Starting phenix.real_space_refine on Thu Jan 23 05:53:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8i_47721/01_2025/9e8i_47721.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8i_47721/01_2025/9e8i_47721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e8i_47721/01_2025/9e8i_47721.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8i_47721/01_2025/9e8i_47721.map" model { file = "/net/cci-nas-00/data/ceres_data/9e8i_47721/01_2025/9e8i_47721.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8i_47721/01_2025/9e8i_47721.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.038 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 45094 2.51 5 N 12244 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 287 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': 9, 'TRANS': 141} Chain breaks: 1 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: 28.87, per 1000 atoms: 0.40 Number of scatterers: 71304 At special positions: 0 Unit cell: (220.08, 219.032, 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 12244 7.00 C 45094 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: 13.72 Conformation dependent library (CDL) restraints added in 7.4 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 " 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 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: 429 helices and 37 sheets defined 60.4% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.66 Creating SS restraints... Processing helix chain 'A' and resid 41 through 63 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.571A pdb=" N GLN A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.535A pdb=" N ILE A 134 " --> pdb=" O PRO A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.684A 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: 3.501A 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 266 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 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 418 through 422 removed outlier: 4.235A pdb=" N LYS A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 433 removed outlier: 4.312A pdb=" N THR A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.778A 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 Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 168 through 175 removed outlier: 3.556A 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: 3.763A 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 208 through 215 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: 3.714A pdb=" N LYS B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 379 through 385 removed outlier: 3.633A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) removed outlier: 3.983A 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 Processing helix chain 'C' and resid 20 through 67 removed outlier: 3.548A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 154 through 171 removed outlier: 3.681A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.908A 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: 4.215A 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 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 240 removed outlier: 4.379A pdb=" N MET C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 283 removed outlier: 4.333A 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 333 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' 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 391 Processing helix chain 'D' and resid 40 through 80 removed outlier: 3.502A pdb=" N LYS D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 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 removed outlier: 3.541A pdb=" N LEU D 185 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) 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 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' 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 360 through 365 Processing helix chain 'D' and resid 371 through 389 Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 414 through 418 Processing helix chain 'E' and resid 37 through 51 removed outlier: 3.560A 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: 3.743A 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: 4.042A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 3.823A 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 286 through 291 Processing helix chain 'E' and resid 305 through 318 Processing helix chain 'E' and resid 327 through 334 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 removed outlier: 3.505A pdb=" N VAL F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN F 83 " --> pdb=" O LYS F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 191 through 203 removed outlier: 3.986A pdb=" N ALA F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 209 through 216 removed outlier: 3.800A pdb=" N LEU F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) 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 287 through 291 Processing helix chain 'F' and resid 303 through 318 Processing helix chain 'F' and resid 358 through 369 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 392 through 410 Processing helix chain 'F' and resid 416 through 429 removed outlier: 3.620A pdb=" N LEU F 425 " --> pdb=" O MET F 421 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 31 Processing helix chain 'G' and resid 32 through 36 removed outlier: 3.904A pdb=" N GLY G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 removed outlier: 3.519A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 185 removed outlier: 3.639A 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: 3.550A pdb=" N HIS G 238 " --> pdb=" O GLU G 234 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG G 245 " --> pdb=" O ALA G 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 31 Processing helix chain 'H' and resid 79 through 102 removed outlier: 3.755A pdb=" N VAL H 100 " --> pdb=" O GLN H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 121 removed outlier: 3.602A pdb=" N TYR H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 176 Processing helix chain 'H' and resid 183 through 199 removed outlier: 4.047A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 234 removed outlier: 3.585A pdb=" N ALA H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE H 233 " --> pdb=" O TYR H 229 " (cutoff:3.500A) removed outlier: 3.688A 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 121 Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 185 through 201 removed outlier: 3.586A pdb=" N LYS I 199 " --> pdb=" O LYS I 195 " (cutoff:3.500A) 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: 3.518A pdb=" N GLN I 235 " --> pdb=" O LYS I 231 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) removed outlier: 3.707A 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: 3.539A pdb=" N ILE J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 118 Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.584A pdb=" N LYS J 174 " --> pdb=" O GLU J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 182 Processing helix chain 'J' and resid 183 through 196 removed outlier: 3.506A 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: 3.612A pdb=" N GLU J 237 " --> pdb=" O GLU J 233 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU J 238 " --> pdb=" O LYS J 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 32 removed outlier: 3.841A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.009A 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: 3.520A pdb=" N ALA K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS K 91 " --> pdb=" O THR K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 104 Processing helix chain 'K' and resid 108 through 120 removed outlier: 3.829A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA K 120 " --> pdb=" O VAL K 116 " (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: 3.536A pdb=" N VAL K 237 " --> pdb=" O GLU K 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.591A pdb=" N ALA L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.794A 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: 3.539A pdb=" N LEU L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 175 removed outlier: 4.144A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 180 removed outlier: 3.932A pdb=" N MET L 180 " --> pdb=" O SER L 177 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 197 removed outlier: 3.590A pdb=" N GLU L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 234 removed outlier: 3.761A 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 32 removed outlier: 3.575A 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 121 Processing helix chain 'M' and resid 122 through 124 No H-bonds generated for 'chain 'M' and resid 122 through 124' Processing helix chain 'M' and resid 168 through 178 removed outlier: 3.585A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 201 removed outlier: 4.242A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) removed outlier: 3.647A 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: 3.653A 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 16 through 31 removed outlier: 4.452A pdb=" N ALA U 29 " --> pdb=" O HIS U 25 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 39 Processing helix chain 'U' and resid 42 through 51 removed outlier: 3.863A pdb=" N VAL U 47 " --> pdb=" O ASP U 43 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU U 48 " --> pdb=" O LYS U 44 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR U 49 " --> pdb=" O ILE U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 Processing helix chain 'U' and resid 73 through 85 removed outlier: 3.727A 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: 3.826A pdb=" N ASP U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) removed outlier: 3.531A 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 145 removed outlier: 3.601A pdb=" N VAL U 134 " --> pdb=" O LEU U 130 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS U 141 " --> pdb=" O MET U 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU U 142 " --> pdb=" O PHE U 138 " (cutoff:3.500A) Processing helix chain 'U' and resid 146 through 157 Processing helix chain 'U' and resid 159 through 170 removed outlier: 3.573A 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 190 through 208 removed outlier: 3.683A pdb=" N LYS U 196 " --> pdb=" O GLN U 192 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS U 203 " --> pdb=" O ARG U 199 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 3.819A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE U 222 " --> pdb=" O GLN U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 239 Processing helix chain 'U' and resid 241 through 255 removed outlier: 3.644A pdb=" N ALA U 245 " --> pdb=" O ASN U 241 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE U 250 " --> pdb=" O TYR U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 270 Processing helix chain 'U' and resid 321 through 330 removed outlier: 3.732A pdb=" N ILE U 328 " --> pdb=" O LYS U 324 " (cutoff:3.500A) Processing helix chain 'U' and resid 333 through 345 removed outlier: 3.614A pdb=" N ARG U 344 " --> pdb=" O GLN U 340 " (cutoff:3.500A) Processing helix chain 'U' and resid 349 through 358 removed outlier: 3.869A 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 388 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: 3.800A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 427 Processing helix chain 'U' and resid 434 through 450 removed outlier: 4.353A pdb=" N GLN U 438 " --> pdb=" O GLY U 434 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 467 removed outlier: 4.187A pdb=" N TYR U 460 " --> pdb=" O ASP U 456 " (cutoff:3.500A) 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: 3.513A 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: 3.581A pdb=" N ALA U 553 " --> pdb=" O ALA U 549 " (cutoff:3.500A) removed outlier: 3.834A 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: 3.625A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 3.647A 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 739 through 742 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 781 Processing helix chain 'V' and resid 59 through 89 removed outlier: 3.794A pdb=" N VAL V 70 " --> pdb=" O GLU V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 100 removed outlier: 4.367A pdb=" N ARG V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA V 97 " --> pdb=" O PHE V 93 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET V 100 " --> pdb=" O ARG V 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 107 removed outlier: 3.868A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG V 107 " --> pdb=" O SER V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 121 removed outlier: 3.949A pdb=" N PHE V 121 " --> pdb=" O VAL V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 132 removed outlier: 3.623A 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: 3.596A pdb=" N ALA V 165 " --> pdb=" O PRO V 161 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR V 166 " --> pdb=" O GLU V 162 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 198 removed outlier: 3.711A pdb=" N LYS V 194 " --> pdb=" O ASP V 190 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 220 removed outlier: 3.628A pdb=" N VAL V 206 " --> pdb=" O ALA V 202 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR V 218 " --> pdb=" O HIS V 214 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 242 removed outlier: 4.170A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG V 241 " --> pdb=" O THR V 237 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 261 removed outlier: 3.809A 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 Processing helix chain 'V' and resid 301 through 316 Processing helix chain 'V' and resid 321 through 339 removed outlier: 3.514A pdb=" N VAL V 334 " --> pdb=" O LYS V 330 " (cutoff:3.500A) Processing helix chain 'V' and resid 345 through 350 removed outlier: 3.559A pdb=" N GLN V 350 " --> pdb=" O GLN V 347 " (cutoff:3.500A) Processing helix chain 'V' and resid 357 through 370 Processing helix chain 'V' and resid 371 through 389 removed outlier: 6.430A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 397 removed outlier: 3.790A pdb=" N ARG V 397 " --> pdb=" O THR V 393 " (cutoff:3.500A) Processing helix chain 'V' and resid 397 through 413 removed outlier: 3.931A 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 Processing helix chain 'V' and resid 465 through 469 Processing helix chain 'V' and resid 470 through 493 Processing helix chain 'V' and resid 507 through 525 removed outlier: 3.623A pdb=" N ARG V 514 " --> pdb=" O GLU V 510 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU V 515 " --> pdb=" O ARG V 511 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 38 Proline residue: W 29 - end of helix Processing helix chain 'W' and resid 40 through 58 removed outlier: 3.663A pdb=" N GLU W 45 " --> pdb=" O GLN W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 59 through 77 Processing helix chain 'W' and resid 79 through 92 Processing helix chain 'W' and resid 97 through 115 removed outlier: 3.554A pdb=" N THR W 110 " --> pdb=" O GLN W 106 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR W 111 " --> pdb=" O GLN W 107 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU W 113 " --> pdb=" O CYS W 109 " (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 removed outlier: 3.612A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) 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: 3.657A 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 removed outlier: 3.511A pdb=" N GLU W 216 " --> pdb=" O PHE W 213 " (cutoff:3.500A) Processing helix chain 'W' and resid 219 through 238 removed outlier: 3.669A pdb=" N HIS W 236 " --> pdb=" O GLN W 232 " (cutoff:3.500A) removed outlier: 3.911A 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: 3.636A 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: 3.846A pdb=" N LEU W 296 " --> pdb=" O ASP W 293 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU W 297 " --> pdb=" O LYS W 294 " (cutoff:3.500A) Processing helix chain 'W' and resid 299 through 309 Processing helix chain 'W' and resid 316 through 330 removed outlier: 6.347A pdb=" N MET W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 342 removed outlier: 4.017A pdb=" N PHE W 341 " --> pdb=" O THR W 338 " (cutoff:3.500A) removed outlier: 3.842A 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 Processing helix chain 'X' and resid 5 through 15 Processing helix chain 'X' and resid 19 through 33 removed outlier: 3.611A pdb=" N ASP X 25 " --> pdb=" O GLU X 21 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE X 26 " --> pdb=" O ALA X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 61 removed outlier: 3.632A pdb=" N GLN X 44 " --> pdb=" O GLU X 40 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS X 59 " --> pdb=" O SER X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 73 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 141 removed outlier: 3.516A pdb=" N SER X 135 " --> pdb=" O ALA X 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 161 Processing helix chain 'X' and resid 162 through 180 removed outlier: 3.930A 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: 3.755A 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: 4.348A pdb=" N GLN X 268 " --> pdb=" O PRO X 264 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA X 269 " --> pdb=" O GLU X 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 278 removed outlier: 4.271A pdb=" N ARG X 278 " --> pdb=" O LYS X 274 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 297 removed outlier: 3.571A pdb=" N LEU X 287 " --> pdb=" O GLN X 283 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 309 removed outlier: 3.534A pdb=" N PHE X 302 " --> pdb=" O SER X 298 " (cutoff:3.500A) Processing helix chain 'X' and resid 309 through 315 removed outlier: 3.646A pdb=" N ASP X 315 " --> pdb=" O ALA X 311 " (cutoff:3.500A) Processing helix chain 'X' and resid 316 through 340 removed outlier: 3.547A pdb=" N THR X 321 " --> pdb=" O PRO X 317 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA X 324 " --> pdb=" O SER X 320 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS X 325 " --> pdb=" O THR X 321 " (cutoff:3.500A) Processing helix chain 'X' and resid 347 through 355 Processing helix chain 'X' and resid 357 through 371 Processing helix chain 'X' and resid 394 through 422 Processing helix chain 'Y' and resid 5 through 10 removed outlier: 3.705A pdb=" N GLY Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 28 removed outlier: 3.875A 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 61 Processing helix chain 'Y' and resid 66 through 94 removed outlier: 3.583A pdb=" N ALA Y 76 " --> pdb=" O LYS Y 72 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 114 Processing helix chain 'Y' and resid 116 through 130 removed outlier: 3.618A 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: 3.704A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 240 removed outlier: 3.528A pdb=" N GLU Y 238 " --> pdb=" O PRO Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 243 through 251 Processing helix chain 'Y' and resid 253 through 265 removed outlier: 3.941A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 284 Processing helix chain 'Y' and resid 291 through 310 removed outlier: 4.290A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 323 Processing helix chain 'Y' and resid 326 through 340 Processing helix chain 'Y' and resid 360 through 389 removed outlier: 3.854A pdb=" N TRP Y 364 " --> pdb=" O ASP Y 360 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET Y 389 " --> pdb=" O ARG Y 385 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 27 Processing helix chain 'Z' and resid 71 through 86 removed outlier: 3.792A pdb=" N VAL Z 85 " --> pdb=" O MET Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 104 through 114 removed outlier: 3.739A 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 237 removed outlier: 3.533A pdb=" N ASP Z 232 " --> pdb=" O TYR Z 228 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 289 removed outlier: 3.870A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 14 removed outlier: 4.002A pdb=" N ASN a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 31 Processing helix chain 'a' and resid 33 through 46 removed outlier: 3.995A pdb=" N THR a 38 " --> pdb=" O TRP a 34 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU a 39 " --> pdb=" O HIS a 35 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN a 40 " --> pdb=" O GLN a 36 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN a 46 " --> pdb=" O LEU a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 63 removed outlier: 3.978A pdb=" N GLU a 61 " --> pdb=" O ILE a 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 67 through 71 removed outlier: 3.534A pdb=" N ARG a 70 " --> pdb=" O PHE a 67 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL a 71 " --> pdb=" O GLU a 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 67 through 71' Processing helix chain 'a' and resid 72 through 87 removed outlier: 3.697A pdb=" N GLU a 78 " --> pdb=" O LEU a 74 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE a 79 " --> pdb=" O SER a 75 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL a 83 " --> pdb=" O ILE a 79 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET a 87 " --> pdb=" O VAL a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 104 removed outlier: 3.802A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 126 Processing helix chain 'a' and resid 127 through 145 removed outlier: 3.747A pdb=" N GLU a 140 " --> pdb=" O GLU a 136 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN a 143 " --> pdb=" O GLU a 139 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN a 144 " --> pdb=" O GLU a 140 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 167 removed outlier: 4.317A pdb=" N SER a 153 " --> pdb=" O THR a 149 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ARG a 154 " --> pdb=" O SER a 150 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR a 165 " --> pdb=" O LYS a 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 168 through 183 Processing helix chain 'a' and resid 189 through 207 Processing helix chain 'a' and resid 212 through 218 removed outlier: 3.988A pdb=" N LEU a 216 " --> pdb=" O ASN a 212 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET a 218 " --> pdb=" O GLY a 214 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 226 removed outlier: 3.596A pdb=" N ARG a 226 " --> pdb=" O GLU a 223 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 243 removed outlier: 4.216A 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 removed outlier: 3.691A pdb=" N ASN a 264 " --> pdb=" O ASP a 260 " (cutoff:3.500A) 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 300 Processing helix chain 'a' and resid 303 through 305 No H-bonds generated for 'chain 'a' and resid 303 through 305' Processing helix chain 'a' and resid 306 through 318 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: 3.713A pdb=" N ASN b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 68 through 77 removed outlier: 4.240A pdb=" N THR b 77 " --> pdb=" O SER b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 99 removed outlier: 3.538A pdb=" N ILE b 90 " --> pdb=" O PHE b 86 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 134 removed outlier: 3.590A pdb=" N LEU b 124 " --> pdb=" O ASN b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 150 Processing helix chain 'b' and resid 151 through 162 Processing helix chain 'b' and resid 179 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: 3.656A pdb=" N PHE c 133 " --> pdb=" O THR c 129 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU c 136 " --> pdb=" O SER c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 170 removed outlier: 3.547A pdb=" N LEU c 170 " --> pdb=" O ASN c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 184 removed outlier: 4.117A 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: 3.755A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) Processing helix chain 'c' and resid 233 through 264 removed outlier: 3.589A pdb=" N GLU c 250 " --> pdb=" O LYS c 246 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS c 257 " --> pdb=" O LYS c 253 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS c 264 " --> pdb=" O GLU c 260 " (cutoff:3.500A) Processing helix chain 'c' and resid 268 through 273 removed outlier: 4.055A pdb=" N ILE c 272 " --> pdb=" O GLU c 268 " (cutoff:3.500A) Processing helix chain 'c' and resid 279 through 309 removed outlier: 3.922A pdb=" N VAL c 307 " --> pdb=" O MET c 303 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 104 removed outlier: 3.620A pdb=" N GLN d 97 " --> pdb=" O GLY d 93 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG d 104 " --> pdb=" O GLY d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 126 removed outlier: 3.786A pdb=" N GLU d 115 " --> pdb=" O LYS d 111 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU d 121 " --> pdb=" O GLY d 117 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL d 122 " --> pdb=" O ARG d 118 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU d 125 " --> pdb=" O LEU d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 158 removed outlier: 3.933A pdb=" N LEU d 141 " --> pdb=" O THR d 137 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU d 148 " --> pdb=" O ALA d 144 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE d 156 " --> pdb=" O ALA d 152 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU d 157 " --> pdb=" O GLN d 153 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG d 158 " --> pdb=" O TRP d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 177 removed outlier: 3.893A pdb=" N PHE d 164 " --> pdb=" O ASP d 160 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS d 173 " --> pdb=" O ALA d 169 " (cutoff:3.500A) removed outlier: 3.638A 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 214 removed outlier: 3.606A pdb=" N ARG d 214 " --> pdb=" O THR d 210 " (cutoff:3.500A) Processing helix chain 'd' and resid 216 through 223 removed outlier: 3.623A pdb=" N ILE d 220 " --> pdb=" O PRO d 216 " (cutoff:3.500A) removed outlier: 4.109A 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: 3.530A pdb=" N ILE d 260 " --> pdb=" O TYR d 256 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR d 266 " --> pdb=" O ILE d 262 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP d 269 " --> pdb=" O ASP d 265 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS d 277 " --> pdb=" O GLY d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 285 through 291 removed outlier: 4.406A pdb=" N ARG d 289 " --> pdb=" O THR d 285 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE d 290 " --> pdb=" O GLU d 286 " (cutoff:3.500A) Processing helix chain 'd' and resid 296 through 307 removed outlier: 3.716A pdb=" N THR d 300 " --> pdb=" O PRO d 296 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP d 301 " --> pdb=" O LYS d 297 " (cutoff:3.500A) removed outlier: 3.690A 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: 3.794A pdb=" N ASP e 45 " --> pdb=" O ASN e 42 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN e 47 " --> pdb=" O ASP e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 61 removed outlier: 4.079A 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: 3.585A pdb=" N ALA f 74 " --> pdb=" O LEU f 70 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG f 83 " --> pdb=" O ARG f 79 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER f 85 " --> pdb=" O GLN f 81 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 98 removed outlier: 3.591A pdb=" N PHE f 98 " --> pdb=" O LYS f 94 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 105 removed outlier: 3.564A pdb=" N GLY f 104 " --> pdb=" O PRO f 101 " (cutoff:3.500A) Processing helix chain 'f' and resid 117 through 129 removed outlier: 4.001A pdb=" N PHE f 121 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 3.752A 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: 3.667A pdb=" N ILE f 125 " --> pdb=" O PHE f 121 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE f 126 " --> pdb=" O ALA f 122 " (cutoff:3.500A) Processing helix chain 'f' and resid 138 through 146 Processing helix chain 'f' and resid 150 through 154 Processing helix chain 'f' and resid 155 through 173 removed outlier: 3.514A pdb=" N ALA f 167 " --> pdb=" O ALA f 163 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU f 172 " --> pdb=" O LYS f 168 " (cutoff:3.500A) Processing helix chain 'f' and resid 174 through 180 removed outlier: 4.753A pdb=" N VAL f 179 " --> pdb=" O ALA f 176 " (cutoff:3.500A) Processing helix chain 'f' and resid 181 through 198 removed outlier: 3.722A pdb=" N THR f 186 " --> pdb=" O GLU f 182 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL f 188 " --> pdb=" O LEU f 184 " (cutoff:3.500A) Proline residue: f 193 - end of helix removed outlier: 3.666A pdb=" N HIS f 198 " --> pdb=" O TYR f 194 " (cutoff:3.500A) Processing helix chain 'f' and resid 200 through 211 removed outlier: 3.865A pdb=" N ALA f 204 " --> pdb=" O ALA f 200 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS f 205 " --> pdb=" O GLU f 201 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU f 208 " --> pdb=" O ALA f 204 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU f 210 " --> pdb=" O ASP f 206 " (cutoff:3.500A) Processing helix chain 'f' and resid 213 through 221 removed outlier: 3.676A pdb=" N MET f 216 " --> pdb=" O GLN f 213 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU f 218 " --> pdb=" O ASP f 215 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS f 219 " --> pdb=" O MET f 216 " (cutoff:3.500A) Processing helix chain 'f' and resid 225 through 237 Processing helix chain 'f' and resid 243 through 259 removed outlier: 3.566A pdb=" N LEU f 249 " --> pdb=" O ASN f 245 " (cutoff:3.500A) Processing helix chain 'f' and resid 261 through 272 Processing helix chain 'f' and resid 274 through 285 removed outlier: 3.788A pdb=" N GLU f 279 " --> pdb=" O MET f 275 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS f 285 " --> pdb=" O ILE f 281 " (cutoff:3.500A) Processing helix chain 'f' and resid 287 through 302 removed outlier: 3.975A pdb=" N GLN f 293 " --> pdb=" O VAL f 289 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET f 294 " --> pdb=" O VAL f 290 " (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: 3.559A 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 removed outlier: 3.558A pdb=" N PHE f 376 " --> pdb=" O LEU f 372 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN f 382 " --> pdb=" O ASN f 378 " (cutoff:3.500A) Processing helix chain 'f' and resid 394 through 402 removed outlier: 4.254A pdb=" N TRP f 398 " --> pdb=" O ASP f 394 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 417 removed outlier: 3.898A pdb=" N LEU f 414 " --> pdb=" O ALA f 410 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET f 416 " --> pdb=" O ALA f 412 " (cutoff:3.500A) Processing helix chain 'f' and resid 421 through 434 removed outlier: 3.591A pdb=" N GLN f 428 " --> pdb=" O GLY f 424 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP f 430 " --> pdb=" O LEU f 426 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR f 434 " --> pdb=" O ASP f 430 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 452 removed outlier: 3.673A pdb=" N LYS f 441 " --> pdb=" O GLU f 437 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY f 449 " --> pdb=" O LEU f 445 " (cutoff:3.500A) Processing helix chain 'f' and resid 461 through 468 removed outlier: 4.473A pdb=" N ASP f 468 " --> pdb=" O ALA f 464 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 489 removed outlier: 3.636A pdb=" N SER f 481 " --> pdb=" O MET f 477 " (cutoff:3.500A) removed outlier: 3.782A 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: 4.114A 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 Processing helix chain 'f' and resid 548 through 555 removed outlier: 5.272A pdb=" N THR f 553 " --> pdb=" O LEU f 550 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N TYR f 554 " --> pdb=" O LYS f 551 " (cutoff:3.500A) Processing helix chain 'f' and resid 556 through 566 removed outlier: 3.871A pdb=" N LEU f 560 " --> pdb=" O ARG f 556 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS f 566 " --> pdb=" O LEU f 562 " (cutoff:3.500A) Processing helix chain 'f' and resid 573 through 580 Processing helix chain 'f' and resid 581 through 583 No H-bonds generated for 'chain 'f' and resid 581 through 583' Processing helix chain 'f' and resid 586 through 600 Processing helix chain 'f' and resid 605 through 618 removed outlier: 3.656A pdb=" N GLU f 618 " --> pdb=" O HIS f 614 " (cutoff:3.500A) Processing helix chain 'f' and resid 648 through 662 removed outlier: 4.251A pdb=" N VAL f 652 " --> pdb=" O ALA f 648 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA f 658 " --> pdb=" O VAL f 654 " (cutoff:3.500A) Processing helix chain 'f' and resid 664 through 682 removed outlier: 3.876A pdb=" N ARG f 673 " --> pdb=" O GLU f 669 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR f 674 " --> pdb=" O MET f 670 " (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: 3.669A 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: 3.528A pdb=" N HIS f 770 " --> pdb=" O GLN f 766 " (cutoff:3.500A) Processing helix chain 'f' and resid 771 through 775 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 removed outlier: 3.666A pdb=" N VAL f 817 " --> pdb=" O SER f 814 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU f 821 " --> pdb=" O LEU f 818 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 120 removed outlier: 3.718A pdb=" N SER g 114 " --> pdb=" O ARG g 110 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA g 117 " --> pdb=" O ARG g 113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE g 120 " --> pdb=" O ILE g 116 " (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: 4.244A pdb=" N PHE g 169 " --> pdb=" O ALA g 165 " (cutoff:3.500A) Processing helix chain 'u' and resid 127 through 130 Processing helix chain 'u' and resid 145 through 151 removed outlier: 3.608A pdb=" N ARG u 151 " --> pdb=" O ASP u 147 " (cutoff:3.500A) Processing helix chain 'u' and resid 221 through 226 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 102 removed outlier: 5.802A pdb=" N CYS A 98 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASN A 114 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 3.622A 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 84 through 89 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 93 through 98 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 69 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 236 through 241 removed outlier: 3.681A 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: 7.328A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N VAL B 250 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER B 280 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE B 328 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 282 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ALA B 330 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE B 284 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY B 221 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE B 351 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 6.202A 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: 6.280A pdb=" N THR C 210 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N PHE C 247 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ASP C 249 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N SER C 244 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE C 292 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE C 246 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA C 294 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET C 248 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY C 185 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE C 315 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 6.237A 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: 6.446A pdb=" N ALA D 226 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N PHE D 263 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE D 228 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ASP D 265 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL D 230 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ALA D 260 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE D 308 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE D 262 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA D 310 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE D 264 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY D 201 " --> pdb=" O ARG D 329 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE D 331 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 6.052A 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 removed outlier: 6.428A pdb=" N CYS E 228 " --> pdb=" O LYS E 274 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE E 276 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE E 230 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ALA E 278 " --> pdb=" O ILE E 230 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET E 232 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 247 through 252 removed outlier: 6.276A pdb=" N THR F 247 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE F 284 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU F 249 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASP F 286 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU F 251 " --> pdb=" O ASP F 286 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER F 281 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ILE F 329 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE F 283 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ALA F 331 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE F 285 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU F 224 " --> pdb=" O ILE F 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.688A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.558A 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 70 removed outlier: 3.562A pdb=" N LYS G 153 " --> pdb=" O CYS G 161 " (cutoff:3.500A) removed outlier: 3.872A 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 67 removed outlier: 3.875A 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: 6.294A pdb=" N ILE K 67 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N MET K 78 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLU K 69 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N CYS K 76 " --> pdb=" O GLU K 69 " (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: 3.588A pdb=" N ASP L 138 " --> pdb=" O GLY L 141 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.868A 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 67 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 788 through 791 removed outlier: 5.697A pdb=" N ILE U 789 " --> pdb=" O ILE U 912 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU U 914 " --> pdb=" O ILE U 789 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU U 791 " --> pdb=" O LEU U 914 " (cutoff:3.500A) removed outlier: 7.162A 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: 3.506A pdb=" N TYR V 457 " --> pdb=" O ASN V 452 " (cutoff:3.500A) removed outlier: 6.109A 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: 5.546A pdb=" N SER X 343 " --> pdb=" O ILE X 387 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N VAL W 406 " --> pdb=" O SER X 343 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL X 345 " --> pdb=" O VAL W 406 " (cutoff:3.500A) removed outlier: 6.389A 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: 3.911A pdb=" N ALA Z 137 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) removed outlier: 9.657A pdb=" N VAL Z 120 " --> pdb=" O ARG Z 90 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL Z 92 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL Z 122 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP Z 94 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE Z 124 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N HIS Z 96 " --> pdb=" O ILE Z 124 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ILE Z 91 " --> pdb=" O GLY Z 41 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLY Z 41 " --> pdb=" O ILE Z 91 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY Z 93 " --> pdb=" O LEU Z 39 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N SER Z 42 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL Z 50 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN Z 44 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LEU Z 48 " --> pdb=" O GLN Z 44 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS Z 8 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL Z 50 " --> pdb=" O LYS Z 8 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL Z 10 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASN Z 52 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL Z 9 " --> pdb=" O GLU Z 161 " (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 60 through 65 removed outlier: 5.855A pdb=" N VAL b 60 " --> pdb=" O THR b 53 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR b 53 " --> pdb=" O VAL b 60 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU b 64 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL b 49 " --> pdb=" O LEU b 64 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ASP b 139 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE b 109 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE b 141 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA b 111 " --> pdb=" O ILE b 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.210A pdb=" N VAL c 25 " --> pdb=" O GLN c 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'c' and resid 30 through 34 removed outlier: 6.684A pdb=" N GLN c 30 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL c 69 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR c 32 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP c 71 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N SER c 34 " --> pdb=" O ASP c 71 " (cutoff:3.500A) removed outlier: 11.207A pdb=" N PHE c 73 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL c 67 " --> pdb=" O VAL c 62 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL c 62 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N VAL c 69 " --> pdb=" O GLU c 60 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLU c 60 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY c 55 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TRP c 111 " --> pdb=" O GLY c 55 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N MET c 57 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N VAL c 141 " --> pdb=" O MET c 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL c 109 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL c 143 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N TRP c 111 " --> pdb=" O VAL c 143 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N VAL c 145 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N HIS c 113 " --> pdb=" O VAL c 145 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL c 156 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ILE c 148 " --> pdb=" O LYS c 154 " (cutoff:3.500A) removed outlier: 10.502A pdb=" N LYS c 154 " --> pdb=" O ILE c 148 " (cutoff:3.500A) removed outlier: 12.668A pdb=" N VAL c 155 " --> pdb=" O TYR c 207 " (cutoff:3.500A) removed outlier: 10.592A pdb=" N TYR c 207 " --> pdb=" O VAL c 155 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 281 through 283 removed outlier: 3.559A pdb=" N ILE d 282 " --> pdb=" O TYR d 316 " (cutoff:3.500A) 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: 5.736A pdb=" N GLY f 864 " --> pdb=" O GLN f 848 " (cutoff:3.500A) removed outlier: 4.796A 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: 4.228A pdb=" N ASN g 99 " --> pdb=" O VAL g 87 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR g 103 " --> pdb=" O ALA g 83 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA g 83 " --> pdb=" O THR g 103 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N VAL g 151 " --> pdb=" O ILE g 82 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR g 84 " --> pdb=" O VAL g 151 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA g 153 " --> pdb=" O THR g 84 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU g 86 " --> pdb=" O ALA g 153 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL g 155 " --> pdb=" O GLU g 86 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET g 154 " --> pdb=" O VAL g 130 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N VAL g 130 " --> pdb=" O MET g 154 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'u' and resid 124 through 125 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 124 through 125 current: chain 'u' and resid 165 through 181 No H-bonds generated for sheet with id=AE1 3885 hydrogen bonds defined for protein. 11208 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: 27.36 Time building geometry restraints manager: 16.16 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: 23729 1.34 - 1.46: 14602 1.46 - 1.58: 33515 1.58 - 1.70: 20 1.70 - 1.82: 637 Bond restraints: 72503 Sorted by residual: bond pdb=" C SER U 432 " pdb=" N PRO U 433 " ideal model delta sigma weight residual 1.335 1.356 -0.021 8.70e-03 1.32e+04 5.95e+00 bond pdb=" CA ASP J 4 " pdb=" CB ASP J 4 " ideal model delta sigma weight residual 1.531 1.606 -0.076 3.28e-02 9.30e+02 5.30e+00 bond pdb=" CA THR B 373 " pdb=" CB THR B 373 " ideal model delta sigma weight residual 1.529 1.549 -0.020 1.38e-02 5.25e+03 2.18e+00 bond pdb=" CB LYS d 111 " pdb=" CG LYS d 111 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.90e+00 bond pdb=" CB ASN D 304 " pdb=" CG ASN D 304 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.85e+00 ... (remaining 72498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 97013 2.44 - 4.87: 826 4.87 - 7.31: 82 7.31 - 9.75: 23 9.75 - 12.18: 8 Bond angle restraints: 97952 Sorted by residual: angle pdb=" N ILE d 226 " pdb=" CA ILE d 226 " pdb=" C ILE d 226 " ideal model delta sigma weight residual 112.96 108.33 4.63 1.00e+00 1.00e+00 2.14e+01 angle pdb=" CA GLU U 120 " pdb=" CB GLU U 120 " pdb=" CG GLU U 120 " ideal model delta sigma weight residual 114.10 122.44 -8.34 2.00e+00 2.50e-01 1.74e+01 angle pdb=" CB MET L 180 " pdb=" CG MET L 180 " pdb=" SD MET L 180 " ideal model delta sigma weight residual 112.70 124.88 -12.18 3.00e+00 1.11e-01 1.65e+01 angle pdb=" CA ARG f 143 " pdb=" CB ARG f 143 " pdb=" CG ARG f 143 " ideal model delta sigma weight residual 114.10 122.18 -8.08 2.00e+00 2.50e-01 1.63e+01 angle pdb=" CB MET W 312 " pdb=" CG MET W 312 " pdb=" SD MET W 312 " ideal model delta sigma weight residual 112.70 124.28 -11.58 3.00e+00 1.11e-01 1.49e+01 ... (remaining 97947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.12: 37662 18.12 - 36.25: 5044 36.25 - 54.37: 1564 54.37 - 72.50: 265 72.50 - 90.62: 99 Dihedral angle restraints: 44634 sinusoidal: 18424 harmonic: 26210 Sorted by residual: dihedral pdb=" CA CYS f 459 " pdb=" C CYS f 459 " pdb=" N ASP f 460 " pdb=" CA ASP f 460 " ideal model delta harmonic sigma weight residual -180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+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 180.00 158.16 21.84 0 5.00e+00 4.00e-02 1.91e+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 -158.23 -21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 44631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 10188 0.069 - 0.138: 954 0.138 - 0.207: 12 0.207 - 0.277: 2 0.277 - 0.346: 1 Chirality restraints: 11157 Sorted by residual: 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 -2.24 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CG LEU U 337 " pdb=" CB LEU U 337 " pdb=" CD1 LEU U 337 " pdb=" CD2 LEU U 337 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB ILE f 339 " pdb=" CA ILE f 339 " pdb=" CG1 ILE f 339 " pdb=" CG2 ILE f 339 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 11154 not shown) Planarity restraints: 12612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE V 174 " 0.014 2.00e-02 2.50e+03 1.78e-02 5.53e+00 pdb=" CG PHE V 174 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE V 174 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE V 174 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE V 174 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE V 174 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE V 174 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN U 340 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" CD GLN U 340 " -0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN U 340 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN U 340 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP L 100 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ASP L 100 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP L 100 " -0.013 2.00e-02 2.50e+03 pdb=" N ARG L 101 " -0.012 2.00e-02 2.50e+03 ... (remaining 12609 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 494 2.52 - 3.12: 53792 3.12 - 3.71: 117892 3.71 - 4.31: 166918 4.31 - 4.90: 273510 Nonbonded interactions: 612606 Sorted by model distance: nonbonded pdb=" OG1 THR E 181 " pdb="MG MG E 502 " model vdw 1.930 2.170 nonbonded pdb=" OG1 THR A 223 " pdb="MG MG A 502 " model vdw 1.971 2.170 nonbonded pdb=" OG1 THR D 213 " pdb="MG MG D 502 " model vdw 1.972 2.170 nonbonded pdb=" O1G ATP B 501 " pdb="MG MG B 502 " model vdw 2.019 2.170 nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 501 " model vdw 2.058 2.230 ... (remaining 612601 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 2.050 Check model and map are aligned: 0.400 Set scattering table: 0.480 Process input model: 129.470 Find NCS groups from input model: 1.830 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 0.076 72503 Z= 0.200 Angle : 0.579 12.182 97952 Z= 0.303 Chirality : 0.040 0.346 11157 Planarity : 0.004 0.055 12612 Dihedral : 18.215 90.623 27673 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.46 % Favored : 97.53 % Rotamer: Outliers : 2.36 % Allowed : 31.60 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 0.41 (0.09), residues: 8913 helix: 0.55 (0.07), residues: 4872 sheet: -0.12 (0.16), residues: 993 loop : 0.24 (0.12), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 139 HIS 0.012 0.001 HIS Z 72 PHE 0.040 0.001 PHE V 174 TYR 0.031 0.001 TYR a 162 ARG 0.012 0.001 ARG f 807 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1949 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 1765 time to evaluate : 6.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 GLN cc_start: 0.8402 (tp40) cc_final: 0.7891 (tm-30) REVERT: A 51 ASP cc_start: 0.8058 (m-30) cc_final: 0.7382 (m-30) REVERT: A 55 LEU cc_start: 0.8698 (mt) cc_final: 0.8480 (mp) REVERT: A 62 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8226 (mm) REVERT: A 239 ARG cc_start: 0.8770 (ptm-80) cc_final: 0.8410 (ppt90) REVERT: A 333 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7585 (ttt90) REVERT: B 91 LYS cc_start: 0.6633 (mmtt) cc_final: 0.6332 (mttt) REVERT: B 288 ASP cc_start: 0.8291 (p0) cc_final: 0.7991 (p0) REVERT: C 60 ARG cc_start: 0.8831 (mtp85) cc_final: 0.8619 (mtt-85) REVERT: C 111 ASN cc_start: 0.8548 (m-40) cc_final: 0.8344 (t0) REVERT: C 165 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8858 (mt) REVERT: C 209 CYS cc_start: 0.8422 (m) cc_final: 0.8164 (m) REVERT: C 290 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8278 (mmpt) REVERT: E 48 LYS cc_start: 0.9301 (mtpp) cc_final: 0.9052 (mttt) REVERT: E 122 MET cc_start: 0.8872 (mtt) cc_final: 0.8634 (mtt) REVERT: G 113 MET cc_start: 0.8644 (mmm) cc_final: 0.8387 (mmt) REVERT: H 51 LYS cc_start: 0.8795 (ttpt) cc_final: 0.7750 (ttpt) REVERT: H 179 ASN cc_start: 0.8427 (p0) cc_final: 0.7043 (p0) REVERT: I 210 LYS cc_start: 0.8566 (mtmp) cc_final: 0.8353 (mtmt) REVERT: J 110 TYR cc_start: 0.8573 (t80) cc_final: 0.8229 (t80) REVERT: L 7 ASP cc_start: 0.8595 (p0) cc_final: 0.8380 (p0) REVERT: L 68 ASN cc_start: 0.8698 (m-40) cc_final: 0.8433 (m110) REVERT: L 100 ASP cc_start: 0.8154 (t0) cc_final: 0.7928 (t0) REVERT: M 75 MET cc_start: 0.8615 (ttt) cc_final: 0.8274 (ttt) REVERT: U 470 ASN cc_start: 0.7535 (t0) cc_final: 0.7223 (t0) REVERT: V 132 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8362 (mm) REVERT: V 212 TYR cc_start: 0.8758 (t80) cc_final: 0.8351 (t80) REVERT: V 496 PHE cc_start: 0.8456 (m-10) cc_final: 0.8211 (m-10) REVERT: V 507 SER cc_start: 0.8054 (OUTLIER) cc_final: 0.6991 (p) REVERT: W 109 CYS cc_start: 0.7552 (p) cc_final: 0.7257 (p) REVERT: W 118 LEU cc_start: 0.8568 (mm) cc_final: 0.8352 (tt) REVERT: X 48 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8427 (tp40) REVERT: Y 50 MET cc_start: 0.8803 (mtp) cc_final: 0.8585 (mtm) REVERT: Y 74 LYS cc_start: 0.9105 (mttm) cc_final: 0.8893 (mttt) REVERT: Y 173 ASP cc_start: 0.8302 (t0) cc_final: 0.8097 (t0) REVERT: Y 184 GLN cc_start: 0.8669 (tt0) cc_final: 0.8467 (mt0) REVERT: a 173 TYR cc_start: 0.8802 (t80) cc_final: 0.8537 (t80) REVERT: b 47 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7181 (m-40) REVERT: f 118 ASN cc_start: 0.7825 (m-40) cc_final: 0.7448 (t0) REVERT: f 131 MET cc_start: 0.6604 (mpp) cc_final: 0.6273 (ppp) REVERT: f 168 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8160 (tppp) REVERT: f 224 ASN cc_start: 0.7268 (m-40) cc_final: 0.6516 (t0) REVERT: f 294 MET cc_start: 0.6790 (mmt) cc_final: 0.6156 (mmt) REVERT: f 319 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6445 (tp30) REVERT: f 646 MET cc_start: 0.7341 (mmm) cc_final: 0.7069 (mmm) REVERT: f 888 LEU cc_start: 0.8023 (mt) cc_final: 0.7761 (mt) REVERT: u 225 ILE cc_start: 0.7484 (pt) cc_final: 0.6531 (pt) outliers start: 184 outliers final: 39 residues processed: 1881 average time/residue: 1.5900 time to fit residues: 3857.6716 Evaluate side-chains 1032 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 986 time to evaluate : 6.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 165 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 143 ASN Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 632 GLN Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 342 ILE Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 466 ILE Chi-restraints excluded: chain V residue 507 SER Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 136 LEU Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 47 ASN Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 690 VAL Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 220 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 6.9990 chunk 673 optimal weight: 4.9990 chunk 373 optimal weight: 0.5980 chunk 229 optimal weight: 2.9990 chunk 454 optimal weight: 1.9990 chunk 359 optimal weight: 9.9990 chunk 696 optimal weight: 7.9990 chunk 269 optimal weight: 0.9990 chunk 423 optimal weight: 10.0000 chunk 518 optimal weight: 7.9990 chunk 806 optimal weight: 6.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN B 82 GLN C 182 GLN D 135 HIS D 221 HIS D 222 HIS D 301 GLN D 302 ASN ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN G 172 GLN H 179 ASN L 16 GLN L 65 HIS L 90 GLN M 97 ASN M 170 GLN U 189 GLN U 398 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 463 ASN U 632 GLN U 708 GLN U 749 GLN ** V 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 365 GLN W 107 GLN W 416 GLN X 283 GLN X 375 HIS ** Y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 32 GLN Z 72 HIS Z 194 GLN ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 229 GLN a 36 GLN a 168 ASN b 29 GLN b 79 GLN b 105 HIS c 77 GLN c 164 ASN c 274 ASN c 283 HIS ** d 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 355 ASN f 565 ASN f 786 GLN ** f 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 173 GLN ** u 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.104062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.071582 restraints weight = 140730.806| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.61 r_work: 0.2884 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 72503 Z= 0.294 Angle : 0.655 15.723 97952 Z= 0.338 Chirality : 0.043 0.240 11157 Planarity : 0.004 0.050 12612 Dihedral : 6.431 82.001 10000 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.65 % Favored : 97.34 % Rotamer: Outliers : 5.52 % Allowed : 28.55 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 0.87 (0.09), residues: 8913 helix: 1.06 (0.07), residues: 4995 sheet: -0.23 (0.16), residues: 970 loop : 0.27 (0.12), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 139 HIS 0.007 0.001 HIS f 472 PHE 0.033 0.002 PHE X 9 TYR 0.029 0.002 TYR U 444 ARG 0.011 0.001 ARG U 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1446 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 430 poor density : 1016 time to evaluate : 6.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ILE cc_start: 0.8403 (tp) cc_final: 0.8090 (tp) REVERT: A 54 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8566 (tm-30) REVERT: A 55 LEU cc_start: 0.8765 (mt) cc_final: 0.8312 (mp) REVERT: A 138 MET cc_start: 0.9260 (ttp) cc_final: 0.9046 (ttp) REVERT: A 186 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8424 (mttm) REVERT: B 48 LYS cc_start: 0.8975 (tppt) cc_final: 0.8189 (mppt) REVERT: B 51 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7741 (pt) REVERT: B 65 LEU cc_start: 0.9399 (mm) cc_final: 0.9168 (mm) REVERT: B 69 LYS cc_start: 0.9189 (tmmm) cc_final: 0.8791 (tmmt) REVERT: B 144 LEU cc_start: 0.8886 (mt) cc_final: 0.8683 (mp) REVERT: B 288 ASP cc_start: 0.8777 (p0) cc_final: 0.8434 (p0) REVERT: C 58 LEU cc_start: 0.8992 (tp) cc_final: 0.8675 (mp) REVERT: C 60 ARG cc_start: 0.9093 (mtp85) cc_final: 0.8744 (mtt-85) REVERT: C 83 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7882 (mmtm) REVERT: C 111 ASN cc_start: 0.9100 (m-40) cc_final: 0.8716 (t0) REVERT: C 112 CYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7429 (p) REVERT: C 130 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8179 (pptt) REVERT: C 209 CYS cc_start: 0.9049 (m) cc_final: 0.8735 (m) REVERT: C 230 MET cc_start: 0.9385 (mtt) cc_final: 0.9150 (mtp) REVERT: C 336 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8568 (mtm) REVERT: C 380 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8215 (tp40) REVERT: D 42 SER cc_start: 0.9219 (OUTLIER) cc_final: 0.9005 (p) REVERT: D 71 GLU cc_start: 0.9273 (tp30) cc_final: 0.8718 (mm-30) REVERT: D 337 ASP cc_start: 0.8261 (t0) cc_final: 0.7958 (m-30) REVERT: D 338 ARG cc_start: 0.8669 (ttt180) cc_final: 0.8385 (ttt90) REVERT: E 48 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8791 (mtmt) REVERT: E 122 MET cc_start: 0.9165 (mtt) cc_final: 0.8765 (mtt) REVERT: E 125 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: E 264 MET cc_start: 0.9238 (mtp) cc_final: 0.9008 (mtp) REVERT: E 277 MET cc_start: 0.9183 (mtt) cc_final: 0.8811 (mtt) REVERT: E 335 SER cc_start: 0.9443 (m) cc_final: 0.9080 (p) REVERT: F 69 MET cc_start: 0.5407 (ppp) cc_final: 0.5100 (pp-130) REVERT: F 277 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8903 (pt0) REVERT: F 325 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8514 (pm20) REVERT: F 349 ASP cc_start: 0.8977 (OUTLIER) cc_final: 0.8627 (m-30) REVERT: G 113 MET cc_start: 0.9013 (mmm) cc_final: 0.8687 (mmt) REVERT: G 147 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: G 232 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: H 124 SER cc_start: 0.8982 (OUTLIER) cc_final: 0.8724 (t) REVERT: H 165 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8661 (tttm) REVERT: H 179 ASN cc_start: 0.8265 (p0) cc_final: 0.7647 (p0) REVERT: H 181 ASP cc_start: 0.8777 (p0) cc_final: 0.8267 (p0) REVERT: H 209 GLU cc_start: 0.8741 (tt0) cc_final: 0.8000 (tt0) REVERT: I 210 LYS cc_start: 0.8504 (mtmp) cc_final: 0.7882 (mtmt) REVERT: I 232 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8603 (mt-10) REVERT: I 235 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8832 (tm-30) REVERT: J 30 SER cc_start: 0.9010 (m) cc_final: 0.8554 (p) REVERT: J 103 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8446 (t) REVERT: J 110 TYR cc_start: 0.9253 (t80) cc_final: 0.8730 (t80) REVERT: K 29 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8633 (mp0) REVERT: K 196 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8103 (ttpp) REVERT: L 68 ASN cc_start: 0.9312 (m-40) cc_final: 0.9086 (m-40) REVERT: L 180 MET cc_start: 0.9395 (mmm) cc_final: 0.9181 (mmm) REVERT: L 220 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8331 (tp30) REVERT: L 224 TYR cc_start: 0.9129 (m-80) cc_final: 0.8770 (m-80) REVERT: M 75 MET cc_start: 0.9479 (ttt) cc_final: 0.9005 (ttt) REVERT: M 114 ARG cc_start: 0.9004 (mmm160) cc_final: 0.8745 (mtp85) REVERT: U 76 GLU cc_start: 0.9067 (mp0) cc_final: 0.8857 (mp0) REVERT: U 98 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: U 131 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8271 (mm-30) REVERT: U 470 ASN cc_start: 0.7867 (t0) cc_final: 0.7309 (t0) REVERT: V 120 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7393 (t80) REVERT: V 212 TYR cc_start: 0.8901 (t80) cc_final: 0.8553 (t80) REVERT: V 279 GLN cc_start: 0.9043 (pm20) cc_final: 0.8748 (pm20) REVERT: V 318 GLN cc_start: 0.8723 (mm-40) cc_final: 0.7934 (mt0) REVERT: V 354 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8267 (ttmm) REVERT: V 399 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7498 (ttm-80) REVERT: V 515 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8108 (tm-30) REVERT: V 525 MET cc_start: 0.6737 (mpp) cc_final: 0.6211 (mpm) REVERT: W 73 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8267 (mpp) REVERT: W 118 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8069 (tt) REVERT: W 152 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8452 (mp) REVERT: W 161 GLU cc_start: 0.8320 (mp0) cc_final: 0.8054 (mp0) REVERT: W 168 GLU cc_start: 0.8408 (pp20) cc_final: 0.8171 (pp20) REVERT: W 348 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8712 (tp30) REVERT: W 383 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8398 (m-30) REVERT: W 436 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8669 (mtp) REVERT: W 443 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9001 (p) REVERT: X 329 ASN cc_start: 0.8696 (t0) cc_final: 0.8381 (m110) REVERT: X 332 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: X 394 ASP cc_start: 0.8027 (t0) cc_final: 0.7800 (t0) REVERT: Y 8 GLU cc_start: 0.7939 (pt0) cc_final: 0.7691 (pt0) REVERT: Y 42 MET cc_start: 0.8503 (mmm) cc_final: 0.8272 (mmt) REVERT: Y 184 GLN cc_start: 0.8903 (tt0) cc_final: 0.8688 (mt0) REVERT: Y 199 GLU cc_start: 0.8901 (tt0) cc_final: 0.8618 (tm-30) REVERT: Y 321 GLU cc_start: 0.9161 (tt0) cc_final: 0.8770 (tp30) REVERT: Y 368 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: Y 382 LYS cc_start: 0.8962 (ttmm) cc_final: 0.8669 (tttp) REVERT: Z 79 TYR cc_start: 0.8876 (t80) cc_final: 0.8418 (t80) REVERT: Z 143 GLU cc_start: 0.7348 (tm-30) cc_final: 0.7108 (tp30) REVERT: Z 177 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8611 (ttt-90) REVERT: Z 244 GLU cc_start: 0.8668 (mp0) cc_final: 0.8288 (pm20) REVERT: Z 283 ARG cc_start: 0.8346 (ttm110) cc_final: 0.7753 (ttm170) REVERT: a 40 GLN cc_start: 0.8334 (tt0) cc_final: 0.7755 (mm110) REVERT: a 127 ASP cc_start: 0.8390 (t0) cc_final: 0.8169 (t0) REVERT: a 182 CYS cc_start: 0.8711 (m) cc_final: 0.8502 (m) REVERT: a 231 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.7987 (tp-100) REVERT: a 316 SER cc_start: 0.9533 (OUTLIER) cc_final: 0.9254 (p) REVERT: b 11 ASP cc_start: 0.8509 (t0) cc_final: 0.7749 (t0) REVERT: b 108 ARG cc_start: 0.6783 (tpp80) cc_final: 0.6322 (tpp80) REVERT: b 139 ASP cc_start: 0.7464 (m-30) cc_final: 0.7178 (m-30) REVERT: c 227 GLU cc_start: 0.8435 (mp0) cc_final: 0.7949 (mp0) REVERT: c 236 GLU cc_start: 0.8969 (mp0) cc_final: 0.8680 (mp0) REVERT: c 257 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8457 (mtpp) REVERT: c 261 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8244 (mm-30) REVERT: c 303 MET cc_start: 0.9553 (OUTLIER) cc_final: 0.8929 (mtt) REVERT: d 123 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8939 (tt) REVERT: d 146 ASP cc_start: 0.8940 (m-30) cc_final: 0.8579 (m-30) REVERT: d 165 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8942 (mt-10) REVERT: d 269 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8806 (t70) REVERT: d 270 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8422 (tp30) REVERT: e 18 GLU cc_start: 0.8082 (pp20) cc_final: 0.7664 (pp20) REVERT: e 20 GLU cc_start: 0.8400 (pm20) cc_final: 0.8187 (pm20) REVERT: e 21 GLU cc_start: 0.8188 (pt0) cc_final: 0.7850 (pt0) REVERT: f 58 MET cc_start: 0.3869 (ppp) cc_final: 0.3380 (ppp) REVERT: f 118 ASN cc_start: 0.7737 (m-40) cc_final: 0.7349 (t0) REVERT: f 133 MET cc_start: 0.4360 (pmm) cc_final: 0.4072 (pmm) REVERT: f 168 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8101 (pttt) REVERT: f 224 ASN cc_start: 0.7790 (m-40) cc_final: 0.6868 (t0) REVERT: f 235 SER cc_start: 0.8889 (m) cc_final: 0.8460 (p) REVERT: f 279 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8647 (mp0) REVERT: f 294 MET cc_start: 0.6356 (mmt) cc_final: 0.5710 (mmt) REVERT: f 354 GLU cc_start: 0.8080 (mp0) cc_final: 0.7857 (mp0) REVERT: f 387 GLN cc_start: 0.8754 (tp40) cc_final: 0.6911 (pm20) REVERT: f 389 LYS cc_start: 0.8786 (tmmt) cc_final: 0.8524 (mtmt) REVERT: f 407 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7770 (mmm) REVERT: f 452 ASN cc_start: 0.8963 (t160) cc_final: 0.8701 (t0) REVERT: f 471 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7866 (mm) REVERT: f 680 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7252 (ttp80) REVERT: f 895 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: g 105 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7648 (mp) REVERT: u 129 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7669 (t80) REVERT: u 151 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7709 (ptp-170) REVERT: u 257 THR cc_start: 0.7833 (p) cc_final: 0.7586 (t) REVERT: u 266 ILE cc_start: 0.7509 (mt) cc_final: 0.7152 (tp) outliers start: 430 outliers final: 115 residues processed: 1351 average time/residue: 1.4361 time to fit residues: 2580.5039 Evaluate side-chains 1055 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 892 time to evaluate : 6.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 177 GLU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 380 GLN Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 325 GLN Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 232 GLU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 107 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 78 MET Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 90 ILE Chi-restraints excluded: chain M residue 143 ASN Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain U residue 98 GLU Chi-restraints excluded: chain U residue 112 CYS Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain U residue 233 LEU Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 514 LEU Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 892 LEU Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 176 MET Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 342 ILE Chi-restraints excluded: chain V residue 354 LYS Chi-restraints excluded: chain V residue 363 LEU Chi-restraints excluded: chain V residue 399 ARG Chi-restraints excluded: chain V residue 491 VAL Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 318 SER Chi-restraints excluded: chain W residue 348 GLU Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 241 SER Chi-restraints excluded: chain X residue 318 ILE Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 159 ARG Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 177 ARG Chi-restraints excluded: chain Z residue 268 SER Chi-restraints excluded: chain a residue 42 LEU Chi-restraints excluded: chain a residue 74 LEU Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 231 GLN Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 306 GLU Chi-restraints excluded: chain a residue 309 LEU Chi-restraints excluded: chain a residue 316 SER Chi-restraints excluded: chain b residue 41 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 204 THR Chi-restraints excluded: chain c residue 261 GLU Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 112 CYS Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 178 TYR Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 269 ASP Chi-restraints excluded: chain d residue 332 SER Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain f residue 205 CYS Chi-restraints excluded: chain f residue 230 CYS Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain f residue 333 LEU Chi-restraints excluded: chain f residue 407 MET Chi-restraints excluded: chain f residue 471 LEU Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 652 VAL Chi-restraints excluded: chain f residue 654 VAL Chi-restraints excluded: chain f residue 655 LEU Chi-restraints excluded: chain f residue 680 ARG Chi-restraints excluded: chain f residue 690 VAL Chi-restraints excluded: chain f residue 842 VAL Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain u residue 129 PHE Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 220 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 0.0670 chunk 396 optimal weight: 9.9990 chunk 706 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 594 optimal weight: 0.0470 chunk 135 optimal weight: 4.9990 chunk 397 optimal weight: 5.9990 chunk 661 optimal weight: 4.9990 chunk 458 optimal weight: 1.9990 chunk 871 optimal weight: 5.9990 overall best weight: 2.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 HIS D 135 HIS D 390 ASN G 172 GLN H 179 ASN I 155 ASN M 97 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 GLN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 375 HIS ** Y 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 72 HIS Z 194 GLN ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN a 370 GLN b 47 ASN b 79 GLN b 101 GLN b 169 HIS c 101 GLN d 103 ASN ** d 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 355 ASN ** u 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.103019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.070513 restraints weight = 141289.159| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.63 r_work: 0.2867 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 72503 Z= 0.282 Angle : 0.602 10.597 97952 Z= 0.309 Chirality : 0.042 0.252 11157 Planarity : 0.004 0.049 12612 Dihedral : 6.157 80.569 9950 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.63 % Favored : 97.36 % Rotamer: Outliers : 5.08 % Allowed : 27.53 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 0.97 (0.09), residues: 8913 helix: 1.19 (0.07), residues: 5005 sheet: -0.32 (0.16), residues: 986 loop : 0.25 (0.12), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 34 HIS 0.010 0.001 HIS C 90 PHE 0.019 0.001 PHE X 9 TYR 0.029 0.001 TYR U 444 ARG 0.009 0.001 ARG b 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 396 poor density : 966 time to evaluate : 6.247 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 51 ASP cc_start: 0.8856 (t0) cc_final: 0.8527 (t0) REVERT: A 54 GLN cc_start: 0.8826 (tm-30) cc_final: 0.8581 (tm-30) REVERT: A 55 LEU cc_start: 0.8468 (mt) cc_final: 0.8077 (mt) REVERT: A 85 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8327 (tp40) REVERT: A 128 GLN cc_start: 0.9068 (OUTLIER) cc_final: 0.8079 (tm-30) REVERT: A 138 MET cc_start: 0.9310 (ttp) cc_final: 0.9065 (ttp) REVERT: A 186 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8438 (mttm) REVERT: A 400 ARG cc_start: 0.8573 (mmp80) cc_final: 0.8176 (tpp-160) REVERT: B 51 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7788 (pt) REVERT: B 69 LYS cc_start: 0.9078 (tmmm) cc_final: 0.8770 (tmmt) REVERT: B 118 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8181 (m-30) REVERT: B 276 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: C 60 ARG cc_start: 0.9097 (mtp85) cc_final: 0.8881 (mtt-85) REVERT: C 83 LYS cc_start: 0.8259 (mmmt) cc_final: 0.8048 (mmtm) REVERT: C 111 ASN cc_start: 0.9200 (m-40) cc_final: 0.8732 (t0) REVERT: C 112 CYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7623 (p) REVERT: C 130 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8237 (pptt) REVERT: C 150 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8762 (ptm) REVERT: C 290 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8288 (mmpt) REVERT: C 297 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8342 (ttp-110) REVERT: D 60 TYR cc_start: 0.9327 (OUTLIER) cc_final: 0.8713 (t80) REVERT: D 71 GLU cc_start: 0.9302 (tp30) cc_final: 0.8842 (mm-30) REVERT: D 153 MET cc_start: 0.9192 (mtm) cc_final: 0.8904 (mtm) REVERT: D 337 ASP cc_start: 0.8245 (t0) cc_final: 0.7911 (m-30) REVERT: E 122 MET cc_start: 0.9244 (mtt) cc_final: 0.8826 (mtt) REVERT: E 125 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: E 264 MET cc_start: 0.9209 (mtp) cc_final: 0.8966 (mtp) REVERT: E 277 MET cc_start: 0.9260 (mtt) cc_final: 0.8828 (mtt) REVERT: E 335 SER cc_start: 0.9479 (m) cc_final: 0.9162 (t) REVERT: F 69 MET cc_start: 0.5412 (ppp) cc_final: 0.5027 (pp-130) REVERT: F 249 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9003 (mp) REVERT: F 349 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8673 (m-30) REVERT: G 19 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8696 (mp0) REVERT: G 92 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8372 (tm-30) REVERT: G 113 MET cc_start: 0.9038 (mmm) cc_final: 0.8708 (mmt) REVERT: G 147 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: H 165 LYS cc_start: 0.9198 (ttpp) cc_final: 0.8723 (tttm) REVERT: H 209 GLU cc_start: 0.8750 (tt0) cc_final: 0.8151 (tt0) REVERT: I 174 MET cc_start: 0.8458 (mtp) cc_final: 0.8256 (ttm) REVERT: I 178 ASP cc_start: 0.9147 (m-30) cc_final: 0.8867 (m-30) REVERT: I 201 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8256 (mtm) REVERT: I 210 LYS cc_start: 0.8596 (mtmp) cc_final: 0.8023 (mtmt) REVERT: I 232 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8621 (mt-10) REVERT: J 30 SER cc_start: 0.9047 (m) cc_final: 0.8651 (p) REVERT: J 103 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8481 (t) REVERT: J 110 TYR cc_start: 0.9271 (t80) cc_final: 0.8666 (t80) REVERT: J 239 ASN cc_start: 0.9207 (m-40) cc_final: 0.8982 (m110) REVERT: K 20 ARG cc_start: 0.8643 (mtp-110) cc_final: 0.8348 (mtp85) REVERT: K 29 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: K 65 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8171 (pm20) REVERT: K 91 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8588 (tppt) REVERT: K 95 GLU cc_start: 0.8941 (tp30) cc_final: 0.8710 (tp30) REVERT: K 147 ASP cc_start: 0.8160 (p0) cc_final: 0.7954 (p0) REVERT: K 196 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8154 (ttpp) REVERT: L 45 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8520 (p) REVERT: L 68 ASN cc_start: 0.9359 (m-40) cc_final: 0.9096 (m-40) REVERT: L 220 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8368 (tp30) REVERT: L 224 TYR cc_start: 0.9100 (m-80) cc_final: 0.8798 (m-80) REVERT: M 75 MET cc_start: 0.9503 (ttt) cc_final: 0.9138 (ttt) REVERT: M 223 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.7934 (ttp80) REVERT: U 76 GLU cc_start: 0.9148 (mp0) cc_final: 0.8888 (mp0) REVERT: U 98 GLU cc_start: 0.8045 (mp0) cc_final: 0.7777 (mp0) REVERT: U 131 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8186 (mm-30) REVERT: U 240 ASP cc_start: 0.8781 (t0) cc_final: 0.8563 (t0) REVERT: U 470 ASN cc_start: 0.7924 (t0) cc_final: 0.7557 (t0) REVERT: U 479 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9222 (mp) REVERT: U 542 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8332 (mt-10) REVERT: U 714 SER cc_start: 0.9284 (OUTLIER) cc_final: 0.9051 (p) REVERT: V 95 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8656 (mm) REVERT: V 99 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7937 (tmt170) REVERT: V 139 MET cc_start: 0.6311 (pmm) cc_final: 0.6078 (ppp) REVERT: V 279 GLN cc_start: 0.9063 (pm20) cc_final: 0.8562 (pm20) REVERT: V 318 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8394 (mp10) REVERT: V 354 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8372 (ttmm) REVERT: V 399 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7533 (ttm-80) REVERT: V 515 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8252 (tm-30) REVERT: V 519 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8203 (tm) REVERT: V 520 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8239 (mm-30) REVERT: W 40 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8585 (tm) REVERT: W 118 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8156 (tt) REVERT: W 161 GLU cc_start: 0.8504 (mp0) cc_final: 0.8030 (mp0) REVERT: W 168 GLU cc_start: 0.8604 (pp20) cc_final: 0.8313 (pp20) REVERT: W 312 MET cc_start: 0.9161 (mmt) cc_final: 0.8934 (mmp) REVERT: W 348 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8809 (tp30) REVERT: W 383 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8369 (m-30) REVERT: W 436 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8751 (mtp) REVERT: W 443 THR cc_start: 0.9396 (OUTLIER) cc_final: 0.8962 (p) REVERT: X 72 TYR cc_start: 0.8401 (t80) cc_final: 0.8115 (t80) REVERT: X 246 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8163 (mtpp) REVERT: X 258 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8550 (tppt) REVERT: X 277 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9169 (mm) REVERT: X 329 ASN cc_start: 0.8802 (t0) cc_final: 0.8460 (m110) REVERT: X 332 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: X 389 ASP cc_start: 0.8562 (p0) cc_final: 0.8124 (p0) REVERT: X 394 ASP cc_start: 0.7921 (t0) cc_final: 0.7644 (t0) REVERT: Y 8 GLU cc_start: 0.7980 (pt0) cc_final: 0.7765 (pt0) REVERT: Y 42 MET cc_start: 0.8597 (mmm) cc_final: 0.8198 (mmp) REVERT: Y 50 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8790 (mtp) REVERT: Y 196 GLN cc_start: 0.9274 (tt0) cc_final: 0.8999 (tt0) REVERT: Y 199 GLU cc_start: 0.8897 (tt0) cc_final: 0.8668 (tm-30) REVERT: Y 238 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8569 (mp0) REVERT: Y 321 GLU cc_start: 0.9151 (tt0) cc_final: 0.8774 (tp30) REVERT: Y 368 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: Z 143 GLU cc_start: 0.7429 (tm-30) cc_final: 0.7083 (tp30) REVERT: Z 156 GLU cc_start: 0.9130 (tt0) cc_final: 0.8852 (tt0) REVERT: Z 177 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8621 (ttt-90) REVERT: Z 244 GLU cc_start: 0.8731 (mp0) cc_final: 0.8381 (pm20) REVERT: Z 283 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7838 (ttm170) REVERT: Z 288 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8217 (pttt) REVERT: a 40 GLN cc_start: 0.8396 (tt0) cc_final: 0.7713 (mm-40) REVERT: a 127 ASP cc_start: 0.8495 (t0) cc_final: 0.8209 (t0) REVERT: a 231 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7965 (tp-100) REVERT: a 306 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8837 (pm20) REVERT: a 316 SER cc_start: 0.9573 (OUTLIER) cc_final: 0.9293 (p) REVERT: b 11 ASP cc_start: 0.8680 (t0) cc_final: 0.8140 (t0) REVERT: b 42 ARG cc_start: 0.8649 (mtm110) cc_final: 0.8432 (ptp-110) REVERT: b 47 ASN cc_start: 0.7807 (OUTLIER) cc_final: 0.7331 (m-40) REVERT: b 108 ARG cc_start: 0.7015 (tpp80) cc_final: 0.6540 (tpp80) REVERT: c 226 MET cc_start: 0.8842 (mpp) cc_final: 0.8621 (mpp) REVERT: c 227 GLU cc_start: 0.8568 (mp0) cc_final: 0.8018 (mp0) REVERT: c 236 GLU cc_start: 0.9108 (mp0) cc_final: 0.8694 (mp0) REVERT: c 257 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8452 (mtpp) REVERT: c 261 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8247 (mm-30) REVERT: c 303 MET cc_start: 0.9552 (OUTLIER) cc_final: 0.8919 (mtt) REVERT: d 146 ASP cc_start: 0.9015 (m-30) cc_final: 0.8614 (m-30) REVERT: d 265 ASP cc_start: 0.8566 (m-30) cc_final: 0.8359 (m-30) REVERT: d 269 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8778 (t70) REVERT: d 299 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8065 (tpp) REVERT: e 18 GLU cc_start: 0.8182 (pp20) cc_final: 0.7649 (pp20) REVERT: e 20 GLU cc_start: 0.8445 (pm20) cc_final: 0.7995 (pm20) REVERT: e 21 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7948 (pt0) REVERT: f 118 ASN cc_start: 0.7712 (m-40) cc_final: 0.7286 (t0) REVERT: f 168 LYS cc_start: 0.8519 (mmmt) cc_final: 0.8073 (mmtt) REVERT: f 207 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8573 (tp) REVERT: f 224 ASN cc_start: 0.8073 (m-40) cc_final: 0.6783 (t0) REVERT: f 235 SER cc_start: 0.8931 (m) cc_final: 0.8436 (p) REVERT: f 275 MET cc_start: 0.9149 (tpp) cc_final: 0.8797 (tpp) REVERT: f 294 MET cc_start: 0.6956 (mmt) cc_final: 0.6229 (mmt) REVERT: f 319 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7930 (tp30) REVERT: f 354 GLU cc_start: 0.8130 (mp0) cc_final: 0.7850 (mp0) REVERT: f 389 LYS cc_start: 0.8820 (tmmt) cc_final: 0.8546 (ttmt) REVERT: f 407 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7628 (mmm) REVERT: f 452 ASN cc_start: 0.9052 (t160) cc_final: 0.8714 (t0) REVERT: f 560 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8721 (pp) REVERT: f 670 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8263 (mpp) REVERT: f 680 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7416 (ttp80) REVERT: f 788 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.7924 (tpp) REVERT: f 895 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7853 (pt0) REVERT: g 132 ASN cc_start: 0.6608 (OUTLIER) cc_final: 0.6149 (p0) REVERT: g 134 LYS cc_start: 0.6107 (pptt) cc_final: 0.5731 (pptt) REVERT: u 140 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: u 157 LEU cc_start: 0.7736 (tt) cc_final: 0.7387 (tm) REVERT: u 220 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7794 (tm) REVERT: u 225 ILE cc_start: 0.7253 (pt) cc_final: 0.6539 (pt) REVERT: u 237 LYS cc_start: 0.8613 (mptp) cc_final: 0.8149 (mppt) outliers start: 396 outliers final: 124 residues processed: 1262 average time/residue: 1.4187 time to fit residues: 2383.0471 Evaluate side-chains 1047 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 860 time to evaluate : 6.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 90 HIS Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 130 LYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 249 LEU Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 179 ASN Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain I residue 232 GLU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 196 LYS Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain U residue 112 CYS Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain U residue 200 VAL Chi-restraints excluded: chain U residue 233 LEU Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 479 LEU Chi-restraints excluded: chain U residue 514 LEU Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 890 LYS Chi-restraints excluded: chain U residue 892 LEU Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 342 ILE Chi-restraints excluded: chain V residue 354 LYS Chi-restraints excluded: chain V residue 399 ARG Chi-restraints excluded: chain V residue 491 VAL Chi-restraints excluded: chain V residue 516 GLN Chi-restraints excluded: chain V residue 519 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 272 LEU Chi-restraints excluded: chain W residue 348 GLU Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 241 SER Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 246 LYS Chi-restraints excluded: chain X residue 258 LYS Chi-restraints excluded: chain X residue 277 LEU Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 159 ARG Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain Z residue 177 ARG Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 288 LYS Chi-restraints excluded: chain a residue 74 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 145 LEU Chi-restraints excluded: chain a residue 231 GLN Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 309 LEU Chi-restraints excluded: chain a residue 316 SER Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 47 ASN Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 75 MET Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 204 THR Chi-restraints excluded: chain c residue 263 ASP Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 201 SER Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 269 ASP Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain f residue 205 CYS Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 230 CYS Chi-restraints excluded: chain f residue 237 VAL Chi-restraints excluded: chain f residue 246 SER Chi-restraints excluded: chain f residue 271 MET Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 407 MET Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 527 VAL Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 560 LEU Chi-restraints excluded: chain f residue 652 VAL Chi-restraints excluded: chain f residue 670 MET Chi-restraints excluded: chain f residue 680 ARG Chi-restraints excluded: chain f residue 690 VAL Chi-restraints excluded: chain f residue 788 MET Chi-restraints excluded: chain f residue 830 LEU Chi-restraints excluded: chain f residue 842 VAL Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 111 GLU Chi-restraints excluded: chain g residue 132 ASN Chi-restraints excluded: chain u residue 129 PHE Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 428 optimal weight: 7.9990 chunk 348 optimal weight: 4.9990 chunk 451 optimal weight: 6.9990 chunk 825 optimal weight: 0.0170 chunk 575 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 536 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 533 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 769 optimal weight: 6.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN B 425 ASN C 90 HIS C 343 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN F 325 GLN G 172 GLN G 193 GLN H 179 ASN M 97 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 453 HIS U 698 GLN V 282 ASN ** V 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 375 HIS Y 184 GLN Z 194 GLN ** Z 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN b 47 ASN b 169 HIS c 164 ASN d 103 ASN ** u 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 251 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.069951 restraints weight = 141807.772| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.61 r_work: 0.2855 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 72503 Z= 0.287 Angle : 0.594 11.436 97952 Z= 0.301 Chirality : 0.042 0.277 11157 Planarity : 0.004 0.046 12612 Dihedral : 6.128 80.112 9944 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 4.81 % Allowed : 27.98 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 1.04 (0.09), residues: 8913 helix: 1.26 (0.07), residues: 5015 sheet: -0.31 (0.16), residues: 966 loop : 0.26 (0.12), residues: 2932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 34 HIS 0.017 0.001 HIS C 90 PHE 0.019 0.001 PHE a 63 TYR 0.025 0.001 TYR U 444 ARG 0.011 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1293 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 375 poor density : 918 time to evaluate : 6.368 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 51 ASP cc_start: 0.8910 (t0) cc_final: 0.8559 (t0) REVERT: A 52 ILE cc_start: 0.8359 (tp) cc_final: 0.8150 (pp) REVERT: A 54 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8550 (tm-30) REVERT: A 55 LEU cc_start: 0.8437 (mt) cc_final: 0.7959 (mt) REVERT: A 85 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8348 (tp40) REVERT: A 138 MET cc_start: 0.9338 (ttp) cc_final: 0.9079 (ttp) REVERT: A 186 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8425 (mttm) REVERT: A 400 ARG cc_start: 0.8557 (mmp80) cc_final: 0.8165 (tpp-160) REVERT: B 69 LYS cc_start: 0.9098 (tmmm) cc_final: 0.8751 (tmmt) REVERT: B 118 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8240 (m-30) REVERT: B 276 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: B 377 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8219 (t0) REVERT: B 405 MET cc_start: 0.9269 (mmt) cc_final: 0.8867 (mtt) REVERT: C 83 LYS cc_start: 0.8311 (mmmt) cc_final: 0.8098 (mmtm) REVERT: C 112 CYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7530 (p) REVERT: C 149 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8779 (pt0) REVERT: C 150 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8736 (ptm) REVERT: C 290 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8325 (mmpt) REVERT: C 297 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8346 (ttp-110) REVERT: D 42 SER cc_start: 0.9224 (OUTLIER) cc_final: 0.8948 (p) REVERT: D 60 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.8689 (t80) REVERT: D 71 GLU cc_start: 0.9322 (tp30) cc_final: 0.8703 (mm-30) REVERT: D 153 MET cc_start: 0.9200 (mtm) cc_final: 0.8924 (mtm) REVERT: D 337 ASP cc_start: 0.8256 (t0) cc_final: 0.7990 (m-30) REVERT: E 48 LYS cc_start: 0.9289 (mtpp) cc_final: 0.9059 (mtmt) REVERT: E 100 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8499 (mt) REVERT: E 122 MET cc_start: 0.9241 (mtt) cc_final: 0.8817 (mtt) REVERT: E 125 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: E 264 MET cc_start: 0.9222 (mtp) cc_final: 0.8959 (mtp) REVERT: E 277 MET cc_start: 0.9240 (mtt) cc_final: 0.8765 (mtt) REVERT: E 335 SER cc_start: 0.9481 (m) cc_final: 0.9164 (t) REVERT: F 69 MET cc_start: 0.5362 (ppp) cc_final: 0.5081 (pp-130) REVERT: F 299 GLU cc_start: 0.8694 (mp0) cc_final: 0.8444 (mp0) REVERT: F 349 ASP cc_start: 0.9050 (OUTLIER) cc_final: 0.8673 (m-30) REVERT: F 434 ASN cc_start: 0.8054 (OUTLIER) cc_final: 0.7824 (t0) REVERT: G 19 GLU cc_start: 0.9227 (OUTLIER) cc_final: 0.8689 (mp0) REVERT: G 61 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8804 (tt) REVERT: G 92 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8375 (tm-30) REVERT: G 113 MET cc_start: 0.9009 (mmm) cc_final: 0.8722 (mmt) REVERT: G 130 GLU cc_start: 0.8519 (pm20) cc_final: 0.8107 (pm20) REVERT: G 147 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: G 223 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8833 (tm-30) REVERT: G 232 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8289 (mm-30) REVERT: H 165 LYS cc_start: 0.9163 (ttpp) cc_final: 0.8696 (tttm) REVERT: H 179 ASN cc_start: 0.8669 (p0) cc_final: 0.8034 (p0) REVERT: H 181 ASP cc_start: 0.8768 (p0) cc_final: 0.8325 (p0) REVERT: H 209 GLU cc_start: 0.8730 (tt0) cc_final: 0.8174 (tt0) REVERT: I 108 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8211 (tp30) REVERT: I 210 LYS cc_start: 0.8555 (mtmp) cc_final: 0.7965 (mtmt) REVERT: I 232 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8595 (mt-10) REVERT: J 30 SER cc_start: 0.9098 (m) cc_final: 0.8706 (p) REVERT: J 103 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8484 (t) REVERT: J 110 TYR cc_start: 0.9235 (t80) cc_final: 0.8635 (t80) REVERT: J 177 THR cc_start: 0.8955 (OUTLIER) cc_final: 0.8736 (p) REVERT: J 239 ASN cc_start: 0.9183 (m-40) cc_final: 0.8939 (m110) REVERT: K 65 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8150 (pm20) REVERT: K 91 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8572 (tppt) REVERT: K 95 GLU cc_start: 0.8963 (tp30) cc_final: 0.8733 (tp30) REVERT: L 68 ASN cc_start: 0.9336 (m-40) cc_final: 0.9091 (m-40) REVERT: L 220 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8343 (tp30) REVERT: L 224 TYR cc_start: 0.9073 (m-80) cc_final: 0.8747 (m-80) REVERT: M 75 MET cc_start: 0.9515 (ttt) cc_final: 0.9249 (ttt) REVERT: M 223 ARG cc_start: 0.8201 (ttp-110) cc_final: 0.7849 (ttp-110) REVERT: U 76 GLU cc_start: 0.9118 (mp0) cc_final: 0.8865 (mp0) REVERT: U 131 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8258 (mm-30) REVERT: U 239 GLU cc_start: 0.8960 (tp30) cc_final: 0.8579 (mp0) REVERT: U 240 ASP cc_start: 0.8922 (t0) cc_final: 0.8713 (t0) REVERT: U 252 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9233 (mm) REVERT: U 470 ASN cc_start: 0.7997 (t0) cc_final: 0.7522 (t0) REVERT: U 479 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9238 (mp) REVERT: U 714 SER cc_start: 0.9266 (OUTLIER) cc_final: 0.9003 (p) REVERT: V 95 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8624 (mm) REVERT: V 99 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.7960 (tmt170) REVERT: V 120 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.6999 (t80) REVERT: V 266 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8780 (mp10) REVERT: V 279 GLN cc_start: 0.8927 (pm20) cc_final: 0.8688 (pm20) REVERT: V 354 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8356 (ttmm) REVERT: V 399 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7524 (ttm-80) REVERT: V 515 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8289 (tm-30) REVERT: V 519 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8249 (tm) REVERT: V 520 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8273 (mm-30) REVERT: W 40 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8609 (tp) REVERT: W 73 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8375 (mpp) REVERT: W 118 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8122 (tt) REVERT: W 161 GLU cc_start: 0.8540 (mp0) cc_final: 0.8035 (mp0) REVERT: W 168 GLU cc_start: 0.8637 (pp20) cc_final: 0.8358 (pp20) REVERT: W 203 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8486 (tm-30) REVERT: W 312 MET cc_start: 0.9157 (mmt) cc_final: 0.8944 (mpp) REVERT: W 340 VAL cc_start: 0.9190 (t) cc_final: 0.8982 (t) REVERT: W 348 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8768 (tp30) REVERT: W 383 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8326 (m-30) REVERT: W 436 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8753 (mtp) REVERT: W 443 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.8974 (p) REVERT: X 72 TYR cc_start: 0.8372 (t80) cc_final: 0.8092 (t80) REVERT: X 223 LYS cc_start: 0.8669 (mmmm) cc_final: 0.8253 (mmpt) REVERT: X 277 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9222 (mp) REVERT: X 329 ASN cc_start: 0.8802 (t0) cc_final: 0.8456 (m110) REVERT: X 332 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: X 389 ASP cc_start: 0.8590 (p0) cc_final: 0.8154 (p0) REVERT: X 394 ASP cc_start: 0.7878 (t0) cc_final: 0.7554 (t0) REVERT: Y 42 MET cc_start: 0.8587 (mmm) cc_final: 0.8179 (mmp) REVERT: Y 50 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.8775 (mtp) REVERT: Y 196 GLN cc_start: 0.9277 (tt0) cc_final: 0.9000 (tt0) REVERT: Y 199 GLU cc_start: 0.8855 (tt0) cc_final: 0.8651 (tm-30) REVERT: Y 238 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8531 (mp0) REVERT: Y 321 GLU cc_start: 0.9162 (tt0) cc_final: 0.8783 (tp30) REVERT: Y 368 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: Z 79 TYR cc_start: 0.8765 (t80) cc_final: 0.8228 (t80) REVERT: Z 143 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7031 (tm-30) REVERT: Z 177 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8688 (ttt-90) REVERT: Z 244 GLU cc_start: 0.8751 (mp0) cc_final: 0.8410 (pm20) REVERT: Z 283 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7905 (ttm170) REVERT: a 40 GLN cc_start: 0.8448 (tt0) cc_final: 0.7784 (mm-40) REVERT: a 103 LYS cc_start: 0.9097 (ptpt) cc_final: 0.8746 (mtmt) REVERT: a 109 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8884 (mm-30) REVERT: a 127 ASP cc_start: 0.8447 (t0) cc_final: 0.8116 (t0) REVERT: a 231 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.7951 (tp-100) REVERT: a 306 GLU cc_start: 0.9353 (mt-10) cc_final: 0.8847 (pm20) REVERT: a 312 MET cc_start: 0.9324 (mmm) cc_final: 0.8998 (mtm) REVERT: a 316 SER cc_start: 0.9571 (OUTLIER) cc_final: 0.9280 (p) REVERT: b 11 ASP cc_start: 0.8692 (t0) cc_final: 0.8171 (t0) REVERT: b 108 ARG cc_start: 0.7016 (tpp80) cc_final: 0.6388 (tpp80) REVERT: b 139 ASP cc_start: 0.7578 (m-30) cc_final: 0.7127 (m-30) REVERT: b 147 GLU cc_start: 0.8858 (pm20) cc_final: 0.8631 (pm20) REVERT: c 32 TYR cc_start: 0.8818 (m-80) cc_final: 0.8580 (m-80) REVERT: c 106 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8656 (mp0) REVERT: c 152 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.9045 (mttp) REVERT: c 227 GLU cc_start: 0.8572 (mp0) cc_final: 0.7998 (mp0) REVERT: c 236 GLU cc_start: 0.9128 (mp0) cc_final: 0.8657 (mp0) REVERT: c 257 LYS cc_start: 0.8769 (mtpt) cc_final: 0.8433 (mtpp) REVERT: c 261 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8227 (mm-30) REVERT: c 303 MET cc_start: 0.9538 (OUTLIER) cc_final: 0.9334 (mtm) REVERT: d 140 GLN cc_start: 0.8928 (mt0) cc_final: 0.8523 (mt0) REVERT: d 146 ASP cc_start: 0.9052 (m-30) cc_final: 0.8663 (m-30) REVERT: d 158 ARG cc_start: 0.8519 (ptm160) cc_final: 0.8216 (ttm110) REVERT: d 261 ASP cc_start: 0.9189 (p0) cc_final: 0.8907 (p0) REVERT: d 270 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8218 (tp30) REVERT: d 299 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7798 (tpt) REVERT: d 332 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8824 (m) REVERT: e 18 GLU cc_start: 0.8129 (pp20) cc_final: 0.7619 (pp20) REVERT: e 20 GLU cc_start: 0.8479 (pm20) cc_final: 0.8031 (pm20) REVERT: e 21 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: e 57 ARG cc_start: 0.8875 (mtp85) cc_final: 0.8575 (ttm-80) REVERT: e 61 GLU cc_start: 0.8157 (pm20) cc_final: 0.7816 (pm20) REVERT: f 118 ASN cc_start: 0.7721 (m-40) cc_final: 0.7259 (t0) REVERT: f 168 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8044 (mmtt) REVERT: f 207 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8625 (tp) REVERT: f 209 MET cc_start: 0.7754 (mtm) cc_final: 0.7549 (mtm) REVERT: f 224 ASN cc_start: 0.8057 (m-40) cc_final: 0.6702 (t0) REVERT: f 235 SER cc_start: 0.8888 (m) cc_final: 0.8367 (p) REVERT: f 275 MET cc_start: 0.9182 (tpp) cc_final: 0.8413 (tpp) REVERT: f 279 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8341 (mp0) REVERT: f 294 MET cc_start: 0.7141 (mmt) cc_final: 0.6502 (mmt) REVERT: f 319 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7999 (tp30) REVERT: f 354 GLU cc_start: 0.8121 (mp0) cc_final: 0.7634 (mp0) REVERT: f 389 LYS cc_start: 0.8684 (tmmt) cc_final: 0.8462 (ttmt) REVERT: f 407 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7527 (mmm) REVERT: f 440 ILE cc_start: 0.8229 (mp) cc_final: 0.7941 (mt) REVERT: f 452 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8687 (t0) REVERT: f 466 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8571 (mm) REVERT: f 471 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7810 (mm) REVERT: f 560 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8720 (pp) REVERT: f 670 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8271 (mpp) REVERT: f 680 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7536 (ttp80) REVERT: f 788 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7853 (tpp) REVERT: f 895 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: g 101 LEU cc_start: 0.4026 (OUTLIER) cc_final: 0.3441 (mm) REVERT: g 132 ASN cc_start: 0.6661 (OUTLIER) cc_final: 0.6204 (t0) REVERT: g 142 LEU cc_start: 0.6905 (tm) cc_final: 0.6230 (mt) REVERT: u 129 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7820 (t80) REVERT: u 140 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: u 220 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7883 (tm) REVERT: u 225 ILE cc_start: 0.7390 (pt) cc_final: 0.6514 (pt) outliers start: 375 outliers final: 137 residues processed: 1193 average time/residue: 1.4122 time to fit residues: 2240.2040 Evaluate side-chains 1073 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 862 time to evaluate : 6.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain C residue 65 LEU 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 167 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 209 LYS Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 434 ASN Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 232 GLU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain U residue 112 CYS Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain U residue 233 LEU Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 479 LEU Chi-restraints excluded: chain U residue 514 LEU Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 890 LYS Chi-restraints excluded: chain U residue 892 LEU Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 266 GLN Chi-restraints excluded: chain V residue 342 ILE Chi-restraints excluded: chain V residue 354 LYS Chi-restraints excluded: chain V residue 399 ARG Chi-restraints excluded: chain V residue 491 VAL Chi-restraints excluded: chain V residue 516 GLN Chi-restraints excluded: chain V residue 519 LEU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 169 LEU Chi-restraints excluded: chain W residue 203 GLN Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 348 GLU Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain W residue 443 THR Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 241 SER Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 277 LEU Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 67 VAL Chi-restraints excluded: chain Y residue 159 ARG Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 368 GLU Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain Z residue 177 ARG Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 283 ARG Chi-restraints excluded: chain a residue 74 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 87 MET Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 231 GLN Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 299 SER Chi-restraints excluded: chain a residue 309 LEU Chi-restraints excluded: chain a residue 316 SER Chi-restraints excluded: chain a residue 375 LEU Chi-restraints excluded: chain b residue 2 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 152 LYS Chi-restraints excluded: chain c residue 204 THR Chi-restraints excluded: chain c residue 230 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 332 SER Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain f residue 205 CYS Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 230 CYS Chi-restraints excluded: chain f residue 237 VAL Chi-restraints excluded: chain f residue 246 SER Chi-restraints excluded: chain f residue 271 MET Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 407 MET Chi-restraints excluded: chain f residue 452 ASN Chi-restraints excluded: chain f residue 466 LEU Chi-restraints excluded: chain f residue 471 LEU Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 560 LEU Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 652 VAL Chi-restraints excluded: chain f residue 670 MET Chi-restraints excluded: chain f residue 680 ARG Chi-restraints excluded: chain f residue 690 VAL Chi-restraints excluded: chain f residue 788 MET Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 830 LEU Chi-restraints excluded: chain f residue 842 VAL Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 111 GLU Chi-restraints excluded: chain g residue 132 ASN Chi-restraints excluded: chain u residue 129 PHE Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 150 LEU Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 347 optimal weight: 3.9990 chunk 362 optimal weight: 7.9990 chunk 635 optimal weight: 0.9990 chunk 511 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 767 optimal weight: 0.9980 chunk 381 optimal weight: 0.8980 chunk 256 optimal weight: 4.9990 chunk 550 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 386 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 197 HIS C 90 HIS C 111 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN G 193 GLN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 283 ASN ** V 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 235 GLN X 127 GLN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 375 HIS Y 184 GLN Z 194 GLN Z 202 ASN ** Z 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN b 30 GLN b 169 HIS ** c 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 242 ASN u 251 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.104086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.071923 restraints weight = 141025.248| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.61 r_work: 0.2898 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 72503 Z= 0.178 Angle : 0.567 12.299 97952 Z= 0.285 Chirality : 0.041 0.299 11157 Planarity : 0.004 0.058 12612 Dihedral : 5.976 78.353 9944 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.49 % Favored : 97.50 % Rotamer: Outliers : 4.38 % Allowed : 28.29 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 1.16 (0.09), residues: 8913 helix: 1.37 (0.07), residues: 5015 sheet: -0.31 (0.16), residues: 982 loop : 0.30 (0.12), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP W 263 HIS 0.008 0.001 HIS C 90 PHE 0.018 0.001 PHE a 63 TYR 0.027 0.001 TYR f 349 ARG 0.011 0.001 ARG b 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 341 poor density : 999 time to evaluate : 6.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8964 (t0) cc_final: 0.8640 (t0) REVERT: A 52 ILE cc_start: 0.8324 (tp) cc_final: 0.8045 (pp) REVERT: A 54 GLN cc_start: 0.8885 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 55 LEU cc_start: 0.8520 (mt) cc_final: 0.8043 (mt) REVERT: A 85 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8382 (tp-100) REVERT: A 138 MET cc_start: 0.9294 (ttp) cc_final: 0.9058 (ttp) REVERT: A 158 ASP cc_start: 0.8759 (t0) cc_final: 0.8309 (t0) REVERT: A 186 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8439 (mttm) REVERT: A 366 ARG cc_start: 0.8847 (mmm-85) cc_final: 0.8484 (ttt90) REVERT: A 400 ARG cc_start: 0.8531 (mmp80) cc_final: 0.8306 (mmp80) REVERT: B 48 LYS cc_start: 0.8715 (tppp) cc_final: 0.7939 (mppt) REVERT: B 69 LYS cc_start: 0.9139 (tmmm) cc_final: 0.8762 (tmmt) REVERT: B 118 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8204 (m-30) REVERT: B 276 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: B 302 GLU cc_start: 0.8812 (mp0) cc_final: 0.7979 (mm-30) REVERT: B 377 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8164 (t0) REVERT: B 405 MET cc_start: 0.9247 (mmt) cc_final: 0.8908 (mtt) REVERT: C 83 LYS cc_start: 0.8297 (mmmt) cc_final: 0.8013 (mmtm) REVERT: C 112 CYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7460 (p) REVERT: C 150 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8706 (ptm) REVERT: C 290 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8213 (mmpt) REVERT: C 297 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8304 (ttp-110) REVERT: D 60 TYR cc_start: 0.9271 (OUTLIER) cc_final: 0.8712 (t80) REVERT: D 63 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8597 (t0) REVERT: D 71 GLU cc_start: 0.9280 (tp30) cc_final: 0.9023 (mm-30) REVERT: D 153 MET cc_start: 0.9170 (mtm) cc_final: 0.8913 (mtm) REVERT: D 337 ASP cc_start: 0.8172 (t0) cc_final: 0.7893 (m-30) REVERT: E 48 LYS cc_start: 0.9276 (mtpp) cc_final: 0.9024 (mtmt) REVERT: E 122 MET cc_start: 0.9195 (mtt) cc_final: 0.8854 (mtt) REVERT: E 264 MET cc_start: 0.9142 (mtp) cc_final: 0.8890 (mtp) REVERT: E 277 MET cc_start: 0.9230 (mtt) cc_final: 0.8739 (mtt) REVERT: E 335 SER cc_start: 0.9476 (m) cc_final: 0.9189 (t) REVERT: E 342 ASP cc_start: 0.8807 (m-30) cc_final: 0.8522 (m-30) REVERT: F 69 MET cc_start: 0.5413 (ppp) cc_final: 0.5136 (pp-130) REVERT: F 299 GLU cc_start: 0.8726 (mp0) cc_final: 0.8498 (mp0) REVERT: F 349 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8666 (m-30) REVERT: G 19 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: G 92 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8374 (tm-30) REVERT: G 113 MET cc_start: 0.8979 (mmm) cc_final: 0.8641 (mmt) REVERT: G 147 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7856 (mp10) REVERT: G 223 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8763 (tm-30) REVERT: G 232 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8288 (mm-30) REVERT: H 165 LYS cc_start: 0.9125 (ttpp) cc_final: 0.8697 (tttm) REVERT: H 209 GLU cc_start: 0.8684 (tt0) cc_final: 0.8174 (tt0) REVERT: I 108 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8222 (tp30) REVERT: I 210 LYS cc_start: 0.8607 (mtmp) cc_final: 0.8007 (mtmt) REVERT: I 232 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: J 30 SER cc_start: 0.9047 (m) cc_final: 0.8641 (p) REVERT: J 103 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8427 (t) REVERT: J 110 TYR cc_start: 0.9248 (t80) cc_final: 0.8608 (t80) REVERT: J 175 ASN cc_start: 0.9430 (m110) cc_final: 0.9047 (m-40) REVERT: J 177 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8723 (p) REVERT: J 239 ASN cc_start: 0.9129 (m-40) cc_final: 0.8873 (m110) REVERT: K 20 ARG cc_start: 0.8711 (mtm110) cc_final: 0.8385 (mtp85) REVERT: K 65 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8307 (pm20) REVERT: K 95 GLU cc_start: 0.8922 (tp30) cc_final: 0.8668 (tp30) REVERT: K 147 ASP cc_start: 0.8232 (p0) cc_final: 0.8030 (p0) REVERT: L 68 ASN cc_start: 0.9345 (m-40) cc_final: 0.9100 (m-40) REVERT: L 140 MET cc_start: 0.6365 (mmt) cc_final: 0.5994 (tpp) REVERT: L 220 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8350 (tp30) REVERT: L 226 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: M 19 ARG cc_start: 0.9020 (ptm160) cc_final: 0.8668 (ptm160) REVERT: M 75 MET cc_start: 0.9519 (ttt) cc_final: 0.9276 (ttt) REVERT: M 223 ARG cc_start: 0.8234 (ttp-110) cc_final: 0.7943 (ttp80) REVERT: U 43 ASP cc_start: 0.9208 (OUTLIER) cc_final: 0.8897 (m-30) REVERT: U 76 GLU cc_start: 0.9123 (mp0) cc_final: 0.8875 (mp0) REVERT: U 131 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8236 (mm-30) REVERT: U 239 GLU cc_start: 0.8859 (tp30) cc_final: 0.8270 (tm-30) REVERT: U 240 ASP cc_start: 0.8904 (t0) cc_final: 0.8694 (t0) REVERT: U 252 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9200 (mm) REVERT: U 470 ASN cc_start: 0.7974 (t0) cc_final: 0.7602 (t0) REVERT: U 479 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9162 (mp) REVERT: U 714 SER cc_start: 0.9177 (OUTLIER) cc_final: 0.8928 (p) REVERT: V 84 LYS cc_start: 0.9019 (tppp) cc_final: 0.8787 (tptp) REVERT: V 95 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8571 (mm) REVERT: V 99 ARG cc_start: 0.8259 (mmm-85) cc_final: 0.7914 (tmt170) REVERT: V 266 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8783 (mp10) REVERT: V 279 GLN cc_start: 0.8935 (pm20) cc_final: 0.8587 (pm20) REVERT: V 354 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8289 (ttmm) REVERT: V 399 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7484 (ttm-80) REVERT: V 503 LYS cc_start: 0.8070 (mmpt) cc_final: 0.7813 (mmmt) REVERT: V 515 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8303 (tm-30) REVERT: V 519 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8312 (tm) REVERT: V 520 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8294 (mm-30) REVERT: W 30 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8468 (mp0) REVERT: W 40 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8673 (tp) REVERT: W 73 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8436 (mtp) REVERT: W 118 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8206 (tt) REVERT: W 152 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8337 (mp) REVERT: W 161 GLU cc_start: 0.8578 (mp0) cc_final: 0.8069 (mp0) REVERT: W 168 GLU cc_start: 0.8638 (pp20) cc_final: 0.8316 (pp20) REVERT: W 203 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8376 (tm-30) REVERT: W 312 MET cc_start: 0.9129 (mmt) cc_final: 0.8906 (mpp) REVERT: W 348 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8773 (tp30) REVERT: W 383 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8300 (m-30) REVERT: W 430 GLN cc_start: 0.8966 (mm110) cc_final: 0.8689 (mm-40) REVERT: X 72 TYR cc_start: 0.8336 (t80) cc_final: 0.8017 (t80) REVERT: X 223 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8283 (mmpt) REVERT: X 277 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9193 (mm) REVERT: X 329 ASN cc_start: 0.8783 (t0) cc_final: 0.8465 (m110) REVERT: X 332 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: X 389 ASP cc_start: 0.8547 (p0) cc_final: 0.8037 (p0) REVERT: Y 42 MET cc_start: 0.8575 (mmm) cc_final: 0.8349 (mmm) REVERT: Y 50 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8639 (mtp) REVERT: Y 184 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8557 (mt0) REVERT: Y 196 GLN cc_start: 0.9253 (tt0) cc_final: 0.8975 (tt0) REVERT: Y 199 GLU cc_start: 0.8848 (tt0) cc_final: 0.8631 (tm-30) REVERT: Y 321 GLU cc_start: 0.9121 (tt0) cc_final: 0.8704 (tp30) REVERT: Z 79 TYR cc_start: 0.8649 (t80) cc_final: 0.8024 (t80) REVERT: Z 143 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7037 (tm-30) REVERT: Z 156 GLU cc_start: 0.8915 (tt0) cc_final: 0.8631 (tt0) REVERT: Z 161 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8597 (mt-10) REVERT: Z 244 GLU cc_start: 0.8720 (mp0) cc_final: 0.8389 (pm20) REVERT: Z 283 ARG cc_start: 0.8314 (ttm110) cc_final: 0.7926 (ttm170) REVERT: a 40 GLN cc_start: 0.8410 (tp40) cc_final: 0.7768 (mm-40) REVERT: a 70 ARG cc_start: 0.8404 (ttm110) cc_final: 0.8017 (ttm110) REVERT: a 103 LYS cc_start: 0.9099 (ptpt) cc_final: 0.8771 (ptpt) REVERT: a 109 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8876 (mm-30) REVERT: a 127 ASP cc_start: 0.8438 (t0) cc_final: 0.8084 (t0) REVERT: a 139 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8819 (mm-30) REVERT: a 306 GLU cc_start: 0.9351 (mt-10) cc_final: 0.8818 (pm20) REVERT: a 316 SER cc_start: 0.9534 (OUTLIER) cc_final: 0.9236 (p) REVERT: b 11 ASP cc_start: 0.8658 (t0) cc_final: 0.8285 (OUTLIER) REVERT: b 42 ARG cc_start: 0.8455 (mtm110) cc_final: 0.8228 (ptp-110) REVERT: b 108 ARG cc_start: 0.7158 (tpp80) cc_final: 0.6498 (tpp80) REVERT: b 134 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: b 139 ASP cc_start: 0.7519 (m-30) cc_final: 0.7136 (m-30) REVERT: b 147 GLU cc_start: 0.8902 (pm20) cc_final: 0.8598 (pm20) REVERT: c 227 GLU cc_start: 0.8573 (mp0) cc_final: 0.7976 (mp0) REVERT: c 236 GLU cc_start: 0.9132 (mp0) cc_final: 0.8597 (mp0) REVERT: c 257 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8422 (mtpp) REVERT: c 261 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8230 (mm-30) REVERT: c 303 MET cc_start: 0.9528 (OUTLIER) cc_final: 0.8925 (mtt) REVERT: d 140 GLN cc_start: 0.8882 (mt0) cc_final: 0.8656 (mt0) REVERT: d 146 ASP cc_start: 0.9077 (m-30) cc_final: 0.8693 (m-30) REVERT: d 158 ARG cc_start: 0.8453 (ptm160) cc_final: 0.8156 (ttm110) REVERT: d 237 MET cc_start: 0.9111 (tpp) cc_final: 0.8808 (mmm) REVERT: d 265 ASP cc_start: 0.8465 (m-30) cc_final: 0.8224 (m-30) REVERT: d 270 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8308 (tp30) REVERT: d 299 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8015 (tpp) REVERT: e 18 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: e 20 GLU cc_start: 0.8459 (pm20) cc_final: 0.8152 (pm20) REVERT: e 21 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7954 (pt0) REVERT: f 118 ASN cc_start: 0.7690 (m-40) cc_final: 0.7356 (t0) REVERT: f 168 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8032 (mmtt) REVERT: f 207 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8650 (tp) REVERT: f 209 MET cc_start: 0.7803 (mtm) cc_final: 0.7582 (mtm) REVERT: f 235 SER cc_start: 0.8984 (m) cc_final: 0.8465 (p) REVERT: f 275 MET cc_start: 0.9152 (tpp) cc_final: 0.8389 (tpp) REVERT: f 279 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: f 294 MET cc_start: 0.7361 (mmt) cc_final: 0.6779 (mmt) REVERT: f 319 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7949 (tp30) REVERT: f 344 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.7998 (m) REVERT: f 354 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: f 387 GLN cc_start: 0.9003 (tp40) cc_final: 0.7343 (pm20) REVERT: f 389 LYS cc_start: 0.8718 (tmmt) cc_final: 0.8463 (mtmt) REVERT: f 407 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7472 (mmm) REVERT: f 440 ILE cc_start: 0.8203 (mp) cc_final: 0.7943 (mt) REVERT: f 452 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8779 (t0) REVERT: f 466 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8557 (mm) REVERT: f 471 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7890 (mm) REVERT: f 670 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8415 (mpp) REVERT: f 788 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7855 (tpp) REVERT: f 829 MET cc_start: 0.7809 (tpp) cc_final: 0.7536 (tpp) REVERT: f 895 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: g 101 LEU cc_start: 0.4098 (OUTLIER) cc_final: 0.3487 (mm) REVERT: g 132 ASN cc_start: 0.6595 (OUTLIER) cc_final: 0.6373 (t0) REVERT: g 142 LEU cc_start: 0.7108 (tm) cc_final: 0.6709 (mt) REVERT: g 154 MET cc_start: 0.5230 (pmm) cc_final: 0.5019 (pmm) REVERT: u 140 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: u 182 PHE cc_start: 0.7482 (OUTLIER) cc_final: 0.7007 (t80) REVERT: u 220 LEU cc_start: 0.8188 (tp) cc_final: 0.7964 (tm) REVERT: u 225 ILE cc_start: 0.7378 (pt) cc_final: 0.6598 (pt) REVERT: u 263 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7533 (t80) outliers start: 341 outliers final: 118 residues processed: 1233 average time/residue: 1.4185 time to fit residues: 2340.3262 Evaluate side-chains 1080 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 897 time to evaluate : 6.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain H residue 179 ASN Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 232 GLU Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 115 LYS 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 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain U residue 233 LEU Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 479 LEU Chi-restraints excluded: chain U residue 514 LEU Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 890 LYS Chi-restraints excluded: chain U residue 892 LEU Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 266 GLN Chi-restraints excluded: chain V residue 342 ILE Chi-restraints excluded: chain V residue 354 LYS Chi-restraints excluded: chain V residue 399 ARG Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 516 GLN Chi-restraints excluded: chain V residue 519 LEU Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 203 GLN Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 348 GLU Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 241 SER Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 277 LEU Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain a residue 74 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 139 GLU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 299 SER Chi-restraints excluded: chain a residue 309 LEU Chi-restraints excluded: chain a residue 316 SER Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 204 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 339 VAL Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain f residue 205 CYS Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 237 VAL Chi-restraints excluded: chain f residue 271 MET Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 354 GLU Chi-restraints excluded: chain f residue 407 MET Chi-restraints excluded: chain f residue 452 ASN Chi-restraints excluded: chain f residue 466 LEU Chi-restraints excluded: chain f residue 471 LEU Chi-restraints excluded: chain f residue 477 MET Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 527 VAL Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 541 THR Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 652 VAL Chi-restraints excluded: chain f residue 670 MET Chi-restraints excluded: chain f residue 690 VAL Chi-restraints excluded: chain f residue 788 MET Chi-restraints excluded: chain f residue 830 LEU Chi-restraints excluded: chain f residue 842 VAL Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 132 ASN Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain u residue 140 GLU Chi-restraints excluded: chain u residue 149 CYS Chi-restraints excluded: chain u residue 150 LEU Chi-restraints excluded: chain u residue 155 THR Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 263 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 693 optimal weight: 0.2980 chunk 391 optimal weight: 0.4980 chunk 797 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 339 optimal weight: 0.4980 chunk 816 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 chunk 362 optimal weight: 6.9990 chunk 668 optimal weight: 5.9990 chunk 521 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN C 111 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 GLN G 172 GLN ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN b 169 HIS ** d 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 758 ASN u 242 ASN u 251 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.103289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.070979 restraints weight = 141602.502| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.64 r_work: 0.2880 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2754 r_free = 0.2754 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 72503 Z= 0.222 Angle : 0.574 14.424 97952 Z= 0.287 Chirality : 0.041 0.320 11157 Planarity : 0.004 0.051 12612 Dihedral : 5.927 78.450 9939 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.57 % Favored : 97.42 % Rotamer: Outliers : 4.39 % Allowed : 28.83 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 1.24 (0.09), residues: 8913 helix: 1.43 (0.07), residues: 5013 sheet: -0.22 (0.16), residues: 965 loop : 0.32 (0.12), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP W 263 HIS 0.006 0.001 HIS f 782 PHE 0.020 0.001 PHE V 496 TYR 0.033 0.001 TYR a 162 ARG 0.012 0.000 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 342 poor density : 932 time to evaluate : 6.642 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 51 ASP cc_start: 0.8955 (t0) cc_final: 0.8641 (t0) REVERT: A 54 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8578 (tm-30) REVERT: A 55 LEU cc_start: 0.8507 (mt) cc_final: 0.8079 (mt) REVERT: A 85 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8366 (tp40) REVERT: A 138 MET cc_start: 0.9309 (ttp) cc_final: 0.9066 (ttp) REVERT: A 158 ASP cc_start: 0.8834 (t0) cc_final: 0.8406 (t0) REVERT: A 186 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8376 (mttm) REVERT: A 362 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.8909 (mtm) REVERT: B 69 LYS cc_start: 0.9156 (tmmm) cc_final: 0.8759 (tmmt) REVERT: B 118 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: B 276 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: B 377 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8132 (t0) REVERT: B 405 MET cc_start: 0.9244 (mmt) cc_final: 0.8939 (mtt) REVERT: B 408 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8713 (tpp80) REVERT: C 51 GLU cc_start: 0.9037 (tt0) cc_final: 0.8776 (pt0) REVERT: C 83 LYS cc_start: 0.8353 (mmmt) cc_final: 0.8148 (mmtm) REVERT: C 112 CYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7493 (p) REVERT: C 150 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8748 (ptm) REVERT: C 290 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8304 (mmpt) REVERT: C 297 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8353 (ttp-110) REVERT: C 336 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8434 (mtp) REVERT: D 60 TYR cc_start: 0.9306 (OUTLIER) cc_final: 0.8698 (t80) REVERT: D 63 ASP cc_start: 0.9069 (OUTLIER) cc_final: 0.8619 (t0) REVERT: D 71 GLU cc_start: 0.9304 (tp30) cc_final: 0.8844 (mm-30) REVERT: D 153 MET cc_start: 0.9164 (mtm) cc_final: 0.8952 (mtm) REVERT: D 337 ASP cc_start: 0.8160 (t0) cc_final: 0.7954 (m-30) REVERT: D 399 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: E 48 LYS cc_start: 0.9304 (mtpp) cc_final: 0.9037 (mtmt) REVERT: E 113 ARG cc_start: 0.9071 (ttm-80) cc_final: 0.8840 (mtp-110) REVERT: E 122 MET cc_start: 0.9231 (mtt) cc_final: 0.8872 (mtt) REVERT: E 125 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: E 258 MET cc_start: 0.8755 (mtm) cc_final: 0.8497 (mtp) REVERT: E 277 MET cc_start: 0.9259 (mtt) cc_final: 0.8757 (mtt) REVERT: E 335 SER cc_start: 0.9497 (m) cc_final: 0.9210 (t) REVERT: E 342 ASP cc_start: 0.8830 (m-30) cc_final: 0.8534 (m-30) REVERT: F 69 MET cc_start: 0.5523 (ppp) cc_final: 0.5205 (pp-130) REVERT: F 299 GLU cc_start: 0.8732 (mp0) cc_final: 0.8505 (mp0) REVERT: F 349 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8694 (m-30) REVERT: G 19 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: G 92 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8416 (tm-30) REVERT: G 113 MET cc_start: 0.9036 (mmm) cc_final: 0.8744 (mmt) REVERT: G 147 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: G 223 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8724 (tm-30) REVERT: H 18 LYS cc_start: 0.9067 (mtmm) cc_final: 0.8736 (mttm) REVERT: H 163 MET cc_start: 0.8521 (ptp) cc_final: 0.8270 (ptm) REVERT: H 165 LYS cc_start: 0.9173 (ttpp) cc_final: 0.8707 (tttm) REVERT: H 209 GLU cc_start: 0.8683 (tt0) cc_final: 0.8188 (tt0) REVERT: I 108 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8301 (tp30) REVERT: I 210 LYS cc_start: 0.8602 (mtmp) cc_final: 0.7846 (mtmt) REVERT: J 30 SER cc_start: 0.9055 (m) cc_final: 0.8647 (p) REVERT: J 175 ASN cc_start: 0.9470 (m110) cc_final: 0.9090 (m-40) REVERT: J 177 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8762 (p) REVERT: J 239 ASN cc_start: 0.9057 (m-40) cc_final: 0.8786 (m110) REVERT: K 20 ARG cc_start: 0.8776 (mtm110) cc_final: 0.8513 (mtp85) REVERT: K 65 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8297 (pm20) REVERT: K 95 GLU cc_start: 0.8883 (tp30) cc_final: 0.8581 (tp30) REVERT: K 147 ASP cc_start: 0.8224 (p0) cc_final: 0.8018 (p0) REVERT: K 203 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.9002 (ttmm) REVERT: L 68 ASN cc_start: 0.9356 (m-40) cc_final: 0.9114 (m-40) REVERT: L 220 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: L 224 TYR cc_start: 0.9097 (m-10) cc_final: 0.8824 (m-80) REVERT: M 19 ARG cc_start: 0.9051 (ptm160) cc_final: 0.8646 (ptm160) REVERT: M 75 MET cc_start: 0.9533 (ttt) cc_final: 0.9262 (ttt) REVERT: M 223 ARG cc_start: 0.8246 (ttp-110) cc_final: 0.7933 (ttp-110) REVERT: U 43 ASP cc_start: 0.9187 (OUTLIER) cc_final: 0.8891 (m-30) REVERT: U 76 GLU cc_start: 0.9129 (mp0) cc_final: 0.8884 (mp0) REVERT: U 92 ASP cc_start: 0.9247 (OUTLIER) cc_final: 0.8680 (m-30) REVERT: U 131 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8264 (mm-30) REVERT: U 239 GLU cc_start: 0.8752 (tp30) cc_final: 0.8451 (tp30) REVERT: U 240 ASP cc_start: 0.8956 (t0) cc_final: 0.8680 (t0) REVERT: U 252 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9227 (mm) REVERT: U 470 ASN cc_start: 0.8029 (t0) cc_final: 0.7661 (t0) REVERT: U 479 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9188 (mp) REVERT: U 714 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8937 (p) REVERT: U 797 MET cc_start: 0.8839 (mtp) cc_final: 0.8473 (ttp) REVERT: V 84 LYS cc_start: 0.9027 (tppp) cc_final: 0.8783 (tptp) REVERT: V 95 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8581 (mm) REVERT: V 99 ARG cc_start: 0.8380 (mmm-85) cc_final: 0.8027 (tmt170) REVERT: V 113 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9004 (mp) REVERT: V 120 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7086 (t80) REVERT: V 162 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: V 266 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8750 (mp10) REVERT: V 279 GLN cc_start: 0.8925 (pm20) cc_final: 0.8592 (pm20) REVERT: V 354 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8327 (ttmm) REVERT: V 399 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7556 (ttm-80) REVERT: V 515 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8284 (tm-30) REVERT: V 519 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8303 (tm) REVERT: V 520 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8322 (mm-30) REVERT: W 30 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: W 40 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8685 (tp) REVERT: W 118 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8199 (tt) REVERT: W 152 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8359 (mp) REVERT: W 161 GLU cc_start: 0.8625 (mp0) cc_final: 0.8055 (mp0) REVERT: W 168 GLU cc_start: 0.8705 (pp20) cc_final: 0.8380 (pp20) REVERT: W 203 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8514 (tm-30) REVERT: W 312 MET cc_start: 0.9141 (mmt) cc_final: 0.8918 (mpp) REVERT: W 348 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8753 (tp30) REVERT: W 383 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8326 (m-30) REVERT: W 424 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8961 (tt) REVERT: W 436 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8733 (mtp) REVERT: X 72 TYR cc_start: 0.8352 (t80) cc_final: 0.8066 (t80) REVERT: X 223 LYS cc_start: 0.8728 (mmmm) cc_final: 0.8347 (mmpt) REVERT: X 277 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9218 (mm) REVERT: X 329 ASN cc_start: 0.8820 (t0) cc_final: 0.8505 (m110) REVERT: X 332 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: Y 42 MET cc_start: 0.8578 (mmm) cc_final: 0.8346 (mmm) REVERT: Y 50 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8699 (mtp) REVERT: Y 85 ASP cc_start: 0.8907 (m-30) cc_final: 0.8681 (m-30) REVERT: Y 196 GLN cc_start: 0.9279 (tt0) cc_final: 0.9030 (tt0) REVERT: Y 199 GLU cc_start: 0.8869 (tt0) cc_final: 0.8655 (tm-30) REVERT: Y 321 GLU cc_start: 0.9117 (tt0) cc_final: 0.8700 (tp30) REVERT: Z 79 TYR cc_start: 0.8594 (t80) cc_final: 0.7964 (t80) REVERT: Z 143 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7101 (tm-30) REVERT: Z 161 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8587 (mt-10) REVERT: Z 244 GLU cc_start: 0.8690 (mp0) cc_final: 0.8351 (pm20) REVERT: Z 283 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7968 (ttm170) REVERT: a 40 GLN cc_start: 0.8482 (tp40) cc_final: 0.7851 (mm-40) REVERT: a 70 ARG cc_start: 0.8434 (ttm110) cc_final: 0.7757 (ttp-110) REVERT: a 103 LYS cc_start: 0.9112 (ptpt) cc_final: 0.8789 (ptpt) REVERT: a 109 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8913 (mm-30) REVERT: a 127 ASP cc_start: 0.8442 (t0) cc_final: 0.8086 (t0) REVERT: a 139 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8835 (mm-30) REVERT: a 306 GLU cc_start: 0.9387 (mt-10) cc_final: 0.8865 (pm20) REVERT: a 316 SER cc_start: 0.9541 (OUTLIER) cc_final: 0.9278 (p) REVERT: b 11 ASP cc_start: 0.8749 (t0) cc_final: 0.8392 (OUTLIER) REVERT: b 108 ARG cc_start: 0.7216 (tpp80) cc_final: 0.6494 (tpp80) REVERT: b 134 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: b 139 ASP cc_start: 0.7501 (m-30) cc_final: 0.7076 (m-30) REVERT: b 147 GLU cc_start: 0.8902 (pm20) cc_final: 0.8670 (pm20) REVERT: c 152 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8972 (mttp) REVERT: c 227 GLU cc_start: 0.8594 (mp0) cc_final: 0.7978 (mp0) REVERT: c 236 GLU cc_start: 0.9161 (mp0) cc_final: 0.8594 (mp0) REVERT: c 257 LYS cc_start: 0.8825 (mtpt) cc_final: 0.8442 (mtpp) REVERT: c 261 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8239 (mm-30) REVERT: c 303 MET cc_start: 0.9522 (OUTLIER) cc_final: 0.8933 (mtt) REVERT: d 140 GLN cc_start: 0.8880 (mt0) cc_final: 0.8591 (mt0) REVERT: d 146 ASP cc_start: 0.9114 (m-30) cc_final: 0.8705 (m-30) REVERT: d 158 ARG cc_start: 0.8451 (ptm160) cc_final: 0.8160 (ttm110) REVERT: d 165 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8868 (mt-10) REVERT: d 261 ASP cc_start: 0.9141 (p0) cc_final: 0.8890 (p0) REVERT: d 265 ASP cc_start: 0.8502 (m-30) cc_final: 0.8290 (m-30) REVERT: d 270 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8497 (tp30) REVERT: d 299 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7994 (tpp) REVERT: e 18 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7692 (tm-30) REVERT: e 20 GLU cc_start: 0.8507 (pm20) cc_final: 0.8218 (pm20) REVERT: e 21 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: f 118 ASN cc_start: 0.7628 (m-40) cc_final: 0.7355 (t0) REVERT: f 168 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8014 (mmtt) REVERT: f 207 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8692 (tp) REVERT: f 235 SER cc_start: 0.8979 (m) cc_final: 0.8448 (p) REVERT: f 275 MET cc_start: 0.9158 (tpp) cc_final: 0.8407 (tpp) REVERT: f 279 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: f 294 MET cc_start: 0.7432 (mmt) cc_final: 0.6889 (mmt) REVERT: f 319 GLU cc_start: 0.8434 (mm-30) cc_final: 0.8010 (tp30) REVERT: f 344 VAL cc_start: 0.8375 (OUTLIER) cc_final: 0.7999 (m) REVERT: f 354 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: f 387 GLN cc_start: 0.9009 (tp40) cc_final: 0.7210 (pm20) REVERT: f 407 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7424 (mmm) REVERT: f 440 ILE cc_start: 0.8187 (mp) cc_final: 0.7973 (mt) REVERT: f 452 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8815 (t0) REVERT: f 466 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8587 (mm) REVERT: f 471 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7838 (mm) REVERT: f 670 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8366 (mpp) REVERT: f 788 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7825 (tpp) REVERT: f 895 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: g 101 LEU cc_start: 0.4108 (OUTLIER) cc_final: 0.3314 (mm) REVERT: g 107 ILE cc_start: 0.4792 (OUTLIER) cc_final: 0.4359 (pt) REVERT: g 111 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6325 (pm20) REVERT: g 132 ASN cc_start: 0.6454 (OUTLIER) cc_final: 0.6187 (t0) REVERT: g 142 LEU cc_start: 0.7148 (tm) cc_final: 0.6628 (mt) REVERT: u 124 MET cc_start: 0.7806 (ptp) cc_final: 0.7398 (ppp) REVERT: u 182 PHE cc_start: 0.7497 (OUTLIER) cc_final: 0.7016 (t80) REVERT: u 225 ILE cc_start: 0.7392 (pt) cc_final: 0.6669 (pt) REVERT: u 263 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7522 (t80) outliers start: 342 outliers final: 128 residues processed: 1183 average time/residue: 1.4243 time to fit residues: 2250.5806 Evaluate side-chains 1089 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 887 time to evaluate : 6.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 181 LYS Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 399 PHE Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 168 VAL Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 203 LYS Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 205 LYS Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain U residue 43 ASP Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain U residue 233 LEU Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 479 LEU Chi-restraints excluded: chain U residue 514 LEU Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 678 ASP Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 890 LYS Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 162 GLU Chi-restraints excluded: chain V residue 266 GLN Chi-restraints excluded: chain V residue 342 ILE Chi-restraints excluded: chain V residue 354 LYS Chi-restraints excluded: chain V residue 399 ARG Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 516 GLN Chi-restraints excluded: chain V residue 519 LEU Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 169 LEU Chi-restraints excluded: chain W residue 203 GLN Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 348 GLU Chi-restraints excluded: chain W residue 383 ASP Chi-restraints excluded: chain W residue 424 LEU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 241 SER Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 277 LEU Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 87 GLU Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 283 ARG Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 74 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 139 GLU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 299 SER Chi-restraints excluded: chain a residue 316 SER Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 152 LYS Chi-restraints excluded: chain c residue 204 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 313 ASN Chi-restraints excluded: chain d residue 339 VAL Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 237 VAL Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 268 LEU Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 354 GLU Chi-restraints excluded: chain f residue 407 MET Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 452 ASN Chi-restraints excluded: chain f residue 466 LEU Chi-restraints excluded: chain f residue 471 LEU Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 527 VAL Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 541 THR Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 652 VAL Chi-restraints excluded: chain f residue 670 MET Chi-restraints excluded: chain f residue 690 VAL Chi-restraints excluded: chain f residue 788 MET Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 830 LEU Chi-restraints excluded: chain f residue 842 VAL Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 111 GLU Chi-restraints excluded: chain g residue 132 ASN Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain u residue 149 CYS Chi-restraints excluded: chain u residue 150 LEU Chi-restraints excluded: chain u residue 155 THR Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 182 PHE Chi-restraints excluded: chain u residue 243 SER Chi-restraints excluded: chain u residue 263 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 789 optimal weight: 7.9990 chunk 552 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 596 optimal weight: 7.9990 chunk 313 optimal weight: 9.9990 chunk 877 optimal weight: 6.9990 chunk 626 optimal weight: 4.9990 chunk 805 optimal weight: 9.9990 chunk 607 optimal weight: 3.9990 chunk 883 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN C 111 ASN D 65 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 ASN G 172 GLN ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 184 GLN Z 7 GLN Z 194 GLN Z 223 ASN ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 242 ASN u 251 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.100896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.068607 restraints weight = 142586.709| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.61 r_work: 0.2831 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 72503 Z= 0.393 Angle : 0.633 14.330 97952 Z= 0.317 Chirality : 0.044 0.333 11157 Planarity : 0.004 0.060 12612 Dihedral : 6.100 80.332 9935 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 4.53 % Allowed : 28.98 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 1.17 (0.09), residues: 8913 helix: 1.36 (0.07), residues: 5042 sheet: -0.19 (0.16), residues: 958 loop : 0.27 (0.12), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 34 HIS 0.006 0.001 HIS f 715 PHE 0.026 0.002 PHE V 496 TYR 0.028 0.002 TYR f 349 ARG 0.012 0.001 ARG Z 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 353 poor density : 884 time to evaluate : 6.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.9029 (t0) cc_final: 0.8702 (t0) REVERT: A 54 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 55 LEU cc_start: 0.8512 (mt) cc_final: 0.8091 (mt) REVERT: A 85 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7999 (tp40) REVERT: A 88 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8319 (pm20) REVERT: A 138 MET cc_start: 0.9358 (ttp) cc_final: 0.9114 (ttp) REVERT: A 158 ASP cc_start: 0.8871 (t0) cc_final: 0.8484 (t0) REVERT: A 182 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8700 (pm20) REVERT: A 186 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8494 (mttm) REVERT: A 239 ARG cc_start: 0.9229 (ptm-80) cc_final: 0.8223 (ppt90) REVERT: A 361 SER cc_start: 0.9181 (OUTLIER) cc_final: 0.8546 (t) REVERT: A 362 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.9053 (mtm) REVERT: A 366 ARG cc_start: 0.8969 (mmm-85) cc_final: 0.8767 (tpt-90) REVERT: A 400 ARG cc_start: 0.8498 (mmp80) cc_final: 0.8298 (tpp-160) REVERT: B 69 LYS cc_start: 0.9175 (tmmm) cc_final: 0.8808 (tmmt) REVERT: B 118 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: B 276 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: B 302 GLU cc_start: 0.8909 (mp0) cc_final: 0.8216 (mm-30) REVERT: B 377 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8164 (t0) REVERT: B 405 MET cc_start: 0.9262 (mmt) cc_final: 0.8946 (mtt) REVERT: B 408 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8864 (tpp80) REVERT: C 51 GLU cc_start: 0.9047 (tt0) cc_final: 0.8845 (pt0) REVERT: C 61 GLU cc_start: 0.9107 (pt0) cc_final: 0.8789 (pt0) REVERT: C 83 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8213 (mmtm) REVERT: C 112 CYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7414 (p) REVERT: C 150 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8768 (ptm) REVERT: C 290 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8440 (mmpt) REVERT: C 297 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8428 (ttp-110) REVERT: C 336 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.8559 (mtp) REVERT: D 60 TYR cc_start: 0.9399 (OUTLIER) cc_final: 0.8710 (t80) REVERT: D 63 ASP cc_start: 0.9141 (OUTLIER) cc_final: 0.8677 (t0) REVERT: D 71 GLU cc_start: 0.9250 (tp30) cc_final: 0.8915 (mm-30) REVERT: E 48 LYS cc_start: 0.9307 (mtpp) cc_final: 0.9030 (mtmt) REVERT: E 113 ARG cc_start: 0.9097 (ttm-80) cc_final: 0.8880 (mtp-110) REVERT: E 122 MET cc_start: 0.9306 (mtt) cc_final: 0.8852 (mtt) REVERT: E 125 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.8320 (tt0) REVERT: E 335 SER cc_start: 0.9489 (m) cc_final: 0.9200 (t) REVERT: E 342 ASP cc_start: 0.8895 (m-30) cc_final: 0.8564 (m-30) REVERT: F 69 MET cc_start: 0.5430 (ppp) cc_final: 0.5117 (pp-130) REVERT: F 183 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: F 349 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8737 (m-30) REVERT: G 19 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8679 (mp0) REVERT: G 61 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8814 (tt) REVERT: G 92 GLN cc_start: 0.9040 (tm-30) cc_final: 0.8485 (tm-30) REVERT: G 113 MET cc_start: 0.9113 (mmm) cc_final: 0.8737 (mmt) REVERT: G 117 ARG cc_start: 0.8560 (ttt90) cc_final: 0.7359 (ttm170) REVERT: G 147 GLN cc_start: 0.8450 (mp10) cc_final: 0.7920 (mp10) REVERT: G 223 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8737 (tm-30) REVERT: H 163 MET cc_start: 0.8696 (ptp) cc_final: 0.8425 (ptm) REVERT: H 165 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8752 (tttm) REVERT: H 209 GLU cc_start: 0.8696 (tt0) cc_final: 0.8429 (tt0) REVERT: I 108 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8418 (tp30) REVERT: I 210 LYS cc_start: 0.8642 (mtmp) cc_final: 0.7986 (mtmt) REVERT: J 30 SER cc_start: 0.9074 (m) cc_final: 0.8762 (p) REVERT: J 177 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8761 (p) REVERT: J 239 ASN cc_start: 0.9053 (m-40) cc_final: 0.8786 (m110) REVERT: K 20 ARG cc_start: 0.8863 (mtm110) cc_final: 0.8625 (mtp85) REVERT: K 29 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8289 (mp0) REVERT: K 65 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8240 (pm20) REVERT: K 95 GLU cc_start: 0.8959 (tp30) cc_final: 0.8661 (tp30) REVERT: K 147 ASP cc_start: 0.8288 (p0) cc_final: 0.8086 (p0) REVERT: K 228 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8817 (tpp) REVERT: L 68 ASN cc_start: 0.9356 (m-40) cc_final: 0.9107 (m-40) REVERT: L 220 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8354 (tp30) REVERT: L 224 TYR cc_start: 0.9070 (m-10) cc_final: 0.8631 (m-10) REVERT: M 75 MET cc_start: 0.9522 (ttt) cc_final: 0.9229 (ttt) REVERT: M 97 ASN cc_start: 0.8885 (m110) cc_final: 0.8313 (m110) REVERT: M 136 MET cc_start: 0.9436 (mtm) cc_final: 0.9087 (mtm) REVERT: M 223 ARG cc_start: 0.8263 (ttp-110) cc_final: 0.7940 (ttp-110) REVERT: U 57 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8373 (ptm-80) REVERT: U 76 GLU cc_start: 0.9135 (mp0) cc_final: 0.8882 (mp0) REVERT: U 92 ASP cc_start: 0.9265 (OUTLIER) cc_final: 0.8744 (m-30) REVERT: U 131 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: U 239 GLU cc_start: 0.8764 (tp30) cc_final: 0.8473 (tp30) REVERT: U 240 ASP cc_start: 0.9042 (t0) cc_final: 0.8803 (t0) REVERT: U 252 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9242 (mm) REVERT: U 470 ASN cc_start: 0.7963 (t0) cc_final: 0.7619 (t0) REVERT: U 479 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9204 (mp) REVERT: U 714 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8957 (p) REVERT: U 797 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8602 (ttp) REVERT: V 84 LYS cc_start: 0.9035 (tppp) cc_final: 0.8759 (tptp) REVERT: V 95 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8658 (mm) REVERT: V 99 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.7988 (tmt170) REVERT: V 113 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8993 (mp) REVERT: V 120 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7170 (t80) REVERT: V 139 MET cc_start: 0.6433 (pmm) cc_final: 0.6187 (ppp) REVERT: V 162 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8202 (mp0) REVERT: V 266 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8736 (mp10) REVERT: V 279 GLN cc_start: 0.9001 (pm20) cc_final: 0.8649 (pm20) REVERT: V 354 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8521 (tmmt) REVERT: V 399 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7619 (ttm-80) REVERT: V 515 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8274 (tm-30) REVERT: V 519 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8319 (tm) REVERT: V 520 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8400 (mm-30) REVERT: V 524 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8143 (tp30) REVERT: W 30 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: W 40 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8707 (tp) REVERT: W 118 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8096 (tt) REVERT: W 152 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8457 (mp) REVERT: W 161 GLU cc_start: 0.8660 (mp0) cc_final: 0.8159 (mp0) REVERT: W 168 GLU cc_start: 0.8760 (pp20) cc_final: 0.8417 (pp20) REVERT: W 203 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: W 312 MET cc_start: 0.9161 (mmt) cc_final: 0.8942 (mmp) REVERT: W 348 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8756 (tp30) REVERT: W 424 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9021 (tt) REVERT: W 436 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8754 (mtp) REVERT: X 72 TYR cc_start: 0.8390 (t80) cc_final: 0.8127 (t80) REVERT: X 223 LYS cc_start: 0.8753 (mmmm) cc_final: 0.8366 (mmpt) REVERT: X 277 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9256 (mp) REVERT: X 329 ASN cc_start: 0.8865 (t0) cc_final: 0.8527 (m110) REVERT: X 332 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: X 389 ASP cc_start: 0.8625 (p0) cc_final: 0.8175 (p0) REVERT: Y 42 MET cc_start: 0.8632 (mmm) cc_final: 0.8233 (mmp) REVERT: Y 184 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8636 (mt0) REVERT: Y 196 GLN cc_start: 0.9284 (tt0) cc_final: 0.9026 (tt0) REVERT: Y 321 GLU cc_start: 0.9130 (tt0) cc_final: 0.8733 (tp30) REVERT: Y 389 MET cc_start: 0.7125 (ptt) cc_final: 0.6319 (ppp) REVERT: Z 79 TYR cc_start: 0.8697 (t80) cc_final: 0.8103 (t80) REVERT: Z 143 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7338 (tm-30) REVERT: Z 194 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8572 (mt0) REVERT: Z 244 GLU cc_start: 0.8737 (mp0) cc_final: 0.8407 (pm20) REVERT: Z 283 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7993 (ttm170) REVERT: a 40 GLN cc_start: 0.8577 (tp40) cc_final: 0.7912 (mp10) REVERT: a 70 ARG cc_start: 0.8545 (ttm110) cc_final: 0.7834 (ttp-110) REVERT: a 103 LYS cc_start: 0.9160 (ptpt) cc_final: 0.8909 (ptmt) REVERT: a 109 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8901 (mm-30) REVERT: a 128 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7743 (pp) REVERT: a 139 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8869 (mm-30) REVERT: a 306 GLU cc_start: 0.9382 (mt-10) cc_final: 0.9031 (pt0) REVERT: b 11 ASP cc_start: 0.8764 (t0) cc_final: 0.8265 (t0) REVERT: b 14 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8174 (mm-30) REVERT: b 108 ARG cc_start: 0.7288 (tpp80) cc_final: 0.6436 (tpp80) REVERT: b 134 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: b 139 ASP cc_start: 0.7692 (m-30) cc_final: 0.7302 (m-30) REVERT: c 106 GLU cc_start: 0.9124 (OUTLIER) cc_final: 0.8662 (mp0) REVERT: c 152 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9027 (mttp) REVERT: c 227 GLU cc_start: 0.8638 (mp0) cc_final: 0.8024 (mp0) REVERT: c 257 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8463 (mtpp) REVERT: c 261 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8127 (mm-30) REVERT: c 303 MET cc_start: 0.9512 (OUTLIER) cc_final: 0.8994 (mtt) REVERT: d 140 GLN cc_start: 0.8910 (mt0) cc_final: 0.8605 (mt0) REVERT: d 146 ASP cc_start: 0.9138 (m-30) cc_final: 0.8750 (m-30) REVERT: d 158 ARG cc_start: 0.8504 (ptm160) cc_final: 0.8218 (ttm110) REVERT: d 299 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8116 (tpp) REVERT: d 332 SER cc_start: 0.9087 (OUTLIER) cc_final: 0.8855 (m) REVERT: e 18 GLU cc_start: 0.8164 (pp20) cc_final: 0.7491 (pp20) REVERT: e 20 GLU cc_start: 0.8577 (pm20) cc_final: 0.7910 (pm20) REVERT: e 21 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: f 118 ASN cc_start: 0.7633 (m-40) cc_final: 0.7416 (t0) REVERT: f 168 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8047 (mmtt) REVERT: f 207 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8759 (tp) REVERT: f 209 MET cc_start: 0.7947 (mtm) cc_final: 0.7452 (ptp) REVERT: f 235 SER cc_start: 0.8877 (m) cc_final: 0.8359 (p) REVERT: f 275 MET cc_start: 0.9130 (tpp) cc_final: 0.8383 (tpp) REVERT: f 279 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8331 (mp0) REVERT: f 294 MET cc_start: 0.7673 (mmt) cc_final: 0.7213 (mmt) REVERT: f 344 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7960 (m) REVERT: f 354 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: f 387 GLN cc_start: 0.8785 (tp40) cc_final: 0.7339 (pm20) REVERT: f 389 LYS cc_start: 0.8654 (tmmt) cc_final: 0.8404 (tmtt) REVERT: f 407 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7381 (mmm) REVERT: f 452 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8728 (t0) REVERT: f 466 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8593 (mm) REVERT: f 471 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7833 (mm) REVERT: f 573 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8063 (mm) REVERT: f 574 GLU cc_start: 0.8773 (mp0) cc_final: 0.8359 (mp0) REVERT: f 670 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8254 (mpp) REVERT: f 680 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7891 (ttp-170) REVERT: f 788 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.7747 (tpp) REVERT: f 895 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7779 (pt0) REVERT: g 101 LEU cc_start: 0.4313 (OUTLIER) cc_final: 0.3590 (mm) REVERT: g 107 ILE cc_start: 0.4781 (OUTLIER) cc_final: 0.4342 (pt) REVERT: g 111 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6524 (pm20) REVERT: g 142 LEU cc_start: 0.7129 (tm) cc_final: 0.6610 (mt) REVERT: u 129 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7677 (t80) outliers start: 353 outliers final: 144 residues processed: 1142 average time/residue: 1.4556 time to fit residues: 2230.7399 Evaluate side-chains 1068 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 841 time to evaluate : 6.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain I residue 190 LEU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain L residue 115 LYS 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 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 205 LYS Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain U residue 160 LEU Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 322 THR Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 457 ILE Chi-restraints excluded: chain U residue 479 LEU Chi-restraints excluded: chain U residue 514 LEU Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 643 SER Chi-restraints excluded: chain U residue 678 ASP Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 797 MET Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 162 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 266 GLN Chi-restraints excluded: chain V residue 281 ASN Chi-restraints excluded: chain V residue 342 ILE Chi-restraints excluded: chain V residue 354 LYS Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 399 ARG Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 486 ILE Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 516 GLN Chi-restraints excluded: chain V residue 519 LEU Chi-restraints excluded: chain V residue 524 GLU Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 169 LEU Chi-restraints excluded: chain W residue 203 GLN Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 348 GLU Chi-restraints excluded: chain W residue 424 LEU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain X residue 92 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 103 THR Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 241 SER Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 277 LEU Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 87 GLU Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 184 GLN Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Z residue 26 ILE Chi-restraints excluded: chain Z residue 28 LYS Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 149 THR Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 194 GLN Chi-restraints excluded: chain Z residue 283 ARG Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 74 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 139 GLU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 299 SER Chi-restraints excluded: chain a residue 309 LEU Chi-restraints excluded: chain a residue 316 SER Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 4 GLU Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 97 ASP Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 152 LYS Chi-restraints excluded: chain c residue 204 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 119 LEU Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 313 ASN Chi-restraints excluded: chain d residue 332 SER Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 208 LEU Chi-restraints excluded: chain f residue 237 VAL Chi-restraints excluded: chain f residue 255 VAL Chi-restraints excluded: chain f residue 268 LEU Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 354 GLU Chi-restraints excluded: chain f residue 407 MET Chi-restraints excluded: chain f residue 414 LEU Chi-restraints excluded: chain f residue 452 ASN Chi-restraints excluded: chain f residue 466 LEU Chi-restraints excluded: chain f residue 471 LEU Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 527 VAL Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 541 THR Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 652 VAL Chi-restraints excluded: chain f residue 670 MET Chi-restraints excluded: chain f residue 680 ARG Chi-restraints excluded: chain f residue 690 VAL Chi-restraints excluded: chain f residue 788 MET Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 830 LEU Chi-restraints excluded: chain f residue 842 VAL Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 111 GLU Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain u residue 129 PHE Chi-restraints excluded: chain u residue 149 CYS Chi-restraints excluded: chain u residue 150 LEU Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 194 VAL Chi-restraints excluded: chain u residue 198 ILE Chi-restraints excluded: chain u residue 243 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 52 optimal weight: 4.9990 chunk 628 optimal weight: 3.9990 chunk 467 optimal weight: 0.9990 chunk 819 optimal weight: 10.0000 chunk 319 optimal weight: 6.9990 chunk 731 optimal weight: 4.9990 chunk 326 optimal weight: 1.9990 chunk 471 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 436 optimal weight: 0.9980 chunk 240 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 111 ASN D 65 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** U 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 198 ASN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 184 GLN Z 194 GLN ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN b 12 ASN b 137 ASN ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 242 ASN u 251 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.069924 restraints weight = 141941.164| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.62 r_work: 0.2861 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 72503 Z= 0.235 Angle : 0.604 15.087 97952 Z= 0.300 Chirality : 0.042 0.336 11157 Planarity : 0.004 0.058 12612 Dihedral : 6.027 79.436 9935 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.63 % Favored : 97.35 % Rotamer: Outliers : 3.86 % Allowed : 29.70 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 1.23 (0.09), residues: 8913 helix: 1.43 (0.07), residues: 5012 sheet: -0.22 (0.16), residues: 944 loop : 0.28 (0.12), residues: 2957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 263 HIS 0.006 0.001 HIS f 715 PHE 0.022 0.001 PHE V 496 TYR 0.030 0.001 TYR f 349 ARG 0.012 0.000 ARG b 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 301 poor density : 897 time to evaluate : 6.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.9028 (t0) cc_final: 0.8741 (t0) REVERT: A 54 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8574 (tm-30) REVERT: A 55 LEU cc_start: 0.8480 (mt) cc_final: 0.8063 (mt) REVERT: A 85 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7990 (tp40) REVERT: A 88 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: A 138 MET cc_start: 0.9332 (ttp) cc_final: 0.9091 (ttp) REVERT: A 158 ASP cc_start: 0.8816 (t0) cc_final: 0.8409 (t0) REVERT: A 186 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8334 (mttm) REVERT: A 400 ARG cc_start: 0.8480 (mmp80) cc_final: 0.8275 (tpp-160) REVERT: B 48 LYS cc_start: 0.8736 (tppp) cc_final: 0.7789 (mppt) REVERT: B 69 LYS cc_start: 0.9167 (tmmm) cc_final: 0.8786 (tmmt) REVERT: B 118 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: B 276 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: B 302 GLU cc_start: 0.8877 (mp0) cc_final: 0.8114 (mm-30) REVERT: B 377 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8084 (t0) REVERT: B 405 MET cc_start: 0.9241 (mmt) cc_final: 0.8931 (mtt) REVERT: C 83 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8182 (mmtm) REVERT: C 112 CYS cc_start: 0.8097 (OUTLIER) cc_final: 0.7446 (p) REVERT: C 139 MET cc_start: 0.9239 (mtp) cc_final: 0.8921 (mtp) REVERT: C 150 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8756 (ptm) REVERT: C 290 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8376 (mmpt) REVERT: C 297 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8407 (ttp-110) REVERT: C 336 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8496 (mtp) REVERT: D 60 TYR cc_start: 0.9387 (OUTLIER) cc_final: 0.8610 (t80) REVERT: D 63 ASP cc_start: 0.9109 (OUTLIER) cc_final: 0.8616 (t0) REVERT: D 71 GLU cc_start: 0.9254 (tp30) cc_final: 0.8904 (mm-30) REVERT: D 153 MET cc_start: 0.9205 (mtm) cc_final: 0.8958 (mtt) REVERT: E 113 ARG cc_start: 0.9084 (ttm-80) cc_final: 0.8876 (mtp-110) REVERT: E 122 MET cc_start: 0.9270 (mtt) cc_final: 0.8882 (mtt) REVERT: E 125 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: E 335 SER cc_start: 0.9483 (m) cc_final: 0.9224 (t) REVERT: E 342 ASP cc_start: 0.8817 (m-30) cc_final: 0.8508 (m-30) REVERT: F 69 MET cc_start: 0.5439 (ppp) cc_final: 0.5090 (pp-130) REVERT: F 183 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: F 349 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8733 (m-30) REVERT: G 19 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8656 (mp0) REVERT: G 92 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8480 (tm-30) REVERT: G 113 MET cc_start: 0.9079 (mmm) cc_final: 0.8761 (mmt) REVERT: G 117 ARG cc_start: 0.8473 (ttt90) cc_final: 0.7354 (ttm170) REVERT: G 130 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: G 147 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: G 223 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8746 (tm-30) REVERT: H 163 MET cc_start: 0.8585 (ptp) cc_final: 0.8326 (ptm) REVERT: H 165 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8718 (tttm) REVERT: H 209 GLU cc_start: 0.8692 (tt0) cc_final: 0.8209 (tt0) REVERT: I 108 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8313 (tp30) REVERT: I 210 LYS cc_start: 0.8646 (mtmp) cc_final: 0.8017 (mtmt) REVERT: J 30 SER cc_start: 0.9066 (m) cc_final: 0.8758 (p) REVERT: J 175 ASN cc_start: 0.9460 (m110) cc_final: 0.9044 (m-40) REVERT: J 177 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8739 (p) REVERT: J 239 ASN cc_start: 0.9049 (m-40) cc_final: 0.8779 (m110) REVERT: K 20 ARG cc_start: 0.8861 (mtm110) cc_final: 0.8614 (mtp85) REVERT: K 29 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8279 (mp0) REVERT: K 65 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8350 (pm20) REVERT: K 95 GLU cc_start: 0.8926 (tp30) cc_final: 0.8712 (tp30) REVERT: K 228 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8790 (tpp) REVERT: L 53 GLN cc_start: 0.8232 (mt0) cc_final: 0.7986 (pt0) REVERT: L 68 ASN cc_start: 0.9354 (m-40) cc_final: 0.9105 (m-40) REVERT: L 220 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: L 224 TYR cc_start: 0.9006 (m-10) cc_final: 0.8600 (m-10) REVERT: M 136 MET cc_start: 0.9437 (mtm) cc_final: 0.9029 (mtm) REVERT: M 223 ARG cc_start: 0.8282 (ttp-110) cc_final: 0.7968 (ttp-110) REVERT: U 43 ASP cc_start: 0.9190 (m-30) cc_final: 0.8806 (m-30) REVERT: U 57 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8285 (ptm-80) REVERT: U 76 GLU cc_start: 0.9137 (mp0) cc_final: 0.8883 (mp0) REVERT: U 92 ASP cc_start: 0.9264 (OUTLIER) cc_final: 0.8735 (m-30) REVERT: U 131 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8259 (mm-30) REVERT: U 239 GLU cc_start: 0.8713 (tp30) cc_final: 0.8457 (tp30) REVERT: U 240 ASP cc_start: 0.9057 (t0) cc_final: 0.8828 (OUTLIER) REVERT: U 252 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9197 (mm) REVERT: U 470 ASN cc_start: 0.8055 (t0) cc_final: 0.7696 (t0) REVERT: U 479 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9177 (mp) REVERT: U 714 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8932 (p) REVERT: U 797 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8608 (ttp) REVERT: V 84 LYS cc_start: 0.9012 (tppp) cc_final: 0.8701 (tptp) REVERT: V 95 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8644 (mm) REVERT: V 99 ARG cc_start: 0.8384 (mmm-85) cc_final: 0.7990 (tmt170) REVERT: V 120 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7242 (t80) REVERT: V 139 MET cc_start: 0.6446 (pmm) cc_final: 0.6229 (ppp) REVERT: V 162 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: V 266 GLN cc_start: 0.9219 (OUTLIER) cc_final: 0.8755 (mp10) REVERT: V 279 GLN cc_start: 0.8971 (pm20) cc_final: 0.8604 (pm20) REVERT: V 354 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8524 (tmmt) REVERT: V 399 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7608 (ttm-80) REVERT: V 503 LYS cc_start: 0.8922 (tptm) cc_final: 0.8461 (tmmt) REVERT: V 515 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8315 (tm-30) REVERT: V 519 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8330 (tm) REVERT: V 520 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8216 (mm-30) REVERT: V 524 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: W 30 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: W 40 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8735 (tp) REVERT: W 45 GLU cc_start: 0.8716 (mp0) cc_final: 0.8513 (mp0) REVERT: W 73 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8812 (mtt) REVERT: W 118 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8162 (tt) REVERT: W 152 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8407 (mp) REVERT: W 161 GLU cc_start: 0.8682 (mp0) cc_final: 0.8165 (mp0) REVERT: W 168 GLU cc_start: 0.8768 (pp20) cc_final: 0.8470 (pp20) REVERT: W 203 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8389 (tm-30) REVERT: W 348 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8724 (tp30) REVERT: W 424 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8985 (tt) REVERT: W 436 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8744 (mtp) REVERT: X 72 TYR cc_start: 0.8345 (t80) cc_final: 0.8061 (t80) REVERT: X 223 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8355 (mmpt) REVERT: X 277 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9244 (mp) REVERT: X 329 ASN cc_start: 0.8845 (t0) cc_final: 0.8519 (m110) REVERT: X 332 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: X 394 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: Y 50 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8786 (mtp) REVERT: Y 85 ASP cc_start: 0.8925 (m-30) cc_final: 0.8719 (m-30) REVERT: Y 196 GLN cc_start: 0.9285 (tt0) cc_final: 0.9051 (tt0) REVERT: Y 321 GLU cc_start: 0.9129 (tt0) cc_final: 0.8728 (tp30) REVERT: Y 385 ARG cc_start: 0.8799 (tmm-80) cc_final: 0.8571 (tmm-80) REVERT: Y 389 MET cc_start: 0.7109 (ptt) cc_final: 0.6261 (ppp) REVERT: Z 79 TYR cc_start: 0.8652 (t80) cc_final: 0.8018 (t80) REVERT: Z 143 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7285 (tm-30) REVERT: Z 244 GLU cc_start: 0.8720 (mp0) cc_final: 0.8390 (pm20) REVERT: Z 283 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7965 (ttm170) REVERT: a 40 GLN cc_start: 0.8575 (tp40) cc_final: 0.7911 (mp10) REVERT: a 70 ARG cc_start: 0.8493 (ttm110) cc_final: 0.7786 (ttp-110) REVERT: a 103 LYS cc_start: 0.9156 (ptpt) cc_final: 0.8917 (ptmt) REVERT: a 109 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8919 (mm-30) REVERT: a 127 ASP cc_start: 0.8448 (t0) cc_final: 0.8162 (t0) REVERT: a 128 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7686 (pp) REVERT: a 306 GLU cc_start: 0.9387 (mt-10) cc_final: 0.8853 (pm20) REVERT: a 316 SER cc_start: 0.9537 (OUTLIER) cc_final: 0.9259 (p) REVERT: b 11 ASP cc_start: 0.8355 (t0) cc_final: 0.7947 (t0) REVERT: b 14 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8174 (mm-30) REVERT: b 108 ARG cc_start: 0.7253 (tpp80) cc_final: 0.6411 (tpp80) REVERT: b 134 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: b 139 ASP cc_start: 0.7712 (m-30) cc_final: 0.7301 (m-30) REVERT: c 152 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8935 (mttp) REVERT: c 227 GLU cc_start: 0.8609 (mp0) cc_final: 0.7951 (mp0) REVERT: c 257 LYS cc_start: 0.8843 (mtpt) cc_final: 0.8456 (mtpp) REVERT: c 261 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8166 (mm-30) REVERT: c 303 MET cc_start: 0.9498 (OUTLIER) cc_final: 0.9042 (mtt) REVERT: d 140 GLN cc_start: 0.8895 (mt0) cc_final: 0.8654 (mt0) REVERT: d 146 ASP cc_start: 0.9135 (m-30) cc_final: 0.8732 (m-30) REVERT: d 158 ARG cc_start: 0.8467 (ptm160) cc_final: 0.8181 (ttm110) REVERT: d 165 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8838 (mt-10) REVERT: d 270 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8411 (tp30) REVERT: d 299 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8068 (tpp) REVERT: e 18 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: e 20 GLU cc_start: 0.8559 (pm20) cc_final: 0.8230 (pm20) REVERT: e 21 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: f 118 ASN cc_start: 0.7567 (m-40) cc_final: 0.7361 (t0) REVERT: f 168 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8046 (mmtt) REVERT: f 207 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8778 (tp) REVERT: f 209 MET cc_start: 0.7999 (mtm) cc_final: 0.7673 (ptp) REVERT: f 235 SER cc_start: 0.8887 (m) cc_final: 0.8361 (p) REVERT: f 256 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.8168 (m-10) REVERT: f 275 MET cc_start: 0.9131 (tpp) cc_final: 0.8383 (tpp) REVERT: f 279 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8332 (mp0) REVERT: f 294 MET cc_start: 0.7795 (mmt) cc_final: 0.7300 (mmt) REVERT: f 344 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7939 (m) REVERT: f 354 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: f 389 LYS cc_start: 0.8614 (tmmt) cc_final: 0.8279 (tmtt) REVERT: f 398 TRP cc_start: 0.7615 (t-100) cc_final: 0.6950 (t-100) REVERT: f 399 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8012 (tm) REVERT: f 407 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.7406 (mmm) REVERT: f 452 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8735 (t0) REVERT: f 466 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8658 (mm) REVERT: f 471 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7810 (mm) REVERT: f 573 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7920 (mm) REVERT: f 574 GLU cc_start: 0.8778 (mp0) cc_final: 0.8382 (tp30) REVERT: f 670 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8348 (mpp) REVERT: f 747 GLN cc_start: 0.8481 (tp40) cc_final: 0.7860 (mt0) REVERT: f 788 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7691 (tpp) REVERT: f 895 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: g 107 ILE cc_start: 0.4835 (OUTLIER) cc_final: 0.4314 (pt) REVERT: g 111 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6466 (pm20) REVERT: g 142 LEU cc_start: 0.7178 (tm) cc_final: 0.6616 (mt) REVERT: u 129 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7683 (t80) outliers start: 301 outliers final: 136 residues processed: 1120 average time/residue: 1.4114 time to fit residues: 2113.3573 Evaluate side-chains 1077 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 863 time to evaluate : 6.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 197 GLU Chi-restraints excluded: chain F residue 310 MET Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 26 GLU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 115 LYS 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 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 205 LYS Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain U residue 201 LEU Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 479 LEU Chi-restraints excluded: chain U residue 514 LEU Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 759 SER Chi-restraints excluded: chain U residue 797 MET Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 162 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 266 GLN Chi-restraints excluded: chain V residue 342 ILE Chi-restraints excluded: chain V residue 354 LYS Chi-restraints excluded: chain V residue 399 ARG Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 486 ILE Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 516 GLN Chi-restraints excluded: chain V residue 519 LEU Chi-restraints excluded: chain V residue 524 GLU Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 169 LEU Chi-restraints excluded: chain W residue 203 GLN Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 318 SER Chi-restraints excluded: chain W residue 348 GLU Chi-restraints excluded: chain W residue 424 LEU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 241 SER Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 277 LEU Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 394 ASP Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 87 GLU Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 28 LYS Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 283 ARG Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 74 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 158 LEU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 299 SER Chi-restraints excluded: chain a residue 309 LEU Chi-restraints excluded: chain a residue 316 SER Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 152 LYS Chi-restraints excluded: chain c residue 204 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 260 ILE Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 313 ASN Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 208 LEU Chi-restraints excluded: chain f residue 237 VAL Chi-restraints excluded: chain f residue 256 PHE Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 354 GLU Chi-restraints excluded: chain f residue 393 ASP Chi-restraints excluded: chain f residue 399 LEU Chi-restraints excluded: chain f residue 407 MET Chi-restraints excluded: chain f residue 452 ASN Chi-restraints excluded: chain f residue 466 LEU Chi-restraints excluded: chain f residue 471 LEU Chi-restraints excluded: chain f residue 477 MET Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 541 THR Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 652 VAL Chi-restraints excluded: chain f residue 670 MET Chi-restraints excluded: chain f residue 690 VAL Chi-restraints excluded: chain f residue 788 MET Chi-restraints excluded: chain f residue 830 LEU Chi-restraints excluded: chain f residue 842 VAL Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 111 GLU Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain u residue 129 PHE Chi-restraints excluded: chain u residue 149 CYS Chi-restraints excluded: chain u residue 150 LEU Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain u residue 173 GLN Chi-restraints excluded: chain u residue 175 VAL Chi-restraints excluded: chain u residue 194 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 110 optimal weight: 4.9990 chunk 861 optimal weight: 40.0000 chunk 597 optimal weight: 3.9990 chunk 860 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 675 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 539 optimal weight: 6.9990 chunk 332 optimal weight: 8.9990 chunk 284 optimal weight: 3.9990 chunk 516 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN C 111 ASN D 65 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN ** D 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 HIS ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 184 GLN Z 7 GLN ** Z 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 273 GLN ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 242 ASN u 251 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.068112 restraints weight = 142989.425| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.61 r_work: 0.2824 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2699 r_free = 0.2699 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 72503 Z= 0.375 Angle : 0.650 15.257 97952 Z= 0.324 Chirality : 0.044 0.338 11157 Planarity : 0.004 0.062 12612 Dihedral : 6.183 80.755 9935 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.05 % Favored : 96.93 % Rotamer: Outliers : 3.68 % Allowed : 29.82 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 1.13 (0.09), residues: 8913 helix: 1.34 (0.07), residues: 5042 sheet: -0.21 (0.17), residues: 946 loop : 0.23 (0.12), residues: 2925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 34 HIS 0.005 0.001 HIS f 782 PHE 0.028 0.001 PHE V 496 TYR 0.036 0.002 TYR f 349 ARG 0.014 0.001 ARG Z 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 863 time to evaluate : 6.317 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 51 ASP cc_start: 0.9046 (t0) cc_final: 0.8708 (t0) REVERT: A 54 GLN cc_start: 0.8825 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 55 LEU cc_start: 0.8478 (mt) cc_final: 0.8049 (mt) REVERT: A 85 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8381 (tp40) REVERT: A 138 MET cc_start: 0.9371 (ttp) cc_final: 0.9121 (ttp) REVERT: A 158 ASP cc_start: 0.8871 (t0) cc_final: 0.8468 (t0) REVERT: A 182 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: A 186 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8457 (mttm) REVERT: A 361 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8574 (t) REVERT: A 400 ARG cc_start: 0.8497 (mmp80) cc_final: 0.8245 (tpp-160) REVERT: B 69 LYS cc_start: 0.9187 (tmmm) cc_final: 0.8804 (tmmt) REVERT: B 118 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: B 276 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: B 302 GLU cc_start: 0.8914 (mp0) cc_final: 0.8206 (mm-30) REVERT: B 405 MET cc_start: 0.9269 (mmt) cc_final: 0.8919 (mtt) REVERT: B 408 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8837 (tpp80) REVERT: C 51 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8802 (pt0) REVERT: C 112 CYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7277 (p) REVERT: C 139 MET cc_start: 0.9332 (mtp) cc_final: 0.9034 (mtp) REVERT: C 150 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8777 (ptm) REVERT: C 290 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8431 (mmpt) REVERT: C 297 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8434 (ttp-110) REVERT: C 336 MET cc_start: 0.9390 (OUTLIER) cc_final: 0.8525 (mtp) REVERT: D 63 ASP cc_start: 0.9158 (OUTLIER) cc_final: 0.8646 (t0) REVERT: D 71 GLU cc_start: 0.9244 (tp30) cc_final: 0.8818 (mm-30) REVERT: D 153 MET cc_start: 0.9205 (mtm) cc_final: 0.8983 (mtt) REVERT: E 48 LYS cc_start: 0.9318 (mtpp) cc_final: 0.9077 (mtmt) REVERT: E 122 MET cc_start: 0.9311 (mtt) cc_final: 0.8867 (mtt) REVERT: E 125 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: E 277 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8853 (mtt) REVERT: E 335 SER cc_start: 0.9474 (m) cc_final: 0.9218 (t) REVERT: E 342 ASP cc_start: 0.8881 (m-30) cc_final: 0.8561 (m-30) REVERT: F 69 MET cc_start: 0.5620 (ppp) cc_final: 0.5321 (pp-130) REVERT: F 183 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: F 349 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8717 (m-30) REVERT: G 19 GLU cc_start: 0.9216 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: G 92 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8431 (tm-30) REVERT: G 113 MET cc_start: 0.9124 (mmm) cc_final: 0.8829 (mmt) REVERT: G 117 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7317 (ttm170) REVERT: G 147 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7945 (mp10) REVERT: H 163 MET cc_start: 0.8726 (ptp) cc_final: 0.8472 (ptm) REVERT: H 209 GLU cc_start: 0.8700 (tt0) cc_final: 0.8441 (tt0) REVERT: I 57 ASP cc_start: 0.9060 (t0) cc_final: 0.8471 (t0) REVERT: I 108 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: I 210 LYS cc_start: 0.8654 (mtmp) cc_final: 0.8030 (mtmt) REVERT: I 220 ASN cc_start: 0.8764 (t0) cc_final: 0.8409 (p0) REVERT: J 30 SER cc_start: 0.9101 (m) cc_final: 0.8883 (p) REVERT: J 177 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8732 (p) REVERT: J 239 ASN cc_start: 0.9034 (m-40) cc_final: 0.8782 (m110) REVERT: K 20 ARG cc_start: 0.8904 (mtm110) cc_final: 0.8659 (mtp85) REVERT: K 65 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8332 (pm20) REVERT: K 95 GLU cc_start: 0.8951 (tp30) cc_final: 0.8640 (tp30) REVERT: K 147 ASP cc_start: 0.8252 (p0) cc_final: 0.8042 (p0) REVERT: L 53 GLN cc_start: 0.8206 (mt0) cc_final: 0.7916 (pt0) REVERT: L 68 ASN cc_start: 0.9353 (m-40) cc_final: 0.9110 (m-40) REVERT: L 220 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: L 224 TYR cc_start: 0.9028 (m-10) cc_final: 0.8638 (m-10) REVERT: M 97 ASN cc_start: 0.8911 (m110) cc_final: 0.8485 (m110) REVERT: M 136 MET cc_start: 0.9450 (mtm) cc_final: 0.9090 (mtm) REVERT: M 223 ARG cc_start: 0.8279 (ttp-110) cc_final: 0.7947 (ttp-110) REVERT: U 57 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8355 (ptm-80) REVERT: U 76 GLU cc_start: 0.9138 (mp0) cc_final: 0.8881 (mp0) REVERT: U 92 ASP cc_start: 0.9234 (OUTLIER) cc_final: 0.8699 (m-30) REVERT: U 131 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: U 239 GLU cc_start: 0.8791 (tp30) cc_final: 0.8572 (tp30) REVERT: U 252 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9197 (mm) REVERT: U 470 ASN cc_start: 0.7951 (t0) cc_final: 0.7590 (t0) REVERT: U 479 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9198 (mp) REVERT: U 714 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8942 (p) REVERT: U 797 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8656 (ttp) REVERT: V 84 LYS cc_start: 0.9019 (tppp) cc_final: 0.8689 (tptp) REVERT: V 120 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7315 (t80) REVERT: V 162 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: V 279 GLN cc_start: 0.8958 (pm20) cc_final: 0.8619 (pm20) REVERT: V 354 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8557 (tmmt) REVERT: V 399 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7603 (ttm-80) REVERT: V 515 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8298 (tm-30) REVERT: V 519 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8305 (tm) REVERT: V 520 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8218 (mm-30) REVERT: V 524 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8058 (pt0) REVERT: W 30 GLU cc_start: 0.9075 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: W 40 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8684 (tp) REVERT: W 73 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8857 (mtt) REVERT: W 118 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8085 (tt) REVERT: W 152 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8476 (mp) REVERT: W 161 GLU cc_start: 0.8721 (mp0) cc_final: 0.8181 (mp0) REVERT: W 168 GLU cc_start: 0.8762 (pp20) cc_final: 0.8458 (pp20) REVERT: W 203 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8338 (tm-30) REVERT: W 424 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8992 (tt) REVERT: W 436 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8776 (mtp) REVERT: X 72 TYR cc_start: 0.8397 (t80) cc_final: 0.8131 (t80) REVERT: X 223 LYS cc_start: 0.8768 (mmmm) cc_final: 0.8364 (mmpt) REVERT: X 260 MET cc_start: 0.9210 (mmt) cc_final: 0.8993 (mmt) REVERT: X 277 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9259 (mp) REVERT: X 329 ASN cc_start: 0.8862 (t0) cc_final: 0.8515 (m110) REVERT: X 332 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: X 394 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7695 (m-30) REVERT: Y 42 MET cc_start: 0.8775 (mmp) cc_final: 0.8455 (mmt) REVERT: Y 50 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8849 (mtp) REVERT: Y 85 ASP cc_start: 0.8927 (m-30) cc_final: 0.8722 (m-30) REVERT: Y 196 GLN cc_start: 0.9283 (tt0) cc_final: 0.9019 (tt0) REVERT: Y 321 GLU cc_start: 0.9142 (tt0) cc_final: 0.8763 (tp30) REVERT: Y 389 MET cc_start: 0.7165 (ptt) cc_final: 0.6361 (ppp) REVERT: Z 79 TYR cc_start: 0.8719 (t80) cc_final: 0.8092 (t80) REVERT: Z 143 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7243 (tm-30) REVERT: Z 177 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8606 (ttt-90) REVERT: Z 244 GLU cc_start: 0.8716 (mp0) cc_final: 0.8401 (pm20) REVERT: Z 283 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7973 (ttm170) REVERT: a 40 GLN cc_start: 0.8635 (tp40) cc_final: 0.8108 (mp10) REVERT: a 58 LYS cc_start: 0.9440 (mmmm) cc_final: 0.9081 (mmmm) REVERT: a 103 LYS cc_start: 0.9241 (ptpt) cc_final: 0.8927 (ptpp) REVERT: a 109 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8906 (mm-30) REVERT: a 127 ASP cc_start: 0.8385 (t0) cc_final: 0.8114 (t0) REVERT: a 128 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7725 (pp) REVERT: a 139 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8865 (mm-30) REVERT: a 306 GLU cc_start: 0.9385 (mt-10) cc_final: 0.9044 (pt0) REVERT: b 11 ASP cc_start: 0.8566 (t0) cc_final: 0.7986 (t0) REVERT: b 14 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8163 (mm-30) REVERT: b 108 ARG cc_start: 0.7471 (tpp80) cc_final: 0.6474 (tpp80) REVERT: b 130 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.6519 (ttp80) REVERT: b 134 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7157 (mp0) REVERT: b 139 ASP cc_start: 0.7851 (m-30) cc_final: 0.7394 (m-30) REVERT: c 152 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9023 (mttp) REVERT: c 227 GLU cc_start: 0.8661 (mp0) cc_final: 0.8036 (mp0) REVERT: c 257 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8522 (mtpp) REVERT: c 261 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8115 (mm-30) REVERT: c 303 MET cc_start: 0.9499 (OUTLIER) cc_final: 0.9045 (mtt) REVERT: d 140 GLN cc_start: 0.8899 (mt0) cc_final: 0.8619 (mt0) REVERT: d 146 ASP cc_start: 0.9154 (m-30) cc_final: 0.8775 (m-30) REVERT: d 158 ARG cc_start: 0.8505 (ptm160) cc_final: 0.8292 (ttm110) REVERT: d 165 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8831 (mt-10) REVERT: d 289 ARG cc_start: 0.8778 (mtm-85) cc_final: 0.8501 (mtm-85) REVERT: d 299 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8070 (tpp) REVERT: d 332 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8831 (m) REVERT: e 18 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7428 (pp20) REVERT: e 20 GLU cc_start: 0.8598 (pm20) cc_final: 0.7986 (pm20) REVERT: e 21 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: e 61 GLU cc_start: 0.8758 (pt0) cc_final: 0.8404 (pm20) REVERT: f 118 ASN cc_start: 0.7605 (m-40) cc_final: 0.7384 (t0) REVERT: f 168 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8060 (mmtt) REVERT: f 207 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8799 (tp) REVERT: f 209 MET cc_start: 0.8051 (mtm) cc_final: 0.7788 (ptp) REVERT: f 235 SER cc_start: 0.8961 (m) cc_final: 0.8449 (p) REVERT: f 275 MET cc_start: 0.9125 (tpp) cc_final: 0.8396 (tpp) REVERT: f 279 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: f 294 MET cc_start: 0.7768 (mmt) cc_final: 0.7302 (mmt) REVERT: f 344 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7908 (m) REVERT: f 354 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: f 389 LYS cc_start: 0.8664 (tmmt) cc_final: 0.8347 (tmtt) REVERT: f 398 TRP cc_start: 0.7676 (t-100) cc_final: 0.7118 (t-100) REVERT: f 399 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8018 (tm) REVERT: f 407 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7396 (mmm) REVERT: f 471 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7851 (mm) REVERT: f 573 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7980 (mm) REVERT: f 574 GLU cc_start: 0.8730 (mp0) cc_final: 0.8489 (tp30) REVERT: f 670 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8271 (mpp) REVERT: f 747 GLN cc_start: 0.8537 (tp40) cc_final: 0.8018 (tt0) REVERT: f 788 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.7682 (tpp) REVERT: f 895 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: g 107 ILE cc_start: 0.4850 (OUTLIER) cc_final: 0.4314 (pt) REVERT: g 111 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6509 (pm20) REVERT: g 142 LEU cc_start: 0.7233 (tm) cc_final: 0.6669 (mt) REVERT: u 129 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7655 (t80) outliers start: 287 outliers final: 133 residues processed: 1076 average time/residue: 1.4532 time to fit residues: 2086.3723 Evaluate side-chains 1039 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 831 time to evaluate : 6.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 385 MET Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 117 ARG Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 115 LYS 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 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 92 ASP Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 479 LEU Chi-restraints excluded: chain U residue 514 LEU Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 759 SER Chi-restraints excluded: chain U residue 797 MET Chi-restraints excluded: chain V residue 120 PHE Chi-restraints excluded: chain V residue 162 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 281 ASN Chi-restraints excluded: chain V residue 342 ILE Chi-restraints excluded: chain V residue 354 LYS Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 395 ILE Chi-restraints excluded: chain V residue 399 ARG Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 486 ILE Chi-restraints excluded: chain V residue 491 VAL Chi-restraints excluded: chain V residue 504 ASP Chi-restraints excluded: chain V residue 516 GLN Chi-restraints excluded: chain V residue 519 LEU Chi-restraints excluded: chain V residue 524 GLU Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 169 LEU Chi-restraints excluded: chain W residue 203 GLN Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 424 LEU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 241 SER Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 277 LEU Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 394 ASP Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 87 GLU Chi-restraints excluded: chain Y residue 163 LYS Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Z residue 28 LYS Chi-restraints excluded: chain Z residue 33 LYS Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 177 ARG Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 283 ARG Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 74 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 139 GLU Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 299 SER Chi-restraints excluded: chain a residue 309 LEU Chi-restraints excluded: chain a residue 316 SER Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 117 VAL Chi-restraints excluded: chain b residue 130 ARG Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 152 LYS Chi-restraints excluded: chain c residue 204 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 260 ILE Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 313 ASN Chi-restraints excluded: chain d residue 332 SER Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain f residue 180 GLN Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 208 LEU Chi-restraints excluded: chain f residue 237 VAL Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain f residue 344 VAL Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 354 GLU Chi-restraints excluded: chain f residue 399 LEU Chi-restraints excluded: chain f residue 407 MET Chi-restraints excluded: chain f residue 471 LEU Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 527 VAL Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 541 THR Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 652 VAL Chi-restraints excluded: chain f residue 670 MET Chi-restraints excluded: chain f residue 690 VAL Chi-restraints excluded: chain f residue 788 MET Chi-restraints excluded: chain f residue 830 LEU Chi-restraints excluded: chain f residue 842 VAL Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 107 ILE Chi-restraints excluded: chain g residue 111 GLU Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain u residue 129 PHE Chi-restraints excluded: chain u residue 149 CYS Chi-restraints excluded: chain u residue 150 LEU Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain u residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 868 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 682 optimal weight: 0.9990 chunk 884 optimal weight: 7.9990 chunk 478 optimal weight: 1.9990 chunk 772 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 586 optimal weight: 9.9990 chunk 553 optimal weight: 3.9990 chunk 749 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN C 111 ASN D 65 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN G 224 ASN J 205 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 28 HIS ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 160 ASN Z 7 GLN Z 278 ASN a 273 GLN b 105 HIS ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 242 ASN u 251 ASN u 252 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.070063 restraints weight = 141279.308| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.61 r_work: 0.2863 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 72503 Z= 0.226 Angle : 0.631 15.432 97952 Z= 0.311 Chirality : 0.042 0.382 11157 Planarity : 0.004 0.065 12612 Dihedral : 6.061 79.305 9935 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 3.05 % Allowed : 30.55 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 1.21 (0.09), residues: 8913 helix: 1.42 (0.07), residues: 5029 sheet: -0.26 (0.16), residues: 964 loop : 0.29 (0.12), residues: 2920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP a 34 HIS 0.018 0.001 HIS u 144 PHE 0.028 0.001 PHE V 496 TYR 0.032 0.001 TYR f 349 ARG 0.016 0.001 ARG E 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17826 Ramachandran restraints generated. 8913 Oldfield, 0 Emsley, 8913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 889 time to evaluate : 6.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.9027 (t0) cc_final: 0.8706 (t0) REVERT: A 54 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8577 (tm-30) REVERT: A 55 LEU cc_start: 0.8474 (mt) cc_final: 0.8054 (mt) REVERT: A 88 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8665 (pm20) REVERT: A 138 MET cc_start: 0.9293 (ttp) cc_final: 0.9063 (ttp) REVERT: A 158 ASP cc_start: 0.8807 (t0) cc_final: 0.8406 (t0) REVERT: A 182 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8717 (pm20) REVERT: A 186 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8314 (mttm) REVERT: A 239 ARG cc_start: 0.9239 (ptm-80) cc_final: 0.8726 (pmt-80) REVERT: A 361 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8576 (t) REVERT: B 69 LYS cc_start: 0.9202 (tmmm) cc_final: 0.8913 (tmmt) REVERT: B 118 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: B 276 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: B 405 MET cc_start: 0.9233 (mmt) cc_final: 0.8939 (mtt) REVERT: B 408 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8848 (tpp80) REVERT: C 51 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8777 (pt0) REVERT: C 112 CYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7448 (p) REVERT: C 139 MET cc_start: 0.9269 (mtp) cc_final: 0.8881 (mtm) REVERT: C 150 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8764 (ptm) REVERT: C 290 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8361 (mmpt) REVERT: C 297 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8413 (ttp-110) REVERT: C 336 MET cc_start: 0.9327 (OUTLIER) cc_final: 0.8523 (mtp) REVERT: D 63 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8617 (t0) REVERT: D 65 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8592 (mm110) REVERT: D 71 GLU cc_start: 0.9197 (tp30) cc_final: 0.8778 (mm-30) REVERT: D 152 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8862 (mpp) REVERT: E 48 LYS cc_start: 0.9320 (mtpp) cc_final: 0.9073 (mtmt) REVERT: E 122 MET cc_start: 0.9280 (mtt) cc_final: 0.8869 (mtt) REVERT: E 125 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: E 277 MET cc_start: 0.9253 (OUTLIER) cc_final: 0.8875 (mtt) REVERT: E 335 SER cc_start: 0.9473 (m) cc_final: 0.9236 (t) REVERT: E 342 ASP cc_start: 0.8765 (m-30) cc_final: 0.8456 (m-30) REVERT: F 69 MET cc_start: 0.5627 (ppp) cc_final: 0.5314 (pp-130) REVERT: F 183 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8418 (mp0) REVERT: F 349 ASP cc_start: 0.9048 (OUTLIER) cc_final: 0.8701 (m-30) REVERT: F 422 GLU cc_start: 0.8774 (pp20) cc_final: 0.8563 (pp20) REVERT: G 19 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8662 (mp0) REVERT: G 92 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8471 (tm-30) REVERT: G 113 MET cc_start: 0.9061 (mmm) cc_final: 0.8703 (mmt) REVERT: G 117 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7329 (ttm170) REVERT: G 130 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8068 (tp30) REVERT: G 147 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: H 18 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8763 (mttm) REVERT: H 163 MET cc_start: 0.8557 (ptp) cc_final: 0.8291 (ptm) REVERT: H 209 GLU cc_start: 0.8688 (tt0) cc_final: 0.8219 (tt0) REVERT: I 108 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: I 210 LYS cc_start: 0.8670 (mtmp) cc_final: 0.7994 (mtmt) REVERT: I 220 ASN cc_start: 0.8644 (t0) cc_final: 0.8273 (p0) REVERT: J 30 SER cc_start: 0.9069 (m) cc_final: 0.8858 (p) REVERT: J 175 ASN cc_start: 0.9438 (m110) cc_final: 0.9016 (m-40) REVERT: J 177 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8707 (p) REVERT: J 239 ASN cc_start: 0.8998 (m-40) cc_final: 0.8744 (m110) REVERT: K 20 ARG cc_start: 0.8944 (mtm110) cc_final: 0.8705 (mtp85) REVERT: K 65 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8346 (pm20) REVERT: K 95 GLU cc_start: 0.8909 (tp30) cc_final: 0.8607 (tp30) REVERT: K 147 ASP cc_start: 0.8214 (p0) cc_final: 0.7998 (p0) REVERT: L 53 GLN cc_start: 0.8269 (mt0) cc_final: 0.8007 (pt0) REVERT: L 68 ASN cc_start: 0.9347 (m-40) cc_final: 0.9065 (m-40) REVERT: L 220 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8363 (tp30) REVERT: L 224 TYR cc_start: 0.9020 (m-10) cc_final: 0.8611 (m-10) REVERT: M 97 ASN cc_start: 0.8912 (m110) cc_final: 0.8529 (m110) REVERT: M 136 MET cc_start: 0.9445 (mtm) cc_final: 0.9030 (mtm) REVERT: M 223 ARG cc_start: 0.8313 (ttp-110) cc_final: 0.7999 (ttp-110) REVERT: U 43 ASP cc_start: 0.9211 (m-30) cc_final: 0.8823 (m-30) REVERT: U 57 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8316 (ptm-80) REVERT: U 76 GLU cc_start: 0.9140 (mp0) cc_final: 0.8883 (mp0) REVERT: U 131 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8259 (mm-30) REVERT: U 144 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8521 (t0) REVERT: U 252 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9176 (mm) REVERT: U 470 ASN cc_start: 0.7996 (t0) cc_final: 0.7645 (t0) REVERT: U 479 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9196 (mp) REVERT: U 700 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8846 (tp30) REVERT: U 797 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8630 (ttp) REVERT: V 84 LYS cc_start: 0.8955 (tppp) cc_final: 0.8659 (tptp) REVERT: V 162 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: V 279 GLN cc_start: 0.8932 (pm20) cc_final: 0.8636 (pm20) REVERT: V 354 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8556 (tmmt) REVERT: V 399 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7610 (ttm-80) REVERT: V 515 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8332 (tm-30) REVERT: V 519 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8331 (tm) REVERT: V 520 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8379 (mm-30) REVERT: W 30 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8477 (mp0) REVERT: W 40 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8706 (tm) REVERT: W 73 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8758 (mtt) REVERT: W 118 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8151 (tt) REVERT: W 152 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8396 (mp) REVERT: W 161 GLU cc_start: 0.8700 (mp0) cc_final: 0.8153 (mp0) REVERT: W 168 GLU cc_start: 0.8783 (pp20) cc_final: 0.8488 (pp20) REVERT: W 203 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8412 (tm-30) REVERT: W 424 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8974 (tt) REVERT: W 436 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8731 (mtp) REVERT: X 28 HIS cc_start: 0.8503 (m-70) cc_final: 0.7691 (m90) REVERT: X 72 TYR cc_start: 0.8327 (t80) cc_final: 0.8042 (t80) REVERT: X 223 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8349 (mmpt) REVERT: X 277 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9185 (mp) REVERT: X 329 ASN cc_start: 0.8812 (t0) cc_final: 0.8482 (m110) REVERT: X 332 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: X 394 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: X 419 LYS cc_start: 0.8400 (pttp) cc_final: 0.8151 (ttpp) REVERT: Y 42 MET cc_start: 0.8787 (mmp) cc_final: 0.8427 (mmm) REVERT: Y 50 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8588 (mtp) REVERT: Y 85 ASP cc_start: 0.8962 (m-30) cc_final: 0.8734 (m-30) REVERT: Y 173 ASP cc_start: 0.8661 (t0) cc_final: 0.8262 (t0) REVERT: Y 196 GLN cc_start: 0.9281 (tt0) cc_final: 0.9017 (tt0) REVERT: Y 321 GLU cc_start: 0.9114 (tt0) cc_final: 0.8718 (tp30) REVERT: Y 389 MET cc_start: 0.7171 (ptt) cc_final: 0.6362 (ppp) REVERT: Z 79 TYR cc_start: 0.8672 (t80) cc_final: 0.8067 (t80) REVERT: Z 143 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7330 (tm-30) REVERT: Z 244 GLU cc_start: 0.8705 (mp0) cc_final: 0.8413 (pm20) REVERT: Z 283 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.7955 (ttm170) REVERT: a 40 GLN cc_start: 0.8712 (tp40) cc_final: 0.8065 (mp10) REVERT: a 70 ARG cc_start: 0.8399 (ttm110) cc_final: 0.8083 (ttp-110) REVERT: a 103 LYS cc_start: 0.9214 (ptpt) cc_final: 0.8895 (ptpp) REVERT: a 109 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8919 (mm-30) REVERT: a 127 ASP cc_start: 0.8323 (t0) cc_final: 0.8055 (t0) REVERT: a 139 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8812 (mm-30) REVERT: a 306 GLU cc_start: 0.9389 (mt-10) cc_final: 0.8868 (pm20) REVERT: a 316 SER cc_start: 0.9494 (OUTLIER) cc_final: 0.9232 (p) REVERT: b 4 GLU cc_start: 0.8269 (pp20) cc_final: 0.8063 (pp20) REVERT: b 11 ASP cc_start: 0.8507 (t0) cc_final: 0.8253 (t0) REVERT: b 14 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8112 (mm-30) REVERT: b 108 ARG cc_start: 0.7478 (tpp80) cc_final: 0.6360 (tpp80) REVERT: b 134 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: b 139 ASP cc_start: 0.7858 (m-30) cc_final: 0.7292 (m-30) REVERT: c 152 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8934 (mttp) REVERT: c 227 GLU cc_start: 0.8619 (mp0) cc_final: 0.7980 (mp0) REVERT: c 257 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8456 (mtpp) REVERT: c 261 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8105 (mm-30) REVERT: c 303 MET cc_start: 0.9494 (OUTLIER) cc_final: 0.9039 (mtt) REVERT: d 140 GLN cc_start: 0.8881 (mt0) cc_final: 0.8628 (mt0) REVERT: d 146 ASP cc_start: 0.9146 (m-30) cc_final: 0.8750 (m-30) REVERT: d 158 ARG cc_start: 0.8437 (ptm160) cc_final: 0.8216 (ttm110) REVERT: d 165 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8824 (mt-10) REVERT: d 270 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8400 (tp30) REVERT: d 299 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.7977 (tpp) REVERT: d 332 SER cc_start: 0.9054 (OUTLIER) cc_final: 0.8819 (m) REVERT: e 18 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7489 (tm-30) REVERT: e 20 GLU cc_start: 0.8581 (pm20) cc_final: 0.8275 (pm20) REVERT: e 21 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: e 61 GLU cc_start: 0.8735 (pt0) cc_final: 0.8390 (pm20) REVERT: f 168 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8153 (tppp) REVERT: f 207 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8793 (tp) REVERT: f 209 MET cc_start: 0.8015 (mtm) cc_final: 0.7770 (ptp) REVERT: f 235 SER cc_start: 0.9003 (m) cc_final: 0.8480 (p) REVERT: f 275 MET cc_start: 0.9118 (tpp) cc_final: 0.8341 (tpp) REVERT: f 279 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8290 (mp0) REVERT: f 294 MET cc_start: 0.7839 (mmt) cc_final: 0.7319 (mmt) REVERT: f 344 VAL cc_start: 0.8205 (t) cc_final: 0.7807 (m) REVERT: f 354 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: f 398 TRP cc_start: 0.7636 (t-100) cc_final: 0.7134 (t-100) REVERT: f 399 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8067 (tm) REVERT: f 407 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7413 (mmm) REVERT: f 452 ASN cc_start: 0.8958 (t160) cc_final: 0.8695 (t0) REVERT: f 471 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7801 (mm) REVERT: f 477 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7172 (mmp) REVERT: f 573 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7906 (mm) REVERT: f 574 GLU cc_start: 0.8739 (mp0) cc_final: 0.8485 (tp30) REVERT: f 670 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8366 (mpp) REVERT: f 747 GLN cc_start: 0.8502 (tp40) cc_final: 0.7831 (mt0) REVERT: f 788 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7715 (tpp) REVERT: f 895 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7902 (pt0) REVERT: g 111 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: g 112 LEU cc_start: 0.6651 (mp) cc_final: 0.6448 (pt) REVERT: g 142 LEU cc_start: 0.7225 (tm) cc_final: 0.6769 (mt) REVERT: u 121 LYS cc_start: 0.8738 (tppp) cc_final: 0.8331 (tppt) REVERT: u 129 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.7738 (t80) REVERT: u 174 PRO cc_start: 0.8957 (Cg_exo) cc_final: 0.8736 (Cg_endo) outliers start: 238 outliers final: 122 residues processed: 1063 average time/residue: 1.4816 time to fit residues: 2110.2156 Evaluate side-chains 1040 residues out of total 7793 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 846 time to evaluate : 6.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 112 CYS Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 290 LYS Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 196 ILE Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 273 LYS Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 117 ARG Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain I residue 13 SER Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 108 GLU Chi-restraints excluded: chain J residue 85 ASN Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 177 THR Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 240 ASP Chi-restraints excluded: chain L residue 35 THR Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 128 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain U residue 57 ARG Chi-restraints excluded: chain U residue 131 GLU Chi-restraints excluded: chain U residue 144 ASP Chi-restraints excluded: chain U residue 252 LEU Chi-restraints excluded: chain U residue 397 THR Chi-restraints excluded: chain U residue 479 LEU Chi-restraints excluded: chain U residue 514 LEU Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 703 CYS Chi-restraints excluded: chain U residue 759 SER Chi-restraints excluded: chain U residue 797 MET Chi-restraints excluded: chain V residue 134 PHE Chi-restraints excluded: chain V residue 162 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain V residue 281 ASN Chi-restraints excluded: chain V residue 342 ILE Chi-restraints excluded: chain V residue 354 LYS Chi-restraints excluded: chain V residue 399 ARG Chi-restraints excluded: chain V residue 442 ILE Chi-restraints excluded: chain V residue 486 ILE Chi-restraints excluded: chain V residue 516 GLN Chi-restraints excluded: chain V residue 519 LEU Chi-restraints excluded: chain W residue 30 GLU Chi-restraints excluded: chain W residue 40 LEU Chi-restraints excluded: chain W residue 50 LEU Chi-restraints excluded: chain W residue 73 MET Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 152 ILE Chi-restraints excluded: chain W residue 169 LEU Chi-restraints excluded: chain W residue 203 GLN Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 424 LEU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain X residue 51 LEU Chi-restraints excluded: chain X residue 93 LEU Chi-restraints excluded: chain X residue 110 CYS Chi-restraints excluded: chain X residue 125 LEU Chi-restraints excluded: chain X residue 241 SER Chi-restraints excluded: chain X residue 242 ILE Chi-restraints excluded: chain X residue 277 LEU Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 332 GLU Chi-restraints excluded: chain X residue 394 ASP Chi-restraints excluded: chain X residue 415 TYR Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 55 GLU Chi-restraints excluded: chain Y residue 87 GLU Chi-restraints excluded: chain Y residue 319 MET Chi-restraints excluded: chain Y residue 343 LEU Chi-restraints excluded: chain Z residue 28 LYS Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 178 ASP Chi-restraints excluded: chain Z residue 283 ARG Chi-restraints excluded: chain a residue 74 LEU Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 139 GLU Chi-restraints excluded: chain a residue 291 LEU Chi-restraints excluded: chain a residue 299 SER Chi-restraints excluded: chain a residue 309 LEU Chi-restraints excluded: chain a residue 316 SER Chi-restraints excluded: chain a residue 340 VAL Chi-restraints excluded: chain b residue 134 GLU Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain b residue 140 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 125 VAL Chi-restraints excluded: chain c residue 152 LYS Chi-restraints excluded: chain c residue 204 THR Chi-restraints excluded: chain c residue 303 MET Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 131 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 257 THR Chi-restraints excluded: chain d residue 267 ILE Chi-restraints excluded: chain d residue 299 MET Chi-restraints excluded: chain d residue 332 SER Chi-restraints excluded: chain e residue 18 GLU Chi-restraints excluded: chain e residue 21 GLU Chi-restraints excluded: chain e residue 30 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain f residue 207 LEU Chi-restraints excluded: chain f residue 208 LEU Chi-restraints excluded: chain f residue 237 VAL Chi-restraints excluded: chain f residue 279 GLU Chi-restraints excluded: chain f residue 353 LEU Chi-restraints excluded: chain f residue 354 GLU Chi-restraints excluded: chain f residue 399 LEU Chi-restraints excluded: chain f residue 407 MET Chi-restraints excluded: chain f residue 471 LEU Chi-restraints excluded: chain f residue 477 MET Chi-restraints excluded: chain f residue 483 PHE Chi-restraints excluded: chain f residue 538 ILE Chi-restraints excluded: chain f residue 541 THR Chi-restraints excluded: chain f residue 558 LEU Chi-restraints excluded: chain f residue 573 ILE Chi-restraints excluded: chain f residue 583 VAL Chi-restraints excluded: chain f residue 652 VAL Chi-restraints excluded: chain f residue 670 MET Chi-restraints excluded: chain f residue 690 VAL Chi-restraints excluded: chain f residue 788 MET Chi-restraints excluded: chain f residue 830 LEU Chi-restraints excluded: chain f residue 842 VAL Chi-restraints excluded: chain f residue 873 LEU Chi-restraints excluded: chain f residue 895 GLU Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 111 GLU Chi-restraints excluded: chain g residue 147 VAL Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain u residue 129 PHE Chi-restraints excluded: chain u residue 149 CYS Chi-restraints excluded: chain u residue 150 LEU Chi-restraints excluded: chain u residue 153 ASP Chi-restraints excluded: chain u residue 175 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 402 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 216 optimal weight: 0.1980 chunk 672 optimal weight: 5.9990 chunk 659 optimal weight: 10.0000 chunk 428 optimal weight: 0.1980 chunk 828 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 865 optimal weight: 20.0000 chunk 282 optimal weight: 4.9990 chunk 716 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN C 90 HIS C 111 ASN D 65 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN G 224 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 7 GLN a 273 GLN ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 164 GLN ** u 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 216 GLN u 242 ASN u 251 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.102532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.070392 restraints weight = 141437.232| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.62 r_work: 0.2870 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 72503 Z= 0.216 Angle : 0.676 48.235 97952 Z= 0.341 Chirality : 0.043 0.370 11157 Planarity : 0.004 0.068 12612 Dihedral : 6.022 79.009 9935 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.76 % Favored : 97.23 % Rotamer: Outliers : 2.90 % Allowed : 30.81 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.56 % 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: 1.22 (0.09), residues: 8913 helix: 1.43 (0.07), residues: 5013 sheet: -0.26 (0.16), residues: 960 loop : 0.29 (0.12), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP W 263 HIS 0.011 0.001 HIS C 90 PHE 0.088 0.001 PHE V 134 TYR 0.031 0.001 TYR a 162 ARG 0.015 0.000 ARG Z 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 60655.78 seconds wall clock time: 1033 minutes 53.66 seconds (62033.66 seconds total)