182 " pdb=" NZ LYS B 237 " model vdw 1.299 3.120 nonbonded pdb=" OE2 GLU C 381 " pdb=" NH1 ARG X 155 " model vdw 1.364 3.120 ... (remaining 591464 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.030 Check model and map are aligned: 0.390 Set scattering table: 0.480 Process input model: 130.650 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 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 : 0.016 1.471 72092 Z= 1.068 Angle : 1.964 56.547 97434 Z= 1.316 Chirality : 0.115 1.564 11146 Planarity : 0.017 0.390 12551 Dihedral : 16.003 124.890 27284 Min Nonbonded Distance : 1.070 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 2.67 % Allowed : 8.37 % Favored : 88.96 % Rotamer: Outliers : 5.56 % Allowed : 9.78 % Favored : 84.67 % Cbeta Deviations : 1.21 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.08), residues: 8885 helix: -0.74 (0.06), residues: 4946 sheet: -0.14 (0.17), residues: 776 loop : -2.32 (0.11), residues: 3163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.220 0.029 TRP A 78 HIS 0.030 0.004 HIS V 214 PHE 0.148 0.014 PHE U 34 TYR 0.196 0.023 TYR u 178 ARG 0.016 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17770 Ramachandran restraints generated. 8885 Oldfield, 0 Emsley, 8885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17770 Ramachandran restraints generated. 8885 Oldfield, 0 Emsley, 8885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2611 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 427 poor density : 2184 time to evaluate : 6.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 88 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: A 143 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6890 (p0) REVERT: A 250 VAL cc_start: 0.8666 (m) cc_final: 0.8401 (p) REVERT: A 299 MET cc_start: 0.8823 (tmm) cc_final: 0.8114 (tmm) REVERT: A 300 LEU cc_start: 0.9240 (mt) cc_final: 0.9014 (mp) REVERT: A 303 ILE cc_start: 0.9044 (mt) cc_final: 0.8764 (mt) REVERT: C 63 LEU cc_start: 0.9461 (mt) cc_final: 0.9047 (mp) REVERT: C 150 MET cc_start: 0.8271 (mmm) cc_final: 0.8030 (mmp) REVERT: C 397 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.6304 (pttm) REVERT: C 398 ASN cc_start: 0.5819 (OUTLIER) cc_final: 0.5437 (m110) REVERT: D 40 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7072 (mm) REVERT: D 60 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8051 (t80) REVERT: D 146 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: D 151 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6965 (mm) REVERT: D 152 MET cc_start: 0.7901 (mtt) cc_final: 0.7671 (mtm) REVERT: D 183 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8742 (tp) REVERT: D 189 GLU cc_start: 0.7651 (pm20) cc_final: 0.7386 (pm20) REVERT: D 207 PRO cc_start: 0.8563 (OUTLIER) cc_final: 0.8223 (Cg_endo) REVERT: D 245 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7416 (ptm160) REVERT: D 404 LYS cc_start: 0.8441 (ptpt) cc_final: 0.7952 (tmtt) REVERT: H 79 MET cc_start: 0.5857 (pmm) cc_final: 0.5000 (tpt) REVERT: H 136 ILE cc_start: 0.8271 (mp) cc_final: 0.8015 (mt) REVERT: H 203 MET cc_start: 0.7460 (mtp) cc_final: 0.7102 (mmt) REVERT: I 14 PRO cc_start: 0.7718 (Cg_endo) cc_final: 0.7500 (Cg_exo) REVERT: I 48 GLU cc_start: 0.4203 (OUTLIER) cc_final: 0.3519 (tt0) REVERT: L 140 MET cc_start: 0.5288 (mtp) cc_final: 0.4989 (mtt) REVERT: L 222 THR cc_start: 0.6747 (p) cc_final: 0.5997 (m) REVERT: L 234 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: M 72 HIS cc_start: 0.3233 (OUTLIER) cc_final: 0.2923 (p90) REVERT: M 97 ASN cc_start: 0.7532 (t0) cc_final: 0.7228 (t0) REVERT: M 221 ASN cc_start: 0.6666 (p0) cc_final: 0.6433 (t0) REVERT: M 243 LEU cc_start: 0.5616 (OUTLIER) cc_final: 0.5088 (mt) REVERT: W 20 TYR cc_start: 0.3666 (OUTLIER) cc_final: 0.1848 (t80) REVERT: W 192 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7475 (tt) REVERT: W 314 LEU cc_start: 0.6997 (mt) cc_final: 0.6710 (mt) REVERT: W 451 MET cc_start: 0.6672 (mtm) cc_final: 0.6443 (mtm) REVERT: X 138 PHE cc_start: 0.7287 (t80) cc_final: 0.6535 (t80) REVERT: X 148 HIS cc_start: 0.7730 (OUTLIER) cc_final: 0.6897 (p-80) REVERT: Y 222 TYR cc_start: 0.6724 (m-10) cc_final: 0.6376 (m-80) REVERT: a 22 TRP cc_start: 0.5373 (m100) cc_final: 0.4863 (m100) REVERT: a 25 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7210 (pp) REVERT: a 79 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7248 (mp) REVERT: a 127 ASP cc_start: 0.2039 (OUTLIER) cc_final: 0.1747 (m-30) REVERT: a 137 ASP cc_start: 0.6469 (OUTLIER) cc_final: 0.6076 (p0) REVERT: a 211 PHE cc_start: 0.0364 (OUTLIER) cc_final: -0.0773 (p90) REVERT: a 218 MET cc_start: 0.8297 (mpt) cc_final: 0.7736 (mpp) REVERT: a 248 PHE cc_start: 0.5882 (t80) cc_final: 0.5303 (t80) REVERT: b 133 LYS cc_start: 0.7373 (ptpt) cc_final: 0.6999 (tttt) REVERT: d 168 MET cc_start: 0.7449 (tpp) cc_final: 0.7201 (tpp) REVERT: d 208 PHE cc_start: 0.6076 (OUTLIER) cc_final: 0.5840 (t80) REVERT: d 237 MET cc_start: 0.6560 (ttm) cc_final: 0.6159 (mtp) REVERT: d 279 TYR cc_start: 0.4618 (m-80) cc_final: 0.4077 (m-80) REVERT: g 104 ARG cc_start: 0.7393 (mmt90) cc_final: 0.6875 (mmm160) REVERT: g 151 VAL cc_start: 0.4860 (OUTLIER) cc_final: 0.4502 (m) REVERT: u 138 LEU cc_start: 0.6238 (mt) cc_final: 0.5982 (tp) REVERT: u 148 ASN cc_start: 0.6194 (m-40) cc_final: 0.5901 (m-40) REVERT: B 59 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.5384 (tpm170) REVERT: B 62 LEU cc_start: 0.8765 (tp) cc_final: 0.7361 (tp) REVERT: B 96 ARG cc_start: 0.7998 (mmp80) cc_final: 0.7694 (ptp-170) REVERT: B 164 MET cc_start: 0.7664 (tpp) cc_final: 0.7189 (mmm) REVERT: B 178 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8146 (mmtm) REVERT: B 424 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6578 (mt-10) REVERT: E 132 TYR cc_start: 0.8922 (m-80) cc_final: 0.8097 (m-80) REVERT: E 171 LEU cc_start: 0.9196 (tp) cc_final: 0.8968 (tt) REVERT: E 267 PHE cc_start: 0.7903 (t80) cc_final: 0.7660 (t80) REVERT: E 273 VAL cc_start: 0.8993 (t) cc_final: 0.8767 (t) REVERT: E 277 MET cc_start: 0.9089 (mtt) cc_final: 0.8773 (mtm) REVERT: F 150 LEU cc_start: 0.8542 (tp) cc_final: 0.7878 (tt) REVERT: F 161 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8361 (pt) REVERT: F 182 THR cc_start: 0.8970 (p) cc_final: 0.8681 (m) REVERT: F 304 ARG cc_start: 0.7511 (mpt180) cc_final: 0.7207 (mmt-90) REVERT: F 310 MET cc_start: 0.9310 (ttp) cc_final: 0.8820 (tmm) REVERT: F 351 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8788 (mttp) REVERT: c 38 LEU cc_start: 0.9162 (tp) cc_final: 0.8958 (tt) REVERT: c 57 MET cc_start: 0.8623 (mtm) cc_final: 0.8379 (mtp) REVERT: c 64 ASP cc_start: 0.8626 (m-30) cc_final: 0.8003 (t0) REVERT: c 95 MET cc_start: 0.8947 (tpp) cc_final: 0.8478 (tpp) REVERT: c 130 GLN cc_start: 0.9167 (tp40) cc_final: 0.8739 (tp40) REVERT: c 201 TYR cc_start: 0.8616 (p90) cc_final: 0.8274 (p90) REVERT: c 226 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6946 (ptp) REVERT: c 229 LEU cc_start: 0.8271 (mt) cc_final: 0.7947 (mt) REVERT: K 26 TYR cc_start: 0.5313 (m-10) cc_final: 0.5032 (m-10) REVERT: K 225 ASN cc_start: 0.6464 (OUTLIER) cc_final: 0.6224 (m110) REVERT: U 86 ASP cc_start: 0.6213 (OUTLIER) cc_final: 0.5604 (m-30) REVERT: U 130 LEU cc_start: 0.8326 (tp) cc_final: 0.8105 (tp) REVERT: U 176 MET cc_start: 0.7268 (tmm) cc_final: 0.6829 (tmm) REVERT: U 189 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: U 340 GLN cc_start: 0.7858 (tt0) cc_final: 0.7399 (mm-40) REVERT: U 351 MET cc_start: 0.7266 (tmm) cc_final: 0.6988 (tmm) REVERT: U 374 SER cc_start: 0.8860 (p) cc_final: 0.8608 (p) REVERT: U 486 MET cc_start: 0.8168 (ttp) cc_final: 0.7824 (ptm) REVERT: U 524 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8427 (tptp) REVERT: U 795 LEU cc_start: 0.8040 (mm) cc_final: 0.7785 (tp) REVERT: U 885 MET cc_start: 0.6503 (OUTLIER) cc_final: 0.4932 (mtm) REVERT: f 66 LYS cc_start: 0.4054 (OUTLIER) cc_final: 0.3407 (mppt) REVERT: f 129 LEU cc_start: 0.8377 (tp) cc_final: 0.7572 (mt) REVERT: f 209 MET cc_start: 0.8005 (mtp) cc_final: 0.7623 (mtp) REVERT: f 248 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6416 (tt) REVERT: f 275 MET cc_start: 0.8080 (mmm) cc_final: 0.6569 (tmm) REVERT: f 300 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7209 (tpt90) REVERT: f 315 GLU cc_start: 0.6270 (mm-30) cc_final: 0.6010 (tm-30) REVERT: f 542 ILE cc_start: 0.7833 (pt) cc_final: 0.7175 (mm) REVERT: f 552 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.4495 (m-30) REVERT: f 748 LEU cc_start: 0.8520 (mt) cc_final: 0.8270 (mm) REVERT: f 777 THR cc_start: 0.8460 (p) cc_final: 0.8020 (p) REVERT: f 788 MET cc_start: 0.7436 (ppp) cc_final: 0.7068 (tmm) REVERT: f 882 LEU cc_start: 0.8841 (mt) cc_final: 0.8600 (pt) REVERT: V 153 LYS cc_start: 0.5477 (OUTLIER) cc_final: 0.4710 (tptm) REVERT: V 214 HIS cc_start: 0.4733 (OUTLIER) cc_final: 0.4359 (t-90) REVERT: V 254 LEU cc_start: 0.8387 (tp) cc_final: 0.8090 (mt) REVERT: V 278 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6262 (mm-30) REVERT: V 279 GLN cc_start: 0.5958 (mp10) cc_final: 0.5190 (tm-30) REVERT: V 451 ILE cc_start: 0.3456 (mt) cc_final: 0.3188 (mt) outliers start: 427 outliers final: 125 residues processed: 2479 average time/residue: 0.7441 time to fit residues: 3095.6353 Evaluate side-chains 1395 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1229 time to evaluate : 6.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 78 TRP Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 117 GLN Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 397 LYS Chi-restraints excluded: chain C residue 398 ASN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 207 PRO Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 244 PRO Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 174 GLU Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 136 TYR Chi-restraints excluded: chain J residue 55 ASP Chi-restraints excluded: chain J residue 148 ASP Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 63 ASN Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 148 LEU Chi-restraints excluded: chain M residue 173 LYS Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 243 LEU Chi-restraints excluded: chain W residue 20 TYR Chi-restraints excluded: chain W residue 161 GLU Chi-restraints excluded: chain W residue 192 LEU Chi-restraints excluded: chain X residue 148 HIS Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain Y residue 292 TYR Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 127 ASP Chi-restraints excluded: chain a residue 137 ASP Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 363 MET Chi-restraints excluded: chain d residue 208 PHE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain Z residue 118 ASN Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 202 ASN Chi-restraints excluded: chain Z residue 224 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 303 ASP Chi-restraints excluded: chain F residue 344 ARG Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 211 GLU Chi-restraints excluded: chain c residue 216 MET Chi-restraints excluded: chain c residue 226 MET Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 225 ASN Chi-restraints excluded: chain U residue 44 LYS Chi-restraints excluded: chain U residue 86 ASP Chi-restraints excluded: chain U residue 93 ASN Chi-restraints excluded: chain U residue 105 ILE Chi-restraints excluded: chain U residue 140 ARG Chi-restraints excluded: chain U residue 189 GLN Chi-restraints excluded: chain U residue 254 GLU Chi-restraints excluded: chain U residue 258 GLN Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 417 LYS Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 524 LYS Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 694 ILE Chi-restraints excluded: chain U residue 760 VAL Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 806 CYS Chi-restraints excluded: chain U residue 885 MET Chi-restraints excluded: chain U residue 917 THR Chi-restraints excluded: chain f residue 66 LYS Chi-restraints excluded: chain f residue 143 ARG Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 213 GLN Chi-restraints excluded: chain f residue 248 LEU Chi-restraints excluded: chain f residue 300 ARG Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 552 ASP Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 577 LEU Chi-restraints excluded: chain f residue 615 ILE Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 249 THR Chi-restraints excluded: chain V residue 300 LEU Chi-restraints excluded: chain V residue 309 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 747 optimal weight: 6.9990 chunk 670 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 452 optimal weight: 8.9990 chunk 358 optimal weight: 0.9990 chunk 693 optimal weight: 8.9990 chunk 268 optimal weight: 5.9990 chunk 421 optimal weight: 20.0000 chunk 516 optimal weight: 6.9990 chunk 803 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 293 ASN ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 241 HIS C 279 GLN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 ASN D 49 GLN D 57 GLN D 74 HIS D 83 GLN D 294 ASN D 312 ASN D 380 GLN D 390 ASN G 33 ASN G 127 GLN H 112 GLN I 30 HIS I 146 GLN I 149 GLN I 155 ASN ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 HIS M 97 ASN M 101 ASN O 91 GLN W 433 ASN W 454 ASN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 375 HIS ** Y 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 357 ASN Y 388 ASN a 69 HIS a 164 GLN ** a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 264 ASN b 27 GLN ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 137 ASN b 142 ASN d 202 GLN ** u 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS B 81 ASN B 82 GLN B 306 GLN B 314 ASN Z 104 ASN Z 145 HIS Z 174 HIS Z 202 ASN ** Z 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 278 ASN ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN F 428 GLN c 44 HIS ** c 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 HIS c 185 ASN c 190 GLN c 194 HIS c 197 ASN ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 139 GLN U 362 ASN U 467 ASN U 491 GLN U 596 ASN U 697 GLN f 112 ASN f 161 HIS f 323 ASN f 325 GLN ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 371 ASN f 405 HIS ** f 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 540 GLN ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 677 HIS ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 815 HIS ** V 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 193 GLN ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 ASN V 477 HIS Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.122918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.099283 restraints weight = 246299.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.099755 restraints weight = 155624.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.099890 restraints weight = 95420.200| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 72092 Z= 0.377 Angle : 0.938 15.058 97434 Z= 0.489 Chirality : 0.051 0.247 11146 Planarity : 0.006 0.080 12551 Dihedral : 10.242 135.344 10227 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.59 % Favored : 92.66 % Rotamer: Outliers : 6.64 % Allowed : 16.10 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.08), residues: 8895 helix: -0.03 (0.07), residues: 5021 sheet: -0.47 (0.17), residues: 852 loop : -1.88 (0.11), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP a 22 HIS 0.014 0.002 HIS L 175 PHE 0.048 0.003 PHE J 171 TYR 0.046 0.003 TYR Y 304 ARG 0.012 0.001 ARG V 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1871 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 510 poor density : 1361 time to evaluate : 6.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 116 LYS cc_start: 0.8148 (tppt) cc_final: 0.7933 (tppt) REVERT: A 143 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7492 (p0) REVERT: A 299 MET cc_start: 0.8782 (tmm) cc_final: 0.8164 (tmm) REVERT: A 323 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7646 (mtm180) REVERT: C 83 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8102 (mmtm) REVERT: C 230 MET cc_start: 0.7655 (tpp) cc_final: 0.6856 (ptp) REVERT: C 293 MET cc_start: 0.7720 (tmm) cc_final: 0.7499 (tmm) REVERT: C 313 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.5939 (mtm180) REVERT: C 335 LYS cc_start: 0.8599 (mttt) cc_final: 0.7905 (tppt) REVERT: D 60 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.8328 (t80) REVERT: D 77 GLU cc_start: 0.8137 (tp30) cc_final: 0.7934 (tp30) REVERT: D 99 ASN cc_start: 0.8216 (t0) cc_final: 0.7892 (t0) REVERT: D 127 ASN cc_start: 0.7487 (t0) cc_final: 0.6995 (t0) REVERT: D 183 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7669 (tp) REVERT: D 192 LYS cc_start: 0.8036 (tttt) cc_final: 0.7674 (ttpp) REVERT: D 234 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8614 (mt-10) REVERT: D 237 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: D 245 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7495 (ttp80) REVERT: D 248 ARG cc_start: 0.8944 (mtt90) cc_final: 0.8198 (mtt180) REVERT: D 339 ARG cc_start: 0.7345 (tpm170) cc_final: 0.6940 (tpm170) REVERT: D 352 MET cc_start: 0.8260 (mtp) cc_final: 0.7868 (mtp) REVERT: D 374 ASP cc_start: 0.9172 (m-30) cc_final: 0.8822 (m-30) REVERT: D 397 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8538 (mtmm) REVERT: G 14 THR cc_start: 0.8256 (m) cc_final: 0.7835 (t) REVERT: G 62 ASP cc_start: 0.8274 (t0) cc_final: 0.7775 (m-30) REVERT: G 80 MET cc_start: 0.6831 (mmm) cc_final: 0.6560 (mmm) REVERT: G 83 MET cc_start: 0.7560 (mpp) cc_final: 0.6765 (mpp) REVERT: G 127 GLN cc_start: 0.7725 (tm130) cc_final: 0.7267 (tm-30) REVERT: H 49 GLU cc_start: 0.7851 (tm-30) cc_final: 0.6917 (pp20) REVERT: H 58 ASP cc_start: 0.6634 (t0) cc_final: 0.6379 (m-30) REVERT: H 64 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7260 (ttmt) REVERT: H 79 MET cc_start: 0.6399 (pmm) cc_final: 0.4643 (tpt) REVERT: H 118 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7287 (ttm) REVERT: H 150 ASP cc_start: 0.7681 (m-30) cc_final: 0.6920 (m-30) REVERT: H 163 MET cc_start: 0.6679 (pmm) cc_final: 0.6339 (pmm) REVERT: H 166 ASN cc_start: 0.6208 (t0) cc_final: 0.5988 (t0) REVERT: I 48 GLU cc_start: 0.4963 (OUTLIER) cc_final: 0.3849 (tt0) REVERT: I 72 MET cc_start: 0.4605 (mpp) cc_final: 0.4151 (mpp) REVERT: J 116 GLN cc_start: 0.8556 (tm-30) cc_final: 0.7940 (tp40) REVERT: J 211 MET cc_start: 0.6897 (ttp) cc_final: 0.6526 (tmm) REVERT: L 176 MET cc_start: 0.5506 (ppp) cc_final: 0.5016 (ptm) REVERT: L 179 PHE cc_start: 0.5055 (m-10) cc_final: 0.4776 (m-10) REVERT: L 234 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: M 50 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: M 72 HIS cc_start: 0.4740 (OUTLIER) cc_final: 0.4141 (p90) REVERT: M 177 GLU cc_start: 0.5585 (mm-30) cc_final: 0.5372 (mm-30) REVERT: O 86 MET cc_start: 0.8856 (ttp) cc_final: 0.8505 (ptp) REVERT: W 73 MET cc_start: 0.5936 (mmp) cc_final: 0.5596 (mtt) REVERT: W 145 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6972 (pp) REVERT: W 177 MET cc_start: 0.7692 (tpp) cc_final: 0.7372 (tpp) REVERT: W 192 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8016 (tt) REVERT: W 201 ARG cc_start: 0.8346 (ttm110) cc_final: 0.8047 (ttp-170) REVERT: W 247 TYR cc_start: 0.7830 (m-80) cc_final: 0.7497 (m-80) REVERT: W 436 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8569 (mtm) REVERT: W 451 MET cc_start: 0.7194 (mtm) cc_final: 0.6657 (mtm) REVERT: X 137 TYR cc_start: 0.8063 (m-10) cc_final: 0.7670 (m-10) REVERT: X 148 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7426 (p-80) REVERT: X 168 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7884 (mt-10) REVERT: X 211 ASP cc_start: 0.8361 (m-30) cc_final: 0.7884 (t0) REVERT: X 217 ILE cc_start: 0.8638 (mm) cc_final: 0.8402 (tp) REVERT: X 323 LEU cc_start: 0.8628 (mt) cc_final: 0.8378 (mt) REVERT: X 342 PHE cc_start: 0.7129 (m-80) cc_final: 0.6842 (m-80) REVERT: Y 176 ARG cc_start: 0.8554 (mtt90) cc_final: 0.8060 (mtm180) REVERT: Y 222 TYR cc_start: 0.8721 (m-10) cc_final: 0.8313 (m-80) REVERT: Y 282 MET cc_start: 0.6557 (mmm) cc_final: 0.6094 (tpp) REVERT: Y 309 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8021 (mm-30) REVERT: a 34 TRP cc_start: 0.4986 (m100) cc_final: 0.3977 (m100) REVERT: a 70 ARG cc_start: 0.5614 (mmm160) cc_final: 0.4965 (mpt180) REVERT: a 174 LYS cc_start: 0.8727 (ttpp) cc_final: 0.8480 (mmmt) REVERT: a 211 PHE cc_start: -0.0341 (OUTLIER) cc_final: -0.1459 (p90) REVERT: a 238 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7466 (t80) REVERT: b 24 THR cc_start: 0.4436 (OUTLIER) cc_final: 0.3551 (m) REVERT: b 63 THR cc_start: 0.8660 (m) cc_final: 0.8401 (p) REVERT: b 107 MET cc_start: 0.6332 (mtt) cc_final: 0.5846 (mtt) REVERT: b 133 LYS cc_start: 0.8333 (ptpt) cc_final: 0.7946 (tttt) REVERT: b 151 GLU cc_start: 0.8447 (pm20) cc_final: 0.7584 (tp30) REVERT: d 225 TYR cc_start: 0.6966 (m-80) cc_final: 0.6574 (m-10) REVERT: g 104 ARG cc_start: 0.7219 (mmt90) cc_final: 0.6735 (mmm160) REVERT: g 151 VAL cc_start: 0.4899 (OUTLIER) cc_final: 0.4505 (t) REVERT: g 163 GLU cc_start: 0.6064 (pm20) cc_final: 0.5364 (mp0) REVERT: u 124 MET cc_start: 0.6431 (mtt) cc_final: 0.5892 (tpp) REVERT: u 138 LEU cc_start: 0.6358 (mt) cc_final: 0.6134 (tp) REVERT: u 204 MET cc_start: 0.6977 (tpp) cc_final: 0.6673 (tpp) REVERT: u 287 GLU cc_start: 0.7004 (pp20) cc_final: 0.6348 (pp20) REVERT: B 79 ILE cc_start: 0.8881 (mt) cc_final: 0.8614 (mt) REVERT: B 96 ARG cc_start: 0.8218 (mmp80) cc_final: 0.7575 (ptp-170) REVERT: B 164 MET cc_start: 0.7944 (tpp) cc_final: 0.7729 (mmm) REVERT: B 178 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7857 (mmmt) REVERT: B 275 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: B 405 MET cc_start: 0.7942 (tpp) cc_final: 0.7656 (tpp) REVERT: Z 189 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7942 (mm-40) REVERT: Z 257 MET cc_start: 0.8790 (mmm) cc_final: 0.8457 (mmm) REVERT: E 132 TYR cc_start: 0.8823 (m-80) cc_final: 0.8024 (m-80) REVERT: E 295 LEU cc_start: 0.9318 (mt) cc_final: 0.9086 (mt) REVERT: F 150 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7601 (tt) REVERT: F 287 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8020 (mm-30) REVERT: F 437 TYR cc_start: 0.7633 (t80) cc_final: 0.7379 (t80) REVERT: c 36 LEU cc_start: 0.9139 (tt) cc_final: 0.8925 (tt) REVERT: c 130 GLN cc_start: 0.9035 (tp40) cc_final: 0.8298 (tp40) REVERT: c 309 PHE cc_start: 0.7033 (m-80) cc_final: 0.6573 (m-80) REVERT: K 12 VAL cc_start: 0.8164 (t) cc_final: 0.7892 (p) REVERT: U 59 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.6298 (t80) REVERT: U 176 MET cc_start: 0.6962 (tmm) cc_final: 0.6708 (ttp) REVERT: U 188 MET cc_start: 0.7652 (tmm) cc_final: 0.7316 (tmm) REVERT: U 220 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8547 (mt) REVERT: U 337 LEU cc_start: 0.8932 (mt) cc_final: 0.8449 (mt) REVERT: U 351 MET cc_start: 0.7371 (tmm) cc_final: 0.7161 (tmm) REVERT: U 524 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8253 (tptp) REVERT: U 556 MET cc_start: 0.8712 (mmt) cc_final: 0.8447 (tpp) REVERT: U 754 HIS cc_start: 0.5520 (t70) cc_final: 0.4858 (t-90) REVERT: U 755 THR cc_start: 0.7386 (OUTLIER) cc_final: 0.6943 (m) REVERT: f 98 PHE cc_start: 0.6032 (m-80) cc_final: 0.5830 (m-80) REVERT: f 129 LEU cc_start: 0.8301 (tp) cc_final: 0.7952 (mt) REVERT: f 133 MET cc_start: 0.6536 (mtt) cc_final: 0.6115 (mmt) REVERT: f 209 MET cc_start: 0.8184 (mtp) cc_final: 0.7787 (mtp) REVERT: f 231 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7665 (mp) REVERT: f 300 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7473 (tpt90) REVERT: f 315 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5929 (tm-30) REVERT: f 557 TRP cc_start: 0.8123 (m-10) cc_final: 0.7793 (m-10) REVERT: f 681 TYR cc_start: 0.7373 (m-10) cc_final: 0.6582 (m-10) REVERT: f 788 MET cc_start: 0.7630 (ppp) cc_final: 0.7273 (tmm) REVERT: f 807 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.5981 (tmt170) REVERT: V 83 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6212 (tp30) REVERT: V 100 MET cc_start: 0.5637 (mpp) cc_final: 0.5354 (mpp) REVERT: V 153 LYS cc_start: 0.5434 (OUTLIER) cc_final: 0.4614 (tptm) REVERT: V 214 HIS cc_start: 0.4187 (OUTLIER) cc_final: 0.3714 (t-90) REVERT: V 412 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7870 (pp) outliers start: 510 outliers final: 233 residues processed: 1725 average time/residue: 0.6657 time to fit residues: 1958.4581 Evaluate side-chains 1342 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 1074 time to evaluate : 6.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 293 ASN Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 ILE Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 TYR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 179 TYR Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 178 GLU Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 189 ILE Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain W residue 145 LEU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 192 LEU Chi-restraints excluded: chain W residue 244 CYS Chi-restraints excluded: chain W residue 326 MET Chi-restraints excluded: chain W residue 344 THR Chi-restraints excluded: chain W residue 371 THR Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain X residue 76 PHE Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 148 HIS Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 257 CYS Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain X residue 353 LEU Chi-restraints excluded: chain X residue 362 GLU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain Y residue 47 ASP Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 292 TYR Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Y residue 376 LEU Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 238 TYR Chi-restraints excluded: chain a residue 269 LEU Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 9 CYS Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 98 LYS Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain d residue 177 ASP Chi-restraints excluded: chain d residue 198 PHE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain g residue 125 ASN Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 147 ASP Chi-restraints excluded: chain u residue 251 ASN Chi-restraints excluded: chain u residue 273 THR Chi-restraints excluded: chain u residue 282 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain Z residue 78 MET Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 224 HIS Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 386 TYR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 216 MET Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain U residue 33 ASP Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 93 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 220 LEU Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 373 ASN Chi-restraints excluded: chain U residue 453 HIS Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 493 VAL Chi-restraints excluded: chain U residue 524 LYS Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 607 VAL Chi-restraints excluded: chain U residue 625 ILE Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 694 ILE Chi-restraints excluded: chain U residue 731 ILE Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 746 ILE Chi-restraints excluded: chain U residue 755 THR Chi-restraints excluded: chain U residue 763 VAL Chi-restraints excluded: chain U residue 769 PHE Chi-restraints excluded: chain U residue 791 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 806 CYS Chi-restraints excluded: chain U residue 917 THR Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain f residue 168 LYS Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 248 LEU Chi-restraints excluded: chain f residue 278 VAL Chi-restraints excluded: chain f residue 300 ARG Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 355 ASN Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 577 LEU Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 711 SER Chi-restraints excluded: chain f residue 721 VAL Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 764 LEU Chi-restraints excluded: chain f residue 807 ARG Chi-restraints excluded: chain f residue 825 MET Chi-restraints excluded: chain f residue 850 VAL Chi-restraints excluded: chain f residue 870 THR Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 172 VAL Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 249 THR Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 300 LEU Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 412 LEU Chi-restraints excluded: chain V residue 457 TYR Chi-restraints excluded: chain V residue 458 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 841 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 449 optimal weight: 7.9990 chunk 798 optimal weight: 0.5980 chunk 803 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 375 optimal weight: 9.9990 chunk 486 optimal weight: 5.9990 chunk 767 optimal weight: 20.0000 chunk 538 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 ASN ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN H 112 GLN I 149 GLN I 198 ASN J 146 GLN X 367 GLN Y 21 GLN Y 357 ASN ** a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 239 GLN ** u 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN Z 104 ASN Z 189 GLN Z 202 ASN ** Z 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 237 HIS ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 HIS U 189 GLN U 366 HIS ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 701 ASN ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 281 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.124935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.101526 restraints weight = 245544.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.102648 restraints weight = 123275.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.102796 restraints weight = 74784.020| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 72092 Z= 0.241 Angle : 0.804 15.124 97434 Z= 0.413 Chirality : 0.046 0.340 11146 Planarity : 0.005 0.067 12551 Dihedral : 8.817 146.558 10044 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.27 % Favored : 93.16 % Rotamer: Outliers : 5.27 % Allowed : 18.24 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.09), residues: 8895 helix: 0.39 (0.07), residues: 5040 sheet: -0.43 (0.16), residues: 882 loop : -1.63 (0.12), residues: 2973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP a 255 HIS 0.019 0.001 HIS I 30 PHE 0.043 0.002 PHE J 171 TYR 0.050 0.002 TYR G 125 ARG 0.017 0.001 ARG Y 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1711 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 405 poor density : 1306 time to evaluate : 6.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8005 (tppt) cc_final: 0.7724 (tppt) REVERT: A 138 MET cc_start: 0.8372 (tpp) cc_final: 0.8052 (tpp) REVERT: A 143 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7681 (p0) REVERT: C 83 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8161 (mmtm) REVERT: C 138 MET cc_start: 0.6480 (OUTLIER) cc_final: 0.6125 (ttt) REVERT: C 230 MET cc_start: 0.7871 (tpp) cc_final: 0.6740 (mtm) REVERT: C 293 MET cc_start: 0.7812 (tmm) cc_final: 0.7521 (tmm) REVERT: C 313 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5762 (mtm180) REVERT: C 385 MET cc_start: 0.8456 (mpp) cc_final: 0.8243 (mpp) REVERT: D 60 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8225 (t80) REVERT: D 99 ASN cc_start: 0.8219 (t0) cc_final: 0.7971 (t0) REVERT: D 127 ASN cc_start: 0.7438 (t0) cc_final: 0.7059 (t0) REVERT: D 140 VAL cc_start: 0.8909 (m) cc_final: 0.8652 (m) REVERT: D 170 MET cc_start: 0.7649 (ptp) cc_final: 0.7205 (ptp) REVERT: D 183 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7609 (tp) REVERT: D 212 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8868 (tttt) REVERT: D 214 MET cc_start: 0.8047 (mmm) cc_final: 0.7841 (tpt) REVERT: D 234 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8615 (mt-10) REVERT: D 237 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: D 245 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.7380 (ttt-90) REVERT: D 248 ARG cc_start: 0.8564 (mtt90) cc_final: 0.8027 (mtm180) REVERT: D 352 MET cc_start: 0.8202 (mtp) cc_final: 0.7951 (mtp) REVERT: D 374 ASP cc_start: 0.9105 (m-30) cc_final: 0.8824 (m-30) REVERT: D 382 SER cc_start: 0.9105 (m) cc_final: 0.8844 (t) REVERT: D 397 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8489 (mtmm) REVERT: G 14 THR cc_start: 0.8162 (m) cc_final: 0.7855 (t) REVERT: G 37 LEU cc_start: 0.7944 (mt) cc_final: 0.7721 (mm) REVERT: G 62 ASP cc_start: 0.8174 (t0) cc_final: 0.7853 (m-30) REVERT: G 110 PRO cc_start: 0.5168 (Cg_endo) cc_final: 0.4871 (Cg_exo) REVERT: H 23 GLU cc_start: 0.8880 (tp30) cc_final: 0.8301 (mp0) REVERT: H 75 VAL cc_start: 0.7743 (p) cc_final: 0.7528 (m) REVERT: H 79 MET cc_start: 0.6172 (pmm) cc_final: 0.4239 (tpt) REVERT: H 118 MET cc_start: 0.7766 (ttm) cc_final: 0.7289 (ttm) REVERT: H 150 ASP cc_start: 0.7769 (m-30) cc_final: 0.7267 (m-30) REVERT: H 155 TYR cc_start: 0.8529 (p90) cc_final: 0.8242 (p90) REVERT: H 163 MET cc_start: 0.6828 (pmm) cc_final: 0.6540 (pmm) REVERT: H 166 ASN cc_start: 0.6443 (t0) cc_final: 0.5763 (t0) REVERT: H 169 ASN cc_start: 0.8373 (m110) cc_final: 0.8152 (m110) REVERT: H 176 LYS cc_start: 0.8516 (mptt) cc_final: 0.8052 (mmtm) REVERT: J 116 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8010 (tp40) REVERT: J 211 MET cc_start: 0.6866 (ttp) cc_final: 0.6579 (tmm) REVERT: L 49 LEU cc_start: 0.8752 (tp) cc_final: 0.8468 (pp) REVERT: L 234 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.6852 (mm-30) REVERT: M 50 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: M 72 HIS cc_start: 0.4263 (OUTLIER) cc_final: 0.3651 (p90) REVERT: M 118 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.6234 (t80) REVERT: O 64 GLU cc_start: 0.8315 (tp30) cc_final: 0.8053 (tp30) REVERT: O 86 MET cc_start: 0.8813 (ttp) cc_final: 0.8130 (ptp) REVERT: O 87 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8292 (mm) REVERT: W 73 MET cc_start: 0.5505 (mmp) cc_final: 0.5225 (mtt) REVERT: W 104 MET cc_start: 0.6811 (ptm) cc_final: 0.6572 (ptm) REVERT: W 145 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6982 (pp) REVERT: W 192 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7919 (tt) REVERT: X 137 TYR cc_start: 0.8062 (m-10) cc_final: 0.7669 (m-10) REVERT: X 148 HIS cc_start: 0.7685 (OUTLIER) cc_final: 0.7362 (p-80) REVERT: X 158 LYS cc_start: 0.9189 (tppt) cc_final: 0.8841 (mmmm) REVERT: X 168 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7875 (mt-10) REVERT: X 187 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7486 (tpp80) REVERT: X 194 ARG cc_start: 0.8307 (mmm160) cc_final: 0.7004 (ptm-80) REVERT: X 211 ASP cc_start: 0.8236 (m-30) cc_final: 0.7738 (t0) REVERT: X 217 ILE cc_start: 0.8696 (mm) cc_final: 0.8422 (tp) REVERT: X 232 PHE cc_start: 0.6870 (m-10) cc_final: 0.6594 (m-10) REVERT: X 254 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7828 (mmm) REVERT: X 342 PHE cc_start: 0.7476 (m-80) cc_final: 0.7097 (m-80) REVERT: X 397 TYR cc_start: 0.7956 (m-80) cc_final: 0.7562 (m-80) REVERT: Y 50 MET cc_start: 0.4922 (mmm) cc_final: 0.3716 (mmm) REVERT: Y 176 ARG cc_start: 0.8568 (mtt90) cc_final: 0.8065 (mtm180) REVERT: Y 222 TYR cc_start: 0.8662 (m-10) cc_final: 0.8139 (m-80) REVERT: Y 272 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8087 (m-10) REVERT: Y 281 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7339 (tp30) REVERT: Y 282 MET cc_start: 0.6288 (mmm) cc_final: 0.5993 (tpp) REVERT: a 25 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.7008 (pp) REVERT: a 130 VAL cc_start: 0.7445 (p) cc_final: 0.7215 (m) REVERT: a 238 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7371 (t80) REVERT: a 248 PHE cc_start: 0.7164 (t80) cc_final: 0.6879 (t80) REVERT: a 252 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8135 (tppt) REVERT: a 343 LEU cc_start: 0.8557 (tp) cc_final: 0.8162 (pt) REVERT: b 107 MET cc_start: 0.6199 (mtt) cc_final: 0.5584 (mtt) REVERT: b 123 ASP cc_start: 0.7270 (m-30) cc_final: 0.6786 (t70) REVERT: b 133 LYS cc_start: 0.8336 (ptpt) cc_final: 0.7995 (tttt) REVERT: b 151 GLU cc_start: 0.8435 (pm20) cc_final: 0.7584 (tp30) REVERT: d 168 MET cc_start: 0.7360 (tpp) cc_final: 0.7085 (tpt) REVERT: d 334 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: g 104 ARG cc_start: 0.7279 (mmt90) cc_final: 0.6688 (mmm160) REVERT: g 151 VAL cc_start: 0.3888 (OUTLIER) cc_final: 0.3616 (t) REVERT: u 124 MET cc_start: 0.6489 (mtt) cc_final: 0.5928 (tpp) REVERT: u 287 GLU cc_start: 0.6764 (pp20) cc_final: 0.6477 (pp20) REVERT: B 96 ARG cc_start: 0.8280 (mmp80) cc_final: 0.7547 (ptp-170) REVERT: B 112 LEU cc_start: 0.8848 (tt) cc_final: 0.8534 (pt) REVERT: B 178 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7525 (tptp) REVERT: B 275 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6931 (mm-30) REVERT: Z 21 ASP cc_start: 0.7980 (t0) cc_final: 0.7681 (t0) REVERT: Z 68 TRP cc_start: 0.8391 (p-90) cc_final: 0.8090 (p-90) REVERT: Z 90 ARG cc_start: 0.7083 (mtp180) cc_final: 0.6612 (mtm-85) REVERT: Z 108 ILE cc_start: 0.9083 (mp) cc_final: 0.8779 (mm) REVERT: Z 189 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7853 (mm-40) REVERT: Z 257 MET cc_start: 0.8726 (mmm) cc_final: 0.8392 (mmm) REVERT: E 51 GLN cc_start: 0.8683 (mm-40) cc_final: 0.8290 (mm-40) REVERT: E 132 TYR cc_start: 0.8734 (m-80) cc_final: 0.7916 (m-80) REVERT: E 149 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8953 (mm) REVERT: E 197 LYS cc_start: 0.8743 (tptt) cc_final: 0.8522 (tptt) REVERT: E 273 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8672 (t) REVERT: E 295 LEU cc_start: 0.9354 (mt) cc_final: 0.9039 (mt) REVERT: F 69 MET cc_start: 0.4990 (tpp) cc_final: 0.4687 (tpp) REVERT: F 125 LYS cc_start: 0.8924 (tttt) cc_final: 0.8686 (tttp) REVERT: F 141 ASP cc_start: 0.7419 (OUTLIER) cc_final: 0.6952 (m-30) REVERT: F 150 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7566 (tt) REVERT: F 310 MET cc_start: 0.9242 (tmm) cc_final: 0.8830 (tmm) REVERT: F 405 MET cc_start: 0.8979 (mmm) cc_final: 0.8761 (mmt) REVERT: F 437 TYR cc_start: 0.7580 (t80) cc_final: 0.7295 (t80) REVERT: c 64 ASP cc_start: 0.8331 (m-30) cc_final: 0.8125 (t0) REVERT: c 99 LEU cc_start: 0.9380 (mt) cc_final: 0.9121 (mp) REVERT: c 104 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7680 (ttm170) REVERT: c 130 GLN cc_start: 0.8971 (tp40) cc_final: 0.8701 (tp40) REVERT: c 309 PHE cc_start: 0.7055 (m-80) cc_final: 0.6837 (m-80) REVERT: K 12 VAL cc_start: 0.8125 (t) cc_final: 0.7886 (p) REVERT: K 93 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8247 (mtp-110) REVERT: K 135 ARG cc_start: 0.8689 (ptt90) cc_final: 0.8464 (ptt90) REVERT: U 188 MET cc_start: 0.7490 (tmm) cc_final: 0.6799 (tmm) REVERT: U 189 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.6962 (pm20) REVERT: U 220 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8504 (mt) REVERT: U 351 MET cc_start: 0.7298 (tmm) cc_final: 0.7022 (tmm) REVERT: U 466 LYS cc_start: 0.8594 (mttt) cc_final: 0.8233 (tppt) REVERT: U 474 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7498 (mtt90) REVERT: U 504 ASP cc_start: 0.7407 (t0) cc_final: 0.6986 (t70) REVERT: U 524 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8116 (tptp) REVERT: U 532 MET cc_start: 0.7745 (mtm) cc_final: 0.7537 (mmm) REVERT: U 556 MET cc_start: 0.8731 (mmt) cc_final: 0.8503 (tpp) REVERT: f 113 MET cc_start: 0.3074 (ptt) cc_final: 0.2205 (ptt) REVERT: f 133 MET cc_start: 0.6842 (mtt) cc_final: 0.6102 (mmt) REVERT: f 300 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7479 (tpt90) REVERT: f 615 ILE cc_start: 0.8360 (mm) cc_final: 0.8064 (mm) REVERT: f 681 TYR cc_start: 0.7091 (m-10) cc_final: 0.6780 (m-10) REVERT: f 788 MET cc_start: 0.7520 (ppp) cc_final: 0.7180 (tmm) REVERT: f 807 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6098 (tmt170) REVERT: V 153 LYS cc_start: 0.5325 (OUTLIER) cc_final: 0.4528 (tptm) REVERT: V 176 MET cc_start: 0.7010 (tpp) cc_final: 0.6795 (mmt) REVERT: V 214 HIS cc_start: 0.4703 (OUTLIER) cc_final: 0.4108 (t-90) REVERT: V 309 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8063 (tpt) REVERT: V 332 LEU cc_start: 0.8288 (tp) cc_final: 0.7853 (tp) REVERT: V 358 MET cc_start: 0.7194 (tpp) cc_final: 0.6628 (mtt) REVERT: V 412 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7814 (pp) REVERT: V 463 MET cc_start: 0.7671 (tpp) cc_final: 0.7324 (tmm) REVERT: V 485 ASP cc_start: 0.8493 (t70) cc_final: 0.7687 (t70) REVERT: V 489 MET cc_start: 0.8181 (mpp) cc_final: 0.7894 (mpt) outliers start: 405 outliers final: 207 residues processed: 1587 average time/residue: 0.6552 time to fit residues: 1787.5086 Evaluate side-chains 1298 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 1049 time to evaluate : 6.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 166 ASP Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 212 LYS Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 136 TYR Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 146 GLN Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain M residue 118 TYR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 65 ARG Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 145 LEU Chi-restraints excluded: chain W residue 192 LEU Chi-restraints excluded: chain W residue 193 CYS Chi-restraints excluded: chain W residue 244 CYS Chi-restraints excluded: chain W residue 371 THR Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 148 HIS Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 254 MET Chi-restraints excluded: chain X residue 257 CYS Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain X residue 350 ILE Chi-restraints excluded: chain X residue 362 GLU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 398 GLU Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 272 PHE Chi-restraints excluded: chain Y residue 281 GLU Chi-restraints excluded: chain Y residue 344 HIS Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Y residue 376 LEU Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 238 TYR Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 9 CYS Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain d residue 120 LYS Chi-restraints excluded: chain d residue 198 PHE Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain d residue 334 GLU Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain u residue 147 ASP Chi-restraints excluded: chain u residue 150 LEU Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 251 ASN Chi-restraints excluded: chain u residue 257 THR Chi-restraints excluded: chain u residue 273 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 189 GLN Chi-restraints excluded: chain Z residue 224 HIS Chi-restraints excluded: chain Z residue 228 TYR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain c residue 25 VAL Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 60 GLU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 300 LEU Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 93 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 181 LEU Chi-restraints excluded: chain U residue 189 GLN Chi-restraints excluded: chain U residue 220 LEU Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 373 ASN Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 524 LYS Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 626 LEU Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 746 ILE Chi-restraints excluded: chain U residue 752 THR Chi-restraints excluded: chain U residue 769 PHE Chi-restraints excluded: chain U residue 791 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 917 THR Chi-restraints excluded: chain f residue 128 VAL Chi-restraints excluded: chain f residue 248 LEU Chi-restraints excluded: chain f residue 249 LEU Chi-restraints excluded: chain f residue 300 ARG Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 401 LYS Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 577 LEU Chi-restraints excluded: chain f residue 614 HIS Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 711 SER Chi-restraints excluded: chain f residue 725 SER Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 807 ARG Chi-restraints excluded: chain f residue 850 VAL Chi-restraints excluded: chain f residue 870 THR Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 180 ARG Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 284 GLU Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 300 LEU Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 412 LEU Chi-restraints excluded: chain V residue 457 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 618 optimal weight: 10.0000 chunk 753 optimal weight: 9.9990 chunk 280 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 466 optimal weight: 4.9990 chunk 829 optimal weight: 20.0000 chunk 513 optimal weight: 20.0000 chunk 544 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 chunk 470 optimal weight: 10.0000 chunk 437 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS I 100 GLN I 149 GLN J 146 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 HIS ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 182 ASN ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN Y 184 GLN Y 196 GLN Y 388 ASN a 164 GLN ** a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 251 ASN B 306 GLN B 368 HIS Z 44 GLN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 157 HIS ** Z 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 202 ASN Z 223 ASN Z 229 GLN Z 282 ASN E 300 HIS ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 155 HIS U 25 HIS U 189 GLN ** U 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 698 GLN ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 156 HIS ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 750 GLN ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 260 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.121918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.096223 restraints weight = 247239.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.098631 restraints weight = 126346.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.099605 restraints weight = 72786.634| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 72092 Z= 0.354 Angle : 0.820 14.168 97434 Z= 0.420 Chirality : 0.047 0.338 11146 Planarity : 0.005 0.073 12551 Dihedral : 8.531 148.978 10015 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.69 % Favored : 92.76 % Rotamer: Outliers : 6.05 % Allowed : 19.98 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.09), residues: 8895 helix: 0.38 (0.07), residues: 5046 sheet: -0.69 (0.16), residues: 900 loop : -1.66 (0.12), residues: 2949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP a 255 HIS 0.010 0.002 HIS c 113 PHE 0.036 0.003 PHE J 171 TYR 0.045 0.002 TYR d 175 ARG 0.009 0.001 ARG u 259 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 465 poor density : 1103 time to evaluate : 6.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 27 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: A 43 ARG cc_start: 0.8822 (tmt170) cc_final: 0.8574 (tmm-80) REVERT: A 116 LYS cc_start: 0.8080 (tppt) cc_final: 0.7130 (tppt) REVERT: A 143 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7411 (p0) REVERT: C 75 GLU cc_start: 0.7911 (pp20) cc_final: 0.7635 (pp20) REVERT: C 83 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8266 (mmtm) REVERT: C 230 MET cc_start: 0.7868 (tpp) cc_final: 0.6692 (mtm) REVERT: C 293 MET cc_start: 0.7800 (tmm) cc_final: 0.7546 (tmm) REVERT: C 335 LYS cc_start: 0.8330 (mttt) cc_final: 0.7776 (mmtm) REVERT: C 375 ARG cc_start: 0.7623 (ppt170) cc_final: 0.7072 (ptt90) REVERT: C 383 PHE cc_start: 0.8136 (m-80) cc_final: 0.7736 (m-80) REVERT: D 60 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8064 (t80) REVERT: D 61 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8432 (tt) REVERT: D 99 ASN cc_start: 0.8322 (t0) cc_final: 0.7932 (t0) REVERT: D 127 ASN cc_start: 0.7609 (t0) cc_final: 0.7152 (t0) REVERT: D 170 MET cc_start: 0.7872 (ptp) cc_final: 0.7504 (ptp) REVERT: D 227 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: D 245 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7313 (ttt-90) REVERT: D 345 PHE cc_start: 0.7928 (m-80) cc_final: 0.7722 (m-80) REVERT: D 374 ASP cc_start: 0.9169 (m-30) cc_final: 0.8771 (m-30) REVERT: D 397 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8579 (mtmm) REVERT: G 14 THR cc_start: 0.8262 (m) cc_final: 0.7932 (t) REVERT: G 83 MET cc_start: 0.7585 (mpp) cc_final: 0.6915 (mpp) REVERT: G 132 ARG cc_start: 0.6985 (ttp80) cc_final: 0.5839 (ptm-80) REVERT: H 79 MET cc_start: 0.5983 (pmm) cc_final: 0.4116 (tpt) REVERT: H 118 MET cc_start: 0.7825 (ttm) cc_final: 0.7462 (ttm) REVERT: H 150 ASP cc_start: 0.7735 (m-30) cc_final: 0.7062 (m-30) REVERT: H 155 TYR cc_start: 0.8788 (p90) cc_final: 0.8204 (p90) REVERT: H 165 LYS cc_start: 0.7294 (tppt) cc_final: 0.7040 (tptm) REVERT: H 166 ASN cc_start: 0.6514 (t0) cc_final: 0.5868 (t0) REVERT: H 169 ASN cc_start: 0.8410 (m110) cc_final: 0.8160 (m110) REVERT: I 226 ARG cc_start: 0.8560 (tmm-80) cc_final: 0.8102 (tmm-80) REVERT: J 116 GLN cc_start: 0.8450 (tm-30) cc_final: 0.7977 (tp40) REVERT: L 115 LYS cc_start: 0.8459 (tppt) cc_final: 0.8065 (tttp) REVERT: L 123 TYR cc_start: 0.8425 (t80) cc_final: 0.8038 (t80) REVERT: L 176 MET cc_start: 0.6842 (ptm) cc_final: 0.6072 (ptp) REVERT: M 24 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7850 (pt0) REVERT: M 28 LYS cc_start: 0.7848 (tttt) cc_final: 0.7524 (tttt) REVERT: M 50 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: M 56 LYS cc_start: 0.8390 (mmtm) cc_final: 0.7716 (ttmt) REVERT: M 72 HIS cc_start: 0.4300 (OUTLIER) cc_final: 0.3660 (p90) REVERT: M 75 MET cc_start: 0.7677 (tpp) cc_final: 0.7401 (tpp) REVERT: M 118 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.6396 (t80) REVERT: M 124 LEU cc_start: 0.8107 (mt) cc_final: 0.7741 (mt) REVERT: M 243 LEU cc_start: 0.6231 (pp) cc_final: 0.5695 (mm) REVERT: O 64 GLU cc_start: 0.8396 (tp30) cc_final: 0.8130 (tp30) REVERT: O 82 MET cc_start: 0.7368 (ptp) cc_final: 0.6786 (ptm) REVERT: O 86 MET cc_start: 0.8739 (ttp) cc_final: 0.8226 (ptp) REVERT: W 73 MET cc_start: 0.5490 (mmp) cc_final: 0.5166 (mtt) REVERT: W 104 MET cc_start: 0.6850 (ptm) cc_final: 0.6624 (ptm) REVERT: W 174 TYR cc_start: 0.3779 (OUTLIER) cc_final: 0.2791 (m-80) REVERT: W 177 MET cc_start: 0.7676 (tpp) cc_final: 0.7372 (tpp) REVERT: W 451 MET cc_start: 0.7611 (mtm) cc_final: 0.7404 (mtm) REVERT: X 137 TYR cc_start: 0.8201 (m-10) cc_final: 0.7916 (m-10) REVERT: X 148 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7408 (p-80) REVERT: X 168 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7884 (mt-10) REVERT: X 187 ARG cc_start: 0.8204 (tpp80) cc_final: 0.7912 (tpp80) REVERT: X 194 ARG cc_start: 0.8379 (mmm160) cc_final: 0.7170 (ptm-80) REVERT: X 211 ASP cc_start: 0.8277 (m-30) cc_final: 0.7715 (t0) REVERT: X 232 PHE cc_start: 0.7162 (m-10) cc_final: 0.6535 (m-10) REVERT: X 342 PHE cc_start: 0.7793 (m-80) cc_final: 0.7463 (m-80) REVERT: X 373 LYS cc_start: 0.8608 (mttm) cc_final: 0.8325 (mttm) REVERT: X 386 ILE cc_start: 0.7572 (OUTLIER) cc_final: 0.7283 (mt) REVERT: X 397 TYR cc_start: 0.7877 (m-80) cc_final: 0.7570 (m-80) REVERT: X 412 ASP cc_start: 0.8554 (m-30) cc_final: 0.8305 (m-30) REVERT: Y 50 MET cc_start: 0.5024 (mmm) cc_final: 0.4048 (mmm) REVERT: Y 176 ARG cc_start: 0.8688 (mtt90) cc_final: 0.8276 (mtm180) REVERT: Y 222 TYR cc_start: 0.8676 (m-10) cc_final: 0.8229 (m-80) REVERT: Y 272 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.8228 (m-80) REVERT: Y 281 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: Y 343 LEU cc_start: 0.8787 (tt) cc_final: 0.8488 (tt) REVERT: a 125 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7361 (pt) REVERT: a 238 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7453 (t80) REVERT: a 248 PHE cc_start: 0.7483 (t80) cc_final: 0.7156 (t80) REVERT: a 312 MET cc_start: 0.8833 (tpp) cc_final: 0.8400 (tpt) REVERT: a 343 LEU cc_start: 0.8686 (tp) cc_final: 0.8246 (pt) REVERT: b 123 ASP cc_start: 0.7288 (m-30) cc_final: 0.6936 (t70) REVERT: b 133 LYS cc_start: 0.8250 (ptpt) cc_final: 0.7911 (tttt) REVERT: d 168 MET cc_start: 0.7519 (tpp) cc_final: 0.7311 (tpp) REVERT: d 334 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: g 104 ARG cc_start: 0.7145 (mmt90) cc_final: 0.6637 (mmm160) REVERT: g 151 VAL cc_start: 0.3851 (t) cc_final: 0.3605 (t) REVERT: g 163 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.5095 (tp30) REVERT: u 124 MET cc_start: 0.6368 (mtt) cc_final: 0.5812 (tpp) REVERT: u 287 GLU cc_start: 0.6868 (pp20) cc_final: 0.6553 (pp20) REVERT: B 96 ARG cc_start: 0.8300 (mmp80) cc_final: 0.7562 (ptp-170) REVERT: B 112 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8530 (pt) REVERT: B 164 MET cc_start: 0.7931 (tpp) cc_final: 0.7668 (tpp) REVERT: B 178 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7588 (mmmt) REVERT: B 275 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.6961 (mm-30) REVERT: Z 78 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.6909 (tpp) REVERT: Z 83 LYS cc_start: 0.8842 (mtpt) cc_final: 0.8534 (ptpp) REVERT: Z 131 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7301 (tt) REVERT: Z 209 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8127 (mtp-110) REVERT: Z 257 MET cc_start: 0.8797 (mmm) cc_final: 0.8595 (mmm) REVERT: E 62 LYS cc_start: 0.8709 (tptt) cc_final: 0.8452 (tttp) REVERT: E 132 TYR cc_start: 0.8919 (m-80) cc_final: 0.8114 (m-80) REVERT: E 149 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8871 (mm) REVERT: E 171 LEU cc_start: 0.8870 (tp) cc_final: 0.8581 (tt) REVERT: E 234 GLU cc_start: 0.8226 (mp0) cc_final: 0.8008 (mm-30) REVERT: F 141 ASP cc_start: 0.7461 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: F 150 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7666 (tt) REVERT: F 289 ASP cc_start: 0.8510 (p0) cc_final: 0.8287 (p0) REVERT: F 437 TYR cc_start: 0.7563 (t80) cc_final: 0.7331 (t80) REVERT: c 282 ARG cc_start: 0.8702 (ttm-80) cc_final: 0.8379 (ttm-80) REVERT: c 309 PHE cc_start: 0.6840 (m-80) cc_final: 0.6611 (m-80) REVERT: K 12 VAL cc_start: 0.8153 (t) cc_final: 0.7861 (p) REVERT: K 93 ARG cc_start: 0.8614 (mtm-85) cc_final: 0.8163 (mtp180) REVERT: K 105 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: U 59 PHE cc_start: 0.6573 (OUTLIER) cc_final: 0.6173 (t80) REVERT: U 189 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6710 (pm20) REVERT: U 351 MET cc_start: 0.7341 (tmm) cc_final: 0.7096 (tmm) REVERT: U 466 LYS cc_start: 0.8492 (mttt) cc_final: 0.8254 (tppt) REVERT: U 474 ARG cc_start: 0.7979 (ttm170) cc_final: 0.7718 (ttt90) REVERT: U 504 ASP cc_start: 0.7707 (t0) cc_final: 0.7187 (t70) REVERT: U 524 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8142 (tptp) REVERT: U 754 HIS cc_start: 0.5445 (t70) cc_final: 0.4790 (t-90) REVERT: U 755 THR cc_start: 0.7671 (OUTLIER) cc_final: 0.7083 (m) REVERT: f 98 PHE cc_start: 0.6318 (m-80) cc_final: 0.5826 (m-80) REVERT: f 113 MET cc_start: 0.3310 (ptt) cc_final: 0.2523 (ptt) REVERT: f 137 ARG cc_start: 0.5581 (OUTLIER) cc_final: 0.5069 (mmp80) REVERT: f 297 MET cc_start: 0.8695 (ttm) cc_final: 0.8449 (ttm) REVERT: f 300 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7322 (tpt90) REVERT: f 615 ILE cc_start: 0.8332 (mm) cc_final: 0.8060 (mm) REVERT: f 788 MET cc_start: 0.7626 (ppp) cc_final: 0.7274 (tmm) REVERT: f 807 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.6361 (tmt170) REVERT: V 150 ARG cc_start: 0.1242 (OUTLIER) cc_final: 0.1039 (mtm180) REVERT: V 153 LYS cc_start: 0.5329 (OUTLIER) cc_final: 0.4523 (tptm) REVERT: V 180 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7240 (mtm180) REVERT: V 214 HIS cc_start: 0.4434 (OUTLIER) cc_final: 0.3836 (t-90) REVERT: V 242 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.6748 (t-90) REVERT: V 309 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8204 (tpp) REVERT: V 314 ARG cc_start: 0.7719 (ptp-110) cc_final: 0.7395 (ptp-110) REVERT: V 358 MET cc_start: 0.7140 (tpp) cc_final: 0.6589 (mtt) REVERT: V 447 ILE cc_start: 0.6636 (mp) cc_final: 0.6372 (mm) REVERT: V 463 MET cc_start: 0.7614 (tpp) cc_final: 0.7284 (tmm) outliers start: 465 outliers final: 283 residues processed: 1447 average time/residue: 0.6411 time to fit residues: 1602.9404 Evaluate side-chains 1316 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 326 poor density : 990 time to evaluate : 6.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 TYR Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 179 TYR Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain L residue 10 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 72 HIS Chi-restraints excluded: chain M residue 118 TYR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain W residue 48 LEU Chi-restraints excluded: chain W residue 65 ARG Chi-restraints excluded: chain W residue 82 LEU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 174 TYR Chi-restraints excluded: chain W residue 244 CYS Chi-restraints excluded: chain W residue 344 THR Chi-restraints excluded: chain W residue 371 THR Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 74 ARG Chi-restraints excluded: chain X residue 76 PHE Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 148 HIS Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 353 LEU Chi-restraints excluded: chain X residue 362 GLU Chi-restraints excluded: chain X residue 386 ILE Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 272 PHE Chi-restraints excluded: chain Y residue 281 GLU Chi-restraints excluded: chain Y residue 292 TYR Chi-restraints excluded: chain Y residue 301 ILE Chi-restraints excluded: chain Y residue 344 HIS Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Y residue 376 LEU Chi-restraints excluded: chain a residue 25 LEU Chi-restraints excluded: chain a residue 38 THR Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 125 ILE Chi-restraints excluded: chain a residue 164 GLN Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 238 TYR Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 9 CYS Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain b residue 122 LYS Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain d residue 120 LYS Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 160 ASP Chi-restraints excluded: chain d residue 198 PHE Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain d residue 334 GLU Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 150 LEU Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 251 ASN Chi-restraints excluded: chain u residue 257 THR Chi-restraints excluded: chain u residue 273 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 78 MET Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 131 LEU Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 202 ASN Chi-restraints excluded: chain Z residue 209 ARG Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 224 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 80 THR Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 300 LEU Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 93 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 181 LEU Chi-restraints excluded: chain U residue 189 GLN Chi-restraints excluded: chain U residue 258 GLN Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 373 ASN Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 524 LYS Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 607 VAL Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 731 ILE Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 746 ILE Chi-restraints excluded: chain U residue 752 THR Chi-restraints excluded: chain U residue 755 THR Chi-restraints excluded: chain U residue 763 VAL Chi-restraints excluded: chain U residue 769 PHE Chi-restraints excluded: chain U residue 791 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 903 PHE Chi-restraints excluded: chain U residue 922 GLU Chi-restraints excluded: chain f residue 58 MET Chi-restraints excluded: chain f residue 128 VAL Chi-restraints excluded: chain f residue 137 ARG Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 248 LEU Chi-restraints excluded: chain f residue 249 LEU Chi-restraints excluded: chain f residue 300 ARG Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 401 LYS Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 577 LEU Chi-restraints excluded: chain f residue 614 HIS Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 659 LEU Chi-restraints excluded: chain f residue 698 SER Chi-restraints excluded: chain f residue 711 SER Chi-restraints excluded: chain f residue 725 SER Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 771 LEU Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 807 ARG Chi-restraints excluded: chain f residue 850 VAL Chi-restraints excluded: chain f residue 870 THR Chi-restraints excluded: chain V residue 101 LEU Chi-restraints excluded: chain V residue 150 ARG Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 180 ARG Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 242 HIS Chi-restraints excluded: chain V residue 284 GLU Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 300 LEU Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 409 MET Chi-restraints excluded: chain V residue 412 LEU Chi-restraints excluded: chain V residue 457 TYR Chi-restraints excluded: chain V residue 489 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 606 optimal weight: 0.9980 chunk 231 optimal weight: 20.0000 chunk 616 optimal weight: 2.9990 chunk 214 optimal weight: 7.9990 chunk 453 optimal weight: 1.9990 chunk 630 optimal weight: 0.9980 chunk 871 optimal weight: 7.9990 chunk 276 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 561 optimal weight: 1.9990 chunk 332 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN C 205 HIS C 392 GLN ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS I 84 ASN I 100 GLN ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 44 ASN ** u 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 251 ASN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 HIS U 25 HIS U 321 GLN ** U 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 874 ASN ** f 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.124257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.099864 restraints weight = 245646.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.101354 restraints weight = 121757.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.102603 restraints weight = 71045.392| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3777 r_free = 0.3777 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 72092 Z= 0.219 Angle : 0.757 13.637 97434 Z= 0.384 Chirality : 0.045 0.344 11146 Planarity : 0.005 0.075 12551 Dihedral : 8.182 152.807 9997 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.00 % Favored : 93.50 % Rotamer: Outliers : 5.17 % Allowed : 21.17 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.09), residues: 8895 helix: 0.56 (0.07), residues: 5035 sheet: -0.47 (0.16), residues: 847 loop : -1.57 (0.12), residues: 3013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP a 255 HIS 0.010 0.001 HIS d 189 PHE 0.035 0.002 PHE J 171 TYR 0.049 0.002 TYR d 175 ARG 0.008 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1534 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 397 poor density : 1137 time to evaluate : 6.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ARG cc_start: 0.8802 (tmt170) cc_final: 0.8586 (tmm-80) REVERT: A 143 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7619 (p0) REVERT: A 422 LYS cc_start: 0.6480 (OUTLIER) cc_final: 0.5078 (pmtt) REVERT: C 75 GLU cc_start: 0.7874 (pp20) cc_final: 0.7594 (pp20) REVERT: C 83 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8295 (mmtm) REVERT: C 189 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: C 230 MET cc_start: 0.7927 (tpp) cc_final: 0.6766 (mtt) REVERT: C 293 MET cc_start: 0.7936 (tmm) cc_final: 0.7626 (tmm) REVERT: C 383 PHE cc_start: 0.8244 (m-80) cc_final: 0.7738 (m-80) REVERT: D 60 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8399 (t80) REVERT: D 61 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8462 (tt) REVERT: D 99 ASN cc_start: 0.8320 (t0) cc_final: 0.7996 (t0) REVERT: D 127 ASN cc_start: 0.7509 (t0) cc_final: 0.7058 (t0) REVERT: D 170 MET cc_start: 0.7780 (ptp) cc_final: 0.7401 (ptp) REVERT: D 234 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8542 (mt-10) REVERT: D 237 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: D 245 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7327 (ttt-90) REVERT: D 248 ARG cc_start: 0.8647 (mtt90) cc_final: 0.8087 (mtm180) REVERT: D 345 PHE cc_start: 0.7910 (m-80) cc_final: 0.7665 (m-80) REVERT: D 374 ASP cc_start: 0.9093 (m-30) cc_final: 0.8714 (m-30) REVERT: D 397 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8765 (mtmm) REVERT: G 14 THR cc_start: 0.8134 (m) cc_final: 0.7825 (t) REVERT: G 15 ILE cc_start: 0.8359 (mt) cc_final: 0.8043 (mp) REVERT: G 83 MET cc_start: 0.7626 (mpp) cc_final: 0.6845 (mpp) REVERT: G 132 ARG cc_start: 0.6903 (ttp80) cc_final: 0.5779 (ptm-80) REVERT: G 153 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7693 (tppt) REVERT: H 23 GLU cc_start: 0.8947 (tp30) cc_final: 0.8311 (mp0) REVERT: H 79 MET cc_start: 0.5850 (pmm) cc_final: 0.4020 (tpt) REVERT: H 118 MET cc_start: 0.7896 (ttm) cc_final: 0.7475 (ttm) REVERT: H 150 ASP cc_start: 0.7714 (m-30) cc_final: 0.6914 (m-30) REVERT: H 155 TYR cc_start: 0.8754 (p90) cc_final: 0.8198 (p90) REVERT: H 163 MET cc_start: 0.7090 (pmm) cc_final: 0.6615 (pmm) REVERT: H 165 LYS cc_start: 0.7300 (tppt) cc_final: 0.6886 (pmtt) REVERT: H 166 ASN cc_start: 0.6520 (t0) cc_final: 0.5989 (t0) REVERT: I 226 ARG cc_start: 0.8552 (tmm-80) cc_final: 0.8096 (tmm-80) REVERT: I 249 ARG cc_start: 0.7015 (mmt-90) cc_final: 0.6292 (tpt90) REVERT: J 116 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8033 (tp40) REVERT: L 49 LEU cc_start: 0.8777 (tp) cc_final: 0.8492 (pp) REVERT: L 115 LYS cc_start: 0.8283 (tppt) cc_final: 0.7926 (tttp) REVERT: L 123 TYR cc_start: 0.8350 (t80) cc_final: 0.8021 (t80) REVERT: L 176 MET cc_start: 0.6860 (ptm) cc_final: 0.6239 (ptp) REVERT: L 179 PHE cc_start: 0.5547 (m-10) cc_final: 0.4971 (m-10) REVERT: L 234 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.6810 (mm-30) REVERT: M 24 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7858 (pt0) REVERT: M 56 LYS cc_start: 0.8333 (mmtm) cc_final: 0.7666 (ttmt) REVERT: M 118 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6287 (t80) REVERT: M 124 LEU cc_start: 0.8056 (mt) cc_final: 0.7586 (mt) REVERT: M 243 LEU cc_start: 0.6278 (pp) cc_final: 0.5773 (mm) REVERT: O 54 MET cc_start: 0.6877 (ppp) cc_final: 0.6622 (ptp) REVERT: O 64 GLU cc_start: 0.8356 (tp30) cc_final: 0.8086 (tp30) REVERT: O 86 MET cc_start: 0.8880 (ttp) cc_final: 0.8533 (ptp) REVERT: O 87 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7749 (tt) REVERT: W 104 MET cc_start: 0.6868 (ptm) cc_final: 0.6639 (ptm) REVERT: W 145 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6839 (pp) REVERT: W 177 MET cc_start: 0.7584 (tpp) cc_final: 0.7301 (tpp) REVERT: W 382 LEU cc_start: 0.6982 (mt) cc_final: 0.6778 (mt) REVERT: X 148 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7425 (p-80) REVERT: X 168 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7834 (mt-10) REVERT: X 185 LYS cc_start: 0.8979 (mttt) cc_final: 0.8767 (mmtt) REVERT: X 187 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7820 (tpp80) REVERT: X 194 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7140 (ptm-80) REVERT: X 211 ASP cc_start: 0.8155 (m-30) cc_final: 0.7574 (t0) REVERT: X 232 PHE cc_start: 0.7078 (m-10) cc_final: 0.6574 (m-10) REVERT: X 254 MET cc_start: 0.7508 (tpt) cc_final: 0.6911 (tpt) REVERT: X 342 PHE cc_start: 0.7706 (m-80) cc_final: 0.7438 (m-80) REVERT: X 373 LYS cc_start: 0.8643 (mttm) cc_final: 0.8249 (mttt) REVERT: X 386 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7302 (mt) REVERT: Y 50 MET cc_start: 0.5294 (mmm) cc_final: 0.4191 (mmm) REVERT: Y 176 ARG cc_start: 0.8680 (mtt90) cc_final: 0.8295 (mtm180) REVERT: Y 222 TYR cc_start: 0.8744 (m-10) cc_final: 0.8080 (m-80) REVERT: Y 272 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8251 (m-80) REVERT: Y 281 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7238 (tp30) REVERT: Y 328 GLU cc_start: 0.7613 (tt0) cc_final: 0.7298 (tm-30) REVERT: Y 343 LEU cc_start: 0.8718 (tt) cc_final: 0.8392 (tt) REVERT: a 125 ILE cc_start: 0.7549 (mm) cc_final: 0.7294 (pt) REVERT: a 130 VAL cc_start: 0.7352 (p) cc_final: 0.7139 (m) REVERT: a 238 TYR cc_start: 0.8156 (OUTLIER) cc_final: 0.7467 (t80) REVERT: a 248 PHE cc_start: 0.7427 (t80) cc_final: 0.7146 (t80) REVERT: a 312 MET cc_start: 0.8720 (tpp) cc_final: 0.8439 (tpt) REVERT: a 343 LEU cc_start: 0.8642 (tp) cc_final: 0.8232 (pt) REVERT: b 107 MET cc_start: 0.5624 (mtt) cc_final: 0.5061 (mtp) REVERT: b 123 ASP cc_start: 0.7226 (m-30) cc_final: 0.6861 (t70) REVERT: b 133 LYS cc_start: 0.8239 (ptpt) cc_final: 0.7941 (tttt) REVERT: d 168 MET cc_start: 0.7484 (tpp) cc_final: 0.7235 (tpp) REVERT: d 334 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: g 104 ARG cc_start: 0.7151 (mmt90) cc_final: 0.6558 (mmm160) REVERT: g 151 VAL cc_start: 0.4049 (t) cc_final: 0.3766 (t) REVERT: g 163 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5070 (tp30) REVERT: u 124 MET cc_start: 0.6367 (mtt) cc_final: 0.5892 (tpp) REVERT: u 138 LEU cc_start: 0.5658 (tp) cc_final: 0.5240 (tp) REVERT: u 140 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5641 (pm20) REVERT: B 96 ARG cc_start: 0.8145 (mmp80) cc_final: 0.7446 (ptp-170) REVERT: B 112 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8649 (pt) REVERT: B 164 MET cc_start: 0.8086 (tpp) cc_final: 0.7847 (tpp) REVERT: B 175 LYS cc_start: 0.8396 (mtpp) cc_final: 0.7960 (mtmm) REVERT: B 178 LYS cc_start: 0.7505 (OUTLIER) cc_final: 0.7244 (tptp) REVERT: B 275 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: B 293 LYS cc_start: 0.6489 (tmtt) cc_final: 0.6268 (mmmt) REVERT: Z 68 TRP cc_start: 0.8375 (p-90) cc_final: 0.7702 (p-90) REVERT: Z 78 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7292 (tpp) REVERT: Z 83 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8539 (ptpp) REVERT: Z 90 ARG cc_start: 0.7118 (mtp180) cc_final: 0.6655 (mtm-85) REVERT: Z 209 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8188 (mtp-110) REVERT: Z 257 MET cc_start: 0.8618 (mmm) cc_final: 0.8415 (mmm) REVERT: E 78 ARG cc_start: 0.8138 (mtt-85) cc_final: 0.7795 (mtt180) REVERT: E 132 TYR cc_start: 0.8840 (m-80) cc_final: 0.7981 (m-80) REVERT: E 171 LEU cc_start: 0.8769 (tp) cc_final: 0.8538 (tt) REVERT: E 197 LYS cc_start: 0.8787 (tptt) cc_final: 0.8361 (tptt) REVERT: F 141 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6892 (m-30) REVERT: F 150 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7647 (tt) REVERT: F 289 ASP cc_start: 0.8317 (p0) cc_final: 0.8112 (p0) REVERT: c 189 ILE cc_start: 0.8939 (pt) cc_final: 0.8656 (mm) REVERT: c 282 ARG cc_start: 0.8646 (ttm-80) cc_final: 0.8274 (ttm-80) REVERT: c 309 PHE cc_start: 0.7070 (m-80) cc_final: 0.6757 (m-80) REVERT: K 12 VAL cc_start: 0.8043 (t) cc_final: 0.7842 (p) REVERT: U 59 PHE cc_start: 0.6490 (OUTLIER) cc_final: 0.6124 (t80) REVERT: U 188 MET cc_start: 0.7069 (tmm) cc_final: 0.6744 (tmm) REVERT: U 216 VAL cc_start: 0.7814 (t) cc_final: 0.7612 (m) REVERT: U 351 MET cc_start: 0.7300 (tmm) cc_final: 0.6999 (tmm) REVERT: U 474 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7694 (ttt90) REVERT: U 504 ASP cc_start: 0.7572 (t0) cc_final: 0.6774 (t70) REVERT: U 524 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.7999 (tptp) REVERT: U 556 MET cc_start: 0.8740 (tpp) cc_final: 0.8435 (tpp) REVERT: U 694 ILE cc_start: 0.7509 (tt) cc_final: 0.7281 (tt) REVERT: U 754 HIS cc_start: 0.5202 (t70) cc_final: 0.4606 (t-90) REVERT: f 113 MET cc_start: 0.3577 (ptt) cc_final: 0.2873 (ptt) REVERT: f 133 MET cc_start: 0.6724 (mtt) cc_final: 0.6181 (ptp) REVERT: f 137 ARG cc_start: 0.5521 (OUTLIER) cc_final: 0.5022 (mmp80) REVERT: f 209 MET cc_start: 0.8438 (ptp) cc_final: 0.8147 (ptp) REVERT: f 297 MET cc_start: 0.8694 (ttm) cc_final: 0.8480 (ttm) REVERT: f 300 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7156 (tpt90) REVERT: f 788 MET cc_start: 0.7456 (ppp) cc_final: 0.7152 (tmm) REVERT: V 150 ARG cc_start: 0.1410 (OUTLIER) cc_final: 0.1199 (mtm180) REVERT: V 153 LYS cc_start: 0.5332 (OUTLIER) cc_final: 0.4445 (tptm) REVERT: V 180 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6921 (mtm180) REVERT: V 214 HIS cc_start: 0.4282 (OUTLIER) cc_final: 0.3621 (t-90) REVERT: V 254 LEU cc_start: 0.7893 (mt) cc_final: 0.7622 (mt) REVERT: V 309 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8253 (tpt) REVERT: V 314 ARG cc_start: 0.7635 (ptp-110) cc_final: 0.7307 (ptp-110) REVERT: V 358 MET cc_start: 0.7187 (tpp) cc_final: 0.6667 (mtt) REVERT: V 447 ILE cc_start: 0.6626 (mp) cc_final: 0.6407 (mm) REVERT: V 463 MET cc_start: 0.7641 (tpp) cc_final: 0.7291 (tmm) outliers start: 397 outliers final: 253 residues processed: 1426 average time/residue: 0.6567 time to fit residues: 1620.0338 Evaluate side-chains 1317 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 1026 time to evaluate : 6.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 189 TYR Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 392 GLN Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 153 LYS Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 136 TYR Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 118 TYR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 145 LEU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 244 CYS Chi-restraints excluded: chain W residue 344 THR Chi-restraints excluded: chain W residue 371 THR Chi-restraints excluded: chain X residue 74 ARG Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 148 HIS Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 259 ILE Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 362 GLU Chi-restraints excluded: chain X residue 386 ILE Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 153 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 272 PHE Chi-restraints excluded: chain Y residue 281 GLU Chi-restraints excluded: chain Y residue 301 ILE Chi-restraints excluded: chain Y residue 344 HIS Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Y residue 376 LEU Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 123 LEU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 238 TYR Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain b residue 166 THR Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 160 ASP Chi-restraints excluded: chain d residue 205 VAL Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain d residue 334 GLU Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 183 GLN Chi-restraints excluded: chain u residue 251 ASN Chi-restraints excluded: chain u residue 273 THR Chi-restraints excluded: chain u residue 289 HIS Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 78 MET Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 202 ASN Chi-restraints excluded: chain Z residue 209 ARG Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 224 HIS Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 351 LYS Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 38 LEU Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 300 LEU Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain K residue 73 HIS Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 93 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 181 LEU Chi-restraints excluded: chain U residue 258 GLN Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 373 ASN Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 524 LYS Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 746 ILE Chi-restraints excluded: chain U residue 752 THR Chi-restraints excluded: chain U residue 769 PHE Chi-restraints excluded: chain U residue 791 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 903 PHE Chi-restraints excluded: chain f residue 58 MET Chi-restraints excluded: chain f residue 128 VAL Chi-restraints excluded: chain f residue 137 ARG Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 249 LEU Chi-restraints excluded: chain f residue 300 ARG Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 348 ILE Chi-restraints excluded: chain f residue 510 SER Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 577 LEU Chi-restraints excluded: chain f residue 614 HIS Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 698 SER Chi-restraints excluded: chain f residue 725 SER Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 771 LEU Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 850 VAL Chi-restraints excluded: chain f residue 898 VAL Chi-restraints excluded: chain V residue 150 ARG Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 180 ARG Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 284 GLU Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 300 LEU Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain V residue 409 MET Chi-restraints excluded: chain V residue 412 LEU Chi-restraints excluded: chain V residue 457 TYR Chi-restraints excluded: chain V residue 485 ASP Chi-restraints excluded: chain V residue 489 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 399 optimal weight: 10.0000 chunk 446 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 810 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 355 optimal weight: 8.9990 chunk 664 optimal weight: 5.9990 chunk 350 optimal weight: 3.9990 chunk 443 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 GLN ** a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 142 ASN d 195 ASN ** d 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 145 HIS Z 202 ASN ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 HIS F 92 ASN c 240 HIS c 256 ASN ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 HIS U 189 GLN U 321 GLN U 346 ASN U 470 ASN U 527 GLN ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 156 HIS ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 327 ASN f 452 ASN ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 257 ASN ** V 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.120585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.098075 restraints weight = 247954.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.097606 restraints weight = 135556.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.098216 restraints weight = 90528.423| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 72092 Z= 0.405 Angle : 0.828 16.055 97434 Z= 0.425 Chirality : 0.048 0.316 11146 Planarity : 0.006 0.079 12551 Dihedral : 8.219 149.490 9985 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.21 % Favored : 92.30 % Rotamer: Outliers : 6.14 % Allowed : 21.79 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.09), residues: 8895 helix: 0.38 (0.07), residues: 5027 sheet: -0.79 (0.16), residues: 877 loop : -1.65 (0.12), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP a 255 HIS 0.023 0.002 HIS K 73 PHE 0.033 0.003 PHE f 98 TYR 0.052 0.003 TYR d 175 ARG 0.011 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 472 poor density : 1003 time to evaluate : 6.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8356 (p0) cc_final: 0.7511 (p0) REVERT: A 422 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.5107 (pmtt) REVERT: C 75 GLU cc_start: 0.8014 (pp20) cc_final: 0.7656 (pp20) REVERT: C 83 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8411 (mmtm) REVERT: C 230 MET cc_start: 0.7965 (tpp) cc_final: 0.6780 (mtt) REVERT: C 293 MET cc_start: 0.7776 (tmm) cc_final: 0.7481 (tmm) REVERT: C 313 ARG cc_start: 0.6274 (OUTLIER) cc_final: 0.5865 (mtm180) REVERT: C 336 MET cc_start: 0.7965 (ppp) cc_final: 0.7625 (ppp) REVERT: C 383 PHE cc_start: 0.8369 (m-80) cc_final: 0.7699 (m-80) REVERT: D 60 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.7813 (t80) REVERT: D 61 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8486 (tt) REVERT: D 99 ASN cc_start: 0.8516 (t0) cc_final: 0.8135 (t0) REVERT: D 127 ASN cc_start: 0.7642 (t0) cc_final: 0.7138 (t0) REVERT: D 170 MET cc_start: 0.7843 (ptp) cc_final: 0.7550 (ptp) REVERT: D 245 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7329 (ttt-90) REVERT: D 374 ASP cc_start: 0.9144 (m-30) cc_final: 0.8744 (m-30) REVERT: G 83 MET cc_start: 0.7810 (mpp) cc_final: 0.7276 (mpp) REVERT: G 132 ARG cc_start: 0.6960 (ttp80) cc_final: 0.5869 (ptm-80) REVERT: H 8 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6194 (m-80) REVERT: H 49 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.6847 (pp20) REVERT: H 79 MET cc_start: 0.5980 (pmm) cc_final: 0.4151 (tpt) REVERT: H 118 MET cc_start: 0.7898 (mtm) cc_final: 0.7497 (ttm) REVERT: H 150 ASP cc_start: 0.7700 (m-30) cc_final: 0.6775 (m-30) REVERT: H 163 MET cc_start: 0.7211 (pmm) cc_final: 0.6743 (pmm) REVERT: H 165 LYS cc_start: 0.7379 (tppt) cc_final: 0.7004 (pttt) REVERT: H 166 ASN cc_start: 0.6694 (t0) cc_final: 0.6129 (t0) REVERT: I 72 MET cc_start: 0.3742 (mpp) cc_final: 0.3368 (mpp) REVERT: I 226 ARG cc_start: 0.8494 (tmm-80) cc_final: 0.8081 (tmm-80) REVERT: J 116 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8025 (tp40) REVERT: J 206 ILE cc_start: 0.4539 (OUTLIER) cc_final: 0.4301 (mm) REVERT: J 211 MET cc_start: 0.6277 (tmm) cc_final: 0.6048 (tmm) REVERT: L 115 LYS cc_start: 0.8348 (tppt) cc_final: 0.7984 (tttp) REVERT: L 123 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.8086 (t80) REVERT: L 176 MET cc_start: 0.6886 (ptm) cc_final: 0.6187 (ptp) REVERT: L 179 PHE cc_start: 0.5364 (m-10) cc_final: 0.5002 (m-10) REVERT: L 203 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6584 (mt0) REVERT: M 24 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7860 (pt0) REVERT: M 56 LYS cc_start: 0.8379 (mmtm) cc_final: 0.7700 (ttmt) REVERT: M 118 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6532 (t80) REVERT: M 124 LEU cc_start: 0.8114 (mt) cc_final: 0.7604 (mt) REVERT: O 64 GLU cc_start: 0.8458 (tp30) cc_final: 0.8188 (tp30) REVERT: O 86 MET cc_start: 0.8916 (ttp) cc_final: 0.8546 (ptp) REVERT: O 87 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7808 (tt) REVERT: W 73 MET cc_start: 0.5580 (mmt) cc_final: 0.5252 (mtt) REVERT: W 145 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6940 (pp) REVERT: W 174 TYR cc_start: 0.3851 (OUTLIER) cc_final: 0.2899 (m-80) REVERT: W 177 MET cc_start: 0.7757 (tpp) cc_final: 0.7500 (tpp) REVERT: X 194 ARG cc_start: 0.8361 (mmm160) cc_final: 0.7315 (ptm-80) REVERT: X 211 ASP cc_start: 0.8180 (m-30) cc_final: 0.7687 (t0) REVERT: X 254 MET cc_start: 0.7479 (tpt) cc_final: 0.6754 (tpt) REVERT: X 351 SER cc_start: 0.6026 (OUTLIER) cc_final: 0.5419 (p) REVERT: X 373 LYS cc_start: 0.8697 (mttm) cc_final: 0.8341 (mttm) REVERT: X 386 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7239 (mt) REVERT: Y 50 MET cc_start: 0.5456 (mmm) cc_final: 0.4367 (mmm) REVERT: Y 176 ARG cc_start: 0.8721 (mtt90) cc_final: 0.8333 (mtm180) REVERT: Y 222 TYR cc_start: 0.8616 (m-10) cc_final: 0.8199 (m-80) REVERT: Y 283 LYS cc_start: 0.4903 (OUTLIER) cc_final: 0.4692 (tmtt) REVERT: Y 328 GLU cc_start: 0.7675 (tt0) cc_final: 0.7334 (tm-30) REVERT: Y 343 LEU cc_start: 0.8757 (tt) cc_final: 0.8431 (tt) REVERT: a 238 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7551 (t80) REVERT: a 248 PHE cc_start: 0.7388 (t80) cc_final: 0.7088 (t80) REVERT: a 343 LEU cc_start: 0.8661 (tp) cc_final: 0.8247 (pt) REVERT: b 123 ASP cc_start: 0.7389 (m-30) cc_final: 0.7023 (t70) REVERT: d 165 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8208 (mm-30) REVERT: d 334 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7562 (tm-30) REVERT: d 347 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: g 104 ARG cc_start: 0.7083 (mmt90) cc_final: 0.6607 (mmm160) REVERT: g 151 VAL cc_start: 0.4119 (t) cc_final: 0.3879 (t) REVERT: g 163 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.5447 (pm20) REVERT: u 124 MET cc_start: 0.6492 (mtt) cc_final: 0.5937 (tpp) REVERT: B 96 ARG cc_start: 0.8274 (mmp80) cc_final: 0.7588 (ptp-170) REVERT: B 164 MET cc_start: 0.8108 (tpp) cc_final: 0.7880 (tpp) REVERT: B 175 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8029 (mtmm) REVERT: B 178 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7375 (tptp) REVERT: B 275 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6914 (mm-30) REVERT: Z 21 ASP cc_start: 0.7888 (t0) cc_final: 0.6753 (t0) REVERT: Z 78 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7196 (tpp) REVERT: Z 90 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6896 (mtm-85) REVERT: Z 209 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8141 (mtp-110) REVERT: E 78 ARG cc_start: 0.8233 (mtt-85) cc_final: 0.7910 (mtt180) REVERT: E 132 TYR cc_start: 0.9055 (m-80) cc_final: 0.8248 (m-80) REVERT: F 150 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7786 (tt) REVERT: c 104 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7819 (mmt-90) REVERT: c 282 ARG cc_start: 0.8797 (ttm-80) cc_final: 0.8479 (ttm-80) REVERT: c 309 PHE cc_start: 0.6993 (m-80) cc_final: 0.6779 (m-80) REVERT: K 12 VAL cc_start: 0.8189 (t) cc_final: 0.7965 (p) REVERT: K 26 TYR cc_start: 0.7755 (m-10) cc_final: 0.7464 (m-10) REVERT: K 59 MET cc_start: 0.8486 (tpp) cc_final: 0.8086 (tpp) REVERT: K 105 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.6715 (mp0) REVERT: U 59 PHE cc_start: 0.6703 (OUTLIER) cc_final: 0.6285 (t80) REVERT: U 188 MET cc_start: 0.7259 (tmm) cc_final: 0.6339 (tmm) REVERT: U 189 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.6692 (pm20) REVERT: U 351 MET cc_start: 0.7311 (tmm) cc_final: 0.7040 (tmm) REVERT: U 504 ASP cc_start: 0.7701 (t0) cc_final: 0.7294 (t70) REVERT: U 524 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8144 (tptp) REVERT: U 754 HIS cc_start: 0.5528 (t70) cc_final: 0.4870 (t70) REVERT: U 755 THR cc_start: 0.7687 (OUTLIER) cc_final: 0.7339 (m) REVERT: f 98 PHE cc_start: 0.6536 (m-80) cc_final: 0.6173 (m-80) REVERT: f 113 MET cc_start: 0.3541 (ptt) cc_final: 0.2919 (ptt) REVERT: f 137 ARG cc_start: 0.5711 (OUTLIER) cc_final: 0.5068 (mmp80) REVERT: f 297 MET cc_start: 0.8674 (ttm) cc_final: 0.8442 (ttm) REVERT: f 553 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8663 (m) REVERT: f 788 MET cc_start: 0.7592 (ppp) cc_final: 0.7348 (tmm) REVERT: V 150 ARG cc_start: 0.1332 (OUTLIER) cc_final: 0.1016 (mtm180) REVERT: V 153 LYS cc_start: 0.5059 (OUTLIER) cc_final: 0.4235 (tptm) REVERT: V 180 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6499 (mtm180) REVERT: V 214 HIS cc_start: 0.4326 (OUTLIER) cc_final: 0.3707 (t-90) REVERT: V 218 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6939 (t80) REVERT: V 254 LEU cc_start: 0.8174 (mt) cc_final: 0.7876 (tt) REVERT: V 309 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8285 (tpt) REVERT: V 314 ARG cc_start: 0.7817 (ptp-110) cc_final: 0.7508 (ptp-110) REVERT: V 447 ILE cc_start: 0.6240 (mp) cc_final: 0.6017 (mm) REVERT: V 463 MET cc_start: 0.7686 (tpp) cc_final: 0.7475 (tmm) REVERT: V 489 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8073 (mpt) outliers start: 472 outliers final: 314 residues processed: 1361 average time/residue: 0.6407 time to fit residues: 1510.5817 Evaluate side-chains 1303 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 356 poor density : 947 time to evaluate : 6.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 83 LYS Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 233 SER Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 370 ILE Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 145 GLU Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 192 ILE Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 132 VAL Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 151 ASP Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 206 ILE Chi-restraints excluded: chain J residue 215 GLN Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 123 TYR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 203 GLN Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 118 TYR Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 135 PHE Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 145 LEU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 174 TYR Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 244 CYS Chi-restraints excluded: chain W residue 344 THR Chi-restraints excluded: chain W residue 371 THR Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 76 PHE Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 251 LEU Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain X residue 304 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 351 SER Chi-restraints excluded: chain X residue 353 LEU Chi-restraints excluded: chain X residue 362 GLU Chi-restraints excluded: chain X residue 374 PHE Chi-restraints excluded: chain X residue 386 ILE Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 153 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 283 LYS Chi-restraints excluded: chain Y residue 301 ILE Chi-restraints excluded: chain Y residue 344 HIS Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Y residue 376 LEU Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 238 TYR Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain a residue 334 THR Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 9 CYS Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain b residue 122 LYS Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 137 THR Chi-restraints excluded: chain d residue 160 ASP Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain d residue 334 GLU Chi-restraints excluded: chain d residue 347 GLU Chi-restraints excluded: chain g residue 116 ILE Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 183 GLN Chi-restraints excluded: chain u residue 251 ASN Chi-restraints excluded: chain u residue 273 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 78 MET Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 202 ASN Chi-restraints excluded: chain Z residue 209 ARG Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 224 HIS Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 302 ASP Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 80 THR Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 300 LEU Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 93 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 181 LEU Chi-restraints excluded: chain U residue 184 CYS Chi-restraints excluded: chain U residue 189 GLN Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 258 GLN Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 342 LEU Chi-restraints excluded: chain U residue 373 ASN Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 524 LYS Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 602 LEU Chi-restraints excluded: chain U residue 607 VAL Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 731 ILE Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 746 ILE Chi-restraints excluded: chain U residue 755 THR Chi-restraints excluded: chain U residue 763 VAL Chi-restraints excluded: chain U residue 769 PHE Chi-restraints excluded: chain U residue 791 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 903 PHE Chi-restraints excluded: chain U residue 922 GLU Chi-restraints excluded: chain f residue 128 VAL Chi-restraints excluded: chain f residue 137 ARG Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain f residue 177 GLU Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 249 LEU Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 348 ILE Chi-restraints excluded: chain f residue 499 THR Chi-restraints excluded: chain f residue 510 SER Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 577 LEU Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 698 SER Chi-restraints excluded: chain f residue 711 SER Chi-restraints excluded: chain f residue 725 SER Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 870 THR Chi-restraints excluded: chain V residue 150 ARG Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 180 ARG Chi-restraints excluded: chain V residue 204 ASP Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 284 GLU Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 300 LEU Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain V residue 409 MET Chi-restraints excluded: chain V residue 412 LEU Chi-restraints excluded: chain V residue 457 TYR Chi-restraints excluded: chain V residue 485 ASP Chi-restraints excluded: chain V residue 489 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 770 optimal weight: 10.0000 chunk 706 optimal weight: 7.9990 chunk 855 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 884 optimal weight: 9.9990 chunk 448 optimal weight: 20.0000 chunk 226 optimal weight: 0.9990 chunk 715 optimal weight: 8.9990 chunk 333 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 400 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN I 30 HIS ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 145 HIS ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 HIS U 346 ASN ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.121402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.096184 restraints weight = 247759.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.098259 restraints weight = 131027.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.098812 restraints weight = 74449.814| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 72092 Z= 0.313 Angle : 0.793 15.309 97434 Z= 0.403 Chirality : 0.046 0.327 11146 Planarity : 0.005 0.077 12551 Dihedral : 8.046 150.169 9969 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.73 % Favored : 92.79 % Rotamer: Outliers : 5.45 % Allowed : 22.51 % Favored : 72.04 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.09), residues: 8895 helix: 0.41 (0.07), residues: 5038 sheet: -0.77 (0.16), residues: 873 loop : -1.65 (0.12), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 255 HIS 0.011 0.001 HIS D 187 PHE 0.033 0.002 PHE f 98 TYR 0.054 0.002 TYR f 723 ARG 0.010 0.001 ARG Y 267 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1441 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 419 poor density : 1022 time to evaluate : 6.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ASP cc_start: 0.8417 (p0) cc_final: 0.7608 (p0) REVERT: A 422 LYS cc_start: 0.6505 (OUTLIER) cc_final: 0.5131 (pmtt) REVERT: C 75 GLU cc_start: 0.8045 (pp20) cc_final: 0.7756 (pp20) REVERT: C 209 CYS cc_start: 0.4912 (m) cc_final: 0.4608 (m) REVERT: C 230 MET cc_start: 0.7989 (tpp) cc_final: 0.6820 (mtt) REVERT: C 248 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.6711 (mpp) REVERT: C 313 ARG cc_start: 0.6177 (OUTLIER) cc_final: 0.5724 (mtm180) REVERT: C 336 MET cc_start: 0.8220 (ppp) cc_final: 0.7984 (ppp) REVERT: C 383 PHE cc_start: 0.8399 (m-80) cc_final: 0.7739 (m-80) REVERT: D 60 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8251 (t80) REVERT: D 61 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8472 (tt) REVERT: D 99 ASN cc_start: 0.8559 (t0) cc_final: 0.8158 (t0) REVERT: D 127 ASN cc_start: 0.7619 (t0) cc_final: 0.7082 (t0) REVERT: D 170 MET cc_start: 0.7790 (ptp) cc_final: 0.7474 (ptp) REVERT: D 245 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7298 (ttt-90) REVERT: D 374 ASP cc_start: 0.9146 (m-30) cc_final: 0.8714 (m-30) REVERT: D 397 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8722 (mtmm) REVERT: G 14 THR cc_start: 0.8047 (m) cc_final: 0.7714 (t) REVERT: G 83 MET cc_start: 0.7791 (mpp) cc_final: 0.7146 (mpp) REVERT: G 113 MET cc_start: 0.8226 (mmm) cc_final: 0.7866 (mmm) REVERT: H 8 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.5958 (m-80) REVERT: H 49 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6829 (pp20) REVERT: H 79 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.3892 (tpt) REVERT: H 118 MET cc_start: 0.8005 (mtm) cc_final: 0.7581 (ttm) REVERT: H 150 ASP cc_start: 0.7679 (m-30) cc_final: 0.6758 (m-30) REVERT: H 163 MET cc_start: 0.7180 (pmm) cc_final: 0.6692 (pmm) REVERT: H 165 LYS cc_start: 0.7375 (tppt) cc_final: 0.6976 (pttt) REVERT: H 166 ASN cc_start: 0.6638 (t0) cc_final: 0.6027 (t0) REVERT: I 6 ASP cc_start: 0.7587 (p0) cc_final: 0.7300 (p0) REVERT: I 226 ARG cc_start: 0.8504 (tmm-80) cc_final: 0.8061 (tmm-80) REVERT: J 3 TYR cc_start: 0.7385 (m-80) cc_final: 0.7157 (m-80) REVERT: J 116 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7998 (tp40) REVERT: J 211 MET cc_start: 0.6312 (tmm) cc_final: 0.6072 (tmm) REVERT: L 123 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.8030 (t80) REVERT: L 176 MET cc_start: 0.6816 (ptm) cc_final: 0.6015 (ptp) REVERT: L 179 PHE cc_start: 0.5482 (m-10) cc_final: 0.5032 (m-10) REVERT: M 24 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7904 (pt0) REVERT: M 181 MET cc_start: 0.4894 (mmp) cc_final: 0.4514 (mmp) REVERT: O 64 GLU cc_start: 0.8438 (tp30) cc_final: 0.8162 (tp30) REVERT: O 86 MET cc_start: 0.8922 (ttp) cc_final: 0.8558 (ptp) REVERT: O 87 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7800 (tt) REVERT: W 73 MET cc_start: 0.5635 (mmt) cc_final: 0.5253 (mtt) REVERT: W 145 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6818 (pp) REVERT: W 174 TYR cc_start: 0.3850 (OUTLIER) cc_final: 0.2951 (m-80) REVERT: W 177 MET cc_start: 0.7725 (tpp) cc_final: 0.7486 (tpp) REVERT: W 382 LEU cc_start: 0.7065 (mt) cc_final: 0.6858 (mt) REVERT: X 194 ARG cc_start: 0.8286 (mmm160) cc_final: 0.7271 (ptm-80) REVERT: X 211 ASP cc_start: 0.8196 (m-30) cc_final: 0.7687 (t0) REVERT: X 254 MET cc_start: 0.7736 (tpt) cc_final: 0.7297 (tpt) REVERT: X 373 LYS cc_start: 0.8667 (mttm) cc_final: 0.8278 (mttt) REVERT: X 386 ILE cc_start: 0.7598 (OUTLIER) cc_final: 0.7305 (mt) REVERT: Y 176 ARG cc_start: 0.8743 (mtt90) cc_final: 0.8348 (mtm180) REVERT: Y 283 LYS cc_start: 0.4832 (OUTLIER) cc_final: 0.4603 (tmtt) REVERT: Y 328 GLU cc_start: 0.7629 (tt0) cc_final: 0.7329 (tm-30) REVERT: a 202 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7488 (pp) REVERT: a 238 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7631 (t80) REVERT: a 248 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.7076 (t80) REVERT: a 312 MET cc_start: 0.8763 (tpp) cc_final: 0.8411 (tpt) REVERT: a 343 LEU cc_start: 0.8658 (tp) cc_final: 0.8254 (pt) REVERT: a 369 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7684 (t-90) REVERT: b 31 ASP cc_start: 0.8047 (p0) cc_final: 0.7839 (p0) REVERT: b 123 ASP cc_start: 0.7378 (m-30) cc_final: 0.7024 (t70) REVERT: d 334 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7575 (tm-30) REVERT: g 104 ARG cc_start: 0.7122 (mmt90) cc_final: 0.6614 (mmm160) REVERT: g 116 ILE cc_start: 0.5886 (OUTLIER) cc_final: 0.5578 (tt) REVERT: g 151 VAL cc_start: 0.4186 (t) cc_final: 0.3952 (t) REVERT: g 163 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.5377 (pm20) REVERT: u 124 MET cc_start: 0.6332 (mtt) cc_final: 0.5834 (tpp) REVERT: B 96 ARG cc_start: 0.8226 (mmp80) cc_final: 0.7582 (ptp-170) REVERT: B 175 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8082 (mtmm) REVERT: B 178 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7188 (tptp) REVERT: B 275 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6886 (mm-30) REVERT: Z 90 ARG cc_start: 0.7252 (mtp180) cc_final: 0.6822 (mtm-85) REVERT: Z 149 THR cc_start: 0.7156 (p) cc_final: 0.6880 (p) REVERT: Z 209 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8154 (mtp-110) REVERT: Z 257 MET cc_start: 0.8919 (mmp) cc_final: 0.8700 (mmm) REVERT: E 78 ARG cc_start: 0.8198 (mtt-85) cc_final: 0.7895 (mtt180) REVERT: E 132 TYR cc_start: 0.9037 (m-80) cc_final: 0.8212 (m-80) REVERT: E 273 VAL cc_start: 0.9075 (t) cc_final: 0.8864 (t) REVERT: F 437 TYR cc_start: 0.6717 (t80) cc_final: 0.6513 (t80) REVERT: c 168 MET cc_start: 0.8361 (mmm) cc_final: 0.8083 (tpt) REVERT: c 201 TYR cc_start: 0.8527 (p90) cc_final: 0.8252 (p90) REVERT: c 282 ARG cc_start: 0.8768 (ttm-80) cc_final: 0.8473 (ttm-80) REVERT: c 309 PHE cc_start: 0.7051 (m-80) cc_final: 0.6755 (m-80) REVERT: K 12 VAL cc_start: 0.8186 (t) cc_final: 0.7971 (p) REVERT: K 26 TYR cc_start: 0.7714 (m-10) cc_final: 0.7444 (m-10) REVERT: K 59 MET cc_start: 0.8542 (tpp) cc_final: 0.8061 (tpp) REVERT: K 105 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: U 59 PHE cc_start: 0.6557 (OUTLIER) cc_final: 0.6123 (t80) REVERT: U 189 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.6936 (pm20) REVERT: U 351 MET cc_start: 0.7323 (tmm) cc_final: 0.6993 (tmm) REVERT: U 474 ARG cc_start: 0.7980 (ttm170) cc_final: 0.7717 (ttt90) REVERT: U 504 ASP cc_start: 0.7758 (t0) cc_final: 0.7549 (t70) REVERT: U 524 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8189 (tptp) REVERT: U 754 HIS cc_start: 0.5557 (t70) cc_final: 0.4823 (t70) REVERT: f 52 LEU cc_start: 0.8646 (tt) cc_final: 0.8395 (mt) REVERT: f 113 MET cc_start: 0.3781 (ptt) cc_final: 0.3282 (ptt) REVERT: f 137 ARG cc_start: 0.5668 (OUTLIER) cc_final: 0.5057 (mmp80) REVERT: f 553 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8631 (m) REVERT: f 788 MET cc_start: 0.7605 (ppp) cc_final: 0.7334 (tmm) REVERT: f 816 TYR cc_start: 0.7625 (OUTLIER) cc_final: 0.7236 (p90) REVERT: V 150 ARG cc_start: 0.1293 (OUTLIER) cc_final: 0.0954 (mtm180) REVERT: V 153 LYS cc_start: 0.5146 (OUTLIER) cc_final: 0.4218 (tptm) REVERT: V 214 HIS cc_start: 0.4023 (OUTLIER) cc_final: 0.3481 (t-90) REVERT: V 218 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6933 (t80) REVERT: V 254 LEU cc_start: 0.8170 (mt) cc_final: 0.7686 (tt) REVERT: V 314 ARG cc_start: 0.7780 (ptp-110) cc_final: 0.7532 (ptp-110) REVERT: V 358 MET cc_start: 0.6844 (tpp) cc_final: 0.6455 (mtt) REVERT: V 463 MET cc_start: 0.7698 (tpp) cc_final: 0.7473 (tmm) outliers start: 419 outliers final: 302 residues processed: 1344 average time/residue: 0.6692 time to fit residues: 1562.1497 Evaluate side-chains 1301 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 339 poor density : 962 time to evaluate : 6.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 245 ARG Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 362 ASP Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 123 TYR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 145 LEU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 174 TYR Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 244 CYS Chi-restraints excluded: chain W residue 344 THR Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 76 PHE Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 251 LEU Chi-restraints excluded: chain X residue 259 ILE Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain X residue 304 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 362 GLU Chi-restraints excluded: chain X residue 374 PHE Chi-restraints excluded: chain X residue 386 ILE Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain Y residue 45 VAL Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 153 ASP Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 283 LYS Chi-restraints excluded: chain Y residue 301 ILE Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Y residue 344 HIS Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Y residue 376 LEU Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 198 PHE Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 238 TYR Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 330 ARG Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain a residue 334 THR Chi-restraints excluded: chain a residue 335 TRP Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain a residue 369 HIS Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 38 HIS Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain b residue 122 LYS Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 160 ASP Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain d residue 334 GLU Chi-restraints excluded: chain g residue 116 ILE Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 183 GLN Chi-restraints excluded: chain u residue 251 ASN Chi-restraints excluded: chain u residue 273 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 126 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 202 ASN Chi-restraints excluded: chain Z residue 209 ARG Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 224 HIS Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 80 THR Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 300 LEU Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 93 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 181 LEU Chi-restraints excluded: chain U residue 184 CYS Chi-restraints excluded: chain U residue 189 GLN Chi-restraints excluded: chain U residue 258 GLN Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 357 LYS Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 373 ASN Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 524 LYS Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 607 VAL Chi-restraints excluded: chain U residue 625 ILE Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 731 ILE Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 746 ILE Chi-restraints excluded: chain U residue 752 THR Chi-restraints excluded: chain U residue 769 PHE Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 791 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 903 PHE Chi-restraints excluded: chain U residue 922 GLU Chi-restraints excluded: chain f residue 128 VAL Chi-restraints excluded: chain f residue 137 ARG Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 249 LEU Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 348 ILE Chi-restraints excluded: chain f residue 499 THR Chi-restraints excluded: chain f residue 510 SER Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 577 LEU Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 698 SER Chi-restraints excluded: chain f residue 725 SER Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 816 TYR Chi-restraints excluded: chain f residue 870 THR Chi-restraints excluded: chain V residue 150 ARG Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 204 ASP Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 284 GLU Chi-restraints excluded: chain V residue 298 ILE Chi-restraints excluded: chain V residue 300 LEU Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain V residue 409 MET Chi-restraints excluded: chain V residue 412 LEU Chi-restraints excluded: chain V residue 457 TYR Chi-restraints excluded: chain V residue 485 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 219 optimal weight: 20.0000 chunk 411 optimal weight: 20.0000 chunk 449 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 53 optimal weight: 30.0000 chunk 524 optimal weight: 1.9990 chunk 624 optimal weight: 2.9990 chunk 762 optimal weight: 5.9990 chunk 572 optimal weight: 2.9990 chunk 410 optimal weight: 20.0000 chunk 799 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 202 ASN ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 73 HIS ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 25 HIS U 189 GLN U 321 GLN U 346 ASN ** U 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 156 HIS ** f 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 614 HIS ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 326 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.121861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.098803 restraints weight = 247055.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.098878 restraints weight = 126198.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.099406 restraints weight = 83191.710| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3721 r_free = 0.3721 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 72092 Z= 0.288 Angle : 0.791 15.842 97434 Z= 0.399 Chirality : 0.046 0.463 11146 Planarity : 0.005 0.078 12551 Dihedral : 7.874 150.467 9959 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.79 % Favored : 92.77 % Rotamer: Outliers : 5.09 % Allowed : 23.38 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.09), residues: 8895 helix: 0.48 (0.07), residues: 5031 sheet: -0.79 (0.16), residues: 868 loop : -1.57 (0.12), residues: 2996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP a 22 HIS 0.011 0.001 HIS f 161 PHE 0.026 0.002 PHE I 130 TYR 0.053 0.002 TYR f 723 ARG 0.014 0.001 ARG X 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1444 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 391 poor density : 1053 time to evaluate : 6.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: A 143 ASP cc_start: 0.8596 (p0) cc_final: 0.7982 (p0) REVERT: A 422 LYS cc_start: 0.6481 (OUTLIER) cc_final: 0.5115 (pmtt) REVERT: C 75 GLU cc_start: 0.8054 (pp20) cc_final: 0.7745 (pp20) REVERT: C 230 MET cc_start: 0.7975 (tpp) cc_final: 0.6790 (mtt) REVERT: C 246 ILE cc_start: 0.8018 (mt) cc_final: 0.7804 (mp) REVERT: C 313 ARG cc_start: 0.6153 (OUTLIER) cc_final: 0.5857 (mtm-85) REVERT: C 336 MET cc_start: 0.8144 (ppp) cc_final: 0.7755 (ppp) REVERT: C 383 PHE cc_start: 0.8467 (m-80) cc_final: 0.7816 (m-80) REVERT: D 60 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.8291 (t80) REVERT: D 61 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8495 (tt) REVERT: D 99 ASN cc_start: 0.8554 (t0) cc_final: 0.8150 (t0) REVERT: D 127 ASN cc_start: 0.7591 (t0) cc_final: 0.7052 (t0) REVERT: D 139 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8844 (tp) REVERT: D 170 MET cc_start: 0.7745 (ptp) cc_final: 0.7401 (ptp) REVERT: D 362 ASP cc_start: 0.8637 (t70) cc_final: 0.8436 (t0) REVERT: D 374 ASP cc_start: 0.9090 (m-30) cc_final: 0.8683 (m-30) REVERT: D 397 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8705 (mtmm) REVERT: G 14 THR cc_start: 0.7993 (m) cc_final: 0.7697 (t) REVERT: G 83 MET cc_start: 0.7745 (mpp) cc_final: 0.7250 (mpp) REVERT: G 113 MET cc_start: 0.8435 (mmm) cc_final: 0.7904 (mmm) REVERT: G 185 LYS cc_start: 0.5932 (OUTLIER) cc_final: 0.4670 (ttpt) REVERT: H 8 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.5964 (m-80) REVERT: H 23 GLU cc_start: 0.8947 (tp30) cc_final: 0.8351 (mp0) REVERT: H 49 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6819 (pp20) REVERT: H 79 MET cc_start: 0.5686 (pmm) cc_final: 0.3800 (tpt) REVERT: H 118 MET cc_start: 0.7999 (mtm) cc_final: 0.7569 (ttm) REVERT: H 150 ASP cc_start: 0.7667 (m-30) cc_final: 0.6709 (m-30) REVERT: H 163 MET cc_start: 0.7201 (pmm) cc_final: 0.6706 (pmm) REVERT: H 165 LYS cc_start: 0.7369 (tppt) cc_final: 0.6996 (pttt) REVERT: H 166 ASN cc_start: 0.6689 (t0) cc_final: 0.6081 (t0) REVERT: I 6 ASP cc_start: 0.7666 (p0) cc_final: 0.7403 (p0) REVERT: I 15 GLU cc_start: 0.7731 (pm20) cc_final: 0.7451 (pm20) REVERT: I 72 MET cc_start: 0.3229 (mpp) cc_final: 0.2909 (mpp) REVERT: I 226 ARG cc_start: 0.8500 (tmm-80) cc_final: 0.8054 (tmm-80) REVERT: I 249 ARG cc_start: 0.6915 (mmt-90) cc_final: 0.6210 (tpt90) REVERT: J 116 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8065 (tp40) REVERT: J 211 MET cc_start: 0.6201 (tmm) cc_final: 0.5973 (tmm) REVERT: L 115 LYS cc_start: 0.8102 (tppt) cc_final: 0.7728 (tttp) REVERT: L 123 TYR cc_start: 0.8381 (t80) cc_final: 0.7968 (t80) REVERT: L 176 MET cc_start: 0.6826 (ptm) cc_final: 0.5956 (ptp) REVERT: L 179 PHE cc_start: 0.5442 (m-10) cc_final: 0.4946 (m-10) REVERT: L 203 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6717 (mt0) REVERT: M 24 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7906 (pt0) REVERT: M 181 MET cc_start: 0.4930 (mmp) cc_final: 0.4635 (mmp) REVERT: M 243 LEU cc_start: 0.6283 (pp) cc_final: 0.5675 (mm) REVERT: O 64 GLU cc_start: 0.8400 (tp30) cc_final: 0.8121 (tp30) REVERT: O 86 MET cc_start: 0.8913 (ttp) cc_final: 0.8541 (ptp) REVERT: O 87 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7777 (tt) REVERT: W 73 MET cc_start: 0.5633 (mmt) cc_final: 0.5224 (mtt) REVERT: W 145 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6817 (pp) REVERT: W 167 GLN cc_start: 0.8494 (tt0) cc_final: 0.8289 (tm-30) REVERT: W 215 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6588 (tm-30) REVERT: W 382 LEU cc_start: 0.7063 (mt) cc_final: 0.6861 (mt) REVERT: X 187 ARG cc_start: 0.8158 (tpp80) cc_final: 0.7793 (tpp80) REVERT: X 194 ARG cc_start: 0.8334 (mmm160) cc_final: 0.7305 (ptm-80) REVERT: X 211 ASP cc_start: 0.8189 (m-30) cc_final: 0.7744 (t0) REVERT: X 254 MET cc_start: 0.7829 (tpt) cc_final: 0.7219 (tpt) REVERT: X 351 SER cc_start: 0.5738 (OUTLIER) cc_final: 0.5151 (p) REVERT: X 373 LYS cc_start: 0.8660 (mttm) cc_final: 0.8296 (mttm) REVERT: X 386 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7374 (mt) REVERT: X 406 ASN cc_start: 0.8881 (m-40) cc_final: 0.8488 (m-40) REVERT: Y 16 ASP cc_start: 0.6515 (t0) cc_final: 0.6089 (t0) REVERT: Y 50 MET cc_start: 0.5487 (mmm) cc_final: 0.4401 (mmm) REVERT: Y 176 ARG cc_start: 0.8774 (mtt90) cc_final: 0.8372 (mtm180) REVERT: Y 281 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7323 (tp30) REVERT: Y 283 LYS cc_start: 0.4844 (OUTLIER) cc_final: 0.4575 (tmtt) REVERT: Y 328 GLU cc_start: 0.7643 (tt0) cc_final: 0.7400 (tm-30) REVERT: a 202 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7482 (pp) REVERT: a 238 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7609 (t80) REVERT: a 248 PHE cc_start: 0.7476 (OUTLIER) cc_final: 0.7112 (t80) REVERT: a 312 MET cc_start: 0.8843 (tpp) cc_final: 0.8443 (tpt) REVERT: a 343 LEU cc_start: 0.8663 (tp) cc_final: 0.8275 (pt) REVERT: b 42 ARG cc_start: 0.7835 (mmt-90) cc_final: 0.7522 (mmt-90) REVERT: b 107 MET cc_start: 0.5760 (mtt) cc_final: 0.5224 (mtp) REVERT: b 123 ASP cc_start: 0.7360 (m-30) cc_final: 0.7020 (t70) REVERT: d 246 LEU cc_start: 0.2810 (OUTLIER) cc_final: 0.2342 (mt) REVERT: d 334 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: g 104 ARG cc_start: 0.7149 (mmt90) cc_final: 0.6519 (mmm160) REVERT: g 116 ILE cc_start: 0.5848 (OUTLIER) cc_final: 0.5558 (tt) REVERT: g 151 VAL cc_start: 0.4146 (OUTLIER) cc_final: 0.3921 (t) REVERT: g 163 GLU cc_start: 0.5665 (OUTLIER) cc_final: 0.5281 (pm20) REVERT: u 124 MET cc_start: 0.6310 (mtt) cc_final: 0.5814 (tpp) REVERT: u 180 MET cc_start: 0.6809 (ptm) cc_final: 0.6590 (ptm) REVERT: B 96 ARG cc_start: 0.8202 (mmp80) cc_final: 0.7712 (ptp-170) REVERT: B 175 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8056 (mtmm) REVERT: B 178 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7117 (tptp) REVERT: B 275 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.6825 (mm-30) REVERT: Z 68 TRP cc_start: 0.8470 (p-90) cc_final: 0.7786 (p-90) REVERT: Z 90 ARG cc_start: 0.7343 (mtp180) cc_final: 0.6892 (mtm-85) REVERT: Z 149 THR cc_start: 0.7050 (p) cc_final: 0.6793 (p) REVERT: Z 209 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.8149 (mtp-110) REVERT: E 78 ARG cc_start: 0.8174 (mtt-85) cc_final: 0.7866 (mtt180) REVERT: E 132 TYR cc_start: 0.8986 (m-80) cc_final: 0.8138 (m-80) REVERT: E 197 LYS cc_start: 0.8827 (tptt) cc_final: 0.8324 (tptt) REVERT: E 250 ASP cc_start: 0.7473 (m-30) cc_final: 0.7253 (m-30) REVERT: F 437 TYR cc_start: 0.6752 (t80) cc_final: 0.6531 (t80) REVERT: c 167 MET cc_start: 0.7472 (ttt) cc_final: 0.6603 (ttm) REVERT: c 282 ARG cc_start: 0.8785 (ttm-80) cc_final: 0.8507 (ttm-80) REVERT: c 309 PHE cc_start: 0.7043 (m-80) cc_final: 0.6722 (m-80) REVERT: K 12 VAL cc_start: 0.8165 (t) cc_final: 0.7960 (p) REVERT: K 26 TYR cc_start: 0.7707 (m-10) cc_final: 0.7424 (m-10) REVERT: K 59 MET cc_start: 0.8574 (tpp) cc_final: 0.8096 (tpp) REVERT: K 105 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: U 59 PHE cc_start: 0.6619 (OUTLIER) cc_final: 0.6202 (t80) REVERT: U 189 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.6771 (pm20) REVERT: U 339 LEU cc_start: 0.8948 (tt) cc_final: 0.8382 (pp) REVERT: U 351 MET cc_start: 0.7269 (tmm) cc_final: 0.6893 (tmm) REVERT: U 524 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8100 (tptp) REVERT: U 754 HIS cc_start: 0.5597 (t70) cc_final: 0.4847 (t70) REVERT: U 755 THR cc_start: 0.7723 (OUTLIER) cc_final: 0.7338 (m) REVERT: U 797 MET cc_start: 0.7348 (pmm) cc_final: 0.6748 (pmm) REVERT: f 52 LEU cc_start: 0.8647 (tt) cc_final: 0.8352 (mt) REVERT: f 113 MET cc_start: 0.4047 (ptt) cc_final: 0.3507 (ptt) REVERT: f 137 ARG cc_start: 0.5640 (OUTLIER) cc_final: 0.5044 (mmp80) REVERT: f 370 MET cc_start: 0.7444 (ptp) cc_final: 0.7112 (pmm) REVERT: f 788 MET cc_start: 0.7583 (ppp) cc_final: 0.7323 (tmm) REVERT: f 816 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.7388 (p90) REVERT: V 150 ARG cc_start: 0.1266 (OUTLIER) cc_final: 0.0910 (mtm180) REVERT: V 153 LYS cc_start: 0.5103 (OUTLIER) cc_final: 0.4166 (tptm) REVERT: V 214 HIS cc_start: 0.4156 (OUTLIER) cc_final: 0.3635 (t-90) REVERT: V 218 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6953 (t80) REVERT: V 254 LEU cc_start: 0.8120 (mt) cc_final: 0.7602 (tt) REVERT: V 269 LYS cc_start: 0.5628 (OUTLIER) cc_final: 0.4670 (tppt) REVERT: V 294 ARG cc_start: 0.7856 (ttt180) cc_final: 0.7495 (ttm170) REVERT: V 309 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8380 (tpt) REVERT: V 314 ARG cc_start: 0.7851 (ptp-110) cc_final: 0.7602 (ptp-110) REVERT: V 358 MET cc_start: 0.7046 (tpp) cc_final: 0.6564 (mtt) REVERT: V 463 MET cc_start: 0.7680 (tpp) cc_final: 0.7453 (tmm) REVERT: V 489 MET cc_start: 0.8077 (mpt) cc_final: 0.7859 (mpt) outliers start: 391 outliers final: 299 residues processed: 1350 average time/residue: 0.6460 time to fit residues: 1515.0102 Evaluate side-chains 1309 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 341 poor density : 968 time to evaluate : 6.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 215 GLN Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 55 GLU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 203 GLN Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 135 PHE Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 238 TYR Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 145 LEU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 215 GLN Chi-restraints excluded: chain W residue 244 CYS Chi-restraints excluded: chain W residue 344 THR Chi-restraints excluded: chain W residue 371 THR Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 76 PHE Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 251 LEU Chi-restraints excluded: chain X residue 259 ILE Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain X residue 304 LYS Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 351 SER Chi-restraints excluded: chain X residue 362 GLU Chi-restraints excluded: chain X residue 374 PHE Chi-restraints excluded: chain X residue 386 ILE Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 153 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 281 GLU Chi-restraints excluded: chain Y residue 283 LYS Chi-restraints excluded: chain Y residue 301 ILE Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Y residue 344 HIS Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Y residue 376 LEU Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 198 PHE Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 238 TYR Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 330 ARG Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain b residue 122 LYS Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain d residue 334 GLU Chi-restraints excluded: chain g residue 116 ILE Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 138 LEU Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 183 GLN Chi-restraints excluded: chain u residue 251 ASN Chi-restraints excluded: chain u residue 273 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 202 ASN Chi-restraints excluded: chain Z residue 209 ARG Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 224 HIS Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 300 LEU Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain e residue 34 GLU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 93 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 181 LEU Chi-restraints excluded: chain U residue 184 CYS Chi-restraints excluded: chain U residue 189 GLN Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 357 LYS Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 373 ASN Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 524 LYS Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 607 VAL Chi-restraints excluded: chain U residue 626 LEU Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 731 ILE Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 746 ILE Chi-restraints excluded: chain U residue 752 THR Chi-restraints excluded: chain U residue 755 THR Chi-restraints excluded: chain U residue 763 VAL Chi-restraints excluded: chain U residue 769 PHE Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 791 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 903 PHE Chi-restraints excluded: chain U residue 922 GLU Chi-restraints excluded: chain f residue 128 VAL Chi-restraints excluded: chain f residue 137 ARG Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 249 LEU Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 339 ILE Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 348 ILE Chi-restraints excluded: chain f residue 499 THR Chi-restraints excluded: chain f residue 510 SER Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 577 LEU Chi-restraints excluded: chain f residue 614 HIS Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 698 SER Chi-restraints excluded: chain f residue 725 SER Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 816 TYR Chi-restraints excluded: chain f residue 863 THR Chi-restraints excluded: chain f residue 870 THR Chi-restraints excluded: chain V residue 150 ARG Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 269 LYS Chi-restraints excluded: chain V residue 284 GLU Chi-restraints excluded: chain V residue 300 LEU Chi-restraints excluded: chain V residue 309 MET Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain V residue 409 MET Chi-restraints excluded: chain V residue 412 LEU Chi-restraints excluded: chain V residue 457 TYR Chi-restraints excluded: chain V residue 485 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 594 optimal weight: 5.9990 chunk 881 optimal weight: 20.0000 chunk 653 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 chunk 244 optimal weight: 4.9990 chunk 502 optimal weight: 6.9990 chunk 584 optimal weight: 3.9990 chunk 336 optimal weight: 5.9990 chunk 312 optimal weight: 5.9990 chunk 566 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 ASN ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 227 ASN ** a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 273 HIS ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 HIS c 221 HIS U 25 HIS U 346 ASN ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 488 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.120975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.097164 restraints weight = 247907.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.097735 restraints weight = 162719.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.098290 restraints weight = 92572.122| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 72092 Z= 0.340 Angle : 0.831 16.151 97434 Z= 0.419 Chirality : 0.047 0.573 11146 Planarity : 0.005 0.077 12551 Dihedral : 7.886 149.687 9950 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 18.85 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.96 % Favored : 92.59 % Rotamer: Outliers : 5.06 % Allowed : 24.08 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.09), residues: 8895 helix: 0.37 (0.07), residues: 5039 sheet: -0.87 (0.16), residues: 891 loop : -1.60 (0.12), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP a 22 HIS 0.018 0.002 HIS f 614 PHE 0.042 0.002 PHE d 208 TYR 0.048 0.002 TYR d 175 ARG 0.016 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1377 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 389 poor density : 988 time to evaluate : 6.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6845 (ptm160) REVERT: A 53 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7914 (mp10) REVERT: A 143 ASP cc_start: 0.8683 (p0) cc_final: 0.8022 (p0) REVERT: A 422 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.5159 (pmtt) REVERT: C 75 GLU cc_start: 0.8026 (pp20) cc_final: 0.7738 (pp20) REVERT: C 229 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7002 (ttp-110) REVERT: C 230 MET cc_start: 0.7936 (tpp) cc_final: 0.6818 (mtt) REVERT: C 383 PHE cc_start: 0.8367 (m-80) cc_final: 0.7843 (m-80) REVERT: D 60 TYR cc_start: 0.8824 (OUTLIER) cc_final: 0.8168 (t80) REVERT: D 61 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8509 (tt) REVERT: D 99 ASN cc_start: 0.8579 (t0) cc_final: 0.8134 (t0) REVERT: D 122 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7129 (mm-30) REVERT: D 127 ASN cc_start: 0.7580 (t0) cc_final: 0.7040 (t0) REVERT: D 170 MET cc_start: 0.7784 (ptp) cc_final: 0.7455 (ptp) REVERT: D 248 ARG cc_start: 0.8621 (mtt90) cc_final: 0.8142 (mtm180) REVERT: D 362 ASP cc_start: 0.8620 (t70) cc_final: 0.8403 (t0) REVERT: D 374 ASP cc_start: 0.9056 (m-30) cc_final: 0.8665 (m-30) REVERT: D 397 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8745 (mtmm) REVERT: G 14 THR cc_start: 0.8097 (m) cc_final: 0.7691 (t) REVERT: G 80 MET cc_start: 0.5605 (mmm) cc_final: 0.5156 (mmp) REVERT: G 83 MET cc_start: 0.7757 (mpp) cc_final: 0.7251 (mpp) REVERT: G 113 MET cc_start: 0.8466 (mmm) cc_final: 0.8133 (mmm) REVERT: G 185 LYS cc_start: 0.5877 (OUTLIER) cc_final: 0.4613 (ttpt) REVERT: H 8 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.5864 (m-80) REVERT: H 49 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6839 (pp20) REVERT: H 79 MET cc_start: 0.5669 (OUTLIER) cc_final: 0.3787 (tpt) REVERT: H 118 MET cc_start: 0.7973 (mtm) cc_final: 0.7543 (ttm) REVERT: H 150 ASP cc_start: 0.7694 (m-30) cc_final: 0.6877 (m-30) REVERT: H 163 MET cc_start: 0.7269 (pmm) cc_final: 0.6776 (pmm) REVERT: H 165 LYS cc_start: 0.7408 (tppt) cc_final: 0.6998 (pttt) REVERT: H 166 ASN cc_start: 0.6612 (t0) cc_final: 0.6032 (t0) REVERT: I 6 ASP cc_start: 0.7693 (p0) cc_final: 0.7460 (p0) REVERT: I 72 MET cc_start: 0.3487 (mpp) cc_final: 0.3154 (mpp) REVERT: I 142 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.6242 (t-90) REVERT: I 226 ARG cc_start: 0.8484 (tmm-80) cc_final: 0.8060 (tmm-80) REVERT: I 249 ARG cc_start: 0.6940 (mmt-90) cc_final: 0.6233 (tpt90) REVERT: J 116 GLN cc_start: 0.8454 (tm-30) cc_final: 0.8175 (tp40) REVERT: J 118 TYR cc_start: 0.8200 (m-80) cc_final: 0.7993 (m-10) REVERT: J 211 MET cc_start: 0.6156 (tmm) cc_final: 0.5934 (tmm) REVERT: L 115 LYS cc_start: 0.8123 (tppt) cc_final: 0.7782 (tttp) REVERT: L 123 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8016 (t80) REVERT: L 176 MET cc_start: 0.6843 (ptm) cc_final: 0.5972 (ptp) REVERT: L 179 PHE cc_start: 0.5373 (m-10) cc_final: 0.4896 (m-10) REVERT: L 203 GLN cc_start: 0.7084 (OUTLIER) cc_final: 0.6778 (mt0) REVERT: M 24 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7919 (pt0) REVERT: M 181 MET cc_start: 0.4642 (mmp) cc_final: 0.4392 (mmp) REVERT: O 54 MET cc_start: 0.7028 (ppp) cc_final: 0.6613 (ptm) REVERT: O 64 GLU cc_start: 0.8430 (tp30) cc_final: 0.8142 (tp30) REVERT: O 86 MET cc_start: 0.8885 (ttp) cc_final: 0.8507 (ptp) REVERT: O 87 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7781 (tt) REVERT: W 73 MET cc_start: 0.5576 (mmt) cc_final: 0.5238 (mtt) REVERT: W 145 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6944 (pp) REVERT: W 167 GLN cc_start: 0.8502 (tt0) cc_final: 0.8276 (tm-30) REVERT: W 315 MET cc_start: 0.5051 (mpp) cc_final: 0.4748 (mpp) REVERT: X 194 ARG cc_start: 0.8340 (mmm160) cc_final: 0.7350 (ptm-80) REVERT: X 211 ASP cc_start: 0.8139 (m-30) cc_final: 0.7767 (t0) REVERT: X 254 MET cc_start: 0.7879 (tpt) cc_final: 0.7434 (tpt) REVERT: X 351 SER cc_start: 0.5821 (OUTLIER) cc_final: 0.5204 (p) REVERT: X 373 LYS cc_start: 0.8675 (mttm) cc_final: 0.8330 (mttm) REVERT: X 406 ASN cc_start: 0.8866 (m-40) cc_final: 0.8439 (m-40) REVERT: Y 16 ASP cc_start: 0.6609 (t0) cc_final: 0.6267 (t0) REVERT: Y 50 MET cc_start: 0.5146 (mmm) cc_final: 0.3730 (mmm) REVERT: Y 176 ARG cc_start: 0.8755 (mtt90) cc_final: 0.8245 (mtm180) REVERT: Y 281 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7366 (tp30) REVERT: Y 283 LYS cc_start: 0.4759 (OUTLIER) cc_final: 0.4457 (tmtt) REVERT: Y 328 GLU cc_start: 0.7614 (tt0) cc_final: 0.7374 (tm-30) REVERT: a 202 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7503 (pp) REVERT: a 248 PHE cc_start: 0.7437 (OUTLIER) cc_final: 0.7088 (t80) REVERT: a 312 MET cc_start: 0.8888 (tpp) cc_final: 0.8466 (tpt) REVERT: a 366 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8667 (mp) REVERT: a 369 HIS cc_start: 0.8104 (OUTLIER) cc_final: 0.7753 (t-90) REVERT: b 16 MET cc_start: 0.4838 (tpp) cc_final: 0.4296 (tpt) REVERT: b 42 ARG cc_start: 0.7813 (mmt-90) cc_final: 0.7528 (mmt-90) REVERT: b 107 MET cc_start: 0.5803 (mtt) cc_final: 0.5278 (mtp) REVERT: b 123 ASP cc_start: 0.7510 (m-30) cc_final: 0.7121 (t70) REVERT: d 168 MET cc_start: 0.7179 (tpp) cc_final: 0.6920 (tpp) REVERT: d 246 LEU cc_start: 0.2786 (OUTLIER) cc_final: 0.2346 (mt) REVERT: d 334 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: g 104 ARG cc_start: 0.7024 (mmt90) cc_final: 0.6517 (mmm160) REVERT: g 116 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5793 (tt) REVERT: g 151 VAL cc_start: 0.4130 (OUTLIER) cc_final: 0.3898 (t) REVERT: g 163 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.5254 (pm20) REVERT: u 124 MET cc_start: 0.6406 (mtt) cc_final: 0.5873 (tpp) REVERT: u 180 MET cc_start: 0.6862 (ptm) cc_final: 0.6633 (ptm) REVERT: B 96 ARG cc_start: 0.8277 (mmp80) cc_final: 0.7661 (ptp-170) REVERT: B 178 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7113 (tptp) REVERT: B 275 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6835 (mm-30) REVERT: B 309 MET cc_start: 0.8477 (tpp) cc_final: 0.8258 (tpp) REVERT: Z 68 TRP cc_start: 0.8417 (p-90) cc_final: 0.7727 (p-90) REVERT: Z 90 ARG cc_start: 0.7385 (mtp180) cc_final: 0.6941 (mtm-85) REVERT: Z 149 THR cc_start: 0.7070 (OUTLIER) cc_final: 0.6777 (p) REVERT: Z 209 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8144 (mtp-110) REVERT: E 132 TYR cc_start: 0.9028 (m-80) cc_final: 0.8244 (m-80) REVERT: F 266 LYS cc_start: 0.9013 (mptt) cc_final: 0.8745 (mmtm) REVERT: c 167 MET cc_start: 0.7509 (ttt) cc_final: 0.6633 (ttm) REVERT: c 175 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8328 (mtp180) REVERT: c 309 PHE cc_start: 0.7053 (m-80) cc_final: 0.6745 (m-80) REVERT: K 12 VAL cc_start: 0.8195 (t) cc_final: 0.7988 (p) REVERT: K 26 TYR cc_start: 0.7826 (m-10) cc_final: 0.7555 (m-10) REVERT: K 59 MET cc_start: 0.8563 (tpp) cc_final: 0.8362 (tpp) REVERT: U 59 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.6313 (t80) REVERT: U 269 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7606 (ttm170) REVERT: U 351 MET cc_start: 0.7287 (tmm) cc_final: 0.6908 (tmm) REVERT: U 524 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8085 (tptp) REVERT: U 556 MET cc_start: 0.8507 (tpp) cc_final: 0.8217 (tpp) REVERT: U 754 HIS cc_start: 0.5474 (t70) cc_final: 0.4658 (t70) REVERT: U 755 THR cc_start: 0.7722 (OUTLIER) cc_final: 0.7316 (m) REVERT: U 797 MET cc_start: 0.7386 (pmm) cc_final: 0.6872 (pmm) REVERT: f 52 LEU cc_start: 0.8427 (tt) cc_final: 0.8089 (mt) REVERT: f 113 MET cc_start: 0.3871 (ptt) cc_final: 0.3380 (ptt) REVERT: f 137 ARG cc_start: 0.5624 (OUTLIER) cc_final: 0.4996 (mmp80) REVERT: f 209 MET cc_start: 0.8175 (ptp) cc_final: 0.7644 (ptp) REVERT: f 370 MET cc_start: 0.7518 (ptp) cc_final: 0.7155 (pmm) REVERT: f 662 MET cc_start: 0.8340 (ptp) cc_final: 0.7872 (ptp) REVERT: f 788 MET cc_start: 0.7640 (ppp) cc_final: 0.7421 (tmm) REVERT: f 816 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.7382 (p90) REVERT: V 124 ASN cc_start: 0.6854 (m-40) cc_final: 0.6540 (m-40) REVERT: V 150 ARG cc_start: 0.1453 (OUTLIER) cc_final: 0.1126 (mtm180) REVERT: V 153 LYS cc_start: 0.4962 (OUTLIER) cc_final: 0.4025 (tptm) REVERT: V 214 HIS cc_start: 0.3836 (OUTLIER) cc_final: 0.3232 (t-90) REVERT: V 218 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6954 (t80) REVERT: V 254 LEU cc_start: 0.8269 (mt) cc_final: 0.7759 (tt) REVERT: V 269 LYS cc_start: 0.5601 (OUTLIER) cc_final: 0.4638 (tppt) REVERT: V 294 ARG cc_start: 0.7726 (ttt180) cc_final: 0.7392 (ttm170) REVERT: V 314 ARG cc_start: 0.7823 (ptp-110) cc_final: 0.7586 (ptp-110) outliers start: 389 outliers final: 301 residues processed: 1284 average time/residue: 0.6492 time to fit residues: 1446.6103 Evaluate side-chains 1306 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 344 poor density : 962 time to evaluate : 6.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 215 GLN Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 123 TYR Chi-restraints excluded: chain L residue 134 ILE Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 203 GLN Chi-restraints excluded: chain L residue 222 THR Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 14 PHE Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 135 PHE Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 145 LEU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 244 CYS Chi-restraints excluded: chain W residue 344 THR Chi-restraints excluded: chain W residue 371 THR Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 76 PHE Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 251 LEU Chi-restraints excluded: chain X residue 259 ILE Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain X residue 304 LYS Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 351 SER Chi-restraints excluded: chain X residue 362 GLU Chi-restraints excluded: chain X residue 374 PHE Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 153 ASP Chi-restraints excluded: chain Y residue 168 ILE Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 281 GLU Chi-restraints excluded: chain Y residue 283 LYS Chi-restraints excluded: chain Y residue 301 ILE Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Y residue 344 HIS Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Y residue 376 LEU Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 198 PHE Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 330 ARG Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 369 HIS Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 24 THR Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain b residue 122 LYS Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain d residue 334 GLU Chi-restraints excluded: chain g residue 116 ILE Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 138 LEU Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 183 GLN Chi-restraints excluded: chain u residue 251 ASN Chi-restraints excluded: chain u residue 273 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 202 ASN Chi-restraints excluded: chain Z residue 209 ARG Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 224 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 48 LYS Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 155 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 80 THR Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 300 LEU Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain e residue 34 GLU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 93 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 181 LEU Chi-restraints excluded: chain U residue 184 CYS Chi-restraints excluded: chain U residue 258 GLN Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 357 LYS Chi-restraints excluded: chain U residue 366 HIS Chi-restraints excluded: chain U residue 373 ASN Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 462 LEU Chi-restraints excluded: chain U residue 524 LYS Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 607 VAL Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 731 ILE Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 746 ILE Chi-restraints excluded: chain U residue 752 THR Chi-restraints excluded: chain U residue 755 THR Chi-restraints excluded: chain U residue 763 VAL Chi-restraints excluded: chain U residue 769 PHE Chi-restraints excluded: chain U residue 788 VAL Chi-restraints excluded: chain U residue 791 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 903 PHE Chi-restraints excluded: chain U residue 922 GLU Chi-restraints excluded: chain f residue 128 VAL Chi-restraints excluded: chain f residue 137 ARG Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 249 LEU Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 339 ILE Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 348 ILE Chi-restraints excluded: chain f residue 499 THR Chi-restraints excluded: chain f residue 510 SER Chi-restraints excluded: chain f residue 553 THR Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 577 LEU Chi-restraints excluded: chain f residue 614 HIS Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 698 SER Chi-restraints excluded: chain f residue 725 SER Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 816 TYR Chi-restraints excluded: chain f residue 863 THR Chi-restraints excluded: chain f residue 870 THR Chi-restraints excluded: chain V residue 150 ARG Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 204 ASP Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 269 LYS Chi-restraints excluded: chain V residue 284 GLU Chi-restraints excluded: chain V residue 300 LEU Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain V residue 409 MET Chi-restraints excluded: chain V residue 412 LEU Chi-restraints excluded: chain V residue 457 TYR Chi-restraints excluded: chain V residue 485 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 293 optimal weight: 20.0000 chunk 87 optimal weight: 0.1980 chunk 514 optimal weight: 3.9990 chunk 808 optimal weight: 5.9990 chunk 436 optimal weight: 9.9990 chunk 679 optimal weight: 5.9990 chunk 516 optimal weight: 3.9990 chunk 842 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 701 optimal weight: 9.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN I 30 HIS ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN L 4 ASN ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 202 ASN ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN c 183 HIS U 25 HIS U 346 ASN ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.121800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.098610 restraints weight = 245788.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.099201 restraints weight = 125041.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.099662 restraints weight = 77260.375| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 72092 Z= 0.293 Angle : 0.825 19.516 97434 Z= 0.412 Chirality : 0.047 0.736 11146 Planarity : 0.005 0.078 12551 Dihedral : 7.786 149.945 9947 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.77 % Favored : 92.82 % Rotamer: Outliers : 4.57 % Allowed : 24.59 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.09), residues: 8895 helix: 0.43 (0.07), residues: 5037 sheet: -0.85 (0.16), residues: 870 loop : -1.56 (0.12), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP a 22 HIS 0.010 0.001 HIS D 187 PHE 0.041 0.002 PHE d 208 TYR 0.033 0.002 TYR d 175 ARG 0.011 0.001 ARG D 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17790 Ramachandran restraints generated. 8895 Oldfield, 0 Emsley, 8895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1380 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 351 poor density : 1029 time to evaluate : 6.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6944 (ptm160) REVERT: A 43 ARG cc_start: 0.8904 (tmt170) cc_final: 0.8673 (tmm-80) REVERT: A 53 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7964 (mp10) REVERT: A 143 ASP cc_start: 0.8615 (p0) cc_final: 0.7925 (p0) REVERT: A 422 LYS cc_start: 0.6503 (OUTLIER) cc_final: 0.5094 (pmtt) REVERT: C 75 GLU cc_start: 0.8077 (pp20) cc_final: 0.7789 (pp20) REVERT: C 150 MET cc_start: 0.8922 (mmp) cc_final: 0.8639 (mmp) REVERT: C 229 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7020 (ttp-110) REVERT: C 230 MET cc_start: 0.8016 (tpp) cc_final: 0.6881 (mtt) REVERT: C 335 LYS cc_start: 0.7840 (mttt) cc_final: 0.7380 (mmtm) REVERT: C 365 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8370 (tp30) REVERT: C 383 PHE cc_start: 0.8339 (m-80) cc_final: 0.7729 (m-80) REVERT: D 60 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.8371 (t80) REVERT: D 61 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8456 (tt) REVERT: D 99 ASN cc_start: 0.8553 (t0) cc_final: 0.8119 (t0) REVERT: D 122 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7118 (mm-30) REVERT: D 127 ASN cc_start: 0.7567 (t0) cc_final: 0.7023 (t0) REVERT: D 139 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8804 (tp) REVERT: D 152 MET cc_start: 0.7271 (mtt) cc_final: 0.7068 (mtm) REVERT: D 170 MET cc_start: 0.7751 (ptp) cc_final: 0.7419 (ptp) REVERT: D 345 PHE cc_start: 0.7980 (m-80) cc_final: 0.7523 (m-80) REVERT: D 374 ASP cc_start: 0.9031 (m-30) cc_final: 0.8732 (m-30) REVERT: D 397 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8778 (mtmm) REVERT: D 399 PHE cc_start: 0.9038 (m-80) cc_final: 0.8837 (m-80) REVERT: G 14 THR cc_start: 0.8113 (m) cc_final: 0.7715 (t) REVERT: G 80 MET cc_start: 0.5603 (mmm) cc_final: 0.5021 (mmp) REVERT: G 83 MET cc_start: 0.7704 (mpp) cc_final: 0.7112 (mpp) REVERT: G 113 MET cc_start: 0.8464 (mmm) cc_final: 0.8130 (mmm) REVERT: G 132 ARG cc_start: 0.7291 (ptt90) cc_final: 0.6017 (ptm-80) REVERT: G 185 LYS cc_start: 0.5998 (OUTLIER) cc_final: 0.4726 (ttpt) REVERT: H 49 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6976 (pp20) REVERT: H 79 MET cc_start: 0.5619 (OUTLIER) cc_final: 0.3793 (tpt) REVERT: H 118 MET cc_start: 0.8042 (mtm) cc_final: 0.7604 (ttm) REVERT: H 150 ASP cc_start: 0.7675 (m-30) cc_final: 0.6835 (m-30) REVERT: H 163 MET cc_start: 0.7356 (pmm) cc_final: 0.6842 (pmm) REVERT: H 165 LYS cc_start: 0.7417 (tppt) cc_final: 0.6730 (ptpp) REVERT: H 166 ASN cc_start: 0.6718 (t0) cc_final: 0.6219 (t0) REVERT: H 176 LYS cc_start: 0.8639 (mptt) cc_final: 0.8366 (mmtm) REVERT: I 6 ASP cc_start: 0.7688 (p0) cc_final: 0.7432 (p0) REVERT: I 72 MET cc_start: 0.3309 (mpp) cc_final: 0.2983 (mpp) REVERT: I 142 HIS cc_start: 0.6463 (OUTLIER) cc_final: 0.6172 (t-90) REVERT: I 226 ARG cc_start: 0.8494 (tmm-80) cc_final: 0.8049 (tmm-80) REVERT: I 249 ARG cc_start: 0.6823 (mmt-90) cc_final: 0.6171 (tpt90) REVERT: J 116 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8212 (tp40) REVERT: L 115 LYS cc_start: 0.8190 (tppt) cc_final: 0.7793 (tttp) REVERT: L 123 TYR cc_start: 0.8471 (t80) cc_final: 0.8038 (t80) REVERT: L 176 MET cc_start: 0.6679 (ptm) cc_final: 0.5869 (ptp) REVERT: L 203 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6696 (mt0) REVERT: M 24 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7931 (pt0) REVERT: M 170 GLN cc_start: 0.7812 (pm20) cc_final: 0.7537 (mm-40) REVERT: O 54 MET cc_start: 0.6956 (ppp) cc_final: 0.6515 (ptm) REVERT: O 64 GLU cc_start: 0.8371 (tp30) cc_final: 0.8090 (tp30) REVERT: O 86 MET cc_start: 0.8928 (ttp) cc_final: 0.8538 (ptp) REVERT: O 87 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7782 (tt) REVERT: W 73 MET cc_start: 0.5632 (mmt) cc_final: 0.5222 (mtt) REVERT: W 145 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6905 (pp) REVERT: W 167 GLN cc_start: 0.8541 (tt0) cc_final: 0.8254 (tm-30) REVERT: W 185 PHE cc_start: 0.8151 (m-80) cc_final: 0.7898 (m-80) REVERT: W 191 ARG cc_start: 0.7839 (tmt-80) cc_final: 0.7599 (tmt-80) REVERT: W 315 MET cc_start: 0.5117 (mpp) cc_final: 0.4786 (mpp) REVERT: W 451 MET cc_start: 0.8047 (ttm) cc_final: 0.7845 (ttm) REVERT: X 194 ARG cc_start: 0.8316 (mmm160) cc_final: 0.7333 (ptm-80) REVERT: X 211 ASP cc_start: 0.8167 (m-30) cc_final: 0.7739 (t0) REVERT: X 254 MET cc_start: 0.7896 (tpt) cc_final: 0.7483 (tpt) REVERT: X 351 SER cc_start: 0.5822 (OUTLIER) cc_final: 0.5218 (p) REVERT: X 373 LYS cc_start: 0.8702 (mttm) cc_final: 0.8318 (mttm) REVERT: Y 16 ASP cc_start: 0.6557 (t0) cc_final: 0.6179 (t0) REVERT: Y 50 MET cc_start: 0.5163 (mmm) cc_final: 0.3911 (mmm) REVERT: Y 176 ARG cc_start: 0.8636 (mtt90) cc_final: 0.8312 (mtm180) REVERT: Y 281 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7374 (tp30) REVERT: Y 283 LYS cc_start: 0.4740 (OUTLIER) cc_final: 0.4473 (tmtt) REVERT: Y 328 GLU cc_start: 0.7658 (tt0) cc_final: 0.7414 (tm-30) REVERT: a 202 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7479 (pp) REVERT: a 248 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6882 (t80) REVERT: a 335 TRP cc_start: 0.7675 (OUTLIER) cc_final: 0.7301 (t60) REVERT: a 343 LEU cc_start: 0.8520 (tp) cc_final: 0.8195 (pt) REVERT: a 366 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8666 (mp) REVERT: a 369 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7752 (t-90) REVERT: b 42 ARG cc_start: 0.7890 (mmt-90) cc_final: 0.7581 (mmt-90) REVERT: b 107 MET cc_start: 0.5485 (mtt) cc_final: 0.5079 (mtp) REVERT: b 123 ASP cc_start: 0.7491 (m-30) cc_final: 0.7097 (t70) REVERT: d 168 MET cc_start: 0.7793 (tpp) cc_final: 0.7309 (tpp) REVERT: d 246 LEU cc_start: 0.2946 (OUTLIER) cc_final: 0.2622 (mt) REVERT: d 334 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: g 104 ARG cc_start: 0.7050 (mmt90) cc_final: 0.6513 (mmm160) REVERT: g 116 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5783 (tt) REVERT: g 151 VAL cc_start: 0.4028 (OUTLIER) cc_final: 0.3815 (t) REVERT: u 124 MET cc_start: 0.6391 (mtt) cc_final: 0.5878 (tpp) REVERT: B 96 ARG cc_start: 0.8314 (mmp80) cc_final: 0.7653 (ptp-170) REVERT: B 164 MET cc_start: 0.7716 (tpp) cc_final: 0.6576 (mmm) REVERT: B 178 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.7004 (tptp) REVERT: B 275 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6821 (mm-30) REVERT: B 309 MET cc_start: 0.8362 (tpp) cc_final: 0.8141 (tpp) REVERT: B 412 MET cc_start: 0.8011 (mmm) cc_final: 0.7730 (mmt) REVERT: Z 68 TRP cc_start: 0.8414 (p-90) cc_final: 0.7669 (p-90) REVERT: Z 90 ARG cc_start: 0.7329 (mtp180) cc_final: 0.6891 (mtm-85) REVERT: Z 149 THR cc_start: 0.7081 (OUTLIER) cc_final: 0.6825 (p) REVERT: Z 209 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.8245 (mtp-110) REVERT: Z 257 MET cc_start: 0.8847 (mmm) cc_final: 0.8603 (mmm) REVERT: E 132 TYR cc_start: 0.9046 (m-80) cc_final: 0.8272 (m-80) REVERT: E 197 LYS cc_start: 0.8870 (tptt) cc_final: 0.8369 (tptt) REVERT: E 250 ASP cc_start: 0.7566 (m-30) cc_final: 0.7352 (m-30) REVERT: F 266 LYS cc_start: 0.8997 (mptt) cc_final: 0.8681 (mmtm) REVERT: c 167 MET cc_start: 0.7528 (ttt) cc_final: 0.6746 (ttm) REVERT: c 175 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7663 (mtm-85) REVERT: c 282 ARG cc_start: 0.8786 (ttm-80) cc_final: 0.8458 (ttm-80) REVERT: c 305 ASP cc_start: 0.8998 (m-30) cc_final: 0.8682 (m-30) REVERT: c 309 PHE cc_start: 0.7063 (m-80) cc_final: 0.6669 (m-80) REVERT: K 12 VAL cc_start: 0.8155 (t) cc_final: 0.7954 (p) REVERT: K 26 TYR cc_start: 0.7852 (m-10) cc_final: 0.7519 (m-10) REVERT: K 59 MET cc_start: 0.8526 (tpp) cc_final: 0.8132 (tpp) REVERT: K 105 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: U 59 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6222 (t80) REVERT: U 269 ARG cc_start: 0.7995 (ttm170) cc_final: 0.7604 (ttm170) REVERT: U 339 LEU cc_start: 0.8969 (tt) cc_final: 0.8398 (pp) REVERT: U 351 MET cc_start: 0.7255 (tmm) cc_final: 0.6864 (tmm) REVERT: U 524 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8051 (tptp) REVERT: U 556 MET cc_start: 0.8493 (tpp) cc_final: 0.8188 (tpp) REVERT: U 754 HIS cc_start: 0.5425 (t70) cc_final: 0.4587 (t70) REVERT: U 755 THR cc_start: 0.7744 (OUTLIER) cc_final: 0.7355 (m) REVERT: U 758 PRO cc_start: 0.8795 (Cg_exo) cc_final: 0.8578 (Cg_endo) REVERT: U 797 MET cc_start: 0.7499 (pmm) cc_final: 0.7092 (pmm) REVERT: f 54 ASP cc_start: 0.5360 (m-30) cc_final: 0.4594 (p0) REVERT: f 113 MET cc_start: 0.4188 (ptt) cc_final: 0.3687 (ptt) REVERT: f 137 ARG cc_start: 0.5662 (OUTLIER) cc_final: 0.5081 (mmp80) REVERT: f 209 MET cc_start: 0.8347 (ptp) cc_final: 0.7783 (ptp) REVERT: f 370 MET cc_start: 0.7458 (ptp) cc_final: 0.7122 (pmm) REVERT: f 662 MET cc_start: 0.8371 (ptp) cc_final: 0.7863 (ptp) REVERT: f 788 MET cc_start: 0.7582 (ppp) cc_final: 0.7339 (tmm) REVERT: V 150 ARG cc_start: 0.1451 (OUTLIER) cc_final: 0.1144 (mtm180) REVERT: V 153 LYS cc_start: 0.5062 (OUTLIER) cc_final: 0.4140 (tptm) REVERT: V 214 HIS cc_start: 0.3772 (OUTLIER) cc_final: 0.3211 (t-90) REVERT: V 218 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.7017 (t80) REVERT: V 254 LEU cc_start: 0.8175 (mt) cc_final: 0.7632 (tt) REVERT: V 269 LYS cc_start: 0.5562 (OUTLIER) cc_final: 0.4620 (tppt) REVERT: V 294 ARG cc_start: 0.7749 (ttt180) cc_final: 0.7333 (tpp-160) REVERT: V 309 MET cc_start: 0.7801 (tpt) cc_final: 0.7557 (ttm) REVERT: V 314 ARG cc_start: 0.8003 (ptp-110) cc_final: 0.7705 (ptp-110) REVERT: V 358 MET cc_start: 0.6720 (tpp) cc_final: 0.6387 (mtt) outliers start: 351 outliers final: 277 residues processed: 1292 average time/residue: 0.6395 time to fit residues: 1433.7192 Evaluate side-chains 1302 residues out of total 7800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 320 poor density : 982 time to evaluate : 6.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 366 ARG Chi-restraints excluded: chain A residue 377 CYS Chi-restraints excluded: chain A residue 422 LYS Chi-restraints excluded: chain C residue 24 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 229 ARG Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 365 GLU Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 397 LYS Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 160 TYR Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 74 LEU Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 147 PHE Chi-restraints excluded: chain H residue 156 PHE Chi-restraints excluded: chain H residue 214 ASN Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 30 HIS Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 217 THR Chi-restraints excluded: chain I residue 227 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 201 SER Chi-restraints excluded: chain J residue 215 GLN Chi-restraints excluded: chain J residue 231 GLU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 203 GLN Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 120 HIS Chi-restraints excluded: chain M residue 135 PHE Chi-restraints excluded: chain M residue 214 SER Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain M residue 238 TYR Chi-restraints excluded: chain O residue 53 ASP Chi-restraints excluded: chain O residue 87 LEU Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 145 LEU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 202 THR Chi-restraints excluded: chain W residue 244 CYS Chi-restraints excluded: chain W residue 344 THR Chi-restraints excluded: chain W residue 371 THR Chi-restraints excluded: chain W residue 413 ILE Chi-restraints excluded: chain X residue 76 PHE Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 167 VAL Chi-restraints excluded: chain X residue 171 LEU Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 251 LEU Chi-restraints excluded: chain X residue 259 ILE Chi-restraints excluded: chain X residue 263 THR Chi-restraints excluded: chain X residue 267 VAL Chi-restraints excluded: chain X residue 304 LYS Chi-restraints excluded: chain X residue 342 PHE Chi-restraints excluded: chain X residue 345 VAL Chi-restraints excluded: chain X residue 351 SER Chi-restraints excluded: chain X residue 362 GLU Chi-restraints excluded: chain X residue 374 PHE Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 396 THR Chi-restraints excluded: chain X residue 410 VAL Chi-restraints excluded: chain Y residue 42 MET Chi-restraints excluded: chain Y residue 131 THR Chi-restraints excluded: chain Y residue 138 LEU Chi-restraints excluded: chain Y residue 153 ASP Chi-restraints excluded: chain Y residue 189 VAL Chi-restraints excluded: chain Y residue 236 LEU Chi-restraints excluded: chain Y residue 270 VAL Chi-restraints excluded: chain Y residue 281 GLU Chi-restraints excluded: chain Y residue 283 LYS Chi-restraints excluded: chain Y residue 301 ILE Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Y residue 344 HIS Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Y residue 376 LEU Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 84 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 109 GLU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 190 VAL Chi-restraints excluded: chain a residue 198 PHE Chi-restraints excluded: chain a residue 202 LEU Chi-restraints excluded: chain a residue 211 PHE Chi-restraints excluded: chain a residue 248 PHE Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 255 TRP Chi-restraints excluded: chain a residue 330 ARG Chi-restraints excluded: chain a residue 331 VAL Chi-restraints excluded: chain a residue 335 TRP Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain a residue 366 LEU Chi-restraints excluded: chain a residue 369 HIS Chi-restraints excluded: chain b residue 8 VAL Chi-restraints excluded: chain b residue 49 VAL Chi-restraints excluded: chain b residue 87 CYS Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain b residue 122 LYS Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 246 LEU Chi-restraints excluded: chain d residue 255 SER Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 326 GLU Chi-restraints excluded: chain d residue 334 GLU Chi-restraints excluded: chain g residue 116 ILE Chi-restraints excluded: chain g residue 151 VAL Chi-restraints excluded: chain g residue 163 GLU Chi-restraints excluded: chain u residue 119 ILE Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 183 GLN Chi-restraints excluded: chain u residue 251 ASN Chi-restraints excluded: chain u residue 273 THR Chi-restraints excluded: chain B residue 55 HIS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 LYS Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain Z residue 67 VAL Chi-restraints excluded: chain Z residue 73 ASP Chi-restraints excluded: chain Z residue 85 VAL Chi-restraints excluded: chain Z residue 123 ILE Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 202 ASN Chi-restraints excluded: chain Z residue 209 ARG Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 224 HIS Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 305 ASN Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 90 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 425 LEU Chi-restraints excluded: chain c residue 26 ASP Chi-restraints excluded: chain c residue 49 VAL Chi-restraints excluded: chain c residue 58 LEU Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 104 ARG Chi-restraints excluded: chain c residue 108 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 129 THR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 157 ILE Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 203 ILE Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 300 LEU Chi-restraints excluded: chain c residue 306 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 GLU Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 206 MET Chi-restraints excluded: chain e residue 34 GLU Chi-restraints excluded: chain e residue 63 HIS Chi-restraints excluded: chain U residue 59 PHE Chi-restraints excluded: chain U residue 69 TYR Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 93 ASN Chi-restraints excluded: chain U residue 173 VAL Chi-restraints excluded: chain U residue 179 TYR Chi-restraints excluded: chain U residue 181 LEU Chi-restraints excluded: chain U residue 184 CYS Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 373 ASN Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 524 LYS Chi-restraints excluded: chain U residue 555 VAL Chi-restraints excluded: chain U residue 607 VAL Chi-restraints excluded: chain U residue 683 VAL Chi-restraints excluded: chain U residue 689 ILE Chi-restraints excluded: chain U residue 731 ILE Chi-restraints excluded: chain U residue 732 LEU Chi-restraints excluded: chain U residue 746 ILE Chi-restraints excluded: chain U residue 752 THR Chi-restraints excluded: chain U residue 755 THR Chi-restraints excluded: chain U residue 763 VAL Chi-restraints excluded: chain U residue 769 PHE Chi-restraints excluded: chain U residue 791 LEU Chi-restraints excluded: chain U residue 802 TYR Chi-restraints excluded: chain U residue 903 PHE Chi-restraints excluded: chain f residue 128 VAL Chi-restraints excluded: chain f residue 137 ARG Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 249 LEU Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 339 ILE Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 347 ASP Chi-restraints excluded: chain f residue 499 THR Chi-restraints excluded: chain f residue 510 SER Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 577 LEU Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 698 SER Chi-restraints excluded: chain f residue 725 SER Chi-restraints excluded: chain f residue 761 MET Chi-restraints excluded: chain f residue 799 VAL Chi-restraints excluded: chain f residue 863 THR Chi-restraints excluded: chain f residue 870 THR Chi-restraints excluded: chain V residue 150 ARG Chi-restraints excluded: chain V residue 153 LYS Chi-restraints excluded: chain V residue 214 HIS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 269 LYS Chi-restraints excluded: chain V residue 284 GLU Chi-restraints excluded: chain V residue 300 LEU Chi-restraints excluded: chain V residue 337 LEU Chi-restraints excluded: chain V residue 403 ILE Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain V residue 409 MET Chi-restraints excluded: chain V residue 412 LEU Chi-restraints excluded: chain V residue 457 TYR Chi-restraints excluded: chain V residue 485 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 885 random chunks: chunk 74 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 460 optimal weight: 9.9990 chunk 201 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 386 optimal weight: 9.9990 chunk 396 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 388 optimal weight: 5.9990 chunk 409 optimal weight: 8.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 HIS ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 69 HIS ** a 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 44 GLN ** Z 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN c 183 HIS U 25 HIS U 346 ASN ** f 619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 782 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.121673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.099451 restraints weight = 247314.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.099333 restraints weight = 138717.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099514 restraints weight = 91549.120| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 72092 Z= 0.296 Angle : 0.828 16.476 97434 Z= 0.413 Chirality : 0.047 0.456 11146 Planarity : 0.005 0.078 12551 Dihedral : 7.735 149.987 9945 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.40 % Allowed : 6.84 % Favored : 92.76 % Rotamer: Outliers : 4.63 % Allowed : 24.81 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.92 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.09), residues: 8895 helix: 0.41 (0.07), residues: 5050 sheet: -0.93 (0.16), residues: 890 loop : -1.53 (0.12), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP a 22 HIS 0.010 0.001 HIS I 30 PHE 0.044 0.002 PHE d 208 TYR 0.045 0.002 TYR d 175 ARG 0.013 0.001 ARG L 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31435.10 seconds wall clock time: 543 minutes 15.12 seconds (32595.12 seconds total)