Starting phenix.real_space_refine on Thu Jan 23 05:54:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8h_47720/01_2025/9e8h_47720.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8h_47720/01_2025/9e8h_47720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e8h_47720/01_2025/9e8h_47720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8h_47720/01_2025/9e8h_47720.map" model { file = "/net/cci-nas-00/data/ceres_data/9e8h_47720/01_2025/9e8h_47720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8h_47720/01_2025/9e8h_47720.cif" } resolution = 2.9 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= 0.003 sd= 0.038 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 17 5.49 5 Mg 6 5.21 5 S 381 5.16 5 C 45092 2.51 5 N 12246 2.21 5 O 13561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 283 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: 71304 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3107 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 23, 'TRANS': 371} Chain: "B" Number of atoms: 3192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3192 Classifications: {'peptide': 405} Link IDs: {'PCIS': 3, 'PTRANS': 20, 'TRANS': 381} Chain: "C" Number of atoms: 2895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2895 Classifications: {'peptide': 366} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 349} Chain breaks: 1 Chain: "D" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3039 Classifications: {'peptide': 380} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 362} Chain: "E" Number of atoms: 2797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2797 Classifications: {'peptide': 354} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 335} Chain: "F" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2743 Classifications: {'peptide': 351} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 333} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1886 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "H" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1793 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "I" Number of atoms: 1841 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 236, 1838 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 4, 'TRANS': 231} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 236, 1838 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 4, 'TRANS': 231} Chain breaks: 2 bond proxies already assigned to first conformer: 1857 Chain: "J" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1887 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "K" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1790 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "L" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1864 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "M" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1881 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "U" Number of atoms: 6515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 838, 6515 Classifications: {'peptide': 838} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 807} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "V" Number of atoms: 3841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3841 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 16, 'TRANS': 453} 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: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3317 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 408} Chain: "Y" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3179 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 377} Chain: "Z" Number of atoms: 2285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2285 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 9, 'TRANS': 276} 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: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1446 Classifications: {'peptide': 189} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 179} Chain: "c" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2282 Classifications: {'peptide': 290} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 279} Chain: "d" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2166 Classifications: {'peptide': 265} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "e" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 425 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "f" Number of atoms: 6433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 831, 6433 Classifications: {'peptide': 831} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 800} Chain breaks: 2 Chain: "g" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 736 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "u" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1210 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 8, 'TRANS': 142} Chain: "A" 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: "B" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" 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: "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} Time building chain proxies: 28.90, per 1000 atoms: 0.41 Number of scatterers: 71304 At special positions: 0 Unit cell: (220.08, 221.128, 226.368, 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 381 16.00 P 17 15.00 Mg 6 11.99 O 13561 8.00 N 12246 7.00 C 45092 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.82 Conformation dependent library (CDL) restraints added in 7.1 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 " 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16958 Finding SS restraints... Secondary structure from input PDB file: 431 helices and 39 sheets defined 60.8% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.83 Creating SS restraints... Processing helix chain 'A' and resid 41 through 64 removed outlier: 3.568A pdb=" N LEU A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.819A pdb=" N ILE A 134 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 164 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.656A pdb=" N VAL A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.635A pdb=" N ASN A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 292 through 307 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 347 through 359 Processing helix chain 'A' and resid 369 through 376 Processing helix chain 'A' and resid 381 through 399 removed outlier: 3.568A pdb=" N ALA A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 removed outlier: 3.570A pdb=" N PHE A 409 " --> pdb=" O THR A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 424 removed outlier: 4.232A pdb=" N LYS A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 433 removed outlier: 4.427A pdb=" N THR A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.527A pdb=" N LYS B 48 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 86 Processing helix chain 'B' and resid 91 through 104 removed outlier: 3.550A pdb=" N ASP B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.557A pdb=" N MET B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.504A pdb=" N GLU B 199 " --> pdb=" O GLN B 195 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.519A pdb=" N TYR B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 256 Processing helix chain 'B' and resid 261 through 277 Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.689A pdb=" N LYS B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.533A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.779A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 415 through 427 removed outlier: 3.608A pdb=" N GLU B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 425 " --> pdb=" O LYS B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 67 removed outlier: 3.533A pdb=" N ILE C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 132 through 142 removed outlier: 3.512A pdb=" N VAL C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 154 through 171 removed outlier: 3.679A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU C 167 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 171 through 179 removed outlier: 4.392A pdb=" N PHE C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 207 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 230 through 233 Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.506A pdb=" N HIS C 241 " --> pdb=" O MET C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 283 removed outlier: 4.374A pdb=" N GLY C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 321 through 334 removed outlier: 3.521A pdb=" N ARG C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 350 Processing helix chain 'C' and resid 355 through 373 Processing helix chain 'C' and resid 379 through 392 Processing helix chain 'D' and resid 40 through 79 removed outlier: 3.799A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'D' and resid 181 through 187 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 241 through 257 Processing helix chain 'D' and resid 267 through 270 Processing helix chain 'D' and resid 279 through 298 Processing helix chain 'D' and resid 313 through 317 Processing helix chain 'D' and resid 318 through 323 Processing helix chain 'D' and resid 337 through 350 Processing helix chain 'D' and resid 359 through 365 removed outlier: 4.260A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 389 Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.540A pdb=" N PHE D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 Processing helix chain 'E' and resid 37 through 51 removed outlier: 3.585A pdb=" N GLN E 51 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 124 Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.609A pdb=" N VAL E 148 " --> pdb=" O GLU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 155 through 163 removed outlier: 4.148A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 191 Processing helix chain 'E' and resid 201 through 203 No H-bonds generated for 'chain 'E' and resid 201 through 203' Processing helix chain 'E' and resid 209 through 225 Processing helix chain 'E' and resid 235 through 238 Processing helix chain 'E' and resid 247 through 265 Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 305 through 318 Processing helix chain 'E' and resid 327 through 335 removed outlier: 3.582A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 357 Processing helix chain 'E' and resid 363 through 378 Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'F' and resid 70 through 84 Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 169 through 175 Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 191 through 208 removed outlier: 3.862A pdb=" N ALA F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) removed outlier: 4.600A 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 214 Processing helix chain 'F' and resid 232 through 243 Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 288 through 291 Processing helix chain 'F' and resid 303 through 318 Processing helix chain 'F' and resid 358 through 370 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 392 through 410 removed outlier: 3.578A pdb=" N CYS F 400 " --> pdb=" O CYS F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 429 removed outlier: 3.860A pdb=" N LEU F 425 " --> pdb=" O MET F 421 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU F 426 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 31 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.838A pdb=" N GLY G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 removed outlier: 3.525A pdb=" N SER G 89 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 126 removed outlier: 3.665A pdb=" N CYS G 115 " --> pdb=" O VAL G 111 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 185 removed outlier: 3.593A pdb=" N LYS G 185 " --> pdb=" O LYS G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 231 through 245 removed outlier: 3.736A pdb=" N HIS G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 31 Processing helix chain 'H' and resid 79 through 102 Processing helix chain 'H' and resid 106 through 124 removed outlier: 3.598A pdb=" N THR H 122 " --> pdb=" O MET H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 178 Processing helix chain 'H' and resid 183 through 199 removed outlier: 3.818A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 234 removed outlier: 3.681A pdb=" N ALA H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE H 233 " --> pdb=" O TYR H 229 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA H 234 " --> pdb=" O LEU H 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 30 Processing helix chain 'I' and resid 79 through 94 Processing helix chain 'I' and resid 106 through 122 removed outlier: 3.615A pdb=" N THR I 122 " --> pdb=" O LYS I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 179 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 251 removed outlier: 3.696A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 Processing helix chain 'J' and resid 76 through 99 removed outlier: 3.686A pdb=" N ILE J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 119 Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.511A pdb=" N LYS J 174 " --> pdb=" O GLU J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.546A pdb=" N VAL J 191 " --> pdb=" O THR J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 221 through 239 removed outlier: 3.586A pdb=" N GLU J 237 " --> pdb=" O GLU J 233 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU J 238 " --> pdb=" O LYS J 234 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN J 239 " --> pdb=" O GLU J 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 32 removed outlier: 3.781A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS K 32 " --> pdb=" O ILE K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 81 through 96 removed outlier: 3.730A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 104 Processing helix chain 'K' and resid 108 through 120 removed outlier: 3.579A 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 206 Processing helix chain 'K' and resid 230 through 239 removed outlier: 3.583A pdb=" N VAL K 237 " --> pdb=" O GLU K 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.674A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS L 30 " --> pdb=" O MET L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 100 Processing helix chain 'L' and resid 104 through 116 removed outlier: 3.970A pdb=" N LEU L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 175 Processing helix chain 'L' and resid 176 through 179 Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.533A pdb=" N GLU L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'L' and resid 225 through 234 removed outlier: 3.854A pdb=" N SER L 230 " --> pdb=" O ASP L 226 " (cutoff:3.500A) Proline residue: L 231 - end of helix Processing helix chain 'M' and resid 20 through 31 removed outlier: 3.631A pdb=" N ALA M 29 " --> pdb=" O TYR M 25 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL M 30 " --> pdb=" O ALA M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 103 Processing helix chain 'M' and resid 107 through 122 removed outlier: 3.665A pdb=" N MET M 117 " --> pdb=" O ASP M 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR M 122 " --> pdb=" O TYR M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 179 removed outlier: 3.500A pdb=" N THR M 174 " --> pdb=" O GLN M 170 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU M 179 " --> pdb=" O GLU M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 201 removed outlier: 4.203A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU M 192 " --> pdb=" O ASP M 188 " (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 228 through 243 removed outlier: 3.514A pdb=" N LEU M 243 " --> pdb=" O ALA M 239 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 10 Processing helix chain 'U' and resid 11 through 13 No H-bonds generated for 'chain 'U' and resid 11 through 13' Processing helix chain 'U' and resid 16 through 31 removed outlier: 4.203A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 41 removed outlier: 3.547A pdb=" N ILE U 38 " --> pdb=" O PHE U 34 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 removed outlier: 3.740A pdb=" N VAL U 47 " --> pdb=" O ASP U 43 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU U 48 " --> pdb=" O LYS U 44 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.737A pdb=" N GLY U 85 " --> pdb=" O ALA U 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 88 No H-bonds generated for 'chain 'U' and resid 86 through 88' Processing helix chain 'U' and resid 94 through 118 removed outlier: 3.689A pdb=" N ASP U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU U 118 " --> pdb=" O GLU U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 119 through 123 Processing helix chain 'U' and resid 127 through 144 removed outlier: 3.885A pdb=" N CYS U 141 " --> pdb=" O MET U 137 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU U 142 " --> pdb=" O PHE U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 157 removed outlier: 3.546A pdb=" N GLY U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE U 153 " --> pdb=" O GLN U 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 170 removed outlier: 3.912A pdb=" N ILE U 167 " --> pdb=" O PHE U 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 187 Processing helix chain 'U' and resid 191 through 207 removed outlier: 3.621A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 3.755A pdb=" N PHE U 222 " --> pdb=" O GLN U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 239 removed outlier: 3.660A pdb=" N VAL U 237 " --> pdb=" O LEU U 233 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS U 238 " --> pdb=" O GLU U 234 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 255 removed outlier: 3.503A pdb=" N ALA U 245 " --> pdb=" O ASN U 241 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 270 removed outlier: 3.585A pdb=" N GLN U 266 " --> pdb=" O SER U 262 " (cutoff:3.500A) Processing helix chain 'U' and resid 321 through 330 Processing helix chain 'U' and resid 331 through 345 Processing helix chain 'U' and resid 349 through 358 removed outlier: 3.873A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 377 Processing helix chain 'U' and resid 383 through 389 Processing helix chain 'U' and resid 389 through 394 Processing helix chain 'U' and resid 395 through 397 No H-bonds generated for 'chain 'U' and resid 395 through 397' Processing helix chain 'U' and resid 398 through 412 removed outlier: 3.871A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 427 Processing helix chain 'U' and resid 434 through 450 removed outlier: 4.322A pdb=" N GLN U 438 " --> pdb=" O GLY U 434 " (cutoff:3.500A) Processing helix chain 'U' and resid 457 through 467 Processing helix chain 'U' and resid 470 through 485 Processing helix chain 'U' and resid 490 through 502 Processing helix chain 'U' and resid 505 through 520 removed outlier: 3.818A 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 556 removed outlier: 3.514A pdb=" N ALA U 553 " --> pdb=" O ALA U 549 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET U 556 " --> pdb=" O ILE U 552 " (cutoff:3.500A) Processing helix chain 'U' and resid 559 through 562 Processing helix chain 'U' and resid 563 through 572 Processing helix chain 'U' and resid 575 through 590 Processing helix chain 'U' and resid 595 through 608 Processing helix chain 'U' and resid 611 through 627 removed outlier: 3.763A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) Processing helix chain 'U' and resid 629 through 631 No H-bonds generated for 'chain 'U' and resid 629 through 631' Processing helix chain 'U' and resid 632 through 637 Processing helix chain 'U' and resid 639 through 643 Processing helix chain 'U' and resid 645 through 660 Processing helix chain 'U' and resid 665 through 676 Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 680 through 695 Processing helix chain 'U' and resid 705 through 718 Processing helix chain 'U' and resid 723 through 738 Processing helix chain 'U' and resid 756 through 768 Processing helix chain 'U' and resid 769 through 771 No H-bonds generated for 'chain 'U' and resid 769 through 771' Processing helix chain 'U' and resid 772 through 777 Processing helix chain 'U' and resid 778 through 782 removed outlier: 4.096A pdb=" N ALA U 782 " --> pdb=" O PHE U 778 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 778 through 782' Processing helix chain 'U' and resid 888 through 892 Processing helix chain 'V' and resid 59 through 89 removed outlier: 3.767A pdb=" N VAL V 70 " --> pdb=" O GLU V 66 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL V 86 " --> pdb=" O LEU V 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 100 removed outlier: 4.235A pdb=" N ARG V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA V 97 " --> pdb=" O PHE V 93 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET V 100 " --> pdb=" O ARG V 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 107 removed outlier: 3.910A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG V 107 " --> pdb=" O SER V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 121 removed outlier: 3.945A pdb=" N PHE V 121 " --> pdb=" O VAL V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 132 removed outlier: 3.804A pdb=" N LEU V 132 " --> pdb=" O ARG V 128 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 157 Processing helix chain 'V' and resid 160 through 178 removed outlier: 3.778A pdb=" N ALA V 165 " --> pdb=" O PRO V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 198 removed outlier: 3.669A pdb=" N LYS V 194 " --> pdb=" O ASP V 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 222 removed outlier: 3.759A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TYR V 218 " --> pdb=" O HIS V 214 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 241 removed outlier: 4.044A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 261 removed outlier: 3.707A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 Processing helix chain 'V' and resid 281 through 299 removed outlier: 3.786A pdb=" N ARG V 287 " --> pdb=" O ASN V 283 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 315 removed outlier: 3.531A pdb=" N ARG V 307 " --> pdb=" O SER V 303 " (cutoff:3.500A) Processing helix chain 'V' and resid 321 through 339 Processing helix chain 'V' and resid 344 through 349 removed outlier: 3.512A pdb=" N GLN V 347 " --> pdb=" O ASP V 344 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 370 removed outlier: 4.694A pdb=" N ARG V 355 " --> pdb=" O PRO V 351 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER V 356 " --> pdb=" O SER V 352 " (cutoff:3.500A) Proline residue: V 359 - end of helix removed outlier: 3.621A pdb=" N GLY V 370 " --> pdb=" O ALA V 366 " (cutoff:3.500A) Processing helix chain 'V' and resid 371 through 389 removed outlier: 6.477A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 397 Processing helix chain 'V' and resid 397 through 413 removed outlier: 3.859A pdb=" N ASN V 401 " --> pdb=" O ARG V 397 " (cutoff:3.500A) Processing helix chain 'V' and resid 419 through 427 Processing helix chain 'V' and resid 430 through 444 removed outlier: 3.591A pdb=" N PHE V 436 " --> pdb=" O GLU V 432 " (cutoff:3.500A) Processing helix chain 'V' and resid 465 through 469 Processing helix chain 'V' and resid 470 through 493 removed outlier: 3.795A pdb=" N PHE V 482 " --> pdb=" O GLN V 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 507 through 526 removed outlier: 3.758A pdb=" N ARG V 514 " --> pdb=" O GLU V 510 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU V 515 " --> pdb=" O ARG V 511 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA V 526 " --> pdb=" O ALA V 522 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 38 removed outlier: 3.628A pdb=" N ARG W 27 " --> pdb=" O THR W 23 " (cutoff:3.500A) Proline residue: W 29 - end of helix Processing helix chain 'W' and resid 40 through 58 removed outlier: 3.524A pdb=" N GLU W 45 " --> pdb=" O GLN W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 77 removed outlier: 3.928A pdb=" N ARG W 65 " --> pdb=" O VAL W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 92 Processing helix chain 'W' and resid 97 through 115 removed outlier: 3.715A pdb=" N THR W 110 " --> pdb=" O GLN W 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR W 111 " --> pdb=" O GLN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 Processing helix chain 'W' and resid 135 through 137 No H-bonds generated for 'chain 'W' and resid 135 through 137' Processing helix chain 'W' and resid 138 through 156 Processing helix chain 'W' and resid 158 through 168 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 207 removed outlier: 3.690A pdb=" N ILE W 204 " --> pdb=" O ILE W 200 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 209 No H-bonds generated for 'chain 'W' and resid 208 through 209' Processing helix chain 'W' and resid 210 through 216 Processing helix chain 'W' and resid 219 through 238 removed outlier: 3.666A pdb=" N HIS W 236 " --> pdb=" O GLN W 232 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU W 237 " --> pdb=" O LEU W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 252 Processing helix chain 'W' and resid 253 through 258 Processing helix chain 'W' and resid 259 through 277 removed outlier: 3.869A pdb=" N GLN W 265 " --> pdb=" O GLU W 261 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU W 276 " --> pdb=" O LEU W 272 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 292 Processing helix chain 'W' and resid 293 through 298 removed outlier: 3.986A pdb=" N LEU W 296 " --> pdb=" O ASP W 293 " (cutoff:3.500A) Processing helix chain 'W' and resid 299 through 311 Processing helix chain 'W' and resid 316 through 330 removed outlier: 6.372A pdb=" N MET W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 342 removed outlier: 4.268A pdb=" N PHE W 341 " --> pdb=" O THR W 338 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY W 342 " --> pdb=" O ASP W 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 338 through 342' Processing helix chain 'W' and resid 344 through 369 Processing helix chain 'W' and resid 375 through 382 Processing helix chain 'W' and resid 385 through 399 Processing helix chain 'W' and resid 420 through 453 removed outlier: 3.523A pdb=" N GLU W 449 " --> pdb=" O LEU W 445 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 15 removed outlier: 3.543A pdb=" N PHE X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 33 removed outlier: 3.762A pdb=" N ASP X 25 " --> pdb=" O GLU X 21 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE X 26 " --> pdb=" O ALA X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 61 removed outlier: 3.738A pdb=" N GLN X 44 " --> pdb=" O GLU X 40 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS X 59 " --> pdb=" O SER X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 73 removed outlier: 3.535A pdb=" N LEU X 70 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS X 71 " --> pdb=" O GLY X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 79 Processing helix chain 'X' and resid 81 through 99 Processing helix chain 'X' and resid 105 through 121 Processing helix chain 'X' and resid 122 through 140 Processing helix chain 'X' and resid 142 through 160 removed outlier: 3.536A pdb=" N MET X 160 " --> pdb=" O GLU X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 180 removed outlier: 3.609A pdb=" N GLU X 168 " --> pdb=" O ALA X 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 199 Processing helix chain 'X' and resid 203 through 221 Processing helix chain 'X' and resid 224 through 242 removed outlier: 3.779A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 246 through 261 Processing helix chain 'X' and resid 264 through 272 removed outlier: 4.271A pdb=" N GLN X 268 " --> pdb=" O PRO X 264 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA X 269 " --> pdb=" O GLU X 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 278 removed outlier: 4.137A pdb=" N ARG X 278 " --> pdb=" O LYS X 274 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 Processing helix chain 'X' and resid 298 through 309 removed outlier: 3.508A pdb=" N PHE X 302 " --> pdb=" O SER X 298 " (cutoff:3.500A) Processing helix chain 'X' and resid 309 through 314 Processing helix chain 'X' and resid 316 through 322 removed outlier: 3.840A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) Processing helix chain 'X' and resid 322 through 340 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 422 removed outlier: 3.518A pdb=" N VAL X 410 " --> pdb=" O ASN X 406 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 10 removed outlier: 3.777A pdb=" N GLY Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 28 removed outlier: 3.705A pdb=" N ALA Y 20 " --> pdb=" O ASP Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 49 Processing helix chain 'Y' and resid 50 through 62 Processing helix chain 'Y' and resid 66 through 94 removed outlier: 3.507A pdb=" N LYS Y 93 " --> pdb=" O GLU Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 114 Processing helix chain 'Y' and resid 116 through 130 removed outlier: 3.708A pdb=" N LYS Y 130 " --> pdb=" O LYS Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 152 Processing helix chain 'Y' and resid 153 through 171 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 removed outlier: 3.705A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 240 Processing helix chain 'Y' and resid 243 through 251 Processing helix chain 'Y' and resid 253 through 265 removed outlier: 3.991A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR Y 264 " --> pdb=" O LEU Y 260 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 284 Processing helix chain 'Y' and resid 288 through 290 No H-bonds generated for 'chain 'Y' and resid 288 through 290' Processing helix chain 'Y' and resid 291 through 310 removed outlier: 4.304A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 324 Processing helix chain 'Y' and resid 326 through 340 Processing helix chain 'Y' and resid 360 through 389 removed outlier: 3.753A pdb=" N TRP Y 364 " --> pdb=" O ASP Y 360 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU Y 368 " --> pdb=" O TRP Y 364 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET Y 389 " --> pdb=" O ARG Y 385 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 30 removed outlier: 3.693A pdb=" N VAL Z 29 " --> pdb=" O ARG Z 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 removed outlier: 3.501A pdb=" N MET Z 81 " --> pdb=" O ASN Z 77 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 114 removed outlier: 3.561A pdb=" N ARG Z 114 " --> pdb=" O GLU Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 176 Processing helix chain 'Z' and resid 185 through 217 Processing helix chain 'Z' and resid 225 through 236 removed outlier: 3.505A pdb=" N ASP Z 232 " --> pdb=" O TYR Z 228 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 289 removed outlier: 3.719A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL Z 269 " --> pdb=" O LEU Z 265 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 14 removed outlier: 3.803A pdb=" N ASN a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 32 Processing helix chain 'a' and resid 33 through 46 removed outlier: 3.814A pdb=" N THR a 38 " --> pdb=" O TRP a 34 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU a 39 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN a 40 " --> pdb=" O GLN a 36 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN a 46 " --> pdb=" O LEU a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 63 removed outlier: 4.127A pdb=" N GLU a 61 " --> pdb=" O ILE a 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 67 through 71 removed outlier: 3.503A pdb=" N ARG a 70 " --> pdb=" O PHE a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 87 removed outlier: 3.796A pdb=" N GLU a 78 " --> pdb=" O LEU a 74 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE a 79 " --> pdb=" O SER a 75 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN a 86 " --> pdb=" O HIS a 82 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET a 87 " --> pdb=" O VAL a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 104 removed outlier: 3.755A pdb=" N LEU a 94 " --> pdb=" O PRO a 90 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 125 Processing helix chain 'a' and resid 127 through 145 removed outlier: 3.578A pdb=" N GLU a 133 " --> pdb=" O GLN a 129 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU a 140 " --> pdb=" O GLU a 136 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN a 144 " --> pdb=" O GLU a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 167 removed outlier: 4.369A pdb=" N SER a 153 " --> pdb=" O THR a 149 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG a 154 " --> pdb=" O SER a 150 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE a 155 " --> pdb=" O VAL a 151 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 182 Processing helix chain 'a' and resid 189 through 207 Processing helix chain 'a' and resid 212 through 218 removed outlier: 3.787A pdb=" N LEU a 216 " --> pdb=" O ASN a 212 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET a 218 " --> pdb=" O GLY a 214 " (cutoff:3.500A) Processing helix chain 'a' and resid 221 through 226 removed outlier: 3.514A pdb=" N ARG a 226 " --> pdb=" O GLU a 223 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.082A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 251 Processing helix chain 'a' and resid 251 through 256 Processing helix chain 'a' and resid 258 through 264 Processing helix chain 'a' and resid 264 through 284 Processing helix chain 'a' and resid 285 through 288 Processing helix chain 'a' and resid 293 through 301 Processing helix chain 'a' and resid 303 through 318 removed outlier: 4.372A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 371 Processing helix chain 'b' and resid 13 through 18 Processing helix chain 'b' and resid 24 through 44 removed outlier: 3.609A pdb=" N HIS b 38 " --> pdb=" O ASN b 34 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 68 through 77 removed outlier: 3.642A pdb=" N LEU b 72 " --> pdb=" O THR b 68 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR b 77 " --> pdb=" O SER b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 99 removed outlier: 3.838A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 134 Processing helix chain 'b' and resid 145 through 150 Processing helix chain 'b' and resid 151 through 162 Processing helix chain 'b' and resid 178 through 183 Processing helix chain 'c' and resid 35 through 48 Processing helix chain 'c' and resid 88 through 100 Processing helix chain 'c' and resid 101 through 103 No H-bonds generated for 'chain 'c' and resid 101 through 103' Processing helix chain 'c' and resid 123 through 137 removed outlier: 3.585A pdb=" N PHE c 133 " --> pdb=" O THR c 129 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU c 136 " --> pdb=" O SER c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 170 removed outlier: 3.570A pdb=" N LEU c 170 " --> pdb=" O ASN c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 184 removed outlier: 3.675A pdb=" N LEU c 184 " --> pdb=" O LEU c 181 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 194 Processing helix chain 'c' and resid 210 through 218 Processing helix chain 'c' and resid 224 through 230 removed outlier: 3.649A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) Processing helix chain 'c' and resid 233 through 264 removed outlier: 3.642A pdb=" N GLU c 250 " --> pdb=" O LYS c 246 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS c 257 " --> pdb=" O LYS c 253 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP c 263 " --> pdb=" O VAL c 259 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS c 264 " --> pdb=" O GLU c 260 " (cutoff:3.500A) Processing helix chain 'c' and resid 268 through 273 removed outlier: 4.205A pdb=" N ILE c 272 " --> pdb=" O GLU c 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS c 273 " --> pdb=" O GLN c 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 268 through 273' Processing helix chain 'c' and resid 279 through 309 removed outlier: 3.839A pdb=" N VAL c 307 " --> pdb=" O MET c 303 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 104 removed outlier: 3.847A pdb=" N GLY d 93 " --> pdb=" O GLN d 89 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET d 94 " --> pdb=" O ALA d 90 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR d 95 " --> pdb=" O ALA d 91 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU d 96 " --> pdb=" O THR d 92 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN d 97 " --> pdb=" O GLY d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 126 removed outlier: 4.165A pdb=" N LEU d 121 " --> pdb=" O GLY d 117 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL d 122 " --> pdb=" O ARG d 118 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU d 125 " --> pdb=" O LEU d 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU d 126 " --> pdb=" O VAL d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 156 removed outlier: 3.903A pdb=" N LEU d 141 " --> pdb=" O THR d 137 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP d 146 " --> pdb=" O ILE d 142 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE d 156 " --> pdb=" O ALA d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 177 removed outlier: 3.878A pdb=" N PHE d 164 " --> pdb=" O ASP d 160 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS d 173 " --> pdb=" O ALA d 169 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR d 174 " --> pdb=" O GLN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 202 Processing helix chain 'd' and resid 204 through 215 removed outlier: 3.796A pdb=" N THR d 210 " --> pdb=" O ALA d 206 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG d 214 " --> pdb=" O THR d 210 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU d 215 " --> pdb=" O GLU d 211 " (cutoff:3.500A) Processing helix chain 'd' and resid 216 through 223 removed outlier: 3.651A pdb=" N ILE d 220 " --> pdb=" O PRO d 216 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN d 221 " --> pdb=" O ALA d 217 " (cutoff:3.500A) Processing helix chain 'd' and resid 223 through 239 Proline residue: d 229 - end of helix Processing helix chain 'd' and resid 240 through 247 Processing helix chain 'd' and resid 253 through 255 No H-bonds generated for 'chain 'd' and resid 253 through 255' Processing helix chain 'd' and resid 256 through 279 removed outlier: 3.738A pdb=" N ILE d 260 " --> pdb=" O TYR d 256 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP d 261 " --> pdb=" O THR d 257 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE d 262 " --> pdb=" O PHE d 258 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR d 266 " --> pdb=" O ILE d 262 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS d 277 " --> pdb=" O GLY d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 287 through 292 Processing helix chain 'd' and resid 296 through 307 removed outlier: 3.905A pdb=" N THR d 300 " --> pdb=" O PRO d 296 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP d 301 " --> pdb=" O LYS d 297 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR d 302 " --> pdb=" O LYS d 298 " (cutoff:3.500A) Processing helix chain 'd' and resid 331 through 348 Processing helix chain 'e' and resid 42 through 47 removed outlier: 3.724A pdb=" N ASP e 45 " --> pdb=" O ASN e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 61 removed outlier: 4.168A pdb=" N GLU e 61 " --> pdb=" O ARG e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 62 through 64 No H-bonds generated for 'chain 'e' and resid 62 through 64' Processing helix chain 'f' and resid 46 through 56 Processing helix chain 'f' and resid 57 through 63 Processing helix chain 'f' and resid 70 through 87 removed outlier: 3.566A pdb=" N ALA f 74 " --> pdb=" O LEU f 70 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG f 83 " --> pdb=" O ARG f 79 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER f 85 " --> pdb=" O GLN f 81 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 98 removed outlier: 3.590A pdb=" N PHE f 98 " --> pdb=" O LYS f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 105 removed outlier: 3.532A pdb=" N GLY f 104 " --> pdb=" O PRO f 101 " (cutoff:3.500A) Processing helix chain 'f' and resid 117 through 133 removed outlier: 4.030A pdb=" N PHE f 121 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA f 122 " --> pdb=" O ASN f 118 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP f 124 " --> pdb=" O ARG f 120 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE f 125 " --> pdb=" O PHE f 121 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE f 126 " --> pdb=" O ALA f 122 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR f 132 " --> pdb=" O VAL f 128 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET f 133 " --> pdb=" O LEU f 129 " (cutoff:3.500A) Processing helix chain 'f' and resid 138 through 146 removed outlier: 3.640A pdb=" N ARG f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) Processing helix chain 'f' and resid 150 through 154 Processing helix chain 'f' and resid 155 through 173 removed outlier: 3.555A pdb=" N GLU f 172 " --> pdb=" O LYS f 168 " (cutoff:3.500A) Processing helix chain 'f' and resid 174 through 180 removed outlier: 4.592A pdb=" N VAL f 179 " --> pdb=" O ALA f 176 " (cutoff:3.500A) Processing helix chain 'f' and resid 181 through 198 removed outlier: 3.725A pdb=" N THR f 186 " --> pdb=" O GLU f 182 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL f 188 " --> pdb=" O LEU f 184 " (cutoff:3.500A) Proline residue: f 193 - end of helix Processing helix chain 'f' and resid 200 through 212 removed outlier: 3.563A pdb=" N ALA f 204 " --> pdb=" O ALA f 200 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP f 206 " --> pdb=" O HIS f 202 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU f 208 " --> pdb=" O ALA f 204 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE f 211 " --> pdb=" O LEU f 207 " (cutoff:3.500A) Processing helix chain 'f' and resid 213 through 221 removed outlier: 3.587A pdb=" N MET f 216 " --> pdb=" O GLN f 213 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU f 217 " --> pdb=" O VAL f 214 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU f 218 " --> pdb=" O ASP f 215 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS f 219 " --> pdb=" O MET f 216 " (cutoff:3.500A) Processing helix chain 'f' and resid 225 through 237 removed outlier: 3.576A pdb=" N VAL f 229 " --> pdb=" O ALA f 225 " (cutoff:3.500A) Processing helix chain 'f' and resid 243 through 259 Processing helix chain 'f' and resid 261 through 273 Processing helix chain 'f' and resid 274 through 285 removed outlier: 3.838A pdb=" N CYS f 285 " --> pdb=" O ILE f 281 " (cutoff:3.500A) Processing helix chain 'f' and resid 287 through 302 removed outlier: 3.519A pdb=" N PHE f 296 " --> pdb=" O LYS f 292 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET f 297 " --> pdb=" O GLN f 293 " (cutoff:3.500A) Processing helix chain 'f' and resid 313 through 322 Processing helix chain 'f' and resid 325 through 337 Processing helix chain 'f' and resid 344 through 350 removed outlier: 3.591A pdb=" N ILE f 348 " --> pdb=" O VAL f 344 " (cutoff:3.500A) Processing helix chain 'f' and resid 351 through 354 Processing helix chain 'f' and resid 368 through 382 Processing helix chain 'f' and resid 395 through 400 Processing helix chain 'f' and resid 405 through 418 removed outlier: 3.511A pdb=" N SER f 409 " --> pdb=" O HIS f 405 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU f 414 " --> pdb=" O ALA f 410 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET f 416 " --> pdb=" O ALA f 412 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE f 417 " --> pdb=" O SER f 413 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) Processing helix chain 'f' and resid 421 through 434 removed outlier: 3.611A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP f 430 " --> pdb=" O LEU f 426 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR f 434 " --> pdb=" O ASP f 430 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 452 removed outlier: 3.623A pdb=" N LYS f 441 " --> pdb=" O GLU f 437 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY f 449 " --> pdb=" O LEU f 445 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 467 removed outlier: 4.302A pdb=" N ALA f 464 " --> pdb=" O ASP f 460 " (cutoff:3.500A) Processing helix chain 'f' and resid 468 through 470 No H-bonds generated for 'chain 'f' and resid 468 through 470' Processing helix chain 'f' and resid 474 through 489 removed outlier: 3.589A pdb=" N ARG f 478 " --> pdb=" O SER f 474 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE f 483 " --> pdb=" O LEU f 479 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY f 484 " --> pdb=" O GLY f 480 " (cutoff:3.500A) Processing helix chain 'f' and resid 494 through 506 Proline residue: f 503 - end of helix removed outlier: 4.021A pdb=" N GLY f 506 " --> pdb=" O LEU f 502 " (cutoff:3.500A) Processing helix chain 'f' and resid 511 through 526 Processing helix chain 'f' and resid 531 through 545 removed outlier: 3.586A pdb=" N GLU f 544 " --> pdb=" O GLN f 540 " (cutoff:3.500A) Processing helix chain 'f' and resid 548 through 552 Processing helix chain 'f' and resid 556 through 566 removed outlier: 3.718A pdb=" N LEU f 560 " --> pdb=" O ARG f 556 " (cutoff:3.500A) Processing helix chain 'f' and resid 573 through 581 removed outlier: 3.566A pdb=" N GLU f 581 " --> pdb=" O LEU f 577 " (cutoff:3.500A) Processing helix chain 'f' and resid 586 through 600 Processing helix chain 'f' and resid 605 through 618 removed outlier: 3.702A pdb=" N GLN f 611 " --> pdb=" O LEU f 607 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU f 612 " --> pdb=" O LYS f 608 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU f 618 " --> pdb=" O HIS f 614 " (cutoff:3.500A) Processing helix chain 'f' and resid 649 through 662 removed outlier: 3.791A pdb=" N ALA f 658 " --> pdb=" O VAL f 654 " (cutoff:3.500A) Processing helix chain 'f' and resid 664 through 682 removed outlier: 3.555A pdb=" N MET f 670 " --> pdb=" O ILE f 666 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA f 671 " --> pdb=" O GLY f 667 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU f 672 " --> pdb=" O ALA f 668 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG f 673 " --> pdb=" O GLU f 669 " (cutoff:3.500A) Processing helix chain 'f' and resid 683 through 688 Processing helix chain 'f' and resid 689 through 698 Processing helix chain 'f' and resid 703 through 713 removed outlier: 3.664A pdb=" N PHE f 713 " --> pdb=" O THR f 709 " (cutoff:3.500A) 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 770 removed outlier: 3.577A pdb=" N MET f 761 " --> pdb=" O ASN f 757 " (cutoff:3.500A) Processing helix chain 'f' and resid 771 through 774 Processing helix chain 'f' and resid 789 through 803 Processing helix chain 'f' and resid 804 through 806 No H-bonds generated for 'chain 'f' and resid 804 through 806' Processing helix chain 'f' and resid 814 through 825 Processing helix chain 'g' and resid 108 through 120 removed outlier: 3.613A pdb=" N ALA g 117 " --> pdb=" O ARG g 113 " (cutoff:3.500A) 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 141 through 146 Processing helix chain 'g' and resid 161 through 169 removed outlier: 4.090A pdb=" N PHE g 169 " --> pdb=" O ALA g 165 " (cutoff:3.500A) Processing helix chain 'u' and resid 147 through 151 removed outlier: 3.514A pdb=" N ARG u 151 " --> pdb=" O ASN u 148 " (cutoff:3.500A) Processing helix chain 'u' and resid 205 through 211 Processing helix chain 'u' and resid 221 through 226 Processing helix chain 'u' and resid 234 through 238 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 102 removed outlier: 5.729A pdb=" N CYS A 98 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASN A 114 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 100 " --> pdb=" O ILE A 112 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 124 current: chain 'A' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 152 current: chain 'B' and resid 120 through 124 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 134 current: chain 'B' and resid 159 through 162 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 159 through 162 current: chain 'C' and resid 85 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 93 through 97 current: chain 'C' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 123 through 126 current: chain 'D' and resid 100 through 105 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 110 through 114 current: chain 'D' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 139 through 142 current: chain 'E' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 81 current: chain 'E' and resid 107 through 111 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 107 through 111 current: chain 'F' and resid 121 through 126 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 131 through 134 current: chain 'F' and resid 160 through 163 Processing sheet with id=AA2, first strand: chain 'A' and resid 165 through 166 removed outlier: 4.858A pdb=" N PHE A 237 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 272 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 246 through 251 removed outlier: 6.312A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL B 250 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY B 221 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ILE B 351 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE B 223 " --> pdb=" O ILE B 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 210 through 213 removed outlier: 6.193A pdb=" N THR C 210 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N PHE C 247 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASP C 249 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N SER C 244 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE C 292 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE C 246 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA C 294 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET C 248 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLY C 185 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE C 315 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU C 187 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 226 through 231 removed outlier: 6.394A pdb=" N ALA D 260 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE D 308 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE D 262 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ALA D 310 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE D 264 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLY D 201 " --> pdb=" O ARG D 329 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE D 331 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU D 203 " --> pdb=" O ILE D 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 194 through 199 Processing sheet with id=AA7, first strand: chain 'F' and resid 247 through 252 removed outlier: 6.277A pdb=" N THR F 247 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE F 284 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU F 249 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP F 286 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 251 " --> pdb=" O ASP F 286 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER F 281 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ILE F 329 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE F 283 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N ALA F 331 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE F 285 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.620A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 69 through 71 removed outlier: 3.746A pdb=" N CYS G 161 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AB2, first strand: chain 'H' and resid 66 through 67 Processing sheet with id=AB3, first strand: chain 'I' and resid 161 through 164 Processing sheet with id=AB4, first strand: chain 'I' and resid 65 through 69 removed outlier: 6.637A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 158 through 161 Processing sheet with id=AB6, first strand: chain 'J' and resid 62 through 64 Processing sheet with id=AB7, first strand: chain 'K' and resid 167 through 170 Processing sheet with id=AB8, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.480A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 158 through 161 Processing sheet with id=AC1, first strand: chain 'L' and resid 63 through 65 removed outlier: 3.502A pdb=" N ASP L 138 " --> pdb=" O GLY L 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.915A pdb=" N GLY M 44 " --> pdb=" O CYS M 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 66 through 68 Processing sheet with id=AC4, first strand: chain 'U' and resid 744 through 746 Processing sheet with id=AC5, first strand: chain 'U' and resid 882 through 883 removed outlier: 6.355A pdb=" N CYS U 787 " --> pdb=" O GLY U 910 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE U 912 " --> pdb=" O CYS U 787 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE U 789 " --> pdb=" O ILE U 912 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU U 914 " --> pdb=" O ILE U 789 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU U 791 " --> pdb=" O LEU U 914 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ASP U 916 " --> pdb=" O LEU U 791 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 802 through 804 Processing sheet with id=AC7, first strand: chain 'V' and resid 449 through 452 removed outlier: 6.074A pdb=" N SER V 415 " --> pdb=" O SER V 460 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'X' and resid 376 through 379 removed outlier: 5.425A pdb=" N SER X 343 " --> pdb=" O ILE X 387 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL W 406 " --> pdb=" O SER X 343 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL X 345 " --> pdb=" O VAL W 406 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS a 321 " --> pdb=" O THR a 334 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 152 through 158 removed outlier: 3.687A pdb=" N SER Z 152 " --> pdb=" O GLU Z 143 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA Z 137 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) removed outlier: 9.549A pdb=" N VAL Z 120 " --> pdb=" O ARG Z 90 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL Z 92 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL Z 122 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP Z 94 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE Z 124 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N HIS Z 96 " --> pdb=" O ILE Z 124 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU Z 39 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TRP Z 94 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY Z 37 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER Z 42 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL Z 50 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN Z 44 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LEU Z 48 " --> pdb=" O GLN Z 44 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS Z 8 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N VAL Z 50 " --> pdb=" O LYS Z 8 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL Z 10 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ASN Z 52 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 58 through 60 Processing sheet with id=AD2, first strand: chain 'b' and resid 59 through 65 removed outlier: 6.498A pdb=" N LEU b 51 " --> pdb=" O LEU b 61 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N THR b 63 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL b 49 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ASP b 139 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE b 109 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE b 141 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA b 111 " --> pdb=" O ILE b 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 30 through 34 removed outlier: 6.637A pdb=" N GLN c 30 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL c 69 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR c 32 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP c 71 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N SER c 34 " --> pdb=" O ASP c 71 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N PHE c 73 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL c 69 " --> pdb=" O GLU c 60 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N GLU c 60 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY c 55 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP c 111 " --> pdb=" O GLY c 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET c 57 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET c 107 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 10.067A pdb=" N VAL c 141 " --> pdb=" O MET c 107 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL c 109 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL c 143 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TRP c 111 " --> pdb=" O VAL c 143 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL c 145 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N HIS c 113 " --> pdb=" O VAL c 145 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL c 156 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N ILE c 148 " --> pdb=" O LYS c 154 " (cutoff:3.500A) removed outlier: 10.570A pdb=" N LYS c 154 " --> pdb=" O ILE c 148 " (cutoff:3.500A) removed outlier: 12.665A pdb=" N VAL c 155 " --> pdb=" O TYR c 207 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N TYR c 207 " --> pdb=" O VAL c 155 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'd' and resid 281 through 283 Processing sheet with id=AD5, first strand: chain 'f' and resid 776 through 777 Processing sheet with id=AD6, first strand: chain 'f' and resid 781 through 782 Processing sheet with id=AD7, first strand: chain 'f' and resid 830 through 833 Processing sheet with id=AD8, first strand: chain 'f' and resid 862 through 869 removed outlier: 5.935A pdb=" N GLY f 864 " --> pdb=" O GLN f 848 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN f 848 " --> pdb=" O GLY f 864 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'g' and resid 99 through 104 removed outlier: 4.133A pdb=" N ASN g 99 " --> pdb=" O VAL g 87 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR g 103 " --> pdb=" O ALA g 83 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA g 83 " --> pdb=" O THR g 103 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N VAL g 151 " --> pdb=" O ILE g 82 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR g 84 " --> pdb=" O VAL g 151 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ALA g 153 " --> pdb=" O THR g 84 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU g 86 " --> pdb=" O ALA g 153 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL g 155 " --> pdb=" O GLU g 86 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'u' and resid 124 through 125 removed outlier: 6.824A pdb=" N THR u 268 " --> pdb=" O LEU u 177 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU u 177 " --> pdb=" O THR u 268 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'u' and resid 157 through 158 Processing sheet with id=AE3, first strand: chain 'u' and resid 165 through 170 removed outlier: 6.565A pdb=" N TYR u 193 " --> pdb=" O GLN u 249 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASN u 251 " --> pdb=" O PRO u 191 " (cutoff:3.500A) 3932 hydrogen bonds defined for protein. 11316 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: 31.81 Time building geometry restraints manager: 15.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 23759 1.34 - 1.46: 15172 1.46 - 1.59: 32914 1.59 - 1.71: 22 1.71 - 1.83: 637 Bond restraints: 72504 Sorted by residual: bond pdb=" CA ASP J 4 " pdb=" CB ASP J 4 " ideal model delta sigma weight residual 1.531 1.659 -0.128 3.28e-02 9.30e+02 1.53e+01 bond pdb=" N ILE A 65 " pdb=" CA ILE A 65 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.25e-02 6.40e+03 1.46e+01 bond pdb=" N GLU A 67 " pdb=" CA GLU A 67 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.30e+00 bond pdb=" N SER A 68 " pdb=" CA SER A 68 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.49e+00 bond pdb=" CB ASN g 132 " pdb=" CG ASN g 132 " ideal model delta sigma weight residual 1.516 1.577 -0.061 2.50e-02 1.60e+03 5.95e+00 ... (remaining 72499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 96909 2.27 - 4.53: 870 4.53 - 6.80: 129 6.80 - 9.07: 32 9.07 - 11.33: 13 Bond angle restraints: 97953 Sorted by residual: angle pdb=" CA GLU f 836 " pdb=" CB GLU f 836 " pdb=" CG GLU f 836 " ideal model delta sigma weight residual 114.10 124.65 -10.55 2.00e+00 2.50e-01 2.78e+01 angle pdb=" N ASP U 240 " pdb=" CA ASP U 240 " pdb=" CB ASP U 240 " ideal model delta sigma weight residual 114.17 109.30 4.87 1.14e+00 7.69e-01 1.83e+01 angle pdb=" CA MET c 265 " pdb=" CB MET c 265 " pdb=" CG MET c 265 " ideal model delta sigma weight residual 114.10 122.49 -8.39 2.00e+00 2.50e-01 1.76e+01 angle pdb=" CA GLY A 64 " pdb=" C GLY A 64 " pdb=" O GLY A 64 " ideal model delta sigma weight residual 122.43 115.47 6.96 1.69e+00 3.50e-01 1.70e+01 angle pdb=" CA GLN U 18 " pdb=" CB GLN U 18 " pdb=" CG GLN U 18 " ideal model delta sigma weight residual 114.10 122.09 -7.99 2.00e+00 2.50e-01 1.59e+01 ... (remaining 97948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 37643 18.05 - 36.11: 5065 36.11 - 54.16: 1565 54.16 - 72.21: 265 72.21 - 90.27: 98 Dihedral angle restraints: 44636 sinusoidal: 18425 harmonic: 26211 Sorted by residual: dihedral pdb=" CA GLU f 669 " pdb=" C GLU f 669 " pdb=" N MET f 670 " pdb=" CA MET f 670 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLU W 217 " pdb=" C GLU W 217 " pdb=" N ASN W 218 " pdb=" CA ASN W 218 " ideal model delta harmonic sigma weight residual -180.00 -158.32 -21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA GLU K 95 " pdb=" C GLU K 95 " pdb=" N THR K 96 " pdb=" CA THR K 96 " ideal model delta harmonic sigma weight residual 180.00 161.18 18.82 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 44633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 9118 0.050 - 0.099: 1725 0.099 - 0.149: 306 0.149 - 0.198: 4 0.198 - 0.248: 3 Chirality restraints: 11156 Sorted by residual: chirality pdb=" CA ILE g 131 " pdb=" N ILE g 131 " pdb=" C ILE g 131 " pdb=" CB ILE g 131 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CB THR b 85 " pdb=" CA THR b 85 " pdb=" OG1 THR b 85 " pdb=" CG2 THR b 85 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU f 333 " pdb=" CB LEU f 333 " pdb=" CD1 LEU f 333 " pdb=" CD2 LEU f 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 11153 not shown) Planarity restraints: 12612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP U 388 " 0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" CG ASP U 388 " -0.065 2.00e-02 2.50e+03 pdb=" OD1 ASP U 388 " 0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP U 388 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU f 571 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.84e+00 pdb=" CD GLU f 571 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU f 571 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU f 571 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP f 460 " -0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO f 461 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO f 461 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO f 461 " -0.034 5.00e-02 4.00e+02 ... (remaining 12609 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 409 2.49 - 3.09: 50220 3.09 - 3.69: 114243 3.69 - 4.30: 170159 4.30 - 4.90: 276669 Nonbonded interactions: 611700 Sorted by model distance: nonbonded pdb=" CD1 ILE A 65 " pdb=" CA PRO A 74 " model vdw 1.884 3.890 nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 501 " model vdw 1.933 2.230 nonbonded pdb=" OG1 THR B 233 " pdb="MG MG B 502 " model vdw 1.955 2.170 nonbonded pdb=" OG1 THR E 181 " pdb="MG MG E 401 " model vdw 1.959 2.170 nonbonded pdb=" O1G ATP B 501 " pdb="MG MG B 502 " model vdw 1.984 2.170 ... (remaining 611695 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 2.040 Check model and map are aligned: 0.400 Set scattering table: 0.480 Process input model: 133.050 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.260 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: 0.170 Load rotamer database and sin/cos tables:10.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.128 72504 Z= 0.179 Angle : 0.565 11.334 97953 Z= 0.293 Chirality : 0.039 0.248 11156 Planarity : 0.004 0.061 12612 Dihedral : 18.201 90.266 27675 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.47 % Favored : 97.50 % Rotamer: Outliers : 2.45 % Allowed : 31.46 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.72 (0.09), residues: 8915 helix: 0.85 (0.07), residues: 4849 sheet: -0.08 (0.16), residues: 1022 loop : 0.32 (0.12), residues: 3044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 34 HIS 0.013 0.001 HIS A 197 PHE 0.027 0.001 PHE V 482 TYR 0.024 0.001 TYR f 226 ARG 0.015 0.001 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2033 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 1842 time to evaluate : 6.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ASP cc_start: 0.8086 (t0) cc_final: 0.7790 (t0) REVERT: A 80 LEU cc_start: 0.9041 (mt) cc_final: 0.8796 (mm) REVERT: B 381 ASP cc_start: 0.8462 (m-30) cc_final: 0.7967 (m-30) REVERT: C 60 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8326 (mtt90) REVERT: C 336 MET cc_start: 0.8653 (mtm) cc_final: 0.8218 (mtm) REVERT: D 71 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7518 (mm-30) REVERT: E 47 LEU cc_start: 0.8888 (mm) cc_final: 0.8543 (tm) REVERT: E 51 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8100 (mp10) REVERT: E 122 MET cc_start: 0.8817 (mtt) cc_final: 0.8604 (mtt) REVERT: E 264 MET cc_start: 0.9164 (mtp) cc_final: 0.8905 (mtp) REVERT: F 70 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6551 (mptt) REVERT: F 74 LYS cc_start: 0.9050 (mmmt) cc_final: 0.8831 (pttp) REVERT: G 120 ASP cc_start: 0.7984 (m-30) cc_final: 0.7710 (m-30) REVERT: L 68 ASN cc_start: 0.8709 (m-40) cc_final: 0.8384 (m-40) REVERT: L 90 GLN cc_start: 0.8680 (tp40) cc_final: 0.8410 (mm-40) REVERT: L 152 ASN cc_start: 0.8964 (t0) cc_final: 0.8587 (t0) REVERT: M 113 ASP cc_start: 0.8096 (m-30) cc_final: 0.7761 (m-30) REVERT: U 239 GLU cc_start: 0.8304 (tt0) cc_final: 0.7748 (tm-30) REVERT: V 72 LEU cc_start: 0.8990 (mm) cc_final: 0.8743 (mt) REVERT: V 96 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8082 (ptp-110) REVERT: V 212 TYR cc_start: 0.8793 (t80) cc_final: 0.8497 (t80) REVERT: V 518 ASP cc_start: 0.8654 (m-30) cc_final: 0.8241 (m-30) REVERT: V 521 PHE cc_start: 0.8911 (t80) cc_final: 0.8413 (t80) REVERT: Z 63 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7986 (mptt) REVERT: Z 78 MET cc_start: 0.8518 (tpt) cc_final: 0.8259 (tpt) REVERT: a 23 HIS cc_start: 0.7303 (m-70) cc_final: 0.6956 (m-70) REVERT: a 135 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8637 (tt) REVERT: c 98 MET cc_start: 0.8102 (mtp) cc_final: 0.7586 (mtm) REVERT: c 106 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: c 264 LYS cc_start: 0.8840 (ptpt) cc_final: 0.8243 (ptmm) REVERT: c 265 MET cc_start: 0.6756 (tmm) cc_final: 0.6366 (tmm) REVERT: c 289 ASP cc_start: 0.8359 (t70) cc_final: 0.8047 (t0) REVERT: c 303 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8192 (mpp) REVERT: f 113 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5223 (pmm) REVERT: f 131 MET cc_start: 0.4033 (tmt) cc_final: 0.3517 (mtm) REVERT: f 162 LEU cc_start: 0.7992 (tp) cc_final: 0.7685 (mt) REVERT: f 170 TRP cc_start: 0.5520 (t-100) cc_final: 0.4718 (t-100) REVERT: f 179 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.8082 (p) REVERT: f 190 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: f 606 VAL cc_start: 0.8059 (m) cc_final: 0.7524 (m) REVERT: f 705 ASN cc_start: 0.7324 (OUTLIER) cc_final: 0.6839 (p0) REVERT: g 158 LEU cc_start: 0.4325 (mm) cc_final: 0.3991 (mt) REVERT: u 123 TYR cc_start: 0.5854 (m-80) cc_final: 0.5638 (m-80) REVERT: u 176 LYS cc_start: 0.7170 (mttm) cc_final: 0.6657 (ttmm) REVERT: u 257 THR cc_start: 0.7092 (t) cc_final: 0.6769 (p) outliers start: 191 outliers final: 62 residues processed: 1969 average time/residue: 1.5282 time to fit residues: 3923.9393 Evaluate side-chains 1069 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 998 time to evaluate : 6.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 231 THR Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 228 ASP Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 220 THR Chi-restraints excluded: chain U residue 151 ILE Chi-restraints excluded: chain U residue 348 THR Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 874 ASN Chi-restraints excluded: chain V residue 96 ARG Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 269 VAL Chi-restraints excluded: chain a residue 91 ASN Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 171 SER Chi-restraints excluded: chain a residue 287 ASN Chi-restraints excluded: chain b residue 11 ASP Chi-restraints excluded: chain b residue 37 CYS Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 206 ASN Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 348 MET Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 179 VAL Chi-restraints excluded: chain f residue 190 GLU Chi-restraints excluded: chain f residue 246 SER Chi-restraints excluded: chain f residue 429 ILE Chi-restraints excluded: chain f residue 705 ASN Chi-restraints excluded: chain f residue 706 ILE Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain f residue 898 VAL Chi-restraints excluded: chain g residue 87 VAL Chi-restraints excluded: chain u residue 168 THR Chi-restraints excluded: chain u residue 171 PHE Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 231 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 3.9990 chunk 673 optimal weight: 0.0670 chunk 373 optimal weight: 0.9980 chunk 229 optimal weight: 2.9990 chunk 454 optimal weight: 10.0000 chunk 359 optimal weight: 3.9990 chunk 696 optimal weight: 8.9990 chunk 269 optimal weight: 4.9990 chunk 423 optimal weight: 3.9990 chunk 518 optimal weight: 1.9990 chunk 806 optimal weight: 9.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 GLN ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 296 ASN D 65 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN F 130 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN H 148 GLN H 179 ASN I 109 GLN I 155 ASN I 198 ASN I 240 HIS J 205 ASN K 221 GLN L 60 GLN L 203 GLN U 340 GLN U 389 ASN U 398 ASN U 596 ASN U 611 ASN U 708 GLN U 721 HIS ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 HIS ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 299 GLN V 347 GLN W 41 GLN W 96 GLN W 156 ASN X 13 GLN X 127 GLN ** X 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN X 406 ASN Y 184 GLN Z 193 ASN Z 223 ASN ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 GLN a 46 GLN a 72 ASN ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 168 ASN b 27 GLN b 30 GLN c 164 ASN c 172 HIS c 214 GLN ** d 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 234 GLN ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 148 GLN f 199 ASN f 213 GLN f 378 ASN f 396 ASN f 592 ASN f 611 GLN f 649 HIS f 677 HIS f 747 GLN u 139 ASN u 183 GLN u 189 GLN u 239 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.103599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.072156 restraints weight = 145753.189| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.74 r_work: 0.2890 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2898 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2898 r_free = 0.2898 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2898 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 72504 Z= 0.274 Angle : 0.655 11.557 97953 Z= 0.338 Chirality : 0.043 0.267 11156 Planarity : 0.004 0.064 12612 Dihedral : 6.812 151.369 10038 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.80 % Favored : 97.17 % Rotamer: Outliers : 5.54 % Allowed : 29.19 % Favored : 65.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.02 (0.09), residues: 8915 helix: 1.18 (0.07), residues: 4969 sheet: -0.24 (0.16), residues: 1001 loop : 0.37 (0.12), residues: 2945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 139 HIS 0.010 0.001 HIS A 197 PHE 0.026 0.002 PHE u 146 TYR 0.026 0.002 TYR a 162 ARG 0.011 0.001 ARG b 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1539 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 432 poor density : 1107 time to evaluate : 6.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.7906 (OUTLIER) cc_final: 0.7666 (mt) REVERT: A 79 ASP cc_start: 0.8107 (t0) cc_final: 0.7728 (t0) REVERT: A 168 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: A 239 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7122 (ptm-80) REVERT: A 356 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8474 (mtmp) REVERT: B 54 PRO cc_start: 0.6887 (Cg_endo) cc_final: 0.6211 (Cg_exo) REVERT: B 85 MET cc_start: 0.7710 (mtt) cc_final: 0.7388 (tmm) REVERT: B 140 ASP cc_start: 0.8417 (m-30) cc_final: 0.7925 (m-30) REVERT: B 210 TYR cc_start: 0.8794 (m-80) cc_final: 0.8182 (m-80) REVERT: B 249 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.7159 (tmm160) REVERT: C 40 GLN cc_start: 0.9292 (tt0) cc_final: 0.9025 (tm-30) REVERT: C 60 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8226 (mtt90) REVERT: C 75 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8545 (mm-30) REVERT: C 89 VAL cc_start: 0.9113 (t) cc_final: 0.8789 (m) REVERT: C 230 MET cc_start: 0.9118 (ptp) cc_final: 0.8874 (mtm) REVERT: C 336 MET cc_start: 0.9151 (mtm) cc_final: 0.8728 (mtm) REVERT: C 382 ASP cc_start: 0.8873 (m-30) cc_final: 0.8610 (m-30) REVERT: D 52 GLU cc_start: 0.8854 (tt0) cc_final: 0.8435 (tp30) REVERT: D 60 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.8410 (t80) REVERT: D 71 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8105 (mm-30) REVERT: D 94 GLU cc_start: 0.8889 (tt0) cc_final: 0.8604 (tt0) REVERT: D 148 ASP cc_start: 0.7831 (t70) cc_final: 0.7592 (t0) REVERT: E 51 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8006 (mp10) REVERT: E 84 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7832 (mtm180) REVERT: E 122 MET cc_start: 0.8891 (mtt) cc_final: 0.8555 (mtt) REVERT: E 264 MET cc_start: 0.9475 (mtp) cc_final: 0.9012 (mtp) REVERT: E 387 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8649 (mttm) REVERT: F 70 LYS cc_start: 0.5964 (OUTLIER) cc_final: 0.5227 (mptt) REVERT: F 180 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8286 (tpp-160) REVERT: F 213 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8095 (mp0) REVERT: F 249 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8971 (mp) REVERT: F 419 ASP cc_start: 0.8891 (m-30) cc_final: 0.8624 (m-30) REVERT: F 438 TYR cc_start: 0.8808 (m-80) cc_final: 0.8219 (m-80) REVERT: G 120 ASP cc_start: 0.8876 (m-30) cc_final: 0.8426 (m-30) REVERT: G 131 MET cc_start: 0.9278 (ptp) cc_final: 0.9048 (pmm) REVERT: G 144 ASP cc_start: 0.8415 (t0) cc_final: 0.7830 (t70) REVERT: G 232 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8466 (mm-30) REVERT: G 235 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8742 (tt) REVERT: H 50 LYS cc_start: 0.8886 (ttpt) cc_final: 0.8629 (ttmm) REVERT: H 79 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8430 (mtt) REVERT: H 95 GLN cc_start: 0.8410 (mm-40) cc_final: 0.7848 (tp-100) REVERT: H 163 MET cc_start: 0.8683 (ptp) cc_final: 0.8431 (ptm) REVERT: H 166 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8550 (t0) REVERT: I 54 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8919 (pttm) REVERT: I 148 TYR cc_start: 0.8832 (m-80) cc_final: 0.8515 (m-80) REVERT: I 242 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8446 (mm-30) REVERT: K 71 ASP cc_start: 0.8771 (t0) cc_final: 0.8399 (t0) REVERT: K 104 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8561 (t0) REVERT: K 147 ASP cc_start: 0.7763 (p0) cc_final: 0.7524 (p0) REVERT: K 156 MET cc_start: 0.8658 (ttp) cc_final: 0.8362 (ttt) REVERT: K 206 MET cc_start: 0.9244 (mtp) cc_final: 0.8983 (mtp) REVERT: L 27 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: M 75 MET cc_start: 0.9147 (ttt) cc_final: 0.8897 (ttp) REVERT: M 109 LYS cc_start: 0.6928 (tttt) cc_final: 0.6182 (tttm) REVERT: M 113 ASP cc_start: 0.8819 (m-30) cc_final: 0.8324 (m-30) REVERT: M 184 MET cc_start: 0.8868 (ptp) cc_final: 0.8665 (ptp) REVERT: M 219 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8967 (pt) REVERT: M 221 ASN cc_start: 0.8714 (t0) cc_final: 0.8420 (p0) REVERT: M 231 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8916 (tp) REVERT: U 95 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: U 98 GLU cc_start: 0.8037 (pp20) cc_final: 0.7728 (pp20) REVERT: U 239 GLU cc_start: 0.9023 (tt0) cc_final: 0.8027 (tm-30) REVERT: U 241 ASN cc_start: 0.8635 (t0) cc_final: 0.8180 (t0) REVERT: U 462 LEU cc_start: 0.9208 (mt) cc_final: 0.8968 (mt) REVERT: U 530 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: U 793 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8394 (ptpp) REVERT: U 908 ILE cc_start: 0.9052 (tt) cc_final: 0.8739 (pp) REVERT: V 72 LEU cc_start: 0.8883 (mm) cc_final: 0.8623 (mt) REVERT: V 90 GLU cc_start: 0.8562 (tt0) cc_final: 0.8074 (mm-30) REVERT: V 96 ARG cc_start: 0.8500 (ptp-170) cc_final: 0.8040 (ptp-110) REVERT: V 100 MET cc_start: 0.8401 (mpt) cc_final: 0.8173 (mpm) REVERT: V 132 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7980 (mm) REVERT: V 212 TYR cc_start: 0.8851 (t80) cc_final: 0.8557 (t80) REVERT: V 299 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.9064 (mm110) REVERT: V 304 GLU cc_start: 0.8528 (mp0) cc_final: 0.8261 (mp0) REVERT: V 381 GLN cc_start: 0.9531 (OUTLIER) cc_final: 0.9142 (tt0) REVERT: V 471 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8359 (tm-30) REVERT: V 494 MET cc_start: 0.9158 (mtm) cc_final: 0.8803 (mmm) REVERT: V 518 ASP cc_start: 0.9006 (m-30) cc_final: 0.8758 (m-30) REVERT: V 521 PHE cc_start: 0.8335 (t80) cc_final: 0.8070 (t80) REVERT: W 33 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.9058 (mtmm) REVERT: W 230 MET cc_start: 0.9133 (mmm) cc_final: 0.8893 (mmm) REVERT: W 285 ASP cc_start: 0.9144 (t0) cc_final: 0.8940 (t0) REVERT: W 333 LEU cc_start: 0.9117 (tm) cc_final: 0.8864 (pt) REVERT: W 420 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8425 (t0) REVERT: W 441 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8670 (ttmt) REVERT: X 11 ARG cc_start: 0.7958 (mtt180) cc_final: 0.7632 (ttp80) REVERT: X 393 VAL cc_start: 0.8636 (OUTLIER) cc_final: 0.8068 (p) REVERT: Y 31 HIS cc_start: 0.8626 (m-70) cc_final: 0.8309 (m-70) REVERT: Y 165 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8638 (mttp) REVERT: Y 378 ASN cc_start: 0.9097 (m-40) cc_final: 0.8893 (m-40) REVERT: Z 28 LYS cc_start: 0.8449 (mmtm) cc_final: 0.8135 (mmpt) REVERT: Z 283 ARG cc_start: 0.7892 (mtm180) cc_final: 0.7594 (mtm180) REVERT: a 23 HIS cc_start: 0.7645 (m-70) cc_final: 0.7029 (m-70) REVERT: a 100 THR cc_start: 0.9335 (m) cc_final: 0.9115 (p) REVERT: a 127 ASP cc_start: 0.8934 (t0) cc_final: 0.8622 (t0) REVERT: a 166 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8881 (mm) REVERT: a 333 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8946 (mmp) REVERT: b 11 ASP cc_start: 0.8842 (t0) cc_final: 0.8407 (t0) REVERT: b 17 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7169 (ttm-80) REVERT: b 27 GLN cc_start: 0.9022 (mm110) cc_final: 0.8503 (mp10) REVERT: b 29 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: b 31 ASP cc_start: 0.7922 (m-30) cc_final: 0.7243 (p0) REVERT: b 35 ILE cc_start: 0.8984 (mm) cc_final: 0.8721 (mm) REVERT: b 39 SER cc_start: 0.9241 (t) cc_final: 0.8996 (p) REVERT: c 167 MET cc_start: 0.8379 (mmm) cc_final: 0.8022 (mpm) REVERT: c 213 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7658 (mt-10) REVERT: c 223 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.9014 (mtpp) REVERT: c 264 LYS cc_start: 0.9167 (ptpt) cc_final: 0.8490 (ptmm) REVERT: c 289 ASP cc_start: 0.8853 (t70) cc_final: 0.8484 (m-30) REVERT: d 94 MET cc_start: 0.8000 (pmm) cc_final: 0.7751 (pmm) REVERT: d 179 LYS cc_start: 0.9149 (pttt) cc_final: 0.8913 (pttm) REVERT: d 236 LEU cc_start: 0.9414 (OUTLIER) cc_final: 0.9188 (mm) REVERT: d 286 GLU cc_start: 0.8612 (tp30) cc_final: 0.7898 (tt0) REVERT: d 297 LYS cc_start: 0.9352 (tmmt) cc_final: 0.8991 (tptp) REVERT: d 347 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8533 (mt-10) REVERT: f 47 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6485 (tp30) REVERT: f 113 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5269 (ppp) REVERT: f 131 MET cc_start: 0.4253 (tmt) cc_final: 0.3631 (mmt) REVERT: f 161 HIS cc_start: 0.7635 (t70) cc_final: 0.6944 (t70) REVERT: f 162 LEU cc_start: 0.8457 (tp) cc_final: 0.7916 (mt) REVERT: f 171 GLN cc_start: 0.7407 (mm-40) cc_final: 0.7156 (mp10) REVERT: f 272 LEU cc_start: 0.8138 (mt) cc_final: 0.7802 (mt) REVERT: f 340 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7282 (mmm) REVERT: f 398 TRP cc_start: 0.7870 (t-100) cc_final: 0.6807 (t-100) REVERT: f 414 LEU cc_start: 0.8885 (tm) cc_final: 0.8669 (mp) REVERT: f 450 ILE cc_start: 0.8919 (pt) cc_final: 0.8685 (pt) REVERT: f 453 SER cc_start: 0.7680 (m) cc_final: 0.7338 (m) REVERT: f 472 HIS cc_start: 0.8036 (OUTLIER) cc_final: 0.7504 (t70) REVERT: f 502 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7904 (mm) REVERT: f 592 ASN cc_start: 0.8964 (OUTLIER) cc_final: 0.8635 (p0) REVERT: f 619 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.6841 (p90) REVERT: f 681 TYR cc_start: 0.7992 (m-80) cc_final: 0.7767 (m-80) REVERT: f 746 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8564 (tpp80) REVERT: f 747 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8772 (mt0) REVERT: f 851 ASP cc_start: 0.6787 (t0) cc_final: 0.6575 (t0) REVERT: g 136 LEU cc_start: 0.6037 (pt) cc_final: 0.5138 (tm) REVERT: g 158 LEU cc_start: 0.4618 (mm) cc_final: 0.4377 (mt) REVERT: u 139 ASN cc_start: 0.4569 (t0) cc_final: 0.3645 (t160) REVERT: u 157 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8530 (mt) REVERT: u 162 ASP cc_start: 0.7953 (t70) cc_final: 0.7553 (t0) REVERT: u 164 GLN cc_start: 0.7797 (mm110) cc_final: 0.7341 (mm-40) REVERT: u 173 GLN cc_start: 0.8491 (mt0) cc_final: 0.8250 (mm110) REVERT: u 228 ASP cc_start: 0.8575 (t70) cc_final: 0.8206 (p0) outliers start: 432 outliers final: 104 residues processed: 1444 average time/residue: 1.4263 time to fit residues: 2748.9632 Evaluate side-chains 1086 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 933 time to evaluate : 6.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain U residue 151 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 362 ASN Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 374 SER Chi-restraints excluded: chain U residue 389 ASN Chi-restraints excluded: chain U residue 530 GLU Chi-restraints excluded: chain U residue 793 LYS Chi-restraints excluded: chain U residue 891 VAL Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 299 GLN Chi-restraints excluded: chain V residue 381 GLN Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 471 GLU Chi-restraints excluded: chain W residue 33 LYS Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 310 THR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 441 LYS Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 165 LYS Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 269 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 287 ASN Chi-restraints excluded: chain a residue 333 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 17 ARG Chi-restraints excluded: chain b residue 29 GLN Chi-restraints excluded: chain b residue 42 ARG Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 103 LYS Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 223 LYS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 178 TYR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 255 VAL Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 472 HIS Chi-restraints excluded: chain f residue 502 LEU Chi-restraints excluded: chain f residue 514 VAL Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 597 VAL Chi-restraints excluded: chain f residue 619 HIS Chi-restraints excluded: chain f residue 679 LEU Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain f residue 747 GLN Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain u residue 157 LEU Chi-restraints excluded: chain u residue 168 THR Chi-restraints excluded: chain u residue 236 VAL Chi-restraints excluded: chain u residue 268 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 3.9990 chunk 396 optimal weight: 6.9990 chunk 706 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 292 optimal weight: 7.9990 chunk 594 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 397 optimal weight: 0.0570 chunk 661 optimal weight: 6.9990 chunk 458 optimal weight: 0.8980 chunk 871 optimal weight: 10.0000 overall best weight: 2.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN D 65 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 222 HIS E 160 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN H 96 GLN H 140 ASN H 148 GLN I 155 ASN I 198 ASN L 53 GLN M 101 ASN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 115 ASN U 340 GLN ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 118 GLN V 242 HIS V 299 GLN V 401 ASN X 198 ASN ** X 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN Y 94 ASN Z 77 ASN ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 46 GLN a 82 HIS ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 169 HIS b 104 ASN ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 GLN c 194 HIS c 214 GLN d 108 ASN d 195 ASN ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN f 378 ASN ** f 452 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 592 ASN f 747 GLN f 750 GLN u 239 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.101576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.069948 restraints weight = 146483.628| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.73 r_work: 0.2852 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 72504 Z= 0.326 Angle : 0.627 16.648 97953 Z= 0.318 Chirality : 0.043 0.194 11156 Planarity : 0.004 0.059 12612 Dihedral : 6.332 86.013 9970 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.30 % Rotamer: Outliers : 5.20 % Allowed : 28.83 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.05 (0.09), residues: 8915 helix: 1.23 (0.07), residues: 5006 sheet: -0.39 (0.15), residues: 1024 loop : 0.39 (0.12), residues: 2885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 139 HIS 0.012 0.001 HIS Z 145 PHE 0.016 0.001 PHE V 174 TYR 0.024 0.002 TYR L 137 ARG 0.011 0.001 ARG u 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1400 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 405 poor density : 995 time to evaluate : 6.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: A 55 LEU cc_start: 0.8422 (tt) cc_final: 0.8210 (tp) REVERT: A 79 ASP cc_start: 0.8213 (t0) cc_final: 0.7730 (t0) REVERT: A 168 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8331 (mm-30) REVERT: A 185 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8114 (mt-10) REVERT: A 186 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7929 (mtmp) REVERT: A 196 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9054 (mp) REVERT: A 256 MET cc_start: 0.9221 (mtp) cc_final: 0.8969 (ttm) REVERT: A 356 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8537 (mtmp) REVERT: B 54 PRO cc_start: 0.6944 (Cg_endo) cc_final: 0.6135 (Cg_exo) REVERT: B 85 MET cc_start: 0.7842 (mtt) cc_final: 0.7476 (tmm) REVERT: B 101 ASP cc_start: 0.8491 (m-30) cc_final: 0.8025 (p0) REVERT: B 117 ASP cc_start: 0.7501 (t0) cc_final: 0.6903 (t70) REVERT: B 140 ASP cc_start: 0.8498 (m-30) cc_final: 0.8070 (m-30) REVERT: B 210 TYR cc_start: 0.8877 (m-80) cc_final: 0.8511 (m-80) REVERT: B 213 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: C 40 GLN cc_start: 0.9294 (tt0) cc_final: 0.9056 (tm-30) REVERT: C 60 ARG cc_start: 0.8610 (mtp85) cc_final: 0.8324 (mtt90) REVERT: C 78 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.6894 (ptp-170) REVERT: C 89 VAL cc_start: 0.9160 (t) cc_final: 0.8890 (m) REVERT: C 297 ARG cc_start: 0.8604 (ttp-110) cc_final: 0.8382 (ttp-110) REVERT: C 336 MET cc_start: 0.9168 (mtm) cc_final: 0.8813 (mtm) REVERT: C 382 ASP cc_start: 0.8892 (m-30) cc_final: 0.8624 (m-30) REVERT: D 52 GLU cc_start: 0.8932 (tt0) cc_final: 0.8452 (tp30) REVERT: D 60 TYR cc_start: 0.9243 (OUTLIER) cc_final: 0.8605 (t80) REVERT: D 71 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8104 (mm-30) REVERT: D 94 GLU cc_start: 0.8890 (tt0) cc_final: 0.8436 (tt0) REVERT: D 413 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7800 (mp0) REVERT: E 51 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8017 (mp10) REVERT: E 66 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8162 (tp30) REVERT: E 100 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8315 (mt) REVERT: E 122 MET cc_start: 0.8972 (mtt) cc_final: 0.8615 (mtt) REVERT: E 264 MET cc_start: 0.9427 (mtp) cc_final: 0.9112 (mtp) REVERT: F 69 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.5160 (pp-130) REVERT: F 73 ILE cc_start: 0.7009 (mt) cc_final: 0.6673 (mm) REVERT: F 81 LYS cc_start: 0.8634 (tppt) cc_final: 0.8168 (tmmt) REVERT: F 180 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8228 (tpp-160) REVERT: F 213 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8030 (mp0) REVERT: F 318 ASP cc_start: 0.8673 (t0) cc_final: 0.8468 (t0) REVERT: G 39 SER cc_start: 0.9291 (OUTLIER) cc_final: 0.9043 (p) REVERT: G 117 ARG cc_start: 0.8264 (ttt90) cc_final: 0.6571 (mtt180) REVERT: G 120 ASP cc_start: 0.8904 (m-30) cc_final: 0.8468 (m-30) REVERT: G 232 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8319 (mm-30) REVERT: G 235 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8782 (tt) REVERT: H 50 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8652 (ttmm) REVERT: H 79 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8571 (mtp) REVERT: H 95 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7897 (tp-100) REVERT: H 163 MET cc_start: 0.8637 (ptp) cc_final: 0.8408 (ptm) REVERT: H 166 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8563 (t0) REVERT: I 54 LYS cc_start: 0.9188 (OUTLIER) cc_final: 0.8939 (pttm) REVERT: I 148 TYR cc_start: 0.8905 (m-80) cc_final: 0.8628 (m-80) REVERT: I 206 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7758 (pt) REVERT: I 234 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8279 (tp30) REVERT: I 242 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8344 (mm-30) REVERT: J 28 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8701 (mtmt) REVERT: J 59 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8523 (m) REVERT: K 71 ASP cc_start: 0.8683 (t0) cc_final: 0.8369 (t0) REVERT: K 104 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8587 (t0) REVERT: L 27 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: L 218 ASP cc_start: 0.8039 (p0) cc_final: 0.7652 (t0) REVERT: L 220 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8203 (tp30) REVERT: M 75 MET cc_start: 0.9221 (ttt) cc_final: 0.8987 (ttp) REVERT: M 97 ASN cc_start: 0.9099 (m-40) cc_final: 0.8820 (m110) REVERT: M 109 LYS cc_start: 0.6996 (tttt) cc_final: 0.6237 (tttm) REVERT: M 113 ASP cc_start: 0.8789 (m-30) cc_final: 0.8339 (m-30) REVERT: M 184 MET cc_start: 0.8846 (ptp) cc_final: 0.8495 (ptm) REVERT: M 192 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8891 (mp0) REVERT: M 221 ASN cc_start: 0.8786 (t0) cc_final: 0.8445 (p0) REVERT: M 223 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7599 (ptm160) REVERT: U 239 GLU cc_start: 0.8935 (tt0) cc_final: 0.8058 (tm-30) REVERT: U 241 ASN cc_start: 0.8494 (t0) cc_final: 0.8077 (t0) REVERT: U 530 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: U 685 GLN cc_start: 0.9364 (OUTLIER) cc_final: 0.9151 (tt0) REVERT: U 714 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.9053 (p) REVERT: U 931 HIS cc_start: 0.5855 (t-90) cc_final: 0.5565 (t-170) REVERT: V 72 LEU cc_start: 0.8904 (mm) cc_final: 0.8656 (mt) REVERT: V 96 ARG cc_start: 0.8525 (ptp-170) cc_final: 0.8204 (ptm160) REVERT: V 100 MET cc_start: 0.8586 (mpt) cc_final: 0.8331 (mpt) REVERT: V 212 TYR cc_start: 0.8816 (t80) cc_final: 0.8459 (t80) REVERT: V 304 GLU cc_start: 0.8550 (mp0) cc_final: 0.8295 (mp0) REVERT: V 381 GLN cc_start: 0.9533 (OUTLIER) cc_final: 0.9103 (tt0) REVERT: V 471 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: V 485 ASP cc_start: 0.9169 (m-30) cc_final: 0.8739 (m-30) REVERT: V 494 MET cc_start: 0.9134 (mtm) cc_final: 0.8791 (mmm) REVERT: V 514 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7961 (ttm170) REVERT: V 521 PHE cc_start: 0.8313 (t80) cc_final: 0.8101 (t80) REVERT: W 310 THR cc_start: 0.9265 (m) cc_final: 0.8706 (p) REVERT: W 333 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8878 (pt) REVERT: W 448 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8563 (mtmm) REVERT: X 41 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: X 51 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7800 (tt) REVERT: X 52 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8604 (mm-30) REVERT: X 161 ASP cc_start: 0.8532 (t70) cc_final: 0.8170 (t0) REVERT: X 212 MET cc_start: 0.8847 (tpt) cc_final: 0.8242 (tpt) REVERT: Y 31 HIS cc_start: 0.8676 (m-70) cc_final: 0.8357 (m-70) REVERT: Y 195 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8552 (mtmt) REVERT: Y 378 ASN cc_start: 0.9151 (m-40) cc_final: 0.8899 (m-40) REVERT: Y 385 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8426 (tmt-80) REVERT: Z 28 LYS cc_start: 0.8449 (mmtm) cc_final: 0.8220 (mmpt) REVERT: Z 143 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7301 (tm-30) REVERT: Z 165 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7696 (tm-30) REVERT: Z 283 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7733 (mtm180) REVERT: a 23 HIS cc_start: 0.7816 (m-70) cc_final: 0.7435 (m-70) REVERT: a 42 LEU cc_start: 0.8597 (mm) cc_final: 0.8395 (mm) REVERT: a 58 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8746 (ptpt) REVERT: a 127 ASP cc_start: 0.8976 (t0) cc_final: 0.8763 (t0) REVERT: a 166 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8886 (mm) REVERT: a 333 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.8910 (mmp) REVERT: b 5 SER cc_start: 0.8860 (m) cc_final: 0.8652 (m) REVERT: b 11 ASP cc_start: 0.8820 (t0) cc_final: 0.8255 (t0) REVERT: b 27 GLN cc_start: 0.8997 (mm110) cc_final: 0.8485 (mp10) REVERT: b 31 ASP cc_start: 0.8009 (m-30) cc_final: 0.7210 (p0) REVERT: b 42 ARG cc_start: 0.8659 (ptt-90) cc_final: 0.8328 (mpp80) REVERT: b 183 LEU cc_start: 0.9198 (mp) cc_final: 0.8895 (mp) REVERT: c 213 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7668 (mt-10) REVERT: c 223 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8996 (mtpp) REVERT: c 264 LYS cc_start: 0.9163 (ptpt) cc_final: 0.8521 (ptmm) REVERT: c 289 ASP cc_start: 0.8862 (t70) cc_final: 0.8481 (m-30) REVERT: d 179 LYS cc_start: 0.9238 (pttt) cc_final: 0.8913 (pttm) REVERT: d 236 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9147 (mm) REVERT: d 297 LYS cc_start: 0.9358 (tmmt) cc_final: 0.8991 (tptp) REVERT: d 309 VAL cc_start: 0.8884 (t) cc_final: 0.8582 (p) REVERT: d 347 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8597 (mm-30) REVERT: e 42 ASN cc_start: 0.8565 (p0) cc_final: 0.8213 (p0) REVERT: f 47 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6474 (tp30) REVERT: f 113 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5336 (ppp) REVERT: f 131 MET cc_start: 0.4149 (tmt) cc_final: 0.3410 (mmt) REVERT: f 162 LEU cc_start: 0.8501 (tp) cc_final: 0.8215 (mt) REVERT: f 165 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7776 (tt0) REVERT: f 268 LEU cc_start: 0.9313 (mp) cc_final: 0.8891 (tp) REVERT: f 272 LEU cc_start: 0.8175 (mt) cc_final: 0.7873 (mt) REVERT: f 294 MET cc_start: 0.5537 (mmt) cc_final: 0.5192 (mmt) REVERT: f 340 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7448 (mmm) REVERT: f 398 TRP cc_start: 0.8158 (t-100) cc_final: 0.7562 (t-100) REVERT: f 407 MET cc_start: 0.6897 (mtt) cc_final: 0.6262 (mpt) REVERT: f 416 MET cc_start: 0.7592 (ttp) cc_final: 0.7381 (ttp) REVERT: f 472 HIS cc_start: 0.8133 (OUTLIER) cc_final: 0.7697 (t70) REVERT: f 501 LEU cc_start: 0.8912 (tp) cc_final: 0.8643 (tp) REVERT: f 502 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7999 (mm) REVERT: f 512 MET cc_start: 0.7889 (tpt) cc_final: 0.7629 (tpt) REVERT: f 592 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8717 (p0) REVERT: f 681 TYR cc_start: 0.7990 (m-80) cc_final: 0.7721 (m-80) REVERT: f 746 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8619 (tpp80) REVERT: f 747 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8882 (mt0) REVERT: f 786 GLN cc_start: 0.8349 (mt0) cc_final: 0.7911 (mt0) REVERT: f 851 ASP cc_start: 0.6998 (t0) cc_final: 0.6755 (t0) REVERT: f 868 HIS cc_start: 0.7252 (OUTLIER) cc_final: 0.6920 (m90) REVERT: g 136 LEU cc_start: 0.6130 (pt) cc_final: 0.5234 (tm) REVERT: g 158 LEU cc_start: 0.4613 (mm) cc_final: 0.4371 (mt) REVERT: u 164 GLN cc_start: 0.7819 (mm110) cc_final: 0.7390 (mm-40) REVERT: u 173 GLN cc_start: 0.8555 (mt0) cc_final: 0.8220 (mm-40) REVERT: u 176 LYS cc_start: 0.7816 (mtmm) cc_final: 0.7415 (mtmm) REVERT: u 178 TYR cc_start: 0.7539 (m-10) cc_final: 0.7314 (m-10) REVERT: u 181 LYS cc_start: 0.7240 (ptpt) cc_final: 0.6372 (tttp) REVERT: u 228 ASP cc_start: 0.8425 (t70) cc_final: 0.8064 (p0) REVERT: u 268 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8741 (p) outliers start: 405 outliers final: 132 residues processed: 1309 average time/residue: 1.4311 time to fit residues: 2506.0908 Evaluate side-chains 1081 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 894 time to evaluate : 6.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 143 ARG Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 422 GLU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 104 ASN Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain M residue 223 ARG Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 142 LEU Chi-restraints excluded: chain U residue 151 ILE Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 362 ASN Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 530 GLU Chi-restraints excluded: chain U residue 578 LEU Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 793 LYS Chi-restraints excluded: chain U residue 891 VAL Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 227 VAL Chi-restraints excluded: chain V residue 336 GLU Chi-restraints excluded: chain V residue 379 LEU Chi-restraints excluded: chain V residue 381 GLN Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain V residue 471 GLU Chi-restraints excluded: chain V residue 507 SER Chi-restraints excluded: chain V residue 514 ARG Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 255 CYS Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 333 LEU Chi-restraints excluded: chain W residue 448 LYS Chi-restraints excluded: chain X residue 41 GLU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain Y residue 166 SER Chi-restraints excluded: chain Y residue 195 LYS Chi-restraints excluded: chain Y residue 385 ARG Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 165 GLU Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 269 VAL Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 333 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 29 GLN Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 223 LYS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 265 ASP Chi-restraints excluded: chain d residue 281 LYS Chi-restraints excluded: chain d residue 315 TYR Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 255 VAL Chi-restraints excluded: chain f residue 270 LEU Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 337 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 350 LYS Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 472 HIS Chi-restraints excluded: chain f residue 502 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 597 VAL Chi-restraints excluded: chain f residue 704 LEU Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain f residue 747 GLN Chi-restraints excluded: chain f residue 796 LEU Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain f residue 868 HIS Chi-restraints excluded: chain u residue 167 ILE Chi-restraints excluded: chain u residue 171 PHE Chi-restraints excluded: chain u residue 231 VAL Chi-restraints excluded: chain u residue 236 VAL Chi-restraints excluded: chain u residue 268 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 428 optimal weight: 4.9990 chunk 348 optimal weight: 4.9990 chunk 451 optimal weight: 2.9990 chunk 825 optimal weight: 7.9990 chunk 575 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 536 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 533 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 769 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN D 65 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN D 278 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 GLN I 40 ASN I 155 ASN I 198 ASN I 220 ASN J 205 ASN L 53 GLN M 101 ASN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 111 GLN U 340 GLN ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 632 GLN ** U 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 749 GLN ** V 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 347 GLN ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 HIS ** X 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 367 GLN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 HIS ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN f 452 ASN f 493 ASN f 592 ASN f 619 HIS f 747 GLN f 848 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.100793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.069045 restraints weight = 146862.701| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.73 r_work: 0.2837 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 72504 Z= 0.317 Angle : 0.608 14.349 97953 Z= 0.309 Chirality : 0.043 0.234 11156 Planarity : 0.004 0.049 12612 Dihedral : 6.317 83.526 9961 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 4.89 % Allowed : 28.36 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.09), residues: 8915 helix: 1.32 (0.07), residues: 5013 sheet: -0.48 (0.15), residues: 1012 loop : 0.36 (0.12), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 139 HIS 0.010 0.001 HIS a 82 PHE 0.037 0.001 PHE a 50 TYR 0.033 0.001 TYR d 315 ARG 0.009 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1306 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 381 poor density : 925 time to evaluate : 6.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: A 79 ASP cc_start: 0.8246 (t0) cc_final: 0.7786 (t0) REVERT: A 168 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: A 185 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8104 (mt-10) REVERT: A 186 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8056 (mttp) REVERT: A 256 MET cc_start: 0.9228 (mtp) cc_final: 0.9009 (ttm) REVERT: B 26 GLU cc_start: 0.8680 (pp20) cc_final: 0.8203 (pm20) REVERT: B 85 MET cc_start: 0.7876 (mtt) cc_final: 0.7509 (tmm) REVERT: B 101 ASP cc_start: 0.8507 (m-30) cc_final: 0.8056 (p0) REVERT: B 117 ASP cc_start: 0.7557 (t0) cc_final: 0.7284 (t0) REVERT: B 140 ASP cc_start: 0.8532 (m-30) cc_final: 0.8066 (m-30) REVERT: B 164 MET cc_start: 0.8275 (tmm) cc_final: 0.7443 (tmm) REVERT: B 210 TYR cc_start: 0.8840 (m-80) cc_final: 0.8558 (m-80) REVERT: B 213 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: C 40 GLN cc_start: 0.9302 (tt0) cc_final: 0.9034 (tm-30) REVERT: C 78 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8846 (ptt-90) REVERT: C 89 VAL cc_start: 0.9159 (t) cc_final: 0.8903 (m) REVERT: C 297 ARG cc_start: 0.8610 (ttp-110) cc_final: 0.8354 (ttp-110) REVERT: C 336 MET cc_start: 0.9178 (mtm) cc_final: 0.8886 (mtm) REVERT: C 382 ASP cc_start: 0.8890 (m-30) cc_final: 0.8635 (m-30) REVERT: D 52 GLU cc_start: 0.8951 (tt0) cc_final: 0.8501 (tp30) REVERT: D 60 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8593 (t80) REVERT: D 71 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8213 (mm-30) REVERT: D 94 GLU cc_start: 0.8900 (tt0) cc_final: 0.8412 (tt0) REVERT: D 411 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7007 (pp20) REVERT: D 413 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7984 (mp0) REVERT: E 51 GLN cc_start: 0.8694 (mm-40) cc_final: 0.7999 (mp10) REVERT: E 66 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: E 100 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8386 (mt) REVERT: E 122 MET cc_start: 0.8974 (mtt) cc_final: 0.8632 (mtt) REVERT: E 264 MET cc_start: 0.9382 (mtp) cc_final: 0.8927 (mtp) REVERT: E 387 LYS cc_start: 0.8991 (mtmm) cc_final: 0.8624 (mttm) REVERT: F 69 MET cc_start: 0.5730 (OUTLIER) cc_final: 0.5458 (pp-130) REVERT: F 81 LYS cc_start: 0.8526 (tppt) cc_final: 0.8065 (tmmt) REVERT: F 180 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8219 (tpp-160) REVERT: F 213 GLU cc_start: 0.8522 (mt-10) cc_final: 0.7952 (mp0) REVERT: F 318 ASP cc_start: 0.8670 (t0) cc_final: 0.8310 (t0) REVERT: F 390 ASP cc_start: 0.8850 (t0) cc_final: 0.8472 (t0) REVERT: G 39 SER cc_start: 0.9309 (OUTLIER) cc_final: 0.9098 (p) REVERT: G 117 ARG cc_start: 0.8315 (ttt90) cc_final: 0.6930 (tpp-160) REVERT: G 120 ASP cc_start: 0.8857 (m-30) cc_final: 0.8432 (m-30) REVERT: G 232 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: G 235 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8781 (tt) REVERT: H 44 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9020 (m) REVERT: H 50 LYS cc_start: 0.8885 (ttpt) cc_final: 0.8616 (ttmm) REVERT: H 79 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8643 (mtp) REVERT: H 95 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7856 (tp-100) REVERT: H 159 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8198 (ttmm) REVERT: H 166 ASN cc_start: 0.8809 (OUTLIER) cc_final: 0.8522 (t0) REVERT: I 54 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8981 (pttm) REVERT: I 148 TYR cc_start: 0.8838 (m-80) cc_final: 0.8480 (m-80) REVERT: I 178 ASP cc_start: 0.9174 (t0) cc_final: 0.8854 (t0) REVERT: I 242 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8415 (mm-30) REVERT: J 28 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8655 (mtmt) REVERT: K 71 ASP cc_start: 0.8749 (t0) cc_final: 0.8415 (t0) REVERT: L 27 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: L 189 LYS cc_start: 0.9060 (tppp) cc_final: 0.8793 (mmtp) REVERT: L 218 ASP cc_start: 0.8042 (p0) cc_final: 0.7683 (t0) REVERT: L 220 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8245 (tp30) REVERT: L 239 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7273 (ptt90) REVERT: M 34 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8569 (p) REVERT: M 75 MET cc_start: 0.9252 (ttt) cc_final: 0.9026 (ttp) REVERT: M 109 LYS cc_start: 0.7015 (tttt) cc_final: 0.6305 (tttm) REVERT: M 113 ASP cc_start: 0.8869 (m-30) cc_final: 0.8409 (m-30) REVERT: M 184 MET cc_start: 0.9105 (ptp) cc_final: 0.8682 (ptp) REVERT: M 192 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8912 (mp0) REVERT: M 223 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7654 (ptm160) REVERT: U 239 GLU cc_start: 0.8951 (tt0) cc_final: 0.8043 (tm-30) REVERT: U 241 ASN cc_start: 0.8520 (t0) cc_final: 0.8113 (t0) REVERT: U 332 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8221 (pp20) REVERT: U 714 SER cc_start: 0.9278 (OUTLIER) cc_final: 0.9043 (p) REVERT: U 931 HIS cc_start: 0.5787 (t-90) cc_final: 0.5487 (t-170) REVERT: V 72 LEU cc_start: 0.8913 (mm) cc_final: 0.8635 (mt) REVERT: V 96 ARG cc_start: 0.8470 (ptp-170) cc_final: 0.7992 (ptm160) REVERT: V 100 MET cc_start: 0.8632 (mpt) cc_final: 0.8366 (mpt) REVERT: V 304 GLU cc_start: 0.8587 (mp0) cc_final: 0.8323 (mp0) REVERT: V 381 GLN cc_start: 0.9531 (OUTLIER) cc_final: 0.9073 (tt0) REVERT: V 443 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8806 (tmm-80) REVERT: V 471 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8468 (tm-30) REVERT: V 485 ASP cc_start: 0.9152 (m-30) cc_final: 0.8724 (m-30) REVERT: V 494 MET cc_start: 0.9116 (mtm) cc_final: 0.8757 (mmm) REVERT: V 510 GLU cc_start: 0.8162 (pt0) cc_final: 0.7659 (pm20) REVERT: V 514 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7849 (ttm170) REVERT: V 518 ASP cc_start: 0.8927 (m-30) cc_final: 0.8650 (m-30) REVERT: W 313 GLU cc_start: 0.8831 (tt0) cc_final: 0.8415 (mm-30) REVERT: W 333 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8880 (pt) REVERT: X 41 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7248 (tm-30) REVERT: X 51 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7743 (tt) REVERT: X 52 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8616 (mm-30) REVERT: X 161 ASP cc_start: 0.8540 (t70) cc_final: 0.8272 (t0) REVERT: X 212 MET cc_start: 0.8746 (tpt) cc_final: 0.8383 (tpt) REVERT: X 367 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: Y 155 ASP cc_start: 0.9122 (m-30) cc_final: 0.8785 (p0) REVERT: Y 383 LEU cc_start: 0.9284 (tp) cc_final: 0.9010 (tm) REVERT: Y 385 ARG cc_start: 0.8666 (tmm-80) cc_final: 0.8390 (tmt-80) REVERT: Z 28 LYS cc_start: 0.8492 (mmtm) cc_final: 0.8267 (mmpt) REVERT: Z 32 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7289 (mm110) REVERT: Z 88 ARG cc_start: 0.8515 (mmt90) cc_final: 0.8303 (mtt90) REVERT: Z 143 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7310 (tm-30) REVERT: Z 165 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: Z 283 ARG cc_start: 0.8019 (mtm180) cc_final: 0.7745 (mtm180) REVERT: a 23 HIS cc_start: 0.7921 (m-70) cc_final: 0.7600 (m-70) REVERT: a 127 ASP cc_start: 0.8938 (t0) cc_final: 0.8433 (t0) REVERT: a 166 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8856 (mm) REVERT: a 333 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8852 (mmt) REVERT: b 11 ASP cc_start: 0.8769 (t0) cc_final: 0.8077 (t0) REVERT: b 31 ASP cc_start: 0.8048 (m-30) cc_final: 0.7252 (p0) REVERT: b 42 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8132 (ptp-110) REVERT: c 223 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.9032 (mtpp) REVERT: c 264 LYS cc_start: 0.9145 (ptpt) cc_final: 0.8215 (ptmm) REVERT: c 289 ASP cc_start: 0.8863 (t70) cc_final: 0.8482 (m-30) REVERT: d 158 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8794 (pmm-80) REVERT: d 165 GLU cc_start: 0.9426 (mm-30) cc_final: 0.8805 (mm-30) REVERT: d 179 LYS cc_start: 0.9259 (pttt) cc_final: 0.8915 (pttm) REVERT: d 236 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9132 (mm) REVERT: d 265 ASP cc_start: 0.8499 (m-30) cc_final: 0.8289 (p0) REVERT: d 286 GLU cc_start: 0.8588 (tp30) cc_final: 0.7952 (tt0) REVERT: d 297 LYS cc_start: 0.9361 (tmmt) cc_final: 0.8952 (tptp) REVERT: d 309 VAL cc_start: 0.8966 (t) cc_final: 0.8681 (p) REVERT: d 347 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8538 (mm-30) REVERT: e 21 GLU cc_start: 0.7981 (pm20) cc_final: 0.7662 (pm20) REVERT: e 49 GLU cc_start: 0.8384 (pt0) cc_final: 0.8134 (pt0) REVERT: f 47 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6475 (tp30) REVERT: f 113 MET cc_start: 0.6188 (OUTLIER) cc_final: 0.5439 (ppp) REVERT: f 131 MET cc_start: 0.4087 (tmt) cc_final: 0.3317 (mmt) REVERT: f 162 LEU cc_start: 0.8596 (tp) cc_final: 0.8119 (mt) REVERT: f 171 GLN cc_start: 0.7618 (mm-40) cc_final: 0.7278 (mp10) REVERT: f 268 LEU cc_start: 0.9346 (mp) cc_final: 0.9086 (mp) REVERT: f 294 MET cc_start: 0.5487 (mmt) cc_final: 0.5063 (mmt) REVERT: f 340 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7444 (mmm) REVERT: f 398 TRP cc_start: 0.8442 (t-100) cc_final: 0.7625 (t-100) REVERT: f 407 MET cc_start: 0.6973 (mtt) cc_final: 0.6377 (mpt) REVERT: f 501 LEU cc_start: 0.8942 (tp) cc_final: 0.8661 (tp) REVERT: f 502 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8190 (mm) REVERT: f 512 MET cc_start: 0.8145 (tpt) cc_final: 0.7930 (tpt) REVERT: f 592 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8673 (p0) REVERT: f 681 TYR cc_start: 0.8049 (m-80) cc_final: 0.7786 (m-80) REVERT: f 746 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8629 (tpp80) REVERT: f 747 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8720 (mt0) REVERT: f 784 ASP cc_start: 0.7553 (t0) cc_final: 0.7308 (t0) REVERT: f 786 GLN cc_start: 0.8373 (mt0) cc_final: 0.8003 (mt0) REVERT: f 851 ASP cc_start: 0.7066 (t0) cc_final: 0.6818 (t0) REVERT: f 868 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6921 (m90) REVERT: u 127 MET cc_start: 0.8321 (pmm) cc_final: 0.8020 (pmm) REVERT: u 164 GLN cc_start: 0.7846 (mm110) cc_final: 0.7297 (mm-40) REVERT: u 173 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8256 (mm-40) REVERT: u 228 ASP cc_start: 0.8359 (t70) cc_final: 0.7952 (p0) REVERT: u 268 THR cc_start: 0.9013 (OUTLIER) cc_final: 0.8749 (p) outliers start: 381 outliers final: 150 residues processed: 1232 average time/residue: 1.4045 time to fit residues: 2311.1092 Evaluate side-chains 1046 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 840 time to evaluate : 6.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 411 GLU Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 152 SER Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 174 MET Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain I residue 249 ARG Chi-restraints excluded: chain J residue 28 LYS Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 239 ARG Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain M residue 205 LYS Chi-restraints excluded: chain M residue 223 ARG Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain M residue 231 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 170 SER Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 332 GLU Chi-restraints excluded: chain U residue 362 ASN Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 530 GLU Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 793 LYS Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain U residue 925 VAL Chi-restraints excluded: chain V residue 134 PHE Chi-restraints excluded: chain V residue 336 GLU Chi-restraints excluded: chain V residue 379 LEU Chi-restraints excluded: chain V residue 381 GLN Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain V residue 471 GLU Chi-restraints excluded: chain V residue 478 GLN Chi-restraints excluded: chain V residue 507 SER Chi-restraints excluded: chain V residue 514 ARG Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 255 CYS Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 333 LEU Chi-restraints excluded: chain X residue 41 GLU Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 103 THR Chi-restraints excluded: chain X residue 120 GLU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 367 GLN Chi-restraints excluded: chain Y residue 166 SER Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 165 GLU Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 269 VAL Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 333 MET Chi-restraints excluded: chain b residue 29 GLN Chi-restraints excluded: chain b residue 42 ARG Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 132 LYS Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 189 LEU Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 223 LYS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 158 ARG Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 315 TYR Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 255 VAL Chi-restraints excluded: chain f residue 270 LEU Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 337 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 350 LYS Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 502 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 619 HIS Chi-restraints excluded: chain f residue 704 LEU Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain f residue 747 GLN Chi-restraints excluded: chain f residue 796 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain f residue 868 HIS Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain u residue 171 PHE Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 177 LEU Chi-restraints excluded: chain u residue 231 VAL Chi-restraints excluded: chain u residue 236 VAL Chi-restraints excluded: chain u residue 261 SER Chi-restraints excluded: chain u residue 263 PHE Chi-restraints excluded: chain u residue 268 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 347 optimal weight: 1.9990 chunk 362 optimal weight: 7.9990 chunk 635 optimal weight: 1.9990 chunk 511 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 767 optimal weight: 0.7980 chunk 381 optimal weight: 7.9990 chunk 256 optimal weight: 0.9980 chunk 550 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 386 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 84 GLN B 181 GLN C 64 GLN C 90 HIS C 288 ASN D 65 GLN D 110 ASN D 127 ASN D 278 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN ** F 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 ASN I 198 ASN J 205 ASN L 53 GLN M 101 ASN ** U 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 118 GLN V 299 GLN V 347 GLN ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 148 HIS ** X 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 27 GLN ** c 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 592 ASN f 855 GLN ** g 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.102732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.071320 restraints weight = 145818.196| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.74 r_work: 0.2884 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.132 72504 Z= 0.192 Angle : 0.619 42.994 97953 Z= 0.312 Chirality : 0.041 0.278 11156 Planarity : 0.004 0.193 12612 Dihedral : 6.139 83.715 9956 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 3.98 % Allowed : 29.37 % Favored : 66.65 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.20 (0.09), residues: 8915 helix: 1.41 (0.07), residues: 5020 sheet: -0.46 (0.15), residues: 1013 loop : 0.38 (0.12), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 139 HIS 0.030 0.001 HIS f 619 PHE 0.020 0.001 PHE a 67 TYR 0.019 0.001 TYR L 137 ARG 0.018 0.000 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1295 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 310 poor density : 985 time to evaluate : 6.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8107 (mp0) REVERT: A 79 ASP cc_start: 0.8245 (t0) cc_final: 0.7734 (t0) REVERT: A 133 ASP cc_start: 0.8769 (t0) cc_final: 0.8300 (t0) REVERT: A 168 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: A 185 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8065 (mt-10) REVERT: A 186 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8002 (mttp) REVERT: B 85 MET cc_start: 0.7923 (mtt) cc_final: 0.7463 (tmm) REVERT: B 117 ASP cc_start: 0.7485 (t0) cc_final: 0.7184 (t0) REVERT: B 140 ASP cc_start: 0.8546 (m-30) cc_final: 0.8093 (m-30) REVERT: B 164 MET cc_start: 0.8254 (tmm) cc_final: 0.7272 (tmm) REVERT: B 174 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8436 (mtp) REVERT: B 210 TYR cc_start: 0.8815 (m-80) cc_final: 0.8530 (m-80) REVERT: B 213 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8278 (mp0) REVERT: B 260 LEU cc_start: 0.9127 (mp) cc_final: 0.8871 (mm) REVERT: C 40 GLN cc_start: 0.9288 (tt0) cc_final: 0.9029 (tm-30) REVERT: C 89 VAL cc_start: 0.9091 (t) cc_final: 0.8792 (m) REVERT: C 297 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.8316 (ttp-110) REVERT: C 336 MET cc_start: 0.9099 (mtm) cc_final: 0.8771 (mtm) REVERT: C 382 ASP cc_start: 0.8862 (m-30) cc_final: 0.8603 (m-30) REVERT: D 52 GLU cc_start: 0.8899 (tt0) cc_final: 0.8389 (tp30) REVERT: D 60 TYR cc_start: 0.9171 (OUTLIER) cc_final: 0.8535 (t80) REVERT: D 71 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8305 (mm-30) REVERT: D 94 GLU cc_start: 0.8840 (tt0) cc_final: 0.8627 (tt0) REVERT: D 278 GLN cc_start: 0.9112 (OUTLIER) cc_final: 0.8912 (pt0) REVERT: D 301 GLN cc_start: 0.8326 (pp30) cc_final: 0.7934 (pp30) REVERT: D 413 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: E 51 GLN cc_start: 0.8678 (mm-40) cc_final: 0.7919 (mp10) REVERT: E 100 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8422 (mt) REVERT: E 102 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8602 (mtm) REVERT: E 122 MET cc_start: 0.8889 (mtt) cc_final: 0.8646 (mtt) REVERT: E 195 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8121 (t80) REVERT: E 264 MET cc_start: 0.9308 (mtp) cc_final: 0.8785 (mtp) REVERT: E 352 MET cc_start: 0.9319 (mmm) cc_final: 0.9119 (mmm) REVERT: E 387 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8624 (mttm) REVERT: F 69 MET cc_start: 0.5875 (ppp) cc_final: 0.5313 (pp-130) REVERT: F 81 LYS cc_start: 0.8541 (tppt) cc_final: 0.8095 (tmmt) REVERT: F 146 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8582 (mtmm) REVERT: F 180 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8236 (tpp-160) REVERT: F 213 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7981 (mp0) REVERT: F 318 ASP cc_start: 0.8607 (t0) cc_final: 0.8296 (t0) REVERT: F 390 ASP cc_start: 0.8851 (t0) cc_final: 0.8450 (t0) REVERT: F 438 TYR cc_start: 0.9016 (m-80) cc_final: 0.8326 (m-80) REVERT: G 117 ARG cc_start: 0.8253 (ttt90) cc_final: 0.6979 (tpp-160) REVERT: G 120 ASP cc_start: 0.8833 (m-30) cc_final: 0.8446 (m-30) REVERT: G 131 MET cc_start: 0.9223 (ptp) cc_final: 0.8879 (pmm) REVERT: G 187 PHE cc_start: 0.7619 (m-80) cc_final: 0.6815 (t80) REVERT: G 232 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8367 (mm-30) REVERT: G 235 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8779 (tt) REVERT: H 44 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.9005 (m) REVERT: H 50 LYS cc_start: 0.8846 (ttpt) cc_final: 0.8559 (ttmm) REVERT: H 79 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8546 (mtp) REVERT: H 95 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7793 (tp-100) REVERT: H 159 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8195 (ttmm) REVERT: H 166 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8450 (t0) REVERT: I 54 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8959 (pttm) REVERT: I 65 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9056 (mp) REVERT: I 148 TYR cc_start: 0.8848 (m-80) cc_final: 0.8634 (m-80) REVERT: I 178 ASP cc_start: 0.9166 (t0) cc_final: 0.8876 (t0) REVERT: I 234 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8221 (tp30) REVERT: I 242 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8355 (mm-30) REVERT: J 59 VAL cc_start: 0.8804 (t) cc_final: 0.8502 (m) REVERT: J 159 ASN cc_start: 0.9230 (t0) cc_final: 0.8937 (t160) REVERT: K 71 ASP cc_start: 0.8748 (t0) cc_final: 0.8394 (t0) REVERT: L 27 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: L 189 LYS cc_start: 0.9055 (tppp) cc_final: 0.8818 (mmtp) REVERT: L 218 ASP cc_start: 0.7908 (p0) cc_final: 0.7635 (t0) REVERT: L 220 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8227 (tp30) REVERT: L 239 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7262 (ptt90) REVERT: M 19 ARG cc_start: 0.9253 (OUTLIER) cc_final: 0.9041 (ptm-80) REVERT: M 34 SER cc_start: 0.8896 (OUTLIER) cc_final: 0.8510 (p) REVERT: M 109 LYS cc_start: 0.6963 (tttt) cc_final: 0.6269 (tttm) REVERT: M 113 ASP cc_start: 0.8737 (m-30) cc_final: 0.8301 (m-30) REVERT: M 184 MET cc_start: 0.9190 (ptp) cc_final: 0.8743 (ptp) REVERT: M 192 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8903 (mp0) REVERT: U 239 GLU cc_start: 0.8937 (tt0) cc_final: 0.8037 (tm-30) REVERT: U 241 ASN cc_start: 0.8450 (t0) cc_final: 0.8043 (t0) REVERT: U 347 ASN cc_start: 0.9155 (t0) cc_final: 0.8928 (t0) REVERT: U 530 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: U 714 SER cc_start: 0.9227 (t) cc_final: 0.9011 (p) REVERT: U 931 HIS cc_start: 0.5809 (t-90) cc_final: 0.5492 (t-170) REVERT: V 96 ARG cc_start: 0.8571 (ptp-170) cc_final: 0.8200 (ptp-110) REVERT: V 100 MET cc_start: 0.8650 (mpt) cc_final: 0.8353 (mpt) REVERT: V 212 TYR cc_start: 0.8605 (t80) cc_final: 0.8274 (t80) REVERT: V 304 GLU cc_start: 0.8557 (mp0) cc_final: 0.8268 (mp0) REVERT: V 443 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8793 (tmm-80) REVERT: V 471 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8376 (tm-30) REVERT: V 485 ASP cc_start: 0.9124 (m-30) cc_final: 0.8666 (m-30) REVERT: V 494 MET cc_start: 0.9061 (mtm) cc_final: 0.8701 (mmm) REVERT: V 510 GLU cc_start: 0.8200 (pt0) cc_final: 0.7709 (pm20) REVERT: V 514 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7866 (ttm170) REVERT: V 518 ASP cc_start: 0.8941 (m-30) cc_final: 0.8678 (m-30) REVERT: V 521 PHE cc_start: 0.8355 (t80) cc_final: 0.7894 (t80) REVERT: W 313 GLU cc_start: 0.8788 (tt0) cc_final: 0.8360 (mm-30) REVERT: W 333 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8888 (pt) REVERT: X 41 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: X 52 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8369 (tp30) REVERT: X 148 HIS cc_start: 0.8328 (t70) cc_final: 0.8118 (t70) REVERT: X 161 ASP cc_start: 0.8541 (t70) cc_final: 0.8123 (t0) REVERT: X 212 MET cc_start: 0.8753 (tpt) cc_final: 0.8418 (tpt) REVERT: X 332 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8090 (mm-30) REVERT: X 415 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.8221 (m-80) REVERT: Y 39 ASP cc_start: 0.8962 (m-30) cc_final: 0.8598 (m-30) REVERT: Y 173 ASP cc_start: 0.7909 (t0) cc_final: 0.7626 (t0) REVERT: Y 361 SER cc_start: 0.8658 (m) cc_final: 0.8414 (p) REVERT: Y 383 LEU cc_start: 0.9295 (tp) cc_final: 0.9046 (tm) REVERT: Y 385 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8442 (tmt-80) REVERT: Z 32 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7275 (mm110) REVERT: Z 143 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7303 (tm-30) REVERT: Z 165 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: Z 178 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8478 (p0) REVERT: Z 283 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7704 (mtm180) REVERT: a 23 HIS cc_start: 0.7977 (m-70) cc_final: 0.7548 (m-70) REVERT: a 43 ASP cc_start: 0.8784 (t0) cc_final: 0.8464 (t70) REVERT: a 81 LEU cc_start: 0.9095 (mt) cc_final: 0.8884 (mt) REVERT: a 127 ASP cc_start: 0.8971 (t0) cc_final: 0.8582 (t0) REVERT: a 166 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8833 (mm) REVERT: a 333 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.9026 (mmp) REVERT: b 11 ASP cc_start: 0.8708 (t0) cc_final: 0.7957 (t0) REVERT: b 42 ARG cc_start: 0.8722 (ptt-90) cc_final: 0.8331 (mpp80) REVERT: b 183 LEU cc_start: 0.9095 (mp) cc_final: 0.8785 (mp) REVERT: c 106 GLU cc_start: 0.9045 (OUTLIER) cc_final: 0.8427 (mp0) REVERT: c 223 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9026 (mtpp) REVERT: c 289 ASP cc_start: 0.8807 (t70) cc_final: 0.8404 (m-30) REVERT: d 96 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8506 (pm20) REVERT: d 158 ARG cc_start: 0.9174 (OUTLIER) cc_final: 0.8830 (pmm-80) REVERT: d 179 LYS cc_start: 0.9232 (pttt) cc_final: 0.8822 (pttm) REVERT: d 207 GLU cc_start: 0.9078 (tt0) cc_final: 0.8772 (mp0) REVERT: d 265 ASP cc_start: 0.8506 (m-30) cc_final: 0.8288 (p0) REVERT: d 286 GLU cc_start: 0.8507 (tp30) cc_final: 0.7860 (tt0) REVERT: d 297 LYS cc_start: 0.9359 (tmmt) cc_final: 0.8921 (tptp) REVERT: d 309 VAL cc_start: 0.8941 (t) cc_final: 0.8659 (p) REVERT: d 347 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8532 (mm-30) REVERT: f 47 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6690 (tp30) REVERT: f 113 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5397 (ppp) REVERT: f 131 MET cc_start: 0.4113 (tmt) cc_final: 0.3322 (mmt) REVERT: f 162 LEU cc_start: 0.8615 (tp) cc_final: 0.8198 (mm) REVERT: f 268 LEU cc_start: 0.9450 (mp) cc_final: 0.9119 (tp) REVERT: f 340 MET cc_start: 0.7841 (mmm) cc_final: 0.7430 (mmm) REVERT: f 398 TRP cc_start: 0.8407 (t-100) cc_final: 0.7537 (t-100) REVERT: f 493 ASN cc_start: 0.8989 (t0) cc_final: 0.8715 (t0) REVERT: f 501 LEU cc_start: 0.8976 (tp) cc_final: 0.8696 (tp) REVERT: f 512 MET cc_start: 0.8293 (tpt) cc_final: 0.8014 (tpt) REVERT: f 592 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8717 (p0) REVERT: f 619 HIS cc_start: 0.6770 (OUTLIER) cc_final: 0.6437 (p-80) REVERT: f 681 TYR cc_start: 0.8030 (m-80) cc_final: 0.7763 (m-80) REVERT: f 747 GLN cc_start: 0.9031 (mm110) cc_final: 0.8668 (mt0) REVERT: f 784 ASP cc_start: 0.7567 (t0) cc_final: 0.7315 (t0) REVERT: f 786 GLN cc_start: 0.8376 (mt0) cc_final: 0.7918 (mt0) REVERT: f 851 ASP cc_start: 0.7075 (t0) cc_final: 0.6824 (t0) REVERT: g 136 LEU cc_start: 0.6124 (pt) cc_final: 0.5352 (tm) REVERT: g 138 LEU cc_start: 0.7048 (mt) cc_final: 0.6815 (tm) REVERT: g 158 LEU cc_start: 0.4395 (OUTLIER) cc_final: 0.4161 (mt) REVERT: u 164 GLN cc_start: 0.7679 (mm110) cc_final: 0.7209 (mm-40) REVERT: u 173 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8276 (mm-40) REVERT: u 176 LYS cc_start: 0.7923 (mtmm) cc_final: 0.7579 (mtmm) REVERT: u 178 TYR cc_start: 0.7245 (m-10) cc_final: 0.6856 (m-10) REVERT: u 228 ASP cc_start: 0.8370 (t70) cc_final: 0.8034 (p0) REVERT: u 268 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8726 (p) outliers start: 310 outliers final: 106 residues processed: 1224 average time/residue: 1.3607 time to fit residues: 2248.4882 Evaluate side-chains 1034 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 877 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 105 ILE Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain L residue 239 ARG Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain M residue 226 ILE Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 362 ASN Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 530 GLU Chi-restraints excluded: chain U residue 793 LYS Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 134 PHE Chi-restraints excluded: chain V residue 379 LEU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain V residue 471 GLU Chi-restraints excluded: chain V residue 507 SER Chi-restraints excluded: chain V residue 514 ARG Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 252 ASP Chi-restraints excluded: chain W residue 333 LEU Chi-restraints excluded: chain X residue 41 GLU Chi-restraints excluded: chain X residue 120 GLU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 377 LEU Chi-restraints excluded: chain Y residue 385 ARG Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 32 GLN Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 165 GLU Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 269 VAL Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 208 GLU Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 333 MET Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 132 LYS Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 223 LYS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 96 GLU Chi-restraints excluded: chain d residue 106 SER Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 158 ARG Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 315 TYR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 255 VAL Chi-restraints excluded: chain f residue 270 LEU Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 539 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 619 HIS Chi-restraints excluded: chain f residue 796 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain u residue 171 PHE Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 231 VAL Chi-restraints excluded: chain u residue 236 VAL Chi-restraints excluded: chain u residue 268 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 693 optimal weight: 4.9990 chunk 391 optimal weight: 5.9990 chunk 797 optimal weight: 30.0000 chunk 92 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 339 optimal weight: 0.9980 chunk 816 optimal weight: 20.0000 chunk 316 optimal weight: 3.9990 chunk 362 optimal weight: 9.9990 chunk 668 optimal weight: 7.9990 chunk 521 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 296 GLN B 82 GLN B 425 ASN C 64 GLN C 288 ASN D 65 GLN D 127 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 ASN I 198 ASN L 8 ASN M 101 ASN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 340 GLN U 389 ASN ** U 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 596 ASN W 430 GLN ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 72 HIS Z 102 HIS ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 HIS ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 27 GLN ** c 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN f 238 ASN ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 592 ASN f 619 HIS ** g 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 149 HIS u 183 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.068361 restraints weight = 147754.592| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.73 r_work: 0.2824 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 72504 Z= 0.349 Angle : 0.630 14.313 97953 Z= 0.316 Chirality : 0.043 0.204 11156 Planarity : 0.004 0.079 12612 Dihedral : 6.275 87.573 9956 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 4.25 % Allowed : 29.10 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.19 (0.09), residues: 8915 helix: 1.44 (0.07), residues: 5015 sheet: -0.63 (0.16), residues: 1004 loop : 0.36 (0.12), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP f 154 HIS 0.009 0.001 HIS V 329 PHE 0.032 0.001 PHE B 78 TYR 0.025 0.002 TYR u 123 ARG 0.016 0.000 ARG b 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 331 poor density : 904 time to evaluate : 6.409 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: A 49 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: A 128 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7755 (tp40) REVERT: A 133 ASP cc_start: 0.8791 (t0) cc_final: 0.8346 (t0) REVERT: A 168 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8379 (mm-30) REVERT: A 186 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8037 (mttp) REVERT: A 249 TYR cc_start: 0.9262 (m-80) cc_final: 0.9049 (m-80) REVERT: A 356 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8500 (mtmp) REVERT: B 85 MET cc_start: 0.7979 (mtt) cc_final: 0.7544 (tmm) REVERT: B 101 ASP cc_start: 0.8523 (m-30) cc_final: 0.8083 (p0) REVERT: B 140 ASP cc_start: 0.8573 (m-30) cc_final: 0.8127 (m-30) REVERT: B 164 MET cc_start: 0.8334 (tmm) cc_final: 0.7407 (tmm) REVERT: B 210 TYR cc_start: 0.8835 (m-80) cc_final: 0.8633 (m-80) REVERT: B 213 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: B 396 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8891 (tttm) REVERT: C 40 GLN cc_start: 0.9307 (tt0) cc_final: 0.9028 (tm-30) REVERT: C 89 VAL cc_start: 0.9169 (t) cc_final: 0.8915 (m) REVERT: C 104 ASP cc_start: 0.8466 (t0) cc_final: 0.8247 (t0) REVERT: C 382 ASP cc_start: 0.8850 (m-30) cc_final: 0.8622 (m-30) REVERT: D 52 GLU cc_start: 0.8881 (tt0) cc_final: 0.8512 (tp30) REVERT: D 60 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8591 (t80) REVERT: D 71 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8108 (mm-30) REVERT: D 94 GLU cc_start: 0.8836 (tt0) cc_final: 0.8288 (tt0) REVERT: D 413 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: E 51 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8102 (mp10) REVERT: E 66 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8178 (tp30) REVERT: E 100 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8466 (mt) REVERT: E 122 MET cc_start: 0.9026 (mtt) cc_final: 0.8666 (mtt) REVERT: E 264 MET cc_start: 0.9377 (mtp) cc_final: 0.9020 (mtp) REVERT: E 281 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8784 (mmm160) REVERT: E 322 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8836 (pttm) REVERT: F 69 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5401 (pp-130) REVERT: F 81 LYS cc_start: 0.8535 (tppt) cc_final: 0.8107 (tmmt) REVERT: F 213 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8033 (mp0) REVERT: F 318 ASP cc_start: 0.8763 (t0) cc_final: 0.8374 (t0) REVERT: F 390 ASP cc_start: 0.8896 (t0) cc_final: 0.8530 (t0) REVERT: G 39 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.9079 (p) REVERT: G 117 ARG cc_start: 0.8302 (ttt90) cc_final: 0.6868 (tpp-160) REVERT: G 120 ASP cc_start: 0.8878 (m-30) cc_final: 0.8409 (m-30) REVERT: G 232 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8405 (mm-30) REVERT: H 44 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8965 (m) REVERT: H 79 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8643 (mtp) REVERT: H 95 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7869 (tp-100) REVERT: H 166 ASN cc_start: 0.8806 (OUTLIER) cc_final: 0.8496 (t0) REVERT: H 182 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8359 (mp) REVERT: I 54 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8958 (pttm) REVERT: I 80 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.7974 (t) REVERT: I 136 TYR cc_start: 0.9044 (m-80) cc_final: 0.8724 (m-80) REVERT: I 178 ASP cc_start: 0.9164 (t0) cc_final: 0.8860 (t0) REVERT: J 59 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8494 (m) REVERT: J 159 ASN cc_start: 0.9279 (t0) cc_final: 0.8971 (t160) REVERT: K 71 ASP cc_start: 0.8733 (t0) cc_final: 0.8413 (t0) REVERT: L 27 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8084 (mp0) REVERT: L 140 MET cc_start: 0.9379 (mmm) cc_final: 0.9172 (mmm) REVERT: L 189 LYS cc_start: 0.9069 (tppp) cc_final: 0.8833 (mmtp) REVERT: L 218 ASP cc_start: 0.7959 (p0) cc_final: 0.7684 (t0) REVERT: L 220 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8269 (tp30) REVERT: L 224 TYR cc_start: 0.8810 (m-80) cc_final: 0.8606 (m-80) REVERT: M 34 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8616 (p) REVERT: M 109 LYS cc_start: 0.7029 (tttt) cc_final: 0.6396 (tttm) REVERT: M 113 ASP cc_start: 0.8788 (m-30) cc_final: 0.8382 (m-30) REVERT: M 184 MET cc_start: 0.9153 (ptp) cc_final: 0.8747 (ptp) REVERT: M 192 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8916 (mp0) REVERT: U 239 GLU cc_start: 0.8951 (tt0) cc_final: 0.8105 (tm-30) REVERT: U 241 ASN cc_start: 0.8513 (t0) cc_final: 0.8160 (t0) REVERT: U 332 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8312 (pp20) REVERT: U 347 ASN cc_start: 0.9196 (t0) cc_final: 0.8910 (t0) REVERT: U 530 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: U 698 GLN cc_start: 0.9039 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: V 96 ARG cc_start: 0.8520 (ptp-170) cc_final: 0.8144 (ptp-110) REVERT: V 100 MET cc_start: 0.8652 (mpt) cc_final: 0.8321 (mpt) REVERT: V 219 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8791 (tt0) REVERT: V 304 GLU cc_start: 0.8561 (mp0) cc_final: 0.8278 (mp0) REVERT: V 381 GLN cc_start: 0.9447 (OUTLIER) cc_final: 0.8868 (tt0) REVERT: V 443 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8854 (tmm-80) REVERT: V 471 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8496 (tm-30) REVERT: V 485 ASP cc_start: 0.9111 (m-30) cc_final: 0.8664 (m-30) REVERT: V 494 MET cc_start: 0.9063 (mtm) cc_final: 0.8713 (mmm) REVERT: V 513 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8769 (tm-30) REVERT: V 518 ASP cc_start: 0.8928 (m-30) cc_final: 0.8682 (m-30) REVERT: V 521 PHE cc_start: 0.8139 (t80) cc_final: 0.7875 (t80) REVERT: X 41 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: X 47 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7438 (pp20) REVERT: X 52 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8605 (mm-30) REVERT: X 161 ASP cc_start: 0.8668 (t70) cc_final: 0.8148 (t70) REVERT: X 212 MET cc_start: 0.8759 (tpt) cc_final: 0.8063 (tpt) REVERT: X 332 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8039 (mm-30) REVERT: Y 39 ASP cc_start: 0.8961 (m-30) cc_final: 0.8615 (m-30) REVERT: Y 173 ASP cc_start: 0.8093 (t0) cc_final: 0.7678 (t0) REVERT: Y 214 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.8428 (ptt) REVERT: Y 383 LEU cc_start: 0.9278 (tp) cc_final: 0.8994 (tm) REVERT: Z 28 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8197 (mmpt) REVERT: Z 143 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7156 (tm-30) REVERT: Z 165 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: Z 178 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8560 (p0) REVERT: Z 251 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8093 (mt) REVERT: Z 283 ARG cc_start: 0.8027 (mtm180) cc_final: 0.7678 (mtm180) REVERT: a 12 GLN cc_start: 0.7458 (mt0) cc_final: 0.7029 (mm110) REVERT: a 43 ASP cc_start: 0.8851 (t0) cc_final: 0.8629 (t70) REVERT: a 81 LEU cc_start: 0.9179 (mt) cc_final: 0.8954 (mt) REVERT: a 127 ASP cc_start: 0.8956 (t0) cc_final: 0.8529 (t0) REVERT: a 278 MET cc_start: 0.8796 (mtm) cc_final: 0.8592 (mtp) REVERT: a 312 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8836 (mmt) REVERT: a 363 MET cc_start: 0.9105 (tpp) cc_final: 0.8738 (tpp) REVERT: b 11 ASP cc_start: 0.8798 (t0) cc_final: 0.8152 (t0) REVERT: b 29 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: b 46 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8191 (mp0) REVERT: b 175 PRO cc_start: 0.8721 (Cg_endo) cc_final: 0.8441 (Cg_exo) REVERT: c 106 GLU cc_start: 0.9080 (OUTLIER) cc_final: 0.8482 (mp0) REVERT: c 223 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.9081 (mtpp) REVERT: c 264 LYS cc_start: 0.8994 (ptpt) cc_final: 0.8342 (ptmm) REVERT: c 289 ASP cc_start: 0.8869 (t70) cc_final: 0.8472 (m-30) REVERT: d 96 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: d 158 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8809 (pmm-80) REVERT: d 165 GLU cc_start: 0.9424 (mm-30) cc_final: 0.8803 (mm-30) REVERT: d 179 LYS cc_start: 0.9235 (pttt) cc_final: 0.8867 (pttm) REVERT: d 236 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8856 (mm) REVERT: d 286 GLU cc_start: 0.8579 (tp30) cc_final: 0.7961 (tt0) REVERT: d 297 LYS cc_start: 0.9397 (tmmt) cc_final: 0.8988 (tptp) REVERT: d 309 VAL cc_start: 0.8964 (t) cc_final: 0.8671 (p) REVERT: d 347 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8559 (mm-30) REVERT: f 47 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6719 (tp30) REVERT: f 113 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5490 (ppp) REVERT: f 131 MET cc_start: 0.4126 (tmt) cc_final: 0.3288 (mmt) REVERT: f 162 LEU cc_start: 0.8639 (tp) cc_final: 0.8219 (mm) REVERT: f 171 GLN cc_start: 0.7552 (mm-40) cc_final: 0.7319 (mp10) REVERT: f 268 LEU cc_start: 0.9390 (mp) cc_final: 0.8982 (tp) REVERT: f 272 LEU cc_start: 0.8369 (tp) cc_final: 0.8051 (mt) REVERT: f 275 MET cc_start: 0.8597 (tpt) cc_final: 0.7747 (tmm) REVERT: f 340 MET cc_start: 0.7908 (mmm) cc_final: 0.7533 (mmm) REVERT: f 472 HIS cc_start: 0.8156 (OUTLIER) cc_final: 0.7646 (t-90) REVERT: f 502 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7728 (mm) REVERT: f 512 MET cc_start: 0.8400 (tpt) cc_final: 0.8187 (tpt) REVERT: f 592 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8703 (p0) REVERT: f 681 TYR cc_start: 0.8147 (m-80) cc_final: 0.7825 (m-80) REVERT: f 746 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8377 (tpp80) REVERT: f 747 GLN cc_start: 0.9035 (mm110) cc_final: 0.8555 (mt0) REVERT: f 784 ASP cc_start: 0.7642 (t0) cc_final: 0.7399 (t0) REVERT: f 786 GLN cc_start: 0.8336 (mt0) cc_final: 0.7706 (mt0) REVERT: f 797 LEU cc_start: 0.8771 (mt) cc_final: 0.8469 (mt) REVERT: f 868 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.6955 (m90) REVERT: g 158 LEU cc_start: 0.4233 (OUTLIER) cc_final: 0.3788 (mt) REVERT: u 157 LEU cc_start: 0.9216 (tp) cc_final: 0.8895 (mt) REVERT: u 164 GLN cc_start: 0.7737 (mm110) cc_final: 0.7250 (mm-40) REVERT: u 173 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8470 (mm-40) REVERT: u 176 LYS cc_start: 0.7899 (mtmm) cc_final: 0.7608 (mtmm) REVERT: u 181 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6643 (mtpm) REVERT: u 211 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8121 (mtp-110) REVERT: u 228 ASP cc_start: 0.8461 (t70) cc_final: 0.8054 (p0) REVERT: u 259 ARG cc_start: 0.7827 (ttp-110) cc_final: 0.7575 (mtp-110) REVERT: u 268 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8688 (p) outliers start: 331 outliers final: 141 residues processed: 1165 average time/residue: 1.4248 time to fit residues: 2216.6443 Evaluate side-chains 1048 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 850 time to evaluate : 6.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 145 GLU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 281 ARG Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 188 ASP Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 174 MET Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 205 ASN Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 192 LYS Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 237 VAL Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 139 SER Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 332 GLU Chi-restraints excluded: chain U residue 362 ASN Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 530 GLU Chi-restraints excluded: chain U residue 698 GLN Chi-restraints excluded: chain U residue 793 LYS Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 134 PHE Chi-restraints excluded: chain V residue 219 GLU Chi-restraints excluded: chain V residue 336 GLU Chi-restraints excluded: chain V residue 379 LEU Chi-restraints excluded: chain V residue 381 GLN Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain V residue 471 GLU Chi-restraints excluded: chain V residue 478 GLN Chi-restraints excluded: chain V residue 507 SER Chi-restraints excluded: chain V residue 517 GLN Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 252 ASP Chi-restraints excluded: chain W residue 260 SER Chi-restraints excluded: chain X residue 41 GLU Chi-restraints excluded: chain X residue 47 GLU Chi-restraints excluded: chain X residue 103 THR Chi-restraints excluded: chain X residue 120 GLU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain Y residue 214 MET Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 165 GLU Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 269 VAL Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 208 GLU Chi-restraints excluded: chain a residue 287 ASN Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain a residue 312 MET Chi-restraints excluded: chain b residue 29 GLN Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 132 LYS Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain b residue 189 LEU Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 223 LYS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain c residue 307 VAL Chi-restraints excluded: chain d residue 96 GLU Chi-restraints excluded: chain d residue 106 SER Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 158 ARG Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 315 TYR Chi-restraints excluded: chain e residue 50 ASP Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 255 VAL Chi-restraints excluded: chain f residue 270 LEU Chi-restraints excluded: chain f residue 337 LEU Chi-restraints excluded: chain f residue 350 LYS Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 472 HIS Chi-restraints excluded: chain f residue 502 LEU Chi-restraints excluded: chain f residue 539 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 619 HIS Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain f residue 796 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain f residue 868 HIS Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 882 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain u residue 171 PHE Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 181 LYS Chi-restraints excluded: chain u residue 231 VAL Chi-restraints excluded: chain u residue 268 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 789 optimal weight: 0.8980 chunk 552 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 chunk 596 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 877 optimal weight: 20.0000 chunk 626 optimal weight: 4.9990 chunk 805 optimal weight: 6.9990 chunk 607 optimal weight: 6.9990 chunk 883 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN C 90 HIS C 288 ASN D 65 GLN D 127 ASN D 278 GLN D 304 ASN E 39 GLN G 75 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 ASN J 205 ASN L 8 ASN M 101 ASN U 267 ASN U 340 GLN ** U 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 207 GLN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 256 GLN ** a 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 592 ASN f 619 HIS f 747 GLN ** g 135 GLN ** 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 = 0.3538 r_free = 0.3538 target = 0.101188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.069830 restraints weight = 146462.566| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.72 r_work: 0.2855 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 72504 Z= 0.233 Angle : 0.607 15.438 97953 Z= 0.303 Chirality : 0.042 0.297 11156 Planarity : 0.004 0.050 12612 Dihedral : 6.217 89.296 9956 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.85 % Favored : 97.13 % Rotamer: Outliers : 3.78 % Allowed : 29.60 % Favored : 66.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.23 (0.09), residues: 8915 helix: 1.48 (0.07), residues: 5016 sheet: -0.62 (0.16), residues: 1000 loop : 0.38 (0.12), residues: 2899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 139 HIS 0.010 0.001 HIS f 619 PHE 0.033 0.001 PHE a 50 TYR 0.022 0.001 TYR u 123 ARG 0.010 0.000 ARG V 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 295 poor density : 900 time to evaluate : 6.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: A 128 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7762 (tp40) REVERT: A 133 ASP cc_start: 0.8767 (t0) cc_final: 0.8329 (t0) REVERT: A 168 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8338 (mm-30) REVERT: A 186 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8017 (mttp) REVERT: A 191 VAL cc_start: 0.9521 (OUTLIER) cc_final: 0.9313 (p) REVERT: A 213 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8938 (tp) REVERT: A 356 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8400 (mtmp) REVERT: B 85 MET cc_start: 0.8042 (mtt) cc_final: 0.7617 (tmm) REVERT: B 140 ASP cc_start: 0.8610 (m-30) cc_final: 0.8134 (m-30) REVERT: B 164 MET cc_start: 0.8320 (tmm) cc_final: 0.7399 (tmm) REVERT: B 210 TYR cc_start: 0.8818 (m-80) cc_final: 0.8602 (m-80) REVERT: B 213 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: B 217 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8681 (mtpp) REVERT: B 260 LEU cc_start: 0.9110 (mp) cc_final: 0.8854 (mm) REVERT: C 40 GLN cc_start: 0.9284 (tt0) cc_final: 0.9012 (tm-30) REVERT: C 89 VAL cc_start: 0.9144 (t) cc_final: 0.8899 (m) REVERT: C 297 ARG cc_start: 0.8597 (ttp-110) cc_final: 0.8197 (ttp-110) REVERT: C 336 MET cc_start: 0.9056 (mtm) cc_final: 0.8580 (mtm) REVERT: C 382 ASP cc_start: 0.8875 (m-30) cc_final: 0.8625 (m-30) REVERT: D 52 GLU cc_start: 0.8918 (tt0) cc_final: 0.8462 (tp30) REVERT: D 60 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.8626 (t80) REVERT: D 71 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8232 (mm-30) REVERT: D 94 GLU cc_start: 0.8847 (tt0) cc_final: 0.8301 (tt0) REVERT: D 278 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8876 (pm20) REVERT: D 413 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: E 66 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8182 (tp30) REVERT: E 100 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8423 (mt) REVERT: E 122 MET cc_start: 0.8946 (mtt) cc_final: 0.8636 (mtt) REVERT: E 195 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8136 (t80) REVERT: E 281 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8775 (mmm160) REVERT: E 352 MET cc_start: 0.9328 (mmm) cc_final: 0.9110 (mmm) REVERT: E 387 LYS cc_start: 0.8974 (mtmm) cc_final: 0.8599 (mttm) REVERT: F 81 LYS cc_start: 0.8539 (tppt) cc_final: 0.8089 (tmmt) REVERT: F 146 LYS cc_start: 0.8877 (mtmm) cc_final: 0.8625 (mtmm) REVERT: F 180 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8332 (tpp-160) REVERT: F 183 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8426 (mp0) REVERT: F 213 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7992 (mp0) REVERT: F 318 ASP cc_start: 0.8736 (t0) cc_final: 0.8351 (t0) REVERT: F 390 ASP cc_start: 0.8846 (t0) cc_final: 0.8480 (t0) REVERT: F 421 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.8929 (mmm) REVERT: G 39 SER cc_start: 0.9345 (OUTLIER) cc_final: 0.9099 (p) REVERT: G 117 ARG cc_start: 0.8201 (ttt90) cc_final: 0.6699 (ttm170) REVERT: G 120 ASP cc_start: 0.8805 (m-30) cc_final: 0.8349 (m-30) REVERT: G 144 ASP cc_start: 0.8244 (t0) cc_final: 0.7550 (t70) REVERT: G 232 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8417 (mm-30) REVERT: H 44 VAL cc_start: 0.9199 (OUTLIER) cc_final: 0.8954 (m) REVERT: H 79 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8593 (mtp) REVERT: H 95 GLN cc_start: 0.8390 (mm-40) cc_final: 0.7845 (tp-100) REVERT: H 159 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8158 (ttmm) REVERT: H 166 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8501 (t0) REVERT: I 54 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8951 (pttm) REVERT: I 80 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.7895 (t) REVERT: I 148 TYR cc_start: 0.8701 (m-80) cc_final: 0.8493 (m-80) REVERT: I 234 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8212 (tp30) REVERT: I 242 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8420 (mm-30) REVERT: J 59 VAL cc_start: 0.8808 (OUTLIER) cc_final: 0.8520 (m) REVERT: J 159 ASN cc_start: 0.9203 (t0) cc_final: 0.8904 (t160) REVERT: K 71 ASP cc_start: 0.8719 (t0) cc_final: 0.8399 (t0) REVERT: L 27 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: L 140 MET cc_start: 0.9371 (mmm) cc_final: 0.9099 (mmm) REVERT: L 189 LYS cc_start: 0.9065 (tppp) cc_final: 0.8798 (mmtp) REVERT: L 218 ASP cc_start: 0.7928 (p0) cc_final: 0.7683 (m-30) REVERT: L 220 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8243 (tp30) REVERT: L 224 TYR cc_start: 0.8823 (m-80) cc_final: 0.8595 (m-80) REVERT: M 34 SER cc_start: 0.8983 (OUTLIER) cc_final: 0.8565 (p) REVERT: M 109 LYS cc_start: 0.6997 (tttt) cc_final: 0.6380 (tttm) REVERT: M 113 ASP cc_start: 0.8748 (m-30) cc_final: 0.8372 (m-30) REVERT: M 184 MET cc_start: 0.9182 (ptp) cc_final: 0.8776 (ptp) REVERT: M 192 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8932 (mp0) REVERT: U 239 GLU cc_start: 0.8908 (tt0) cc_final: 0.8118 (tm-30) REVERT: U 241 ASN cc_start: 0.8468 (t0) cc_final: 0.8100 (t0) REVERT: U 347 ASN cc_start: 0.9148 (t0) cc_final: 0.8897 (t0) REVERT: U 530 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: U 698 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: U 714 SER cc_start: 0.9249 (t) cc_final: 0.9024 (p) REVERT: V 96 ARG cc_start: 0.8493 (ptp-170) cc_final: 0.8135 (ptp-110) REVERT: V 100 MET cc_start: 0.8664 (mpt) cc_final: 0.8324 (mpt) REVERT: V 212 TYR cc_start: 0.8471 (t80) cc_final: 0.8242 (t80) REVERT: V 304 GLU cc_start: 0.8553 (mp0) cc_final: 0.8282 (mp0) REVERT: V 443 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8838 (tmm-80) REVERT: V 463 MET cc_start: 0.8062 (tpp) cc_final: 0.7636 (tmm) REVERT: V 471 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: V 485 ASP cc_start: 0.9087 (m-30) cc_final: 0.8672 (m-30) REVERT: V 494 MET cc_start: 0.9055 (mtm) cc_final: 0.8697 (mmm) REVERT: V 513 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8773 (tm-30) REVERT: V 515 GLU cc_start: 0.8283 (pt0) cc_final: 0.7877 (pp20) REVERT: V 521 PHE cc_start: 0.8186 (t80) cc_final: 0.7971 (t80) REVERT: W 225 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8768 (tttt) REVERT: W 313 GLU cc_start: 0.8689 (tt0) cc_final: 0.8295 (mm-30) REVERT: X 41 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: X 52 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8605 (mm-30) REVERT: X 99 MET cc_start: 0.8985 (tpp) cc_final: 0.8781 (mmm) REVERT: X 161 ASP cc_start: 0.8680 (t70) cc_final: 0.8177 (t70) REVERT: X 212 MET cc_start: 0.8766 (tpt) cc_final: 0.8080 (tpt) REVERT: X 332 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8075 (mm-30) REVERT: X 395 LYS cc_start: 0.8146 (mppt) cc_final: 0.7791 (mmmm) REVERT: Y 39 ASP cc_start: 0.8972 (m-30) cc_final: 0.8648 (m-30) REVERT: Y 173 ASP cc_start: 0.7988 (t0) cc_final: 0.7642 (t0) REVERT: Y 383 LEU cc_start: 0.9273 (tp) cc_final: 0.9037 (tm) REVERT: Z 28 LYS cc_start: 0.8497 (mmtm) cc_final: 0.8212 (mmpt) REVERT: Z 143 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7162 (tm-30) REVERT: Z 165 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: Z 178 ASP cc_start: 0.8875 (OUTLIER) cc_final: 0.8597 (p0) REVERT: Z 251 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8033 (mt) REVERT: Z 283 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7675 (mtm180) REVERT: a 23 HIS cc_start: 0.8027 (m-70) cc_final: 0.7598 (m-70) REVERT: a 43 ASP cc_start: 0.8837 (t0) cc_final: 0.8555 (t70) REVERT: a 81 LEU cc_start: 0.9226 (mt) cc_final: 0.9015 (mt) REVERT: a 127 ASP cc_start: 0.8956 (t0) cc_final: 0.8523 (t0) REVERT: a 178 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8622 (mmm-85) REVERT: a 278 MET cc_start: 0.8729 (mtm) cc_final: 0.8512 (mtp) REVERT: b 29 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: b 31 ASP cc_start: 0.8070 (m-30) cc_final: 0.7368 (p0) REVERT: b 42 ARG cc_start: 0.8950 (mtm180) cc_final: 0.8131 (ptp-110) REVERT: b 46 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8150 (mp0) REVERT: b 184 ILE cc_start: 0.8455 (mp) cc_final: 0.8020 (mm) REVERT: c 106 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8572 (mp0) REVERT: c 168 MET cc_start: 0.6763 (ppp) cc_final: 0.6385 (pmm) REVERT: c 223 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9083 (mtpp) REVERT: c 264 LYS cc_start: 0.8998 (ptpt) cc_final: 0.8282 (ptmm) REVERT: c 289 ASP cc_start: 0.8864 (t70) cc_final: 0.8473 (m-30) REVERT: d 96 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8549 (pm20) REVERT: d 158 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8854 (pmm-80) REVERT: d 236 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8853 (mm) REVERT: d 286 GLU cc_start: 0.8501 (tp30) cc_final: 0.7933 (tt0) REVERT: d 297 LYS cc_start: 0.9367 (tmmt) cc_final: 0.9058 (tppt) REVERT: d 309 VAL cc_start: 0.8985 (t) cc_final: 0.8705 (p) REVERT: d 328 THR cc_start: 0.7643 (OUTLIER) cc_final: 0.7422 (t) REVERT: d 347 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8508 (mm-30) REVERT: f 47 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6717 (tp30) REVERT: f 113 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5607 (ppp) REVERT: f 131 MET cc_start: 0.4129 (tmt) cc_final: 0.3307 (mmt) REVERT: f 162 LEU cc_start: 0.8598 (tp) cc_final: 0.8157 (mm) REVERT: f 195 ASN cc_start: 0.6592 (OUTLIER) cc_final: 0.6144 (t0) REVERT: f 268 LEU cc_start: 0.9405 (mp) cc_final: 0.9027 (tp) REVERT: f 272 LEU cc_start: 0.8336 (tp) cc_final: 0.8013 (mt) REVERT: f 275 MET cc_start: 0.8599 (tpt) cc_final: 0.7724 (tmm) REVERT: f 340 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7435 (mmm) REVERT: f 398 TRP cc_start: 0.8102 (t-100) cc_final: 0.7396 (t-100) REVERT: f 453 SER cc_start: 0.7485 (m) cc_final: 0.7231 (m) REVERT: f 472 HIS cc_start: 0.8170 (OUTLIER) cc_final: 0.7686 (t-90) REVERT: f 502 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7524 (mm) REVERT: f 512 MET cc_start: 0.8450 (tpt) cc_final: 0.8242 (tpt) REVERT: f 592 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8691 (p0) REVERT: f 681 TYR cc_start: 0.8126 (m-80) cc_final: 0.7768 (m-80) REVERT: f 746 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8381 (tpp80) REVERT: f 747 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8623 (mt0) REVERT: f 784 ASP cc_start: 0.7673 (t0) cc_final: 0.7428 (t0) REVERT: f 786 GLN cc_start: 0.8256 (mt0) cc_final: 0.7616 (mt0) REVERT: f 797 LEU cc_start: 0.8774 (mt) cc_final: 0.8452 (mt) REVERT: f 868 HIS cc_start: 0.7275 (OUTLIER) cc_final: 0.7014 (m90) REVERT: g 158 LEU cc_start: 0.4137 (OUTLIER) cc_final: 0.3861 (mt) REVERT: u 164 GLN cc_start: 0.7724 (mm110) cc_final: 0.7254 (mm-40) REVERT: u 173 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8497 (mm-40) REVERT: u 176 LYS cc_start: 0.7908 (mtmm) cc_final: 0.7512 (mtmm) REVERT: u 181 LYS cc_start: 0.7115 (mtpt) cc_final: 0.6534 (mtpm) REVERT: u 228 ASP cc_start: 0.8481 (t70) cc_final: 0.8071 (p0) REVERT: u 268 THR cc_start: 0.8904 (OUTLIER) cc_final: 0.8637 (p) outliers start: 295 outliers final: 128 residues processed: 1136 average time/residue: 1.4435 time to fit residues: 2201.5833 Evaluate side-chains 1053 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 862 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 217 LYS Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 278 GLN Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain E residue 66 GLU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 281 ARG Chi-restraints excluded: chain E residue 360 ASP Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 79 MET Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 209 LYS Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain L residue 27 GLU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 362 ASN Chi-restraints excluded: chain U residue 373 ASN Chi-restraints excluded: chain U residue 530 GLU Chi-restraints excluded: chain U residue 578 LEU Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 698 GLN Chi-restraints excluded: chain U residue 793 LYS Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 134 PHE Chi-restraints excluded: chain V residue 336 GLU Chi-restraints excluded: chain V residue 379 LEU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain V residue 471 GLU Chi-restraints excluded: chain V residue 478 GLN Chi-restraints excluded: chain V residue 507 SER Chi-restraints excluded: chain V residue 517 GLN Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 225 LYS Chi-restraints excluded: chain W residue 252 ASP Chi-restraints excluded: chain W residue 255 CYS Chi-restraints excluded: chain W residue 260 SER Chi-restraints excluded: chain X residue 41 GLU Chi-restraints excluded: chain X residue 103 THR Chi-restraints excluded: chain X residue 120 GLU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 368 MET Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 165 GLU Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 269 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 178 ARG Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 287 ASN Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain b residue 29 GLN Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 132 LYS Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 223 LYS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 96 GLU Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 158 ARG Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 328 THR Chi-restraints excluded: chain d residue 348 MET Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 50 LYS Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 195 ASN Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 255 VAL Chi-restraints excluded: chain f residue 270 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 472 HIS Chi-restraints excluded: chain f residue 502 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 619 HIS Chi-restraints excluded: chain f residue 746 ARG Chi-restraints excluded: chain f residue 747 GLN Chi-restraints excluded: chain f residue 796 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain f residue 868 HIS Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain u residue 171 PHE Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain u residue 231 VAL Chi-restraints excluded: chain u residue 261 SER Chi-restraints excluded: chain u residue 268 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 52 optimal weight: 10.0000 chunk 628 optimal weight: 0.0670 chunk 467 optimal weight: 2.9990 chunk 819 optimal weight: 0.2980 chunk 319 optimal weight: 9.9990 chunk 731 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 chunk 471 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 436 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN B 425 ASN C 64 GLN C 288 ASN D 65 GLN D 127 ASN D 390 ASN E 39 GLN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 ASN I 198 ASN I 230 GLN J 205 ASN K 13 ASN L 8 ASN M 101 ASN U 340 GLN ** U 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 430 GLN ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 27 GLN b 105 HIS ** c 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 592 ASN f 619 HIS f 747 GLN g 135 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.102686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.071461 restraints weight = 146246.275| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.74 r_work: 0.2888 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 72504 Z= 0.177 Angle : 0.605 15.683 97953 Z= 0.301 Chirality : 0.041 0.284 11156 Planarity : 0.004 0.088 12612 Dihedral : 6.092 87.692 9955 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.76 % Favored : 97.22 % Rotamer: Outliers : 3.07 % Allowed : 30.60 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.31 (0.09), residues: 8915 helix: 1.54 (0.07), residues: 5017 sheet: -0.54 (0.16), residues: 1006 loop : 0.41 (0.12), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 139 HIS 0.019 0.001 HIS f 619 PHE 0.029 0.001 PHE B 78 TYR 0.021 0.001 TYR a 60 ARG 0.010 0.000 ARG b 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 941 time to evaluate : 6.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: A 128 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7647 (tp40) REVERT: A 133 ASP cc_start: 0.8684 (t0) cc_final: 0.8224 (t0) REVERT: A 168 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8332 (mm-30) REVERT: A 191 VAL cc_start: 0.9481 (OUTLIER) cc_final: 0.9243 (p) REVERT: A 213 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9044 (tt) REVERT: A 256 MET cc_start: 0.9099 (mtp) cc_final: 0.8774 (ttm) REVERT: A 356 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8402 (mtmp) REVERT: B 85 MET cc_start: 0.8096 (mtt) cc_final: 0.7577 (tpt) REVERT: B 95 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8692 (mm-30) REVERT: B 140 ASP cc_start: 0.8586 (m-30) cc_final: 0.8118 (m-30) REVERT: B 164 MET cc_start: 0.8280 (tmm) cc_final: 0.7241 (tmm) REVERT: B 213 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: B 260 LEU cc_start: 0.9130 (mp) cc_final: 0.8880 (mm) REVERT: B 269 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: B 304 GLU cc_start: 0.8735 (tp30) cc_final: 0.8518 (mm-30) REVERT: C 40 GLN cc_start: 0.9286 (tt0) cc_final: 0.9049 (pp30) REVERT: C 89 VAL cc_start: 0.9078 (t) cc_final: 0.8786 (m) REVERT: C 297 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.8179 (ttp-110) REVERT: C 336 MET cc_start: 0.9072 (mtm) cc_final: 0.8542 (mtm) REVERT: C 382 ASP cc_start: 0.8866 (m-30) cc_final: 0.8631 (m-30) REVERT: D 52 GLU cc_start: 0.8908 (tt0) cc_final: 0.8445 (tp30) REVERT: D 60 TYR cc_start: 0.9130 (OUTLIER) cc_final: 0.8576 (t80) REVERT: D 71 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8240 (mm-30) REVERT: D 94 GLU cc_start: 0.8836 (tt0) cc_final: 0.8545 (tt0) REVERT: D 413 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: E 100 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8432 (mt) REVERT: E 122 MET cc_start: 0.8895 (mtt) cc_final: 0.8644 (mtt) REVERT: E 195 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8075 (t80) REVERT: E 352 MET cc_start: 0.9307 (mmm) cc_final: 0.9044 (mmm) REVERT: E 387 LYS cc_start: 0.8959 (mtmm) cc_final: 0.8577 (mttt) REVERT: F 81 LYS cc_start: 0.8494 (tppt) cc_final: 0.8040 (tmmt) REVERT: F 146 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8623 (mtmm) REVERT: F 180 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8293 (tpp-160) REVERT: F 318 ASP cc_start: 0.8698 (t0) cc_final: 0.8332 (t0) REVERT: F 390 ASP cc_start: 0.8841 (t0) cc_final: 0.8472 (t0) REVERT: F 421 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.8906 (mmm) REVERT: G 187 PHE cc_start: 0.7468 (m-80) cc_final: 0.6739 (t80) REVERT: G 232 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8461 (mm-30) REVERT: H 44 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8949 (m) REVERT: H 95 GLN cc_start: 0.8241 (mm-40) cc_final: 0.7730 (tp-100) REVERT: H 159 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8156 (ttmm) REVERT: H 166 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8393 (t0) REVERT: H 219 ARG cc_start: 0.8733 (ptm-80) cc_final: 0.8516 (ptm-80) REVERT: I 54 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8958 (pttm) REVERT: I 148 TYR cc_start: 0.8685 (m-80) cc_final: 0.8480 (m-80) REVERT: I 177 GLN cc_start: 0.8632 (tm-30) cc_final: 0.7921 (pp30) REVERT: I 178 ASP cc_start: 0.9080 (t0) cc_final: 0.8691 (m-30) REVERT: I 201 MET cc_start: 0.8193 (mmm) cc_final: 0.7901 (mmm) REVERT: I 205 LYS cc_start: 0.8535 (pmtt) cc_final: 0.7890 (mmtp) REVERT: I 234 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8220 (tp30) REVERT: I 242 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8443 (mm-30) REVERT: J 59 VAL cc_start: 0.8776 (t) cc_final: 0.8517 (m) REVERT: J 159 ASN cc_start: 0.9121 (t0) cc_final: 0.8793 (t160) REVERT: K 18 GLU cc_start: 0.8676 (mp0) cc_final: 0.8390 (mp0) REVERT: K 71 ASP cc_start: 0.8726 (t0) cc_final: 0.8449 (t0) REVERT: L 140 MET cc_start: 0.9433 (mmm) cc_final: 0.9152 (mmm) REVERT: L 148 CYS cc_start: 0.9070 (t) cc_final: 0.8827 (t) REVERT: L 189 LYS cc_start: 0.9051 (tppp) cc_final: 0.8807 (mmtp) REVERT: L 218 ASP cc_start: 0.7950 (p0) cc_final: 0.7709 (m-30) REVERT: L 220 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8245 (tp30) REVERT: L 224 TYR cc_start: 0.8797 (m-80) cc_final: 0.8569 (m-80) REVERT: M 34 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8505 (p) REVERT: M 97 ASN cc_start: 0.9077 (m-40) cc_final: 0.8575 (m110) REVERT: M 109 LYS cc_start: 0.7184 (tttt) cc_final: 0.6592 (tttm) REVERT: M 113 ASP cc_start: 0.8730 (m-30) cc_final: 0.8358 (m-30) REVERT: M 184 MET cc_start: 0.9225 (ptp) cc_final: 0.8796 (ptp) REVERT: M 192 GLU cc_start: 0.9169 (OUTLIER) cc_final: 0.8932 (mp0) REVERT: U 239 GLU cc_start: 0.8892 (tt0) cc_final: 0.8104 (tm-30) REVERT: U 530 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7869 (mp0) REVERT: U 714 SER cc_start: 0.9211 (t) cc_final: 0.9000 (p) REVERT: V 96 ARG cc_start: 0.8488 (ptp-170) cc_final: 0.8086 (ptp-110) REVERT: V 100 MET cc_start: 0.8653 (mpt) cc_final: 0.8298 (mpt) REVERT: V 304 GLU cc_start: 0.8515 (mp0) cc_final: 0.8223 (mp0) REVERT: V 443 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8829 (tmm-80) REVERT: V 471 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8386 (tm-30) REVERT: V 485 ASP cc_start: 0.9054 (m-30) cc_final: 0.8650 (m-30) REVERT: V 494 MET cc_start: 0.9060 (mtm) cc_final: 0.8702 (mmm) REVERT: V 513 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8848 (tm-30) REVERT: V 515 GLU cc_start: 0.8361 (pt0) cc_final: 0.7990 (pp20) REVERT: V 521 PHE cc_start: 0.8239 (t80) cc_final: 0.8027 (t80) REVERT: W 91 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8302 (p) REVERT: W 225 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8728 (tttt) REVERT: W 259 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: W 313 GLU cc_start: 0.8666 (tt0) cc_final: 0.8291 (mm-30) REVERT: X 41 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: X 52 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8573 (mm-30) REVERT: X 161 ASP cc_start: 0.8743 (t70) cc_final: 0.8278 (t0) REVERT: X 212 MET cc_start: 0.8755 (tpt) cc_final: 0.8386 (tpt) REVERT: X 332 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8045 (mm-30) REVERT: Y 39 ASP cc_start: 0.8966 (m-30) cc_final: 0.8649 (m-30) REVERT: Y 173 ASP cc_start: 0.7785 (t0) cc_final: 0.7502 (t0) REVERT: Z 28 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8239 (mmpt) REVERT: Z 78 MET cc_start: 0.9151 (tpt) cc_final: 0.8614 (tpt) REVERT: Z 143 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7298 (tm-30) REVERT: Z 165 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: Z 178 ASP cc_start: 0.8880 (OUTLIER) cc_final: 0.8597 (p0) REVERT: Z 251 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7971 (mt) REVERT: a 23 HIS cc_start: 0.8064 (m-70) cc_final: 0.7491 (m-70) REVERT: a 43 ASP cc_start: 0.8776 (t0) cc_final: 0.8505 (t70) REVERT: a 127 ASP cc_start: 0.8945 (t0) cc_final: 0.8498 (t0) REVERT: a 178 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8380 (mmm-85) REVERT: b 11 ASP cc_start: 0.8814 (t0) cc_final: 0.8290 (t0) REVERT: b 29 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: b 31 ASP cc_start: 0.8070 (m-30) cc_final: 0.7321 (p0) REVERT: b 42 ARG cc_start: 0.8929 (mtm180) cc_final: 0.8212 (mpp80) REVERT: b 46 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8212 (mp0) REVERT: b 184 ILE cc_start: 0.8396 (mp) cc_final: 0.7933 (mm) REVERT: c 106 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8433 (mp0) REVERT: c 223 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9108 (mtpp) REVERT: c 264 LYS cc_start: 0.8957 (ptpt) cc_final: 0.8250 (ptmm) REVERT: c 289 ASP cc_start: 0.8800 (t70) cc_final: 0.8390 (m-30) REVERT: d 96 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8553 (pm20) REVERT: d 158 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.8818 (pmm-80) REVERT: d 236 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8858 (mm) REVERT: d 286 GLU cc_start: 0.8338 (tp30) cc_final: 0.7845 (tt0) REVERT: d 297 LYS cc_start: 0.9352 (tmmt) cc_final: 0.8923 (tptp) REVERT: d 328 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7359 (t) REVERT: d 347 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8509 (mm-30) REVERT: e 44 ASP cc_start: 0.9007 (m-30) cc_final: 0.8325 (t0) REVERT: f 47 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6850 (tp30) REVERT: f 113 MET cc_start: 0.6145 (OUTLIER) cc_final: 0.5692 (ppp) REVERT: f 131 MET cc_start: 0.3957 (tmt) cc_final: 0.3246 (mmt) REVERT: f 162 LEU cc_start: 0.8624 (tp) cc_final: 0.8180 (mm) REVERT: f 170 TRP cc_start: 0.5934 (t-100) cc_final: 0.5698 (t60) REVERT: f 195 ASN cc_start: 0.6627 (OUTLIER) cc_final: 0.6348 (t0) REVERT: f 268 LEU cc_start: 0.9344 (mp) cc_final: 0.8982 (tp) REVERT: f 272 LEU cc_start: 0.8344 (tp) cc_final: 0.8043 (mt) REVERT: f 275 MET cc_start: 0.8620 (tpt) cc_final: 0.7733 (tmm) REVERT: f 340 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7439 (mmm) REVERT: f 398 TRP cc_start: 0.8130 (t-100) cc_final: 0.7374 (t-100) REVERT: f 453 SER cc_start: 0.7422 (m) cc_final: 0.7173 (m) REVERT: f 472 HIS cc_start: 0.8163 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: f 502 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7448 (mm) REVERT: f 512 MET cc_start: 0.8436 (tpt) cc_final: 0.8235 (tpt) REVERT: f 592 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8793 (p0) REVERT: f 600 TYR cc_start: 0.7724 (m-80) cc_final: 0.7487 (m-80) REVERT: f 655 LEU cc_start: 0.8235 (tp) cc_final: 0.7965 (mt) REVERT: f 681 TYR cc_start: 0.8109 (m-80) cc_final: 0.7703 (m-80) REVERT: f 747 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8682 (mt0) REVERT: f 784 ASP cc_start: 0.7628 (t0) cc_final: 0.7388 (t0) REVERT: f 786 GLN cc_start: 0.8285 (mt0) cc_final: 0.7671 (mt0) REVERT: f 797 LEU cc_start: 0.8769 (mt) cc_final: 0.8445 (mt) REVERT: f 868 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6968 (m90) REVERT: g 134 LYS cc_start: 0.7064 (tppt) cc_final: 0.6225 (mppt) REVERT: g 158 LEU cc_start: 0.4188 (OUTLIER) cc_final: 0.3924 (mt) REVERT: u 139 ASN cc_start: 0.6026 (t0) cc_final: 0.5322 (t0) REVERT: u 157 LEU cc_start: 0.9227 (tp) cc_final: 0.8959 (mt) REVERT: u 164 GLN cc_start: 0.7743 (mm110) cc_final: 0.7207 (mm-40) REVERT: u 173 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8615 (mm-40) REVERT: u 176 LYS cc_start: 0.7915 (mtmm) cc_final: 0.7603 (mtmm) REVERT: u 181 LYS cc_start: 0.7073 (mtpt) cc_final: 0.6543 (mtpm) REVERT: u 211 ARG cc_start: 0.8500 (ttm110) cc_final: 0.7864 (mtp-110) REVERT: u 220 LEU cc_start: 0.7403 (mt) cc_final: 0.7101 (mp) REVERT: u 223 ASP cc_start: 0.8601 (t0) cc_final: 0.8345 (m-30) REVERT: u 228 ASP cc_start: 0.8457 (t70) cc_final: 0.8072 (p0) REVERT: u 259 ARG cc_start: 0.8275 (ttm110) cc_final: 0.7818 (mtp-110) outliers start: 239 outliers final: 107 residues processed: 1136 average time/residue: 1.4136 time to fit residues: 2144.2133 Evaluate side-chains 1036 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 879 time to evaluate : 6.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 242 GLU Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 362 ASN Chi-restraints excluded: chain U residue 530 GLU Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 793 LYS Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 131 LEU Chi-restraints excluded: chain V residue 379 LEU Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain V residue 471 GLU Chi-restraints excluded: chain V residue 478 GLN Chi-restraints excluded: chain V residue 507 SER Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 225 LYS Chi-restraints excluded: chain W residue 259 GLU Chi-restraints excluded: chain W residue 260 SER Chi-restraints excluded: chain X residue 41 GLU Chi-restraints excluded: chain X residue 103 THR Chi-restraints excluded: chain X residue 120 GLU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 165 GLU Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 269 VAL Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 158 LEU Chi-restraints excluded: chain a residue 178 ARG Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain b residue 29 GLN Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 223 LYS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 96 GLU Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 158 ARG Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 328 THR Chi-restraints excluded: chain d residue 348 MET Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 50 LYS Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 195 ASN Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 255 VAL Chi-restraints excluded: chain f residue 270 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 472 HIS Chi-restraints excluded: chain f residue 502 LEU Chi-restraints excluded: chain f residue 539 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 619 HIS Chi-restraints excluded: chain f residue 796 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 868 HIS Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain u residue 171 PHE Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain u residue 231 VAL Chi-restraints excluded: chain u residue 261 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 110 optimal weight: 1.9990 chunk 861 optimal weight: 20.0000 chunk 597 optimal weight: 2.9990 chunk 860 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 675 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 539 optimal weight: 1.9990 chunk 332 optimal weight: 9.9990 chunk 284 optimal weight: 0.0170 chunk 516 optimal weight: 9.9990 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 64 GLN C 90 HIS D 65 GLN D 127 ASN D 278 GLN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 ASN I 155 ASN I 198 ASN J 205 ASN K 13 ASN L 8 ASN M 101 ASN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 340 GLN ** U 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 677 ASN ** U 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 246 HIS ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 592 ASN f 610 GLN f 619 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.102488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.071130 restraints weight = 146683.268| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.74 r_work: 0.2882 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 72504 Z= 0.202 Angle : 0.624 15.801 97953 Z= 0.308 Chirality : 0.042 0.405 11156 Planarity : 0.004 0.075 12612 Dihedral : 6.042 89.952 9954 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.71 % Favored : 97.26 % Rotamer: Outliers : 2.89 % Allowed : 31.04 % Favored : 66.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.32 (0.09), residues: 8915 helix: 1.56 (0.07), residues: 5022 sheet: -0.51 (0.16), residues: 1012 loop : 0.36 (0.12), residues: 2881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 364 HIS 0.012 0.001 HIS f 619 PHE 0.029 0.001 PHE a 50 TYR 0.022 0.001 TYR f 194 ARG 0.013 0.000 ARG b 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 919 time to evaluate : 6.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: A 133 ASP cc_start: 0.8691 (t0) cc_final: 0.8245 (t0) REVERT: A 168 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8330 (mm-30) REVERT: A 256 MET cc_start: 0.9118 (mtp) cc_final: 0.8880 (ttm) REVERT: A 356 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8397 (mtmp) REVERT: B 85 MET cc_start: 0.8072 (mtt) cc_final: 0.7558 (tpt) REVERT: B 95 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8687 (mm-30) REVERT: B 140 ASP cc_start: 0.8573 (m-30) cc_final: 0.8100 (m-30) REVERT: B 210 TYR cc_start: 0.8636 (m-80) cc_final: 0.8031 (m-80) REVERT: B 213 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8321 (mp0) REVERT: B 260 LEU cc_start: 0.9152 (mp) cc_final: 0.8902 (mm) REVERT: B 269 GLU cc_start: 0.8722 (tp30) cc_final: 0.8392 (tp30) REVERT: B 304 GLU cc_start: 0.8769 (tp30) cc_final: 0.8477 (mm-30) REVERT: B 332 ASN cc_start: 0.9151 (p0) cc_final: 0.8706 (p0) REVERT: C 40 GLN cc_start: 0.9294 (tt0) cc_final: 0.9034 (pp30) REVERT: C 89 VAL cc_start: 0.9066 (t) cc_final: 0.8813 (m) REVERT: C 297 ARG cc_start: 0.8572 (ttp-110) cc_final: 0.8156 (ttp-110) REVERT: C 336 MET cc_start: 0.9109 (mtm) cc_final: 0.8591 (mtm) REVERT: C 382 ASP cc_start: 0.8868 (m-30) cc_final: 0.8658 (m-30) REVERT: D 52 GLU cc_start: 0.8894 (tt0) cc_final: 0.8433 (tp30) REVERT: D 60 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8571 (t80) REVERT: D 71 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8270 (mm-30) REVERT: D 94 GLU cc_start: 0.8845 (tt0) cc_final: 0.8552 (tt0) REVERT: D 413 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: E 100 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8475 (mt) REVERT: E 122 MET cc_start: 0.8921 (mtt) cc_final: 0.8654 (mtt) REVERT: E 387 LYS cc_start: 0.8950 (mtmm) cc_final: 0.8573 (mttt) REVERT: F 81 LYS cc_start: 0.8475 (tppt) cc_final: 0.8006 (tmmt) REVERT: F 146 LYS cc_start: 0.8910 (mtmm) cc_final: 0.8692 (mtmm) REVERT: F 180 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8293 (tpp-160) REVERT: F 318 ASP cc_start: 0.8688 (t0) cc_final: 0.8342 (t0) REVERT: F 390 ASP cc_start: 0.8851 (t0) cc_final: 0.8486 (t0) REVERT: F 421 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.8838 (mmm) REVERT: G 120 ASP cc_start: 0.8807 (m-30) cc_final: 0.8388 (m-30) REVERT: G 144 ASP cc_start: 0.8230 (t0) cc_final: 0.7533 (t70) REVERT: G 187 PHE cc_start: 0.7615 (m-80) cc_final: 0.6903 (t80) REVERT: G 232 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8506 (mm-30) REVERT: H 44 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8942 (m) REVERT: H 95 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7712 (tp-100) REVERT: H 159 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8197 (ttmm) REVERT: H 166 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8372 (t0) REVERT: H 219 ARG cc_start: 0.8740 (ptm-80) cc_final: 0.8523 (ptm-80) REVERT: I 54 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8970 (pttm) REVERT: I 148 TYR cc_start: 0.8699 (m-80) cc_final: 0.8495 (m-80) REVERT: I 151 ASP cc_start: 0.8611 (p0) cc_final: 0.7605 (p0) REVERT: I 155 ASN cc_start: 0.7977 (t0) cc_final: 0.7676 (p0) REVERT: I 177 GLN cc_start: 0.8652 (tm-30) cc_final: 0.7934 (pp30) REVERT: I 178 ASP cc_start: 0.9085 (t0) cc_final: 0.8694 (m-30) REVERT: I 205 LYS cc_start: 0.8592 (pmtt) cc_final: 0.7953 (mmtp) REVERT: I 209 GLU cc_start: 0.8549 (mp0) cc_final: 0.8077 (pm20) REVERT: I 234 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8123 (tp30) REVERT: J 59 VAL cc_start: 0.8772 (t) cc_final: 0.8506 (m) REVERT: J 159 ASN cc_start: 0.9101 (t0) cc_final: 0.8776 (t160) REVERT: K 18 GLU cc_start: 0.8676 (mp0) cc_final: 0.8385 (mp0) REVERT: K 71 ASP cc_start: 0.8731 (t0) cc_final: 0.8448 (t0) REVERT: L 140 MET cc_start: 0.9441 (mmm) cc_final: 0.9158 (mmm) REVERT: L 148 CYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8836 (t) REVERT: L 189 LYS cc_start: 0.9056 (tppp) cc_final: 0.8815 (mmtp) REVERT: L 220 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8253 (tp30) REVERT: L 224 TYR cc_start: 0.8857 (m-80) cc_final: 0.8634 (m-80) REVERT: M 34 SER cc_start: 0.8889 (OUTLIER) cc_final: 0.8467 (p) REVERT: M 97 ASN cc_start: 0.9094 (m-40) cc_final: 0.8575 (m110) REVERT: M 184 MET cc_start: 0.9213 (ptp) cc_final: 0.8780 (ptp) REVERT: M 192 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8918 (mp0) REVERT: U 239 GLU cc_start: 0.8885 (tt0) cc_final: 0.8109 (tm-30) REVERT: U 520 MET cc_start: 0.8939 (mmm) cc_final: 0.8706 (mtp) REVERT: U 530 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: U 542 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7951 (mt-10) REVERT: U 714 SER cc_start: 0.9206 (t) cc_final: 0.8990 (p) REVERT: V 96 ARG cc_start: 0.8504 (ptp-170) cc_final: 0.8147 (ptp-110) REVERT: V 100 MET cc_start: 0.8662 (mpt) cc_final: 0.8299 (mpt) REVERT: V 304 GLU cc_start: 0.8533 (mp0) cc_final: 0.8242 (mp0) REVERT: V 443 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8817 (tmm-80) REVERT: V 463 MET cc_start: 0.8004 (tpp) cc_final: 0.7586 (tmm) REVERT: V 471 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: V 485 ASP cc_start: 0.9053 (m-30) cc_final: 0.8628 (m-30) REVERT: V 494 MET cc_start: 0.9054 (mtm) cc_final: 0.8702 (mmm) REVERT: V 515 GLU cc_start: 0.8282 (pt0) cc_final: 0.7919 (pp20) REVERT: W 225 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8724 (tttt) REVERT: W 259 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7577 (tm-30) REVERT: W 313 GLU cc_start: 0.8619 (tt0) cc_final: 0.8291 (mm-30) REVERT: X 41 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: X 52 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8574 (mm-30) REVERT: X 87 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.8714 (ttt-90) REVERT: X 161 ASP cc_start: 0.8783 (t70) cc_final: 0.8259 (t0) REVERT: X 212 MET cc_start: 0.8759 (tpt) cc_final: 0.8061 (tpt) REVERT: X 332 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8016 (mm-30) REVERT: X 395 LYS cc_start: 0.8056 (mppt) cc_final: 0.7668 (mmmm) REVERT: X 415 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: X 416 ASN cc_start: 0.8595 (m-40) cc_final: 0.8287 (t0) REVERT: Y 39 ASP cc_start: 0.8966 (m-30) cc_final: 0.8653 (m-30) REVERT: Y 173 ASP cc_start: 0.7739 (t0) cc_final: 0.7460 (t0) REVERT: Z 28 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8251 (mmpt) REVERT: Z 78 MET cc_start: 0.9167 (tpt) cc_final: 0.8615 (tpt) REVERT: Z 143 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7314 (tm-30) REVERT: Z 165 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: Z 178 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8589 (p0) REVERT: Z 251 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7975 (mt) REVERT: a 23 HIS cc_start: 0.8119 (m-70) cc_final: 0.7780 (m-70) REVERT: a 43 ASP cc_start: 0.8780 (t0) cc_final: 0.8500 (t70) REVERT: a 127 ASP cc_start: 0.8939 (t0) cc_final: 0.8490 (t0) REVERT: a 178 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8148 (mmm-85) REVERT: b 11 ASP cc_start: 0.8832 (t0) cc_final: 0.8317 (t0) REVERT: b 29 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: b 31 ASP cc_start: 0.8034 (m-30) cc_final: 0.7324 (p0) REVERT: b 42 ARG cc_start: 0.8939 (mtm180) cc_final: 0.8438 (mpp80) REVERT: b 46 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8212 (mp0) REVERT: b 112 PHE cc_start: 0.7966 (m-10) cc_final: 0.7722 (m-10) REVERT: b 147 GLU cc_start: 0.8852 (pm20) cc_final: 0.8623 (pm20) REVERT: b 184 ILE cc_start: 0.8542 (mp) cc_final: 0.8089 (mm) REVERT: c 106 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8403 (mp0) REVERT: c 168 MET cc_start: 0.6707 (ppp) cc_final: 0.6308 (pmm) REVERT: c 223 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9111 (mtpp) REVERT: c 264 LYS cc_start: 0.8966 (ptpt) cc_final: 0.8274 (ptmm) REVERT: c 289 ASP cc_start: 0.8826 (t70) cc_final: 0.8534 (t0) REVERT: d 96 GLU cc_start: 0.9006 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: d 158 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8956 (pmm-80) REVERT: d 165 GLU cc_start: 0.9381 (mm-30) cc_final: 0.8813 (mp0) REVERT: d 236 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8831 (mm) REVERT: d 286 GLU cc_start: 0.8276 (tp30) cc_final: 0.7829 (tt0) REVERT: d 297 LYS cc_start: 0.9375 (tmmt) cc_final: 0.8940 (tptp) REVERT: d 328 THR cc_start: 0.7573 (OUTLIER) cc_final: 0.7362 (t) REVERT: d 347 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8493 (mm-30) REVERT: e 44 ASP cc_start: 0.8888 (m-30) cc_final: 0.8325 (t0) REVERT: e 59 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: f 47 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7029 (tp30) REVERT: f 113 MET cc_start: 0.6069 (OUTLIER) cc_final: 0.5473 (pp-130) REVERT: f 131 MET cc_start: 0.3854 (tmt) cc_final: 0.3298 (mmt) REVERT: f 162 LEU cc_start: 0.8631 (tp) cc_final: 0.8183 (mm) REVERT: f 170 TRP cc_start: 0.5960 (t-100) cc_final: 0.5593 (t60) REVERT: f 195 ASN cc_start: 0.6465 (OUTLIER) cc_final: 0.6144 (t0) REVERT: f 268 LEU cc_start: 0.9335 (mp) cc_final: 0.8984 (tp) REVERT: f 272 LEU cc_start: 0.8331 (tp) cc_final: 0.8037 (mt) REVERT: f 275 MET cc_start: 0.8657 (tpt) cc_final: 0.7747 (tmm) REVERT: f 340 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7444 (mmm) REVERT: f 407 MET cc_start: 0.6568 (mpt) cc_final: 0.6285 (mmt) REVERT: f 453 SER cc_start: 0.7412 (m) cc_final: 0.7181 (m) REVERT: f 472 HIS cc_start: 0.8164 (OUTLIER) cc_final: 0.7657 (t-90) REVERT: f 502 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7517 (mm) REVERT: f 592 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8747 (p0) REVERT: f 600 TYR cc_start: 0.7819 (m-80) cc_final: 0.7593 (m-80) REVERT: f 655 LEU cc_start: 0.8223 (tp) cc_final: 0.7953 (mt) REVERT: f 681 TYR cc_start: 0.8124 (m-80) cc_final: 0.7707 (m-80) REVERT: f 747 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8590 (mt0) REVERT: f 788 MET cc_start: 0.8484 (tmm) cc_final: 0.7927 (tmm) REVERT: f 797 LEU cc_start: 0.8780 (mt) cc_final: 0.8452 (mt) REVERT: f 868 HIS cc_start: 0.7228 (OUTLIER) cc_final: 0.6995 (m90) REVERT: g 134 LYS cc_start: 0.7187 (tppt) cc_final: 0.6322 (mppt) REVERT: g 158 LEU cc_start: 0.4020 (OUTLIER) cc_final: 0.3790 (mt) REVERT: u 157 LEU cc_start: 0.9147 (tp) cc_final: 0.8875 (mt) REVERT: u 164 GLN cc_start: 0.7726 (mm110) cc_final: 0.7252 (mm-40) REVERT: u 173 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8657 (mm-40) REVERT: u 176 LYS cc_start: 0.7946 (mtmm) cc_final: 0.7415 (ptpp) REVERT: u 178 TYR cc_start: 0.7371 (m-10) cc_final: 0.7075 (m-10) REVERT: u 181 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6617 (mtpm) REVERT: u 211 ARG cc_start: 0.8495 (ttm110) cc_final: 0.7867 (mtp-110) REVERT: u 223 ASP cc_start: 0.8673 (t0) cc_final: 0.8247 (m-30) REVERT: u 226 LYS cc_start: 0.7952 (mmtm) cc_final: 0.7686 (mmtm) REVERT: u 228 ASP cc_start: 0.8456 (t70) cc_final: 0.8076 (p0) REVERT: u 259 ARG cc_start: 0.8172 (ttm110) cc_final: 0.7695 (mtp-110) REVERT: u 268 THR cc_start: 0.9129 (p) cc_final: 0.8384 (t) outliers start: 225 outliers final: 111 residues processed: 1097 average time/residue: 1.4218 time to fit residues: 2086.8469 Evaluate side-chains 1032 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 872 time to evaluate : 6.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 362 ASN Chi-restraints excluded: chain U residue 530 GLU Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 699 THR Chi-restraints excluded: chain U residue 793 LYS Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 379 LEU Chi-restraints excluded: chain V residue 395 ILE Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain V residue 471 GLU Chi-restraints excluded: chain V residue 478 GLN Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 225 LYS Chi-restraints excluded: chain W residue 259 GLU Chi-restraints excluded: chain W residue 260 SER Chi-restraints excluded: chain X residue 41 GLU Chi-restraints excluded: chain X residue 87 ARG Chi-restraints excluded: chain X residue 103 THR Chi-restraints excluded: chain X residue 120 GLU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 159 THR Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 165 GLU Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 269 VAL Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 158 LEU Chi-restraints excluded: chain a residue 178 ARG Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain b residue 29 GLN Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 132 LYS Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 223 LYS Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain d residue 96 GLU Chi-restraints excluded: chain d residue 106 SER Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 158 ARG Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 236 LEU Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 328 THR Chi-restraints excluded: chain d residue 348 MET Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 195 ASN Chi-restraints excluded: chain f residue 270 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 472 HIS Chi-restraints excluded: chain f residue 502 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 619 HIS Chi-restraints excluded: chain f residue 796 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain f residue 868 HIS Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 882 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain u residue 171 PHE Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain u residue 181 LYS Chi-restraints excluded: chain u residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 868 optimal weight: 30.0000 chunk 220 optimal weight: 8.9990 chunk 682 optimal weight: 8.9990 chunk 884 optimal weight: 0.0070 chunk 478 optimal weight: 0.0970 chunk 772 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 586 optimal weight: 20.0000 chunk 553 optimal weight: 2.9990 chunk 749 optimal weight: 0.7980 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 ASN D 65 GLN D 127 ASN E 305 ASN F 307 GLN G 100 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 ASN J 205 ASN K 13 ASN L 8 ASN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 340 GLN ** U 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 677 ASN ** U 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 299 GLN W 430 GLN ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 GLN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 224 HIS ** a 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 592 ASN f 619 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.102849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.071789 restraints weight = 145747.977| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.72 r_work: 0.2894 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 72504 Z= 0.193 Angle : 0.631 14.779 97953 Z= 0.311 Chirality : 0.041 0.311 11156 Planarity : 0.004 0.069 12612 Dihedral : 5.975 86.870 9951 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.71 % Favored : 97.24 % Rotamer: Outliers : 2.31 % Allowed : 31.58 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.33 (0.09), residues: 8915 helix: 1.57 (0.07), residues: 5026 sheet: -0.50 (0.16), residues: 1013 loop : 0.37 (0.12), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 364 HIS 0.007 0.001 HIS b 169 PHE 0.032 0.001 PHE B 78 TYR 0.026 0.001 TYR a 60 ARG 0.013 0.000 ARG b 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17830 Ramachandran restraints generated. 8915 Oldfield, 0 Emsley, 8915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 918 time to evaluate : 6.362 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: A 49 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: A 133 ASP cc_start: 0.8668 (t0) cc_final: 0.8225 (t0) REVERT: A 168 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8344 (mm-30) REVERT: A 256 MET cc_start: 0.9103 (mtp) cc_final: 0.8903 (ttm) REVERT: A 356 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8368 (mtmp) REVERT: B 85 MET cc_start: 0.8171 (mtt) cc_final: 0.7592 (tmm) REVERT: B 140 ASP cc_start: 0.8570 (m-30) cc_final: 0.8089 (m-30) REVERT: B 210 TYR cc_start: 0.8632 (m-80) cc_final: 0.8087 (m-80) REVERT: B 213 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8405 (mp0) REVERT: B 260 LEU cc_start: 0.9135 (mp) cc_final: 0.8866 (mm) REVERT: B 332 ASN cc_start: 0.9116 (p0) cc_final: 0.8680 (p0) REVERT: C 40 GLN cc_start: 0.9281 (tt0) cc_final: 0.9023 (pp30) REVERT: C 75 GLU cc_start: 0.8972 (tt0) cc_final: 0.8580 (tt0) REVERT: C 297 ARG cc_start: 0.8540 (ttp-110) cc_final: 0.8117 (ttp-110) REVERT: C 382 ASP cc_start: 0.8874 (m-30) cc_final: 0.8651 (m-30) REVERT: D 52 GLU cc_start: 0.8875 (tt0) cc_final: 0.8389 (tp30) REVERT: D 60 TYR cc_start: 0.9097 (OUTLIER) cc_final: 0.8525 (t80) REVERT: D 71 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8224 (mm-30) REVERT: D 77 GLU cc_start: 0.8769 (tp30) cc_final: 0.7901 (mt-10) REVERT: D 94 GLU cc_start: 0.8827 (tt0) cc_final: 0.8530 (tt0) REVERT: D 413 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: E 100 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8423 (mt) REVERT: E 122 MET cc_start: 0.8863 (mtt) cc_final: 0.8612 (mtt) REVERT: E 379 LYS cc_start: 0.9461 (mtpt) cc_final: 0.9030 (pttt) REVERT: E 387 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8549 (mttt) REVERT: F 81 LYS cc_start: 0.8408 (tppt) cc_final: 0.7937 (tmmt) REVERT: F 146 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8684 (mtmm) REVERT: F 180 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8249 (tpp-160) REVERT: F 318 ASP cc_start: 0.8649 (t0) cc_final: 0.8306 (t0) REVERT: F 390 ASP cc_start: 0.8856 (t0) cc_final: 0.8504 (t0) REVERT: F 421 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.8919 (mmm) REVERT: G 39 SER cc_start: 0.9354 (OUTLIER) cc_final: 0.9145 (p) REVERT: G 187 PHE cc_start: 0.7624 (m-80) cc_final: 0.6919 (t80) REVERT: H 95 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7572 (tp-100) REVERT: H 159 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8104 (ttmm) REVERT: H 166 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8332 (t0) REVERT: H 219 ARG cc_start: 0.8708 (ptm-80) cc_final: 0.8491 (ptm-80) REVERT: I 148 TYR cc_start: 0.8691 (m-80) cc_final: 0.8393 (m-80) REVERT: I 151 ASP cc_start: 0.8612 (p0) cc_final: 0.7677 (p0) REVERT: I 155 ASN cc_start: 0.7962 (t0) cc_final: 0.7603 (p0) REVERT: I 177 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8330 (tm-30) REVERT: I 178 ASP cc_start: 0.9073 (t0) cc_final: 0.8849 (m-30) REVERT: I 205 LYS cc_start: 0.8591 (pmtt) cc_final: 0.7980 (mmtp) REVERT: I 209 GLU cc_start: 0.8533 (mp0) cc_final: 0.8061 (pm20) REVERT: I 234 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8193 (tp30) REVERT: J 59 VAL cc_start: 0.8763 (t) cc_final: 0.8515 (m) REVERT: J 159 ASN cc_start: 0.9164 (t0) cc_final: 0.8842 (t160) REVERT: K 18 GLU cc_start: 0.8667 (mp0) cc_final: 0.8370 (mp0) REVERT: K 71 ASP cc_start: 0.8683 (t0) cc_final: 0.8392 (t0) REVERT: L 140 MET cc_start: 0.9423 (mmm) cc_final: 0.9145 (mmm) REVERT: L 148 CYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8809 (t) REVERT: L 189 LYS cc_start: 0.9039 (tppp) cc_final: 0.8799 (mmtp) REVERT: L 220 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: L 224 TYR cc_start: 0.8821 (m-80) cc_final: 0.8614 (m-80) REVERT: M 34 SER cc_start: 0.8872 (OUTLIER) cc_final: 0.8443 (p) REVERT: M 97 ASN cc_start: 0.9071 (m-40) cc_final: 0.8556 (m110) REVERT: M 113 ASP cc_start: 0.8696 (m-30) cc_final: 0.8419 (m-30) REVERT: M 184 MET cc_start: 0.9149 (ptp) cc_final: 0.8827 (ptp) REVERT: M 192 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8914 (mp0) REVERT: M 221 ASN cc_start: 0.8648 (p0) cc_final: 0.8385 (p0) REVERT: U 233 LEU cc_start: 0.9250 (mt) cc_final: 0.9006 (mt) REVERT: U 239 GLU cc_start: 0.8902 (tt0) cc_final: 0.8115 (tm-30) REVERT: U 714 SER cc_start: 0.9180 (t) cc_final: 0.8964 (p) REVERT: V 96 ARG cc_start: 0.8467 (ptp-170) cc_final: 0.8124 (ptp-110) REVERT: V 100 MET cc_start: 0.8661 (mpt) cc_final: 0.8308 (mpt) REVERT: V 304 GLU cc_start: 0.8548 (mp0) cc_final: 0.8234 (mp0) REVERT: V 443 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8791 (tmm-80) REVERT: V 463 MET cc_start: 0.8085 (tpp) cc_final: 0.7626 (tmm) REVERT: V 471 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8337 (tm-30) REVERT: V 485 ASP cc_start: 0.8992 (m-30) cc_final: 0.8608 (m-30) REVERT: V 494 MET cc_start: 0.9036 (mtm) cc_final: 0.8684 (mmm) REVERT: V 515 GLU cc_start: 0.8359 (pt0) cc_final: 0.7945 (pp20) REVERT: V 521 PHE cc_start: 0.8203 (t80) cc_final: 0.7969 (t80) REVERT: W 216 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7874 (mt-10) REVERT: W 259 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: W 313 GLU cc_start: 0.8591 (tt0) cc_final: 0.8265 (mm-30) REVERT: W 451 MET cc_start: 0.9246 (tmm) cc_final: 0.8986 (ppp) REVERT: X 41 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7134 (tm-30) REVERT: X 52 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8560 (mm-30) REVERT: X 87 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8713 (ttt-90) REVERT: X 161 ASP cc_start: 0.8756 (t70) cc_final: 0.8274 (t0) REVERT: X 212 MET cc_start: 0.8709 (tpt) cc_final: 0.8015 (tpt) REVERT: X 332 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7981 (mm-30) REVERT: X 395 LYS cc_start: 0.8016 (mppt) cc_final: 0.7614 (mmmm) REVERT: X 416 ASN cc_start: 0.8548 (m-40) cc_final: 0.8262 (t0) REVERT: Y 39 ASP cc_start: 0.8971 (m-30) cc_final: 0.8654 (m-30) REVERT: Y 152 MET cc_start: 0.8998 (tpp) cc_final: 0.8753 (tpp) REVERT: Y 173 ASP cc_start: 0.7678 (t0) cc_final: 0.7399 (t0) REVERT: Z 28 LYS cc_start: 0.8477 (mmtm) cc_final: 0.8209 (mmpt) REVERT: Z 74 TYR cc_start: 0.9048 (t80) cc_final: 0.8706 (t80) REVERT: Z 78 MET cc_start: 0.9132 (tpt) cc_final: 0.8593 (tpt) REVERT: Z 143 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7304 (tm-30) REVERT: Z 165 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: Z 178 ASP cc_start: 0.8891 (OUTLIER) cc_final: 0.8558 (p0) REVERT: Z 251 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7916 (mt) REVERT: a 23 HIS cc_start: 0.8129 (m-70) cc_final: 0.7796 (m-70) REVERT: a 43 ASP cc_start: 0.8780 (t0) cc_final: 0.8522 (t70) REVERT: a 127 ASP cc_start: 0.8944 (t0) cc_final: 0.8485 (t0) REVERT: a 178 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8220 (mmm-85) REVERT: b 11 ASP cc_start: 0.8819 (t0) cc_final: 0.8294 (t0) REVERT: b 29 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: b 31 ASP cc_start: 0.8047 (m-30) cc_final: 0.7372 (p0) REVERT: b 42 ARG cc_start: 0.8955 (mtm180) cc_final: 0.8460 (mpp80) REVERT: b 46 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8236 (mp0) REVERT: b 70 ARG cc_start: 0.8902 (mtm-85) cc_final: 0.8608 (mtm180) REVERT: b 112 PHE cc_start: 0.7901 (m-10) cc_final: 0.7659 (m-10) REVERT: b 147 GLU cc_start: 0.8875 (pm20) cc_final: 0.8649 (pm20) REVERT: c 106 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8461 (mp0) REVERT: c 168 MET cc_start: 0.6682 (ppp) cc_final: 0.6278 (pmm) REVERT: c 216 MET cc_start: 0.9294 (tpp) cc_final: 0.9051 (tpt) REVERT: c 223 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9115 (mtpp) REVERT: c 264 LYS cc_start: 0.8944 (ptpt) cc_final: 0.8341 (ptmm) REVERT: c 289 ASP cc_start: 0.8773 (t70) cc_final: 0.8481 (t0) REVERT: d 96 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8576 (pm20) REVERT: d 158 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8747 (pmm-80) REVERT: d 165 GLU cc_start: 0.9390 (mm-30) cc_final: 0.8806 (mp0) REVERT: d 207 GLU cc_start: 0.9088 (tt0) cc_final: 0.8765 (mp0) REVERT: d 286 GLU cc_start: 0.8275 (tp30) cc_final: 0.7810 (tt0) REVERT: d 297 LYS cc_start: 0.9380 (tmmt) cc_final: 0.8946 (tptp) REVERT: d 347 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8468 (mm-30) REVERT: e 44 ASP cc_start: 0.8781 (m-30) cc_final: 0.8221 (t0) REVERT: f 47 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7098 (tp30) REVERT: f 113 MET cc_start: 0.6085 (OUTLIER) cc_final: 0.5656 (ppp) REVERT: f 131 MET cc_start: 0.3884 (tmt) cc_final: 0.3325 (mmt) REVERT: f 162 LEU cc_start: 0.8628 (tp) cc_final: 0.8183 (mm) REVERT: f 195 ASN cc_start: 0.6476 (OUTLIER) cc_final: 0.6221 (t0) REVERT: f 268 LEU cc_start: 0.9347 (mp) cc_final: 0.9016 (tp) REVERT: f 272 LEU cc_start: 0.8339 (tp) cc_final: 0.8044 (mt) REVERT: f 275 MET cc_start: 0.8706 (tpt) cc_final: 0.7747 (tmm) REVERT: f 340 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7486 (mmm) REVERT: f 398 TRP cc_start: 0.8019 (t-100) cc_final: 0.7560 (t-100) REVERT: f 407 MET cc_start: 0.6744 (mpt) cc_final: 0.6384 (mmt) REVERT: f 414 LEU cc_start: 0.9125 (mm) cc_final: 0.8907 (mm) REVERT: f 453 SER cc_start: 0.7414 (m) cc_final: 0.7178 (m) REVERT: f 472 HIS cc_start: 0.8137 (OUTLIER) cc_final: 0.7632 (t-90) REVERT: f 502 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7490 (mm) REVERT: f 592 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8696 (p0) REVERT: f 600 TYR cc_start: 0.7815 (m-80) cc_final: 0.7570 (m-80) REVERT: f 655 LEU cc_start: 0.8175 (tp) cc_final: 0.7895 (mt) REVERT: f 681 TYR cc_start: 0.8099 (m-80) cc_final: 0.7662 (m-80) REVERT: f 747 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8517 (mt0) REVERT: f 788 MET cc_start: 0.8452 (tmm) cc_final: 0.7917 (tmm) REVERT: f 797 LEU cc_start: 0.8803 (mt) cc_final: 0.8495 (mt) REVERT: f 868 HIS cc_start: 0.7191 (OUTLIER) cc_final: 0.6933 (m90) REVERT: g 134 LYS cc_start: 0.7177 (tppt) cc_final: 0.6359 (mppt) REVERT: g 158 LEU cc_start: 0.3959 (OUTLIER) cc_final: 0.3721 (mt) REVERT: u 154 THR cc_start: 0.8022 (t) cc_final: 0.7804 (p) REVERT: u 157 LEU cc_start: 0.9174 (tp) cc_final: 0.8853 (mt) REVERT: u 164 GLN cc_start: 0.7736 (mm110) cc_final: 0.7247 (mm-40) REVERT: u 176 LYS cc_start: 0.7857 (mtmm) cc_final: 0.7394 (ptpp) REVERT: u 181 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6609 (mtpm) REVERT: u 210 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7989 (tm-30) REVERT: u 211 ARG cc_start: 0.8443 (ttm110) cc_final: 0.8053 (mtm-85) REVERT: u 223 ASP cc_start: 0.8670 (t0) cc_final: 0.8241 (m-30) REVERT: u 226 LYS cc_start: 0.8034 (mmtm) cc_final: 0.7593 (mmtp) REVERT: u 228 ASP cc_start: 0.8464 (t70) cc_final: 0.8061 (p0) REVERT: u 259 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7730 (mtp-110) REVERT: u 268 THR cc_start: 0.9124 (p) cc_final: 0.8397 (t) outliers start: 180 outliers final: 110 residues processed: 1059 average time/residue: 1.4608 time to fit residues: 2088.2490 Evaluate side-chains 1025 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 875 time to evaluate : 6.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 287 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain D residue 171 ASP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 281 SER Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 229 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 159 LYS Chi-restraints excluded: chain H residue 166 ASN Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 20 ARG Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 148 CYS Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain L residue 234 GLU Chi-restraints excluded: chain M residue 34 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 192 GLU Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 90 VAL Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 362 ASN Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 699 THR Chi-restraints excluded: chain U residue 793 LYS Chi-restraints excluded: chain U residue 921 ILE Chi-restraints excluded: chain V residue 379 LEU Chi-restraints excluded: chain V residue 395 ILE Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 443 ARG Chi-restraints excluded: chain V residue 450 SER Chi-restraints excluded: chain V residue 471 GLU Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 224 LEU Chi-restraints excluded: chain W residue 259 GLU Chi-restraints excluded: chain W residue 260 SER Chi-restraints excluded: chain X residue 41 GLU Chi-restraints excluded: chain X residue 87 ARG Chi-restraints excluded: chain X residue 120 GLU Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 144 VAL Chi-restraints excluded: chain Z residue 158 VAL Chi-restraints excluded: chain Z residue 160 SER Chi-restraints excluded: chain Z residue 165 GLU Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 251 LEU Chi-restraints excluded: chain Z residue 269 VAL Chi-restraints excluded: chain a residue 76 LEU Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 158 LEU Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 178 ARG Chi-restraints excluded: chain a residue 206 LEU Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 292 THR Chi-restraints excluded: chain b residue 29 GLN Chi-restraints excluded: chain b residue 38 HIS Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 132 LYS Chi-restraints excluded: chain b residue 150 THR Chi-restraints excluded: chain c residue 33 ILE Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 223 LYS Chi-restraints excluded: chain c residue 230 THR Chi-restraints excluded: chain c residue 266 THR Chi-restraints excluded: chain d residue 96 GLU Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 158 ARG Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 348 MET Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain f residue 47 GLU Chi-restraints excluded: chain f residue 113 MET Chi-restraints excluded: chain f residue 188 VAL Chi-restraints excluded: chain f residue 195 ASN Chi-restraints excluded: chain f residue 231 LEU Chi-restraints excluded: chain f residue 270 LEU Chi-restraints excluded: chain f residue 340 MET Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 451 VAL Chi-restraints excluded: chain f residue 472 HIS Chi-restraints excluded: chain f residue 502 LEU Chi-restraints excluded: chain f residue 592 ASN Chi-restraints excluded: chain f residue 619 HIS Chi-restraints excluded: chain f residue 796 LEU Chi-restraints excluded: chain f residue 798 THR Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain f residue 868 HIS Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain u residue 180 MET Chi-restraints excluded: chain u residue 181 LYS Chi-restraints excluded: chain u residue 231 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 402 optimal weight: 3.9990 chunk 297 optimal weight: 7.9990 chunk 216 optimal weight: 0.7980 chunk 672 optimal weight: 6.9990 chunk 659 optimal weight: 0.0770 chunk 428 optimal weight: 6.9990 chunk 828 optimal weight: 0.4980 chunk 95 optimal weight: 10.0000 chunk 865 optimal weight: 0.5980 chunk 282 optimal weight: 0.8980 chunk 716 optimal weight: 9.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 154 HIS C 64 GLN C 90 HIS D 65 GLN D 127 ASN G 100 ASN ** H 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 ASN J 205 ASN K 13 ASN L 8 ASN ** M 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 647 HIS U 677 ASN ** U 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 218 ASN ** W 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 13 GLN X 334 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 195 ASN ** f 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 592 ASN f 619 HIS u 240 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.103573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.072647 restraints weight = 146235.599| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.73 r_work: 0.2911 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 72504 Z= 0.178 Angle : 0.627 15.153 97953 Z= 0.309 Chirality : 0.041 0.313 11156 Planarity : 0.004 0.067 12612 Dihedral : 5.903 82.163 9950 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.60 % Favored : 97.36 % Rotamer: Outliers : 2.26 % Allowed : 31.87 % Favored : 65.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.36 (0.09), residues: 8915 helix: 1.58 (0.07), residues: 5027 sheet: -0.46 (0.16), residues: 1021 loop : 0.38 (0.12), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Y 364 HIS 0.016 0.001 HIS f 619 PHE 0.034 0.001 PHE J 73 TYR 0.037 0.001 TYR f 194 ARG 0.012 0.000 ARG b 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 52778.19 seconds wall clock time: 901 minutes 53.29 seconds (54113.29 seconds total)