Starting phenix.real_space_refine on Wed Jan 22 22:07:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8usb_42506/01_2025/8usb_42506.cif Found real_map, /net/cci-nas-00/data/ceres_data/8usb_42506/01_2025/8usb_42506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8usb_42506/01_2025/8usb_42506.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8usb_42506/01_2025/8usb_42506.map" model { file = "/net/cci-nas-00/data/ceres_data/8usb_42506/01_2025/8usb_42506.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8usb_42506/01_2025/8usb_42506.cif" } resolution = 2.73 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= 0.004 sd= 0.051 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 373 5.16 5 C 44357 2.51 5 N 12061 2.21 5 O 13328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 138 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 70143 Number of models: 1 Model: "" Number of chains: 34 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: "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: "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: "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: "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: "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: "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: "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: "O" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 49 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} 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: "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: "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: "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: "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: "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: "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: "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: "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: 28.86, per 1000 atoms: 0.41 Number of scatterers: 70143 At special positions: 0 Unit cell: (216.936, 220.08, 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 373 16.00 P 17 15.00 Mg 6 11.99 O 13328 8.00 N 12061 7.00 C 44357 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: 13.02 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 113 " 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16686 Finding SS restraints... Secondary structure from input PDB file: 427 helices and 38 sheets defined 61.5% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... 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 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: 3.836A pdb=" N THR W 110 " --> pdb=" O GLN W 106 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR W 111 " --> pdb=" O GLN W 107 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 Processing helix chain 'W' and resid 135 through 137 No H-bonds generated for 'chain 'W' and resid 135 through 137' Processing helix chain 'W' and resid 138 through 156 removed outlier: 3.659A pdb=" N ASN W 156 " --> pdb=" O ILE W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 168 Processing helix chain 'W' and resid 170 through 174 Processing helix chain 'W' and resid 178 through 196 Processing helix chain 'W' and resid 198 through 207 Processing helix chain 'W' and resid 208 through 209 No H-bonds generated for 'chain 'W' and resid 208 through 209' Processing helix chain 'W' and resid 210 through 216 Processing helix chain 'W' and resid 219 through 238 removed outlier: 3.686A pdb=" N HIS W 236 " --> pdb=" O GLN W 232 " (cutoff:3.500A) removed outlier: 3.798A 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 255 through 258 Processing helix chain 'W' and resid 259 through 277 removed outlier: 3.932A pdb=" N GLN W 265 " --> pdb=" O GLU W 261 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 292 Processing helix chain 'W' and resid 294 through 298 Processing helix chain 'W' and resid 299 through 309 Processing helix chain 'W' and resid 316 through 329 removed outlier: 6.457A pdb=" N MET W 326 " --> pdb=" O GLU W 322 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLU W 327 " --> pdb=" O ASP W 323 " (cutoff:3.500A) Processing helix chain 'W' and resid 338 through 342 removed outlier: 4.032A pdb=" N PHE W 341 " --> pdb=" O THR W 338 " (cutoff:3.500A) removed outlier: 3.635A 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 383 Processing helix chain 'W' and resid 385 through 399 Processing helix chain 'W' and resid 420 through 453 Processing helix chain 'C' and resid 20 through 67 removed outlier: 3.608A pdb=" N ILE C 34 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN C 64 " --> pdb=" O ARG C 60 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 132 through 142 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 154 through 171 removed outlier: 3.579A pdb=" N VAL C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.694A 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: 4.174A pdb=" N PHE C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 207 Processing helix chain 'C' and resid 220 through 225 Processing helix chain 'C' and resid 230 through 233 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 267 through 283 removed outlier: 4.512A pdb=" N GLY C 282 " --> pdb=" O ASN C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 307 Processing helix chain 'C' and resid 321 through 334 Processing helix chain 'C' and resid 343 through 350 Processing helix chain 'C' and resid 355 through 373 removed outlier: 3.512A pdb=" N GLU C 373 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 Processing helix chain 'b' and resid 13 through 18 Processing helix chain 'b' and resid 24 through 44 removed outlier: 3.582A pdb=" N ASN b 44 " --> pdb=" O LYS b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 68 through 77 removed outlier: 3.510A pdb=" N LEU b 72 " --> pdb=" O THR b 68 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR b 77 " --> pdb=" O SER b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 99 removed outlier: 3.788A pdb=" N ARG b 91 " --> pdb=" O CYS b 87 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 134 Processing helix chain 'b' and resid 145 through 150 Processing helix chain 'b' and resid 151 through 162 Processing helix chain 'b' and resid 179 through 184 removed outlier: 3.553A pdb=" N ILE b 184 " --> pdb=" O ALA b 180 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 104 removed outlier: 3.596A pdb=" N ARG d 104 " --> pdb=" O GLY d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 126 removed outlier: 3.624A pdb=" N LEU d 121 " --> pdb=" O GLY d 117 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU d 125 " --> pdb=" O LEU d 121 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU d 126 " --> pdb=" O VAL d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 137 through 156 removed outlier: 3.922A pdb=" N LEU d 141 " --> pdb=" O THR d 137 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE d 156 " --> pdb=" O ALA d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 177 removed outlier: 4.127A pdb=" N PHE d 164 " --> pdb=" O ASP d 160 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS d 173 " --> pdb=" O ALA d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 178 through 181 Processing helix chain 'd' and resid 187 through 202 Processing helix chain 'd' and resid 204 through 213 Processing helix chain 'd' and resid 216 through 223 removed outlier: 3.610A pdb=" N ILE d 220 " --> pdb=" O PRO d 216 " (cutoff:3.500A) removed outlier: 4.080A 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: 3.519A pdb=" N ILE d 260 " --> pdb=" O TYR d 256 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR d 266 " --> pdb=" O ILE d 262 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP d 269 " --> pdb=" O ASP d 265 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS d 277 " --> pdb=" O GLY d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 286 through 291 removed outlier: 3.996A pdb=" N ILE d 290 " --> pdb=" O GLU d 286 " (cutoff:3.500A) Processing helix chain 'd' and resid 296 through 307 removed outlier: 3.873A pdb=" N THR d 300 " --> pdb=" O PRO d 296 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASP d 301 " --> pdb=" O LYS d 297 " (cutoff:3.500A) removed outlier: 3.632A 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 '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: 3.537A pdb=" N ALA f 74 " --> pdb=" O LEU f 70 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG f 83 " --> pdb=" O ARG f 79 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER f 85 " --> pdb=" O GLN f 81 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 98 removed outlier: 3.773A pdb=" N LYS f 97 " --> pdb=" O PRO f 93 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE f 98 " --> pdb=" O LYS f 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 93 through 98' Processing helix chain 'f' and resid 99 through 105 Processing helix chain 'f' and resid 117 through 131 removed outlier: 4.063A pdb=" N PHE f 121 " --> pdb=" O GLU f 117 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA f 122 " --> pdb=" O ASN f 118 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP f 124 " --> pdb=" O ARG f 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE f 125 " --> pdb=" O PHE f 121 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE f 126 " --> pdb=" O ALA f 122 " (cutoff:3.500A) Processing helix chain 'f' and resid 138 through 146 removed outlier: 3.730A pdb=" N ARG f 143 " --> pdb=" O CYS f 139 " (cutoff:3.500A) Processing helix chain 'f' and resid 150 through 154 Processing helix chain 'f' and resid 155 through 173 Processing helix chain 'f' and resid 174 through 180 removed outlier: 4.477A pdb=" N VAL f 179 " --> pdb=" O ALA f 176 " (cutoff:3.500A) Processing helix chain 'f' and resid 181 through 198 removed outlier: 3.964A pdb=" N THR f 186 " --> pdb=" O GLU f 182 " (cutoff:3.500A) Proline residue: f 193 - end of helix Processing helix chain 'f' and resid 200 through 211 removed outlier: 3.646A pdb=" N LEU f 207 " --> pdb=" O GLU f 203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU f 208 " --> pdb=" O ALA f 204 " (cutoff:3.500A) Processing helix chain 'f' and resid 213 through 221 removed outlier: 4.039A pdb=" N MET f 216 " --> pdb=" O GLN f 213 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU f 218 " --> pdb=" O ASP f 215 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE f 221 " --> pdb=" O GLU f 218 " (cutoff:3.500A) Processing helix chain 'f' and resid 225 through 237 Processing helix chain 'f' and resid 243 through 259 Processing helix chain 'f' and resid 261 through 272 Processing helix chain 'f' and resid 274 through 285 removed outlier: 3.643A pdb=" N CYS f 285 " --> pdb=" O ILE f 281 " (cutoff:3.500A) Processing helix chain 'f' and resid 287 through 302 Processing helix chain 'f' and resid 313 through 323 Processing helix chain 'f' and resid 325 through 337 Processing helix chain 'f' and resid 344 through 350 removed outlier: 3.740A pdb=" N ILE f 348 " --> pdb=" O VAL f 344 " (cutoff:3.500A) Processing helix chain 'f' and resid 351 through 354 Processing helix chain 'f' and resid 368 through 382 Processing helix chain 'f' and resid 395 through 402 removed outlier: 3.631A pdb=" N ASN f 402 " --> pdb=" O TRP f 398 " (cutoff:3.500A) Processing helix chain 'f' and resid 405 through 418 removed outlier: 3.766A pdb=" N GLY f 415 " --> pdb=" O ALA f 411 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET f 416 " --> pdb=" O ALA f 412 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE f 417 " --> pdb=" O SER f 413 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU f 418 " --> pdb=" O LEU f 414 " (cutoff:3.500A) Processing helix chain 'f' and resid 421 through 434 removed outlier: 3.697A pdb=" N THR f 427 " --> pdb=" O ASP f 423 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LYS f 431 " --> pdb=" O THR f 427 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR f 432 " --> pdb=" O GLN f 428 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR f 434 " --> pdb=" O ASP f 430 " (cutoff:3.500A) Processing helix chain 'f' and resid 437 through 453 removed outlier: 3.678A pdb=" N LYS f 441 " --> pdb=" O GLU f 437 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER f 442 " --> pdb=" O ASP f 438 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY f 449 " --> pdb=" O LEU f 445 " (cutoff:3.500A) Processing helix chain 'f' and resid 460 through 468 removed outlier: 3.739A pdb=" N ALA f 464 " --> pdb=" O ASP f 460 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP f 468 " --> pdb=" O ALA f 464 " (cutoff:3.500A) Processing helix chain 'f' and resid 474 through 489 Processing helix chain 'f' and resid 494 through 507 Proline residue: f 503 - end of helix removed outlier: 4.031A 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: 5.141A pdb=" N THR f 553 " --> pdb=" O LEU f 550 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N TYR f 554 " --> pdb=" O LYS f 551 " (cutoff:3.500A) Processing helix chain 'f' and resid 556 through 566 removed outlier: 3.755A pdb=" N LEU f 560 " --> pdb=" O ARG f 556 " (cutoff:3.500A) Processing helix chain 'f' and resid 573 through 582 removed outlier: 4.170A pdb=" N VAL f 582 " --> pdb=" O ALA f 578 " (cutoff:3.500A) Processing helix chain 'f' and resid 586 through 600 Processing helix chain 'f' and resid 605 through 618 removed outlier: 3.835A pdb=" N GLU f 618 " --> pdb=" O HIS f 614 " (cutoff:3.500A) Processing helix chain 'f' and resid 647 through 662 removed outlier: 4.282A pdb=" N GLY f 651 " --> pdb=" O GLY f 647 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL f 652 " --> pdb=" O ALA f 648 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA f 658 " --> pdb=" O VAL f 654 " (cutoff:3.500A) Processing helix chain 'f' and resid 664 through 682 removed outlier: 3.948A pdb=" N ARG f 673 " --> pdb=" O GLU f 669 " (cutoff:3.500A) removed outlier: 3.624A 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: 3.592A 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 Processing helix chain 'f' and resid 771 through 774 Processing helix chain 'f' and resid 789 through 803 Processing helix chain 'f' and resid 804 through 806 No H-bonds generated for 'chain 'f' and resid 804 through 806' Processing helix chain 'f' and resid 814 through 825 Processing helix chain 'g' and resid 108 through 120 removed outlier: 3.660A 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: 4.249A pdb=" N PHE g 169 " --> pdb=" O ALA g 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 removed outlier: 3.657A 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 removed outlier: 3.516A pdb=" N LEU B 144 " --> pdb=" O LYS B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.556A pdb=" N SER B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.455A pdb=" N TYR B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 253 through 256 Processing helix chain 'B' and resid 261 through 277 Processing helix chain 'B' and resid 288 through 293 removed outlier: 3.782A pdb=" N LYS B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 317 removed outlier: 3.505A pdb=" N ILE B 305 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 379 through 384 removed outlier: 3.757A pdb=" N LEU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 415 through 427 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 130 through 134 removed outlier: 3.677A 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: 3.571A 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: 3.669A pdb=" N ASN A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 292 through 307 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 347 through 359 Processing helix chain 'A' and resid 369 through 376 Processing helix chain 'A' and resid 381 through 399 Processing helix chain 'A' and resid 405 through 417 Processing helix chain 'A' and resid 418 through 424 removed outlier: 4.290A pdb=" N LYS A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 Processing helix chain 'D' and resid 40 through 79 removed outlier: 3.826A pdb=" N LYS D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'D' and resid 181 through 187 removed outlier: 3.546A pdb=" N LEU D 185 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 3.665A 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 removed outlier: 3.539A pdb=" N ARG D 323 " --> pdb=" O ALA D 320 " (cutoff:3.500A) 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: 3.678A 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: 3.542A 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: 4.007A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) removed outlier: 4.002A 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 removed outlier: 3.529A pdb=" N ASN E 262 " --> pdb=" O MET E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 305 through 317 Processing helix chain 'E' and resid 327 through 334 removed outlier: 3.807A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 357 Processing helix chain 'E' and resid 363 through 378 Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'F' and resid 70 through 84 Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 169 through 175 Processing helix chain 'F' and resid 184 through 188 removed outlier: 3.595A pdb=" N ILE F 188 " --> pdb=" O TYR F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 203 removed outlier: 3.544A 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 214 Processing helix chain 'F' and resid 232 through 243 Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 287 through 291 Processing helix chain 'F' and resid 303 through 318 Processing helix chain 'F' and resid 358 through 370 Processing helix chain 'F' and resid 380 through 387 Processing helix chain 'F' and resid 392 through 410 Processing helix chain 'F' and resid 416 through 429 removed outlier: 3.559A 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: 3.760A 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 126 removed outlier: 3.650A pdb=" N VAL G 124 " --> pdb=" O ASP G 120 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR G 125 " --> pdb=" O ILE G 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 185 removed outlier: 3.766A 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: 3.605A 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 Processing helix chain 'H' and resid 106 through 121 Processing helix chain 'H' and resid 166 through 176 Processing helix chain 'H' and resid 183 through 199 removed outlier: 3.526A pdb=" N SER H 198 " --> pdb=" O THR H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 234 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 124 Processing helix chain 'I' and resid 167 through 179 Processing helix chain 'I' and resid 185 through 201 removed outlier: 3.565A 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: 3.565A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 28 Processing helix chain 'J' and resid 76 through 99 Processing helix chain 'J' and resid 103 through 119 Processing helix chain 'J' and resid 164 through 176 Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'J' and resid 183 through 197 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: 3.526A pdb=" N GLU J 237 " --> pdb=" O GLU J 233 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU J 238 " --> pdb=" O LYS J 234 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 32 removed outlier: 3.790A pdb=" N ILE K 31 " --> pdb=" O ALA K 27 " (cutoff:3.500A) removed outlier: 4.230A 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: 3.504A pdb=" N LYS K 86 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 98 through 104 Processing helix chain 'K' and resid 108 through 120 removed outlier: 3.702A pdb=" N LEU K 119 " --> pdb=" O ALA K 115 " (cutoff:3.500A) removed outlier: 3.708A 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 204 Processing helix chain 'K' and resid 230 through 239 Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.879A pdb=" N VAL L 29 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 3.581A 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: 3.837A pdb=" N LEU L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 117 through 121 Processing helix chain 'L' and resid 164 through 175 removed outlier: 4.382A pdb=" N ALA L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 179 Processing helix chain 'L' and resid 183 through 197 removed outlier: 3.515A pdb=" N GLU L 197 " --> pdb=" O ARG L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 234 removed outlier: 3.808A 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 Processing helix chain 'M' and resid 80 through 103 Processing helix chain 'M' and resid 107 through 121 Processing helix chain 'M' and resid 168 through 178 removed outlier: 3.771A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 201 removed outlier: 4.306A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 219 through 221 No H-bonds generated for 'chain 'M' and resid 219 through 221' Processing helix chain 'M' and resid 228 through 243 Processing helix chain 'O' and resid 66 through 71 Processing helix chain 'U' and resid 5 through 11 Processing helix chain 'U' and resid 16 through 28 Processing helix chain 'U' and resid 34 through 39 removed outlier: 3.557A pdb=" N ILE U 38 " --> pdb=" O PHE U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 51 removed outlier: 4.038A pdb=" N LEU U 48 " --> pdb=" O LYS U 44 " (cutoff:3.500A) removed outlier: 3.935A 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 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: 3.849A pdb=" N ASP U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 144 Processing helix chain 'U' and resid 146 through 158 Processing helix chain 'U' and resid 159 through 170 Processing helix chain 'U' and resid 172 through 187 Processing helix chain 'U' and resid 191 through 207 Processing helix chain 'U' and resid 212 through 224 removed outlier: 3.504A pdb=" N VAL U 216 " --> pdb=" O ASP U 212 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 239 Processing helix chain 'U' and resid 241 through 255 Processing helix chain 'U' and resid 257 through 270 Processing helix chain 'U' and resid 321 through 331 Processing helix chain 'U' and resid 331 through 345 Processing helix chain 'U' and resid 349 through 358 removed outlier: 4.041A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 377 Processing helix chain 'U' and resid 383 through 389 Processing helix chain 'U' and resid 389 through 394 Processing helix chain 'U' and resid 395 through 397 No H-bonds generated for 'chain 'U' and resid 395 through 397' Processing helix chain 'U' and resid 398 through 412 removed outlier: 3.591A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.526A 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: 4.326A pdb=" N GLN U 438 " --> pdb=" O GLY U 434 " (cutoff:3.500A) Processing helix chain 'U' and resid 456 through 467 removed outlier: 4.260A 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 503 Processing helix chain 'U' and resid 505 through 520 removed outlier: 3.827A 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: 3.631A pdb=" N VAL U 550 " --> pdb=" O ARG U 546 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA U 553 " --> pdb=" O ALA U 549 " (cutoff:3.500A) removed outlier: 3.618A 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 removed outlier: 3.515A pdb=" N SER U 569 " --> pdb=" O ALA U 565 " (cutoff:3.500A) 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: 3.766A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) 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 removed outlier: 3.503A pdb=" N SER U 714 " --> pdb=" O ARG U 710 " (cutoff:3.500A) 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 'U' and resid 887 through 892 Processing helix chain 'V' and resid 59 through 89 removed outlier: 3.708A pdb=" N VAL V 70 " --> pdb=" O GLU V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 92 through 100 removed outlier: 4.109A pdb=" N ARG V 96 " --> pdb=" O ARG V 92 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA V 97 " --> pdb=" O PHE V 93 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET V 100 " --> pdb=" O ARG V 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 107 removed outlier: 3.696A pdb=" N ARG V 106 " --> pdb=" O PRO V 102 " (cutoff:3.500A) Processing helix chain 'V' and resid 109 through 121 removed outlier: 3.703A pdb=" N PHE V 121 " --> pdb=" O VAL V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 132 removed outlier: 3.676A 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: 3.661A pdb=" N ALA V 165 " --> pdb=" O PRO V 161 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 198 Processing helix chain 'V' and resid 202 through 222 removed outlier: 4.158A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR V 218 " --> pdb=" O HIS V 214 " (cutoff:3.500A) Processing helix chain 'V' and resid 225 through 241 removed outlier: 4.203A pdb=" N SER V 229 " --> pdb=" O ASP V 225 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE V 230 " --> pdb=" O VAL V 226 " (cutoff:3.500A) Processing helix chain 'V' and resid 243 through 261 removed outlier: 3.688A pdb=" N TYR V 261 " --> pdb=" O ASN V 257 " (cutoff:3.500A) Processing helix chain 'V' and resid 263 through 274 Processing helix chain 'V' and resid 281 through 299 removed outlier: 3.793A pdb=" N ARG V 287 " --> pdb=" O ASN V 283 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 316 Processing helix chain 'V' and resid 321 through 339 Processing helix chain 'V' and resid 345 through 350 removed outlier: 3.752A pdb=" N GLN V 350 " --> pdb=" O GLN V 347 " (cutoff:3.500A) Processing helix chain 'V' and resid 352 through 370 removed outlier: 4.459A pdb=" N SER V 356 " --> pdb=" O SER V 352 " (cutoff:3.500A) Proline residue: V 359 - end of helix Processing helix chain 'V' and resid 371 through 389 removed outlier: 6.270A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 397 removed outlier: 3.752A pdb=" N ARG V 397 " --> pdb=" O THR V 393 " (cutoff:3.500A) Processing helix chain 'V' and resid 397 through 414 removed outlier: 4.001A 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 526 removed outlier: 3.822A pdb=" N ALA V 526 " --> pdb=" O ALA V 522 " (cutoff:3.500A) 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: 3.562A pdb=" N SER c 132 " --> pdb=" O ASN c 128 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE c 133 " --> pdb=" O THR c 129 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 170 removed outlier: 3.515A pdb=" N LEU c 170 " --> pdb=" O ASN c 166 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 184 removed outlier: 3.960A 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 219 removed outlier: 3.696A pdb=" N ASN c 219 " --> pdb=" O LYS c 215 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 230 removed outlier: 3.559A pdb=" N GLY c 228 " --> pdb=" O SER c 224 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU c 229 " --> pdb=" O TRP c 225 " (cutoff:3.500A) Processing helix chain 'c' and resid 233 through 264 removed outlier: 3.634A pdb=" N GLU c 250 " --> pdb=" O LYS c 246 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS c 257 " --> pdb=" O LYS c 253 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS c 264 " --> pdb=" O GLU c 260 " (cutoff:3.500A) Processing helix chain 'c' and resid 265 through 267 No H-bonds generated for 'chain 'c' and resid 265 through 267' Processing helix chain 'c' and resid 268 through 273 removed outlier: 4.137A pdb=" N ILE c 272 " --> pdb=" O GLU c 268 " (cutoff:3.500A) Processing helix chain 'c' and resid 279 through 309 removed outlier: 3.525A pdb=" N VAL c 307 " --> pdb=" O MET c 303 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 removed outlier: 3.596A pdb=" N ASP e 45 " --> pdb=" O ASN e 42 " (cutoff:3.500A) Processing helix chain 'e' and resid 51 through 61 removed outlier: 3.771A 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 'Y' and resid 5 through 10 removed outlier: 3.818A pdb=" N GLY Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 28 removed outlier: 3.707A 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: 3.510A pdb=" N LYS Y 93 " --> pdb=" O GLU Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 96 through 114 Processing helix chain 'Y' and resid 116 through 130 removed outlier: 3.638A 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: 3.710A pdb=" N ILE Y 229 " --> pdb=" O TYR Y 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 232 through 240 Processing helix chain 'Y' and resid 243 through 251 Processing helix chain 'Y' and resid 253 through 265 removed outlier: 3.657A pdb=" N LEU Y 263 " --> pdb=" O TYR Y 259 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 284 removed outlier: 3.838A pdb=" N LYS Y 284 " --> pdb=" O GLN Y 280 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 290 No H-bonds generated for 'chain 'Y' and resid 288 through 290' Processing helix chain 'Y' and resid 291 through 310 removed outlier: 4.175A pdb=" N SER Y 310 " --> pdb=" O GLN Y 306 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 324 Processing helix chain 'Y' and resid 326 through 340 Processing helix chain 'Y' and resid 360 through 389 removed outlier: 3.778A pdb=" N TRP Y 364 " --> pdb=" O ASP Y 360 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU Y 368 " --> pdb=" O TRP Y 364 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET Y 389 " --> pdb=" O ARG Y 385 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 28 Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 104 through 114 removed outlier: 4.000A 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 Processing helix chain 'Z' and resid 242 through 289 removed outlier: 3.661A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 14 removed outlier: 3.734A pdb=" N ASN a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 32 Processing helix chain 'a' and resid 33 through 46 removed outlier: 3.768A pdb=" N GLN a 40 " --> pdb=" O GLN a 36 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN a 46 " --> pdb=" O LEU a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 54 through 63 removed outlier: 3.991A pdb=" N LYS a 58 " --> pdb=" O ASP a 54 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR a 60 " --> pdb=" O LEU a 56 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU a 61 " --> pdb=" O ILE a 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 68 removed outlier: 4.039A pdb=" N PHE a 67 " --> pdb=" O PHE a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 69 through 71 No H-bonds generated for 'chain 'a' and resid 69 through 71' Processing helix chain 'a' and resid 72 through 87 removed outlier: 3.904A pdb=" N GLU a 78 " --> pdb=" O LEU a 74 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE a 79 " --> pdb=" O SER a 75 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE a 80 " --> pdb=" O LEU a 76 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN a 86 " --> pdb=" O HIS a 82 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET a 87 " --> pdb=" O VAL a 83 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 104 removed outlier: 3.534A pdb=" N THR a 95 " --> pdb=" O ASN a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 125 Processing helix chain 'a' and resid 127 through 145 Processing helix chain 'a' and resid 151 through 167 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: 3.735A pdb=" N LEU a 216 " --> pdb=" O ASN a 212 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 226 removed outlier: 3.501A pdb=" N ARG a 226 " --> pdb=" O GLU a 223 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 242 removed outlier: 3.957A pdb=" N ILE a 234 " --> pdb=" O ARG a 230 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 251 Processing helix chain 'a' and resid 251 through 256 Processing helix chain 'a' and resid 258 through 264 Processing helix chain 'a' and resid 264 through 284 removed outlier: 3.617A pdb=" N ARG a 284 " --> pdb=" O MET a 280 " (cutoff:3.500A) 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 318 removed outlier: 4.336A pdb=" N GLU a 308 " --> pdb=" O VAL a 304 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU a 309 " --> pdb=" O ASN a 305 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY a 318 " --> pdb=" O ALA a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 342 through 371 Processing helix chain 'X' and resid 5 through 17 removed outlier: 4.169A pdb=" N SER X 17 " --> pdb=" O GLN X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 33 removed outlier: 3.980A pdb=" N ILE X 26 " --> pdb=" O ALA X 22 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 61 removed outlier: 3.781A pdb=" N GLN X 44 " --> pdb=" O GLU X 40 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS X 59 " --> pdb=" O SER X 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 73 removed outlier: 3.579A pdb=" N LEU X 70 " --> pdb=" O LEU X 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 75 through 79 Processing helix chain 'X' and resid 81 through 99 Processing helix chain 'X' and resid 105 through 121 Processing helix chain 'X' and resid 122 through 140 Processing helix chain 'X' and resid 142 through 161 Processing helix chain 'X' and resid 162 through 180 removed outlier: 3.653A 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: 3.944A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 246 through 261 removed outlier: 3.615A pdb=" N LYS X 258 " --> pdb=" O MET X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 273 removed outlier: 4.179A pdb=" N GLN X 268 " --> pdb=" O PRO X 264 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA X 269 " --> pdb=" O GLU X 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 278 removed outlier: 3.894A pdb=" N ARG X 278 " --> pdb=" O LYS X 274 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 296 Processing helix chain 'X' and resid 298 through 309 Processing helix chain 'X' and resid 309 through 314 Processing helix chain 'X' and resid 316 through 340 removed outlier: 3.649A pdb=" N HIS X 322 " --> pdb=" O ILE X 318 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ALA X 324 " --> pdb=" O SER X 320 " (cutoff:3.500A) removed outlier: 5.127A 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 sheet with id=AA1, first strand: chain 'W' and resid 405 through 407 removed outlier: 6.445A pdb=" N LYS a 321 " --> pdb=" O THR a 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 71 through 80 removed outlier: 6.745A pdb=" N LEU C 86 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA C 79 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS C 84 " --> pdb=" O ALA C 79 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 94 through 97 current: chain 'C' and resid 123 through 126 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 123 through 126 current: chain '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 'A' and resid 110 through 115 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 123 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 'D' and resid 100 through 105 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 110 through 114 current: chain 'D' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 139 through 142 current: chain 'E' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 81 current: chain 'E' and resid 107 through 110 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 107 through 110 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=AA3, first strand: chain 'C' and resid 210 through 213 removed outlier: 6.325A pdb=" N THR C 210 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE C 247 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ASP C 249 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER C 244 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ILE C 292 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ILE C 246 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ALA C 294 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N MET C 248 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY C 185 " --> pdb=" O ARG C 313 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N ILE C 315 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU C 187 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 59 through 65 removed outlier: 5.793A pdb=" N VAL b 60 " --> pdb=" O THR b 53 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR b 53 " --> pdb=" O VAL b 60 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU b 64 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N VAL b 49 " --> pdb=" O LEU b 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 281 through 283 removed outlier: 3.508A pdb=" N ILE d 282 " --> pdb=" O TYR d 316 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 776 through 777 Processing sheet with id=AA7, first strand: chain 'f' and resid 781 through 782 Processing sheet with id=AA8, first strand: chain 'f' and resid 830 through 833 Processing sheet with id=AA9, first strand: chain 'f' and resid 862 through 869 removed outlier: 5.848A pdb=" N GLY f 864 " --> pdb=" O GLN f 848 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLN f 848 " --> pdb=" O GLY f 864 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 99 through 103 removed outlier: 3.903A pdb=" N ASN g 99 " --> pdb=" O VAL g 87 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR g 103 " --> pdb=" O ALA g 83 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR g 84 " --> pdb=" O VAL g 151 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA g 153 " --> pdb=" O THR g 84 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU g 86 " --> pdb=" O ALA g 153 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL g 155 " --> pdb=" O GLU g 86 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N PHE g 88 " --> pdb=" O VAL g 155 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N GLU g 157 " --> pdb=" O PHE g 88 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 246 through 251 removed outlier: 6.320A pdb=" N THR B 246 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N PHE B 283 " --> pdb=" O THR B 246 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 248 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP B 285 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL B 250 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY B 221 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE B 351 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE B 223 " --> pdb=" O ILE B 351 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 236 through 241 removed outlier: 6.207A pdb=" N CYS A 236 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A 273 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 238 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP A 275 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 240 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A 211 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE A 341 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 213 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 226 through 231 removed outlier: 6.459A pdb=" N ALA D 226 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N PHE D 263 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE D 228 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP D 265 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL D 230 " --> pdb=" O ASP D 265 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA D 260 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N ILE D 308 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE D 262 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA D 310 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE D 264 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D 329 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 199 Processing sheet with id=AB6, first strand: chain 'F' and resid 247 through 252 removed outlier: 6.248A pdb=" N THR F 247 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE F 284 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU F 249 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ASP F 286 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU F 251 " --> pdb=" O ASP F 286 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER F 281 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ILE F 329 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ILE F 283 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA F 331 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE F 285 " --> pdb=" O ALA F 331 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL F 223 " --> pdb=" O ALA F 330 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR F 332 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N MET F 225 " --> pdb=" O THR F 332 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.618A pdb=" N THR G 38 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN G 53 " --> pdb=" O THR G 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 69 through 70 removed outlier: 3.546A pdb=" N LYS G 153 " --> pdb=" O CYS G 161 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS G 161 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AC1, first strand: chain 'H' and resid 66 through 67 Processing sheet with id=AC2, first strand: chain 'I' and resid 161 through 164 Processing sheet with id=AC3, first strand: chain 'I' and resid 65 through 67 removed outlier: 4.084A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 158 through 161 Processing sheet with id=AC5, first strand: chain 'J' and resid 62 through 64 Processing sheet with id=AC6, first strand: chain 'K' and resid 167 through 170 Processing sheet with id=AC7, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.370A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 158 through 161 Processing sheet with id=AC9, first strand: chain 'L' and resid 63 through 65 removed outlier: 4.095A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 162 through 165 removed outlier: 3.958A pdb=" N GLY M 44 " --> pdb=" O CYS M 41 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 66 through 67 Processing sheet with id=AD3, first strand: chain 'U' and resid 744 through 746 Processing sheet with id=AD4, first strand: chain 'U' and resid 882 through 883 removed outlier: 3.569A pdb=" N ALA U 882 " --> pdb=" O VAL U 788 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N CYS U 787 " --> pdb=" O GLY U 910 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE U 912 " --> pdb=" O CYS U 787 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE U 789 " --> pdb=" O ILE U 912 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU U 914 " --> pdb=" O ILE U 789 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N LEU U 791 " --> pdb=" O LEU U 914 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP U 916 " --> pdb=" O LEU U 791 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 802 through 804 Processing sheet with id=AD6, first strand: chain 'V' and resid 416 through 418 Processing sheet with id=AD7, first strand: chain 'c' and resid 30 through 34 removed outlier: 6.733A pdb=" N GLN c 30 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL c 69 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR c 32 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP c 71 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N SER c 34 " --> pdb=" O ASP c 71 " (cutoff:3.500A) removed outlier: 11.020A pdb=" N PHE c 73 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N VAL c 67 " --> pdb=" O VAL c 62 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL c 62 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N VAL c 69 " --> pdb=" O GLU c 60 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU c 60 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLY c 55 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TRP c 111 " --> pdb=" O GLY c 55 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N MET c 57 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET c 107 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N VAL c 141 " --> pdb=" O MET c 107 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL c 109 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 7.651A 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: 8.039A pdb=" N VAL c 145 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS c 113 " --> pdb=" O VAL c 145 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL c 156 " --> pdb=" O ASP c 146 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N ILE c 148 " --> pdb=" O LYS c 154 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N LYS c 154 " --> pdb=" O ILE c 148 " (cutoff:3.500A) removed outlier: 12.799A pdb=" N VAL c 155 " --> pdb=" O TYR c 207 " (cutoff:3.500A) removed outlier: 10.562A pdb=" N TYR c 207 " --> pdb=" O VAL c 155 " (cutoff:3.500A) removed outlier: 8.761A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Y' and resid 313 through 315 Processing sheet with id=AD9, first strand: chain 'Z' and resid 152 through 158 removed outlier: 3.528A pdb=" N SER Z 152 " --> pdb=" O GLU Z 143 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA Z 137 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N VAL Z 120 " --> pdb=" O ARG Z 90 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL Z 92 " --> pdb=" O VAL Z 120 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N VAL Z 122 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP Z 94 " --> pdb=" O VAL Z 122 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE Z 124 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS Z 96 " --> pdb=" O ILE Z 124 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU Z 39 " --> pdb=" O VAL Z 92 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP Z 94 " --> pdb=" O GLY Z 37 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY Z 37 " --> pdb=" O TRP Z 94 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N SER Z 42 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N VAL Z 50 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN Z 44 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU Z 48 " --> pdb=" O GLN Z 44 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS Z 8 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL Z 50 " --> pdb=" O LYS Z 8 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N VAL Z 10 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASN Z 52 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Z' and resid 58 through 60 Processing sheet with id=AE2, first strand: chain 'X' and resid 344 through 346 3985 hydrogen bonds defined for protein. 11487 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 31.16 Time building geometry restraints manager: 15.47 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: 23370 1.34 - 1.46: 14694 1.46 - 1.58: 32609 1.58 - 1.70: 20 1.70 - 1.82: 625 Bond restraints: 71318 Sorted by residual: bond pdb=" CG1 ILE f 482 " pdb=" CD1 ILE f 482 " ideal model delta sigma weight residual 1.513 1.426 0.087 3.90e-02 6.57e+02 4.96e+00 bond pdb=" CB GLU f 336 " pdb=" CG GLU f 336 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CB GLU g 162 " pdb=" CG GLU g 162 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" N ASP f 404 " pdb=" CA ASP f 404 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.72e+00 bond pdb=" CB VAL f 597 " pdb=" CG1 VAL f 597 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.69e+00 ... (remaining 71313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 95658 2.65 - 5.30: 609 5.30 - 7.95: 58 7.95 - 10.60: 19 10.60 - 13.26: 5 Bond angle restraints: 96349 Sorted by residual: angle pdb=" CA LEU U 337 " pdb=" CB LEU U 337 " pdb=" CG LEU U 337 " ideal model delta sigma weight residual 116.30 129.56 -13.26 3.50e+00 8.16e-02 1.43e+01 angle pdb=" CB MET f 543 " pdb=" CG MET f 543 " pdb=" SD MET f 543 " ideal model delta sigma weight residual 112.70 123.89 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CB MET V 463 " pdb=" CG MET V 463 " pdb=" SD MET V 463 " ideal model delta sigma weight residual 112.70 123.88 -11.18 3.00e+00 1.11e-01 1.39e+01 angle pdb=" N ILE U 45 " pdb=" CA ILE U 45 " pdb=" C ILE U 45 " ideal model delta sigma weight residual 113.16 108.03 5.13 1.49e+00 4.50e-01 1.18e+01 angle pdb=" CA GLU I 241 " pdb=" CB GLU I 241 " pdb=" CG GLU I 241 " ideal model delta sigma weight residual 114.10 120.90 -6.80 2.00e+00 2.50e-01 1.16e+01 ... (remaining 96344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 37837 18.03 - 36.05: 4558 36.05 - 54.08: 1226 54.08 - 72.11: 216 72.11 - 90.14: 73 Dihedral angle restraints: 43910 sinusoidal: 18120 harmonic: 25790 Sorted by residual: dihedral pdb=" CA MET E 258 " pdb=" C MET E 258 " pdb=" N GLU E 259 " pdb=" CA GLU E 259 " ideal model delta harmonic sigma weight residual 180.00 149.46 30.54 0 5.00e+00 4.00e-02 3.73e+01 dihedral pdb=" CA ARG f 828 " pdb=" C ARG f 828 " pdb=" N MET f 829 " pdb=" CA MET f 829 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+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 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 43907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 10082 0.071 - 0.142: 885 0.142 - 0.213: 14 0.213 - 0.284: 1 0.284 - 0.355: 2 Chirality restraints: 10984 Sorted by residual: 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 -2.23 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CG LEU V 67 " pdb=" CB LEU V 67 " pdb=" CD1 LEU V 67 " pdb=" CD2 LEU V 67 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CG LEU b 97 " pdb=" CB LEU b 97 " pdb=" CD1 LEU b 97 " pdb=" CD2 LEU b 97 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 10981 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP Y 364 " -0.018 2.00e-02 2.50e+03 1.59e-02 6.28e+00 pdb=" CG TRP Y 364 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP Y 364 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP Y 364 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP Y 364 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP Y 364 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP Y 364 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP Y 364 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP Y 364 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP Y 364 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG f 478 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" C ARG f 478 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG f 478 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU f 479 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE V 120 " 0.007 2.00e-02 2.50e+03 1.71e-02 5.11e+00 pdb=" CG PHE V 120 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE V 120 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE V 120 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE V 120 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE V 120 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE V 120 " 0.007 2.00e-02 2.50e+03 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 523 2.52 - 3.11: 53053 3.11 - 3.71: 116414 3.71 - 4.30: 164312 4.30 - 4.90: 270722 Nonbonded interactions: 605024 Sorted by model distance: nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 501 " model vdw 1.925 2.230 nonbonded pdb=" OE1 GLU c 52 " pdb="ZN ZN c 501 " model vdw 1.957 2.230 nonbonded pdb=" OG1 THR A 223 " pdb="MG MG A 502 " model vdw 1.959 2.170 nonbonded pdb=" O3G ATP F 501 " pdb="MG MG F 502 " model vdw 1.964 2.170 nonbonded pdb=" OG1 THR F 234 " pdb="MG MG F 502 " model vdw 1.965 2.170 ... (remaining 605019 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=0.06 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 2.110 Check model and map are aligned: 0.420 Set scattering table: 0.490 Process input model: 133.860 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.270 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: 0.030 Load rotamer database and sin/cos tables:10.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 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 0.087 71318 Z= 0.176 Angle : 0.549 13.256 96349 Z= 0.286 Chirality : 0.040 0.355 10984 Planarity : 0.004 0.075 12396 Dihedral : 16.859 90.136 27221 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.59 % Rotamer: Outliers : 1.81 % Allowed : 25.31 % Favored : 72.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.09), residues: 8771 helix: 1.39 (0.07), residues: 4953 sheet: -0.24 (0.17), residues: 920 loop : 0.44 (0.12), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP Y 364 HIS 0.011 0.001 HIS C 90 PHE 0.034 0.001 PHE V 120 TYR 0.030 0.001 TYR a 173 ARG 0.012 0.000 ARG V 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 835 time to evaluate : 6.050 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: W 76 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: W 112 VAL cc_start: 0.8341 (t) cc_final: 0.8086 (t) REVERT: W 130 MET cc_start: 0.9029 (ttp) cc_final: 0.8790 (ttt) REVERT: W 322 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8381 (mm-30) REVERT: W 368 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8745 (ttpp) REVERT: W 375 MET cc_start: 0.8993 (mmm) cc_final: 0.8773 (tpp) REVERT: W 436 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8491 (mtp) REVERT: C 44 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7717 (ttm110) REVERT: C 60 ARG cc_start: 0.8548 (mtp85) cc_final: 0.8338 (mtt-85) REVERT: C 184 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8174 (pptt) REVERT: b 7 MET cc_start: 0.7756 (mmm) cc_final: 0.7395 (tpp) REVERT: b 52 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7044 (mt) REVERT: d 218 LYS cc_start: 0.9054 (tppt) cc_final: 0.8843 (tppt) REVERT: d 289 ARG cc_start: 0.8272 (mpp-170) cc_final: 0.7747 (ptp90) REVERT: f 341 GLU cc_start: 0.8092 (pp20) cc_final: 0.7824 (pp20) REVERT: f 403 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7986 (tppt) REVERT: g 86 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: g 87 VAL cc_start: 0.8806 (p) cc_final: 0.8315 (m) REVERT: g 110 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7957 (mmm160) REVERT: B 63 LEU cc_start: 0.9046 (mt) cc_final: 0.8819 (mp) REVERT: B 76 GLU cc_start: 0.8529 (tp30) cc_final: 0.8295 (tp30) REVERT: B 170 LEU cc_start: 0.8088 (tt) cc_final: 0.7857 (tt) REVERT: B 349 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8364 (mtt180) REVERT: A 46 LYS cc_start: 0.8019 (mmmm) cc_final: 0.7628 (tppp) REVERT: A 111 TYR cc_start: 0.8990 (m-80) cc_final: 0.8515 (m-80) REVERT: A 133 ASP cc_start: 0.9033 (OUTLIER) cc_final: 0.8703 (t0) REVERT: A 168 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7974 (tm-30) REVERT: D 55 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8017 (tm-30) REVERT: D 60 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8515 (t80) REVERT: E 100 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8521 (mt) REVERT: F 183 GLU cc_start: 0.8982 (OUTLIER) cc_final: 0.8606 (mp0) REVERT: F 321 GLN cc_start: 0.9119 (mm110) cc_final: 0.8719 (mm-40) REVERT: H 60 ARG cc_start: 0.7967 (ptm-80) cc_final: 0.7546 (ppt170) REVERT: H 200 GLU cc_start: 0.8636 (pt0) cc_final: 0.8413 (pt0) REVERT: H 212 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.9132 (pp) REVERT: I 235 GLN cc_start: 0.8742 (tp40) cc_final: 0.8289 (tp-100) REVERT: K 236 GLU cc_start: 0.8499 (tp30) cc_final: 0.8121 (tm-30) REVERT: L 220 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: L 237 GLU cc_start: 0.8353 (pm20) cc_final: 0.7808 (pm20) REVERT: M 59 GLU cc_start: 0.8559 (tt0) cc_final: 0.8347 (mt-10) REVERT: M 71 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7540 (ptt180) REVERT: M 187 ARG cc_start: 0.8408 (mmt-90) cc_final: 0.8096 (mmm160) REVERT: U 188 MET cc_start: 0.8689 (mmm) cc_final: 0.8381 (mmp) REVERT: U 474 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8048 (mtm-85) REVERT: V 92 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.8027 (mmm-85) REVERT: V 93 PHE cc_start: 0.8143 (m-80) cc_final: 0.7746 (m-80) REVERT: V 132 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8411 (mm) REVERT: V 145 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6520 (pt) REVERT: V 463 MET cc_start: 0.7553 (tpp) cc_final: 0.7185 (ppp) REVERT: V 489 MET cc_start: 0.9284 (tpp) cc_final: 0.8952 (mmp) REVERT: c 211 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7977 (tp30) REVERT: c 227 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8232 (pp20) REVERT: Y 282 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8161 (mtp) REVERT: Z 90 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7493 (mtp85) REVERT: Z 231 GLN cc_start: 0.8270 (mt0) cc_final: 0.8016 (mt0) REVERT: Z 252 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7666 (mptt) REVERT: Z 255 ASP cc_start: 0.8895 (m-30) cc_final: 0.8612 (m-30) REVERT: a 26 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8069 (pp20) REVERT: a 121 LEU cc_start: 0.8750 (mt) cc_final: 0.8474 (pp) REVERT: a 166 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8523 (pt) REVERT: X 395 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8342 (mtpp) REVERT: X 416 ASN cc_start: 0.8634 (m110) cc_final: 0.8308 (m-40) outliers start: 139 outliers final: 82 residues processed: 929 average time/residue: 1.4894 time to fit residues: 1817.4370 Evaluate side-chains 895 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 784 time to evaluate : 6.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 272 LEU Chi-restraints excluded: chain W residue 322 GLU Chi-restraints excluded: chain W residue 368 LYS Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain C residue 44 ARG Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 184 LYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain b residue 12 ASN Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 177 ASP Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 237 MET Chi-restraints excluded: chain d residue 251 ILE Chi-restraints excluded: chain d residue 265 ASP Chi-restraints excluded: chain d residue 301 ASP Chi-restraints excluded: chain d residue 332 SER Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 181 ARG Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 403 LYS Chi-restraints excluded: chain f residue 422 VAL Chi-restraints excluded: chain f residue 606 VAL Chi-restraints excluded: chain f residue 705 ASN Chi-restraints excluded: chain f residue 706 ILE Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain g residue 86 GLU Chi-restraints excluded: chain g residue 93 LEU Chi-restraints excluded: chain g residue 110 ARG Chi-restraints excluded: chain g residue 119 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 133 ASP Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 246 MET Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 225 MET Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 289 ASP Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain L residue 140 MET Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain U residue 217 CYS Chi-restraints excluded: chain U residue 337 LEU Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 474 ARG Chi-restraints excluded: chain U residue 538 GLU Chi-restraints excluded: chain U residue 542 GLU Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 639 LEU Chi-restraints excluded: chain U residue 678 ASP Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 363 LEU Chi-restraints excluded: chain c residue 210 ASN Chi-restraints excluded: chain c residue 227 GLU Chi-restraints excluded: chain e residue 53 SER Chi-restraints excluded: chain Y residue 157 ILE Chi-restraints excluded: chain Y residue 214 MET Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Y residue 385 ARG Chi-restraints excluded: chain Z residue 44 GLN Chi-restraints excluded: chain Z residue 90 ARG Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 243 GLN Chi-restraints excluded: chain Z residue 252 LYS Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain X residue 28 HIS Chi-restraints excluded: chain X residue 78 ASN Chi-restraints excluded: chain X residue 218 HIS Chi-restraints excluded: chain X residue 395 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 873 random chunks: chunk 737 optimal weight: 5.9990 chunk 661 optimal weight: 9.9990 chunk 367 optimal weight: 20.0000 chunk 226 optimal weight: 5.9990 chunk 446 optimal weight: 9.9990 chunk 353 optimal weight: 0.9980 chunk 684 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 416 optimal weight: 9.9990 chunk 509 optimal weight: 6.9990 chunk 792 optimal weight: 3.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 203 GLN C 90 HIS b 30 GLN ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 234 GLN d 314 ASN ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 161 HIS f 195 ASN ** f 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 382 ASN f 452 ASN D 49 GLN D 65 GLN D 127 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN I 155 ASN L 68 ASN M 221 ASN U 190 ASN U 398 ASN U 685 GLN V 78 HIS V 318 GLN ** V 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 GLN c 237 HIS e 47 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 256 GLN X 10 GLN X 329 ASN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 367 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.078726 restraints weight = 122559.579| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.17 r_work: 0.2896 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2781 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2781 r_free = 0.2781 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2781 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 71318 Z= 0.362 Angle : 0.571 10.974 96349 Z= 0.295 Chirality : 0.042 0.196 10984 Planarity : 0.004 0.051 12396 Dihedral : 7.513 89.562 10015 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 4.46 % Allowed : 20.79 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.40 (0.09), residues: 8771 helix: 1.51 (0.07), residues: 5021 sheet: -0.34 (0.16), residues: 918 loop : 0.53 (0.13), residues: 2832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 364 HIS 0.009 0.001 HIS C 90 PHE 0.019 0.001 PHE c 73 TYR 0.017 0.002 TYR L 137 ARG 0.008 0.001 ARG V 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 342 poor density : 832 time to evaluate : 6.232 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: W 112 VAL cc_start: 0.8599 (t) cc_final: 0.8319 (t) REVERT: W 212 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8712 (mmmt) REVERT: W 216 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: W 322 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8307 (mm-30) REVERT: W 368 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8747 (ttpp) REVERT: W 375 MET cc_start: 0.9091 (mmm) cc_final: 0.8822 (tpp) REVERT: C 224 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8954 (mt) REVERT: b 54 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7847 (mm) REVERT: d 265 ASP cc_start: 0.8998 (m-30) cc_final: 0.8667 (m-30) REVERT: d 269 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8281 (p0) REVERT: d 289 ARG cc_start: 0.8119 (mpp-170) cc_final: 0.7889 (mpp-170) REVERT: f 181 ARG cc_start: 0.7391 (mpp80) cc_final: 0.7042 (mpp80) REVERT: f 341 GLU cc_start: 0.8277 (pp20) cc_final: 0.8005 (pp20) REVERT: f 392 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8609 (p) REVERT: f 829 MET cc_start: 0.8303 (tpp) cc_final: 0.8063 (tpt) REVERT: g 86 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: g 101 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8796 (tm) REVERT: g 110 ARG cc_start: 0.8795 (tpp80) cc_final: 0.7991 (mmm160) REVERT: g 113 ARG cc_start: 0.9121 (tmt90) cc_final: 0.8806 (tmt90) REVERT: g 157 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.6927 (tt0) REVERT: B 63 LEU cc_start: 0.9202 (mt) cc_final: 0.8952 (mp) REVERT: B 76 GLU cc_start: 0.8615 (tp30) cc_final: 0.8251 (tp30) REVERT: B 174 MET cc_start: 0.8969 (mtt) cc_final: 0.8719 (mtt) REVERT: B 286 GLU cc_start: 0.9312 (OUTLIER) cc_final: 0.8914 (mt-10) REVERT: B 371 ARG cc_start: 0.8711 (mmm160) cc_final: 0.8106 (mmp80) REVERT: B 385 MET cc_start: 0.7893 (mmm) cc_final: 0.7663 (tpt) REVERT: A 46 LYS cc_start: 0.8122 (mmmm) cc_final: 0.7733 (tppp) REVERT: A 168 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 204 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7898 (tt) REVERT: A 232 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8171 (mmm160) REVERT: D 52 GLU cc_start: 0.9026 (tt0) cc_final: 0.8722 (tt0) REVERT: D 60 TYR cc_start: 0.9181 (OUTLIER) cc_final: 0.8702 (t80) REVERT: E 48 LYS cc_start: 0.8755 (mtpp) cc_final: 0.8294 (mmmt) REVERT: E 195 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: E 277 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8737 (mtt) REVERT: E 384 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8301 (mt) REVERT: H 18 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8428 (mtpp) REVERT: I 235 GLN cc_start: 0.8751 (tp40) cc_final: 0.8313 (tp-100) REVERT: L 6 TYR cc_start: 0.9150 (m-80) cc_final: 0.8615 (m-80) REVERT: M 113 ASP cc_start: 0.8341 (m-30) cc_final: 0.8120 (m-30) REVERT: M 187 ARG cc_start: 0.8497 (mmt-90) cc_final: 0.8285 (mmm160) REVERT: U 673 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8784 (tt0) REVERT: V 132 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8472 (mm) REVERT: c 211 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8039 (tp30) REVERT: c 227 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8166 (pp20) REVERT: Y 237 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8466 (ptm-80) REVERT: a 121 LEU cc_start: 0.8722 (mt) cc_final: 0.8513 (pp) REVERT: a 140 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8013 (tm-30) REVERT: a 166 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8631 (pt) REVERT: a 183 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.8123 (m) REVERT: a 218 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8457 (mmm) REVERT: X 254 MET cc_start: 0.8990 (ttm) cc_final: 0.8771 (ttp) REVERT: X 416 ASN cc_start: 0.8718 (m110) cc_final: 0.8377 (m-40) outliers start: 342 outliers final: 124 residues processed: 1094 average time/residue: 1.4543 time to fit residues: 2110.4373 Evaluate side-chains 909 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 759 time to evaluate : 6.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 322 GLU Chi-restraints excluded: chain W residue 368 LYS Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 17 ARG Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 173 CYS Chi-restraints excluded: chain d residue 188 MET Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 263 LEU Chi-restraints excluded: chain d residue 269 ASP Chi-restraints excluded: chain d residue 332 SER Chi-restraints excluded: chain d residue 349 ILE Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 215 ASP Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 375 SER Chi-restraints excluded: chain f residue 392 THR Chi-restraints excluded: chain f residue 403 LYS Chi-restraints excluded: chain f residue 422 VAL Chi-restraints excluded: chain f residue 517 VAL Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 686 LEU Chi-restraints excluded: chain f residue 705 ASN Chi-restraints excluded: chain f residue 797 LEU Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain g residue 86 GLU Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 116 ILE Chi-restraints excluded: chain g residue 155 VAL Chi-restraints excluded: chain g residue 157 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 277 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 15 GLU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 218 ASP Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 184 MET Chi-restraints excluded: chain U residue 217 CYS Chi-restraints excluded: chain U residue 236 LEU Chi-restraints excluded: chain U residue 431 THR Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 538 GLU Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 673 GLU Chi-restraints excluded: chain U residue 699 THR Chi-restraints excluded: chain U residue 878 LEU Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain V residue 237 THR Chi-restraints excluded: chain V residue 489 MET Chi-restraints excluded: chain c residue 227 GLU Chi-restraints excluded: chain Y residue 237 ARG Chi-restraints excluded: chain Z residue 106 ILE Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 218 MET Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain X residue 28 HIS Chi-restraints excluded: chain X residue 48 GLN Chi-restraints excluded: chain X residue 160 MET Chi-restraints excluded: chain X residue 218 HIS Chi-restraints excluded: chain X residue 395 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 873 random chunks: chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 823 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 506 optimal weight: 5.9990 chunk 640 optimal weight: 5.9990 chunk 857 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 434 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS b 38 HIS d 221 GLN ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 198 HIS g 132 ASN ** g 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN D 127 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 HIS I 51 ASN J 239 ASN L 68 ASN M 221 ASN U 685 GLN V 318 GLN ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 243 GLN X 329 ASN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 367 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.112089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.079729 restraints weight = 122009.644| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.21 r_work: 0.2903 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2794 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 71318 Z= 0.247 Angle : 0.531 9.706 96349 Z= 0.273 Chirality : 0.040 0.282 10984 Planarity : 0.004 0.055 12396 Dihedral : 6.755 99.836 9852 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.22 % Rotamer: Outliers : 3.81 % Allowed : 22.02 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.47 (0.09), residues: 8771 helix: 1.60 (0.07), residues: 5011 sheet: -0.38 (0.16), residues: 922 loop : 0.50 (0.13), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP d 154 HIS 0.010 0.001 HIS C 90 PHE 0.015 0.001 PHE c 73 TYR 0.020 0.001 TYR c 32 ARG 0.008 0.000 ARG Z 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 292 poor density : 852 time to evaluate : 6.311 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: W 76 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: W 79 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6838 (mm-30) REVERT: W 112 VAL cc_start: 0.8591 (t) cc_final: 0.8293 (t) REVERT: W 130 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8848 (ttt) REVERT: W 216 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: W 299 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8292 (OUTLIER) REVERT: W 322 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8314 (mm-30) REVERT: W 375 MET cc_start: 0.9061 (mmm) cc_final: 0.8814 (tpp) REVERT: b 54 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7961 (mm) REVERT: d 265 ASP cc_start: 0.8996 (m-30) cc_final: 0.8619 (m-30) REVERT: d 269 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8281 (p0) REVERT: d 289 ARG cc_start: 0.8127 (mpp-170) cc_final: 0.7531 (ptp90) REVERT: f 341 GLU cc_start: 0.8315 (pp20) cc_final: 0.8017 (pp20) REVERT: f 392 THR cc_start: 0.8760 (m) cc_final: 0.8548 (p) REVERT: f 408 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8669 (tp) REVERT: f 815 HIS cc_start: 0.9388 (OUTLIER) cc_final: 0.9054 (p90) REVERT: g 110 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8067 (mmm160) REVERT: g 113 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8700 (tmt90) REVERT: g 137 GLN cc_start: 0.8286 (pm20) cc_final: 0.7916 (pm20) REVERT: g 157 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.6899 (tt0) REVERT: B 63 LEU cc_start: 0.9161 (mt) cc_final: 0.8929 (mp) REVERT: B 76 GLU cc_start: 0.8662 (tp30) cc_final: 0.8253 (tp30) REVERT: B 174 MET cc_start: 0.8944 (mtt) cc_final: 0.8729 (mtt) REVERT: B 286 GLU cc_start: 0.9323 (OUTLIER) cc_final: 0.8921 (mt-10) REVERT: A 46 LYS cc_start: 0.8125 (mmmm) cc_final: 0.7693 (tppp) REVERT: A 168 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 204 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7853 (tt) REVERT: A 232 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8156 (mmm160) REVERT: D 60 TYR cc_start: 0.9170 (OUTLIER) cc_final: 0.8697 (t80) REVERT: E 48 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8258 (mmmt) REVERT: E 157 GLU cc_start: 0.8901 (pm20) cc_final: 0.8681 (pm20) REVERT: E 195 PHE cc_start: 0.9052 (OUTLIER) cc_final: 0.8415 (m-80) REVERT: E 277 MET cc_start: 0.9209 (OUTLIER) cc_final: 0.8692 (mtt) REVERT: E 384 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8295 (mt) REVERT: F 183 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8609 (mp0) REVERT: F 321 GLN cc_start: 0.9097 (mm110) cc_final: 0.8782 (mm-40) REVERT: H 18 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8433 (mtpp) REVERT: I 178 ASP cc_start: 0.8841 (t0) cc_final: 0.8595 (t0) REVERT: I 235 GLN cc_start: 0.8763 (tp40) cc_final: 0.8321 (tp-100) REVERT: J 113 SER cc_start: 0.9011 (p) cc_final: 0.8712 (m) REVERT: K 69 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8281 (tp30) REVERT: L 143 HIS cc_start: 0.8494 (m-70) cc_final: 0.8043 (m170) REVERT: M 71 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7675 (ptt180) REVERT: U 188 MET cc_start: 0.8682 (mmm) cc_final: 0.8365 (mmp) REVERT: V 132 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8443 (mm) REVERT: V 221 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8728 (mm) REVERT: V 489 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8994 (mmp) REVERT: c 106 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8947 (mp0) REVERT: c 211 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7927 (tp30) REVERT: c 227 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8175 (pp20) REVERT: Y 248 GLU cc_start: 0.8518 (tp30) cc_final: 0.8167 (tp30) REVERT: Y 282 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8843 (mtp) REVERT: Z 112 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8698 (mmm) REVERT: Z 231 GLN cc_start: 0.8678 (mt0) cc_final: 0.8410 (mt0) REVERT: a 121 LEU cc_start: 0.8702 (mt) cc_final: 0.8482 (pp) REVERT: a 166 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8629 (pt) REVERT: a 218 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8448 (mmm) REVERT: X 48 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: X 246 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7727 (mtpt) REVERT: X 254 MET cc_start: 0.9021 (ttm) cc_final: 0.8789 (ttp) REVERT: X 395 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8393 (mtpp) REVERT: X 416 ASN cc_start: 0.8711 (m110) cc_final: 0.8372 (m-40) outliers start: 292 outliers final: 118 residues processed: 1072 average time/residue: 1.4650 time to fit residues: 2073.9483 Evaluate side-chains 947 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 796 time to evaluate : 6.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 322 GLU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 173 CYS Chi-restraints excluded: chain d residue 194 LEU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 237 MET Chi-restraints excluded: chain d residue 251 ILE Chi-restraints excluded: chain d residue 263 LEU Chi-restraints excluded: chain d residue 269 ASP Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 375 SER Chi-restraints excluded: chain f residue 408 LEU Chi-restraints excluded: chain f residue 422 VAL Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 686 LEU Chi-restraints excluded: chain f residue 797 LEU Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain g residue 86 GLU Chi-restraints excluded: chain g residue 93 LEU Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 157 GLU Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain g residue 164 ASP Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 294 ARG Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain U residue 45 ILE Chi-restraints excluded: chain U residue 130 LEU Chi-restraints excluded: chain U residue 217 CYS Chi-restraints excluded: chain U residue 431 THR Chi-restraints excluded: chain U residue 538 GLU Chi-restraints excluded: chain U residue 560 MET Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 237 THR Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 489 MET Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 227 GLU Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Z residue 44 GLN Chi-restraints excluded: chain Z residue 106 ILE Chi-restraints excluded: chain Z residue 112 MET Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 244 GLU Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 218 MET Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 303 THR Chi-restraints excluded: chain X residue 28 HIS Chi-restraints excluded: chain X residue 48 GLN Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 218 HIS Chi-restraints excluded: chain X residue 246 LYS Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 395 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 873 random chunks: chunk 548 optimal weight: 4.9990 chunk 817 optimal weight: 7.9990 chunk 709 optimal weight: 9.9990 chunk 815 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 735 optimal weight: 6.9990 chunk 794 optimal weight: 0.9980 chunk 287 optimal weight: 10.0000 chunk 866 optimal weight: 0.3980 chunk 53 optimal weight: 6.9990 chunk 388 optimal weight: 4.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 ASN ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 752 HIS ** g 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN A 88 GLN D 65 GLN D 127 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN I 51 ASN I 155 ASN J 239 ASN L 68 ASN M 221 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 685 GLN V 318 GLN ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 243 GLN X 329 ASN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 367 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.110979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.078274 restraints weight = 122551.926| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.34 r_work: 0.2879 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 71318 Z= 0.334 Angle : 0.556 9.204 96349 Z= 0.285 Chirality : 0.042 0.323 10984 Planarity : 0.004 0.067 12396 Dihedral : 6.628 86.871 9827 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 4.14 % Allowed : 21.91 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.45 (0.09), residues: 8771 helix: 1.60 (0.07), residues: 5014 sheet: -0.41 (0.16), residues: 928 loop : 0.48 (0.13), residues: 2829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP Y 364 HIS 0.009 0.001 HIS C 90 PHE 0.017 0.001 PHE c 73 TYR 0.018 0.001 TYR a 172 ARG 0.008 0.000 ARG c 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 317 poor density : 813 time to evaluate : 6.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 76 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: W 79 GLU cc_start: 0.7165 (mm-30) cc_final: 0.6877 (mm-30) REVERT: W 85 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8546 (mm-30) REVERT: W 130 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8879 (ttt) REVERT: W 212 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8719 (mmmt) REVERT: W 216 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: W 299 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8258 (OUTLIER) REVERT: W 322 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: W 375 MET cc_start: 0.9050 (mmm) cc_final: 0.8825 (tpp) REVERT: C 224 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.9011 (mt) REVERT: C 336 MET cc_start: 0.8960 (mtm) cc_final: 0.8757 (mtp) REVERT: b 54 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8045 (mm) REVERT: d 265 ASP cc_start: 0.8988 (m-30) cc_final: 0.8630 (m-30) REVERT: d 269 ASP cc_start: 0.8601 (t0) cc_final: 0.8244 (p0) REVERT: f 196 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8244 (mtm) REVERT: f 341 GLU cc_start: 0.8334 (pp20) cc_final: 0.8018 (pp20) REVERT: f 392 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8598 (p) REVERT: f 438 ASP cc_start: 0.8369 (t0) cc_final: 0.8133 (t0) REVERT: f 477 MET cc_start: 0.8896 (mmm) cc_final: 0.8675 (mmm) REVERT: g 110 ARG cc_start: 0.8831 (tpp80) cc_final: 0.8056 (mmm160) REVERT: g 113 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8719 (tmt90) REVERT: g 157 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.6890 (tt0) REVERT: B 63 LEU cc_start: 0.9163 (mt) cc_final: 0.8913 (mp) REVERT: B 76 GLU cc_start: 0.8676 (tp30) cc_final: 0.8275 (tp30) REVERT: B 258 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8704 (mtmt) REVERT: B 286 GLU cc_start: 0.9343 (OUTLIER) cc_final: 0.8943 (mt-10) REVERT: B 349 ARG cc_start: 0.9272 (OUTLIER) cc_final: 0.8967 (mtt-85) REVERT: B 371 ARG cc_start: 0.8757 (mmm160) cc_final: 0.8127 (mmp80) REVERT: A 46 LYS cc_start: 0.8103 (mmmm) cc_final: 0.7673 (tppp) REVERT: A 168 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 204 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8026 (tt) REVERT: A 232 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8277 (mmm160) REVERT: D 60 TYR cc_start: 0.9200 (OUTLIER) cc_final: 0.8718 (t80) REVERT: D 163 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8592 (mtm) REVERT: E 100 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8892 (mt) REVERT: E 157 GLU cc_start: 0.8906 (pm20) cc_final: 0.8676 (pm20) REVERT: E 195 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8474 (m-80) REVERT: E 277 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.8771 (mtt) REVERT: E 384 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8295 (mt) REVERT: F 183 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8558 (mp0) REVERT: F 321 GLN cc_start: 0.9124 (mm110) cc_final: 0.8798 (mm-40) REVERT: G 182 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8528 (mptm) REVERT: H 18 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8445 (mtpp) REVERT: H 183 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7498 (tm-30) REVERT: I 178 ASP cc_start: 0.8882 (t0) cc_final: 0.8574 (t0) REVERT: I 235 GLN cc_start: 0.8768 (tp40) cc_final: 0.8325 (tp-100) REVERT: K 69 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8243 (tp30) REVERT: L 6 TYR cc_start: 0.9175 (m-80) cc_final: 0.8660 (m-80) REVERT: L 143 HIS cc_start: 0.8525 (m-70) cc_final: 0.8034 (m170) REVERT: M 71 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7654 (ptt180) REVERT: M 187 ARG cc_start: 0.8652 (mmm160) cc_final: 0.8043 (mmt90) REVERT: U 759 SER cc_start: 0.9205 (OUTLIER) cc_final: 0.8817 (m) REVERT: V 132 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8441 (mm) REVERT: V 145 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6445 (pt) REVERT: V 221 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8749 (mm) REVERT: c 106 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.8981 (mp0) REVERT: c 211 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7865 (tp30) REVERT: c 227 GLU cc_start: 0.8782 (pt0) cc_final: 0.8254 (pp20) REVERT: Y 248 GLU cc_start: 0.8530 (tp30) cc_final: 0.8184 (tp30) REVERT: Y 282 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8267 (mtp) REVERT: Y 364 TRP cc_start: 0.8827 (t60) cc_final: 0.8560 (t60) REVERT: Z 105 ASP cc_start: 0.8869 (m-30) cc_final: 0.8561 (m-30) REVERT: Z 255 ASP cc_start: 0.9124 (m-30) cc_final: 0.8873 (m-30) REVERT: a 166 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8566 (pt) REVERT: X 48 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: X 223 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8670 (mmmm) REVERT: X 246 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7705 (mtpt) REVERT: X 254 MET cc_start: 0.9053 (ttm) cc_final: 0.8796 (ttp) REVERT: X 395 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8374 (mtpp) REVERT: X 416 ASN cc_start: 0.8713 (m110) cc_final: 0.8379 (m-40) outliers start: 317 outliers final: 155 residues processed: 1054 average time/residue: 1.4278 time to fit residues: 2007.9356 Evaluate side-chains 968 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 774 time to evaluate : 6.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 322 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 173 CYS Chi-restraints excluded: chain d residue 194 LEU Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 237 MET Chi-restraints excluded: chain d residue 251 ILE Chi-restraints excluded: chain d residue 332 SER Chi-restraints excluded: chain d residue 349 ILE Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 324 VAL Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 375 SER Chi-restraints excluded: chain f residue 392 THR Chi-restraints excluded: chain f residue 422 VAL Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 686 LEU Chi-restraints excluded: chain f residue 797 LEU Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain g residue 86 GLU Chi-restraints excluded: chain g residue 93 LEU Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 157 GLU Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 176 MET Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain U residue 130 LEU Chi-restraints excluded: chain U residue 217 CYS Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 431 THR Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 538 GLU Chi-restraints excluded: chain U residue 593 SER Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 759 SER Chi-restraints excluded: chain U residue 878 LEU Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain V residue 169 LEU Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 237 THR Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 489 MET Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 214 MET Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Y residue 327 VAL Chi-restraints excluded: chain Z residue 44 GLN Chi-restraints excluded: chain Z residue 106 ILE Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 135 ILE Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 303 THR Chi-restraints excluded: chain X residue 28 HIS Chi-restraints excluded: chain X residue 48 GLN Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 218 HIS Chi-restraints excluded: chain X residue 223 LYS Chi-restraints excluded: chain X residue 246 LYS Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 395 LYS Chi-restraints excluded: chain X residue 419 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 873 random chunks: chunk 181 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 223 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 619 optimal weight: 0.3980 chunk 302 optimal weight: 5.9990 chunk 578 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 815 optimal weight: 9.9990 chunk 658 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 ASN ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 452 ASN B 425 ASN A 88 GLN D 65 GLN D 127 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN I 155 ASN J 239 ASN K 225 ASN L 68 ASN M 221 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 318 GLN ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 ASN e 47 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 243 GLN Z 256 GLN X 44 GLN ** X 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 367 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.079340 restraints weight = 122208.877| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.16 r_work: 0.2897 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 71318 Z= 0.291 Angle : 0.545 9.544 96349 Z= 0.279 Chirality : 0.041 0.264 10984 Planarity : 0.004 0.067 12396 Dihedral : 6.534 87.364 9821 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 4.20 % Allowed : 22.19 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.47 (0.09), residues: 8771 helix: 1.62 (0.07), residues: 5031 sheet: -0.41 (0.16), residues: 923 loop : 0.47 (0.13), residues: 2817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP d 154 HIS 0.009 0.001 HIS C 90 PHE 0.021 0.001 PHE U 250 TYR 0.027 0.001 TYR f 142 ARG 0.008 0.000 ARG Z 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1144 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 322 poor density : 822 time to evaluate : 6.648 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: W 76 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: W 79 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6819 (mm-30) REVERT: W 85 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8509 (mm-30) REVERT: W 130 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8848 (ttt) REVERT: W 212 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8722 (mmmt) REVERT: W 216 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: W 322 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8340 (mp0) REVERT: W 375 MET cc_start: 0.9024 (mmm) cc_final: 0.8790 (tpp) REVERT: W 436 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8743 (mtp) REVERT: C 224 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8984 (mt) REVERT: C 336 MET cc_start: 0.8951 (mtm) cc_final: 0.8693 (mtp) REVERT: d 168 MET cc_start: 0.9101 (mmm) cc_final: 0.8826 (mmm) REVERT: d 265 ASP cc_start: 0.8990 (m-30) cc_final: 0.8536 (m-30) REVERT: d 266 THR cc_start: 0.8843 (p) cc_final: 0.8541 (t) REVERT: d 269 ASP cc_start: 0.8561 (t0) cc_final: 0.8232 (p0) REVERT: f 196 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8190 (mtm) REVERT: f 341 GLU cc_start: 0.8312 (pp20) cc_final: 0.7978 (pp20) REVERT: f 392 THR cc_start: 0.8832 (m) cc_final: 0.8588 (p) REVERT: f 397 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8663 (mtmm) REVERT: f 683 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8375 (mm-30) REVERT: g 104 ARG cc_start: 0.7321 (mmm-85) cc_final: 0.7028 (mmm160) REVERT: g 110 ARG cc_start: 0.8856 (tpp80) cc_final: 0.8075 (mmm160) REVERT: g 113 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8706 (tmt90) REVERT: g 137 GLN cc_start: 0.8635 (mp10) cc_final: 0.8225 (pm20) REVERT: g 157 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: B 63 LEU cc_start: 0.9156 (mt) cc_final: 0.8907 (mp) REVERT: B 76 GLU cc_start: 0.8665 (tp30) cc_final: 0.8245 (tp30) REVERT: B 286 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8862 (mt-10) REVERT: B 349 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8943 (mtt-85) REVERT: B 371 ARG cc_start: 0.8732 (mmm160) cc_final: 0.8095 (mmp80) REVERT: B 385 MET cc_start: 0.7889 (mmm) cc_final: 0.7662 (tpt) REVERT: A 46 LYS cc_start: 0.8056 (mmmm) cc_final: 0.7633 (tppp) REVERT: A 111 TYR cc_start: 0.9080 (m-80) cc_final: 0.8633 (m-80) REVERT: A 168 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8105 (tm-30) REVERT: A 204 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8030 (tt) REVERT: A 232 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8208 (mmm160) REVERT: D 60 TYR cc_start: 0.9152 (OUTLIER) cc_final: 0.8675 (t80) REVERT: D 163 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8557 (mtm) REVERT: D 272 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8988 (m) REVERT: E 48 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8261 (mmmt) REVERT: E 100 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8852 (mt) REVERT: E 157 GLU cc_start: 0.8887 (pm20) cc_final: 0.8638 (pm20) REVERT: E 195 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8431 (m-80) REVERT: E 232 MET cc_start: 0.9346 (mtp) cc_final: 0.9114 (mtp) REVERT: E 277 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8731 (mtt) REVERT: E 384 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8269 (mt) REVERT: F 69 MET cc_start: 0.5228 (OUTLIER) cc_final: 0.4763 (ppp) REVERT: F 183 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8518 (mp0) REVERT: F 321 GLN cc_start: 0.9117 (mm110) cc_final: 0.8781 (mm-40) REVERT: G 182 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8482 (mptm) REVERT: H 183 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: I 15 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8635 (mp0) REVERT: I 178 ASP cc_start: 0.8814 (t0) cc_final: 0.8475 (t0) REVERT: I 235 GLN cc_start: 0.8776 (tp40) cc_final: 0.8330 (tp-100) REVERT: K 69 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8197 (tp30) REVERT: L 6 TYR cc_start: 0.9138 (m-80) cc_final: 0.8579 (m-80) REVERT: L 143 HIS cc_start: 0.8556 (m-70) cc_final: 0.8120 (m170) REVERT: M 71 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7609 (ptt180) REVERT: U 188 MET cc_start: 0.8669 (mmm) cc_final: 0.8342 (mmp) REVERT: U 474 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8290 (mtm-85) REVERT: U 759 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8852 (m) REVERT: V 132 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8491 (mm) REVERT: V 145 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6439 (pt) REVERT: V 221 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8677 (mm) REVERT: c 106 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8974 (mp0) REVERT: c 211 GLU cc_start: 0.8479 (mm-30) cc_final: 0.7739 (tp30) REVERT: c 227 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8215 (pp20) REVERT: c 233 ASP cc_start: 0.9236 (t0) cc_final: 0.8885 (t0) REVERT: c 236 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8618 (mt-10) REVERT: e 18 GLU cc_start: 0.8176 (pp20) cc_final: 0.7947 (pp20) REVERT: Y 215 ASP cc_start: 0.8496 (t0) cc_final: 0.8294 (t0) REVERT: Y 248 GLU cc_start: 0.8499 (tp30) cc_final: 0.8150 (tp30) REVERT: Y 282 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: Y 364 TRP cc_start: 0.8722 (t60) cc_final: 0.8477 (t60) REVERT: Z 105 ASP cc_start: 0.8887 (m-30) cc_final: 0.8596 (m-30) REVERT: Z 255 ASP cc_start: 0.9088 (m-30) cc_final: 0.8776 (m-30) REVERT: a 26 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8104 (pp20) REVERT: a 140 GLU cc_start: 0.8454 (tm-30) cc_final: 0.7967 (tm-30) REVERT: a 166 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8545 (pt) REVERT: X 48 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: X 223 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8658 (mmmm) REVERT: X 246 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7720 (mtpt) REVERT: X 416 ASN cc_start: 0.8689 (m110) cc_final: 0.8340 (m-40) outliers start: 322 outliers final: 158 residues processed: 1074 average time/residue: 1.4468 time to fit residues: 2057.9638 Evaluate side-chains 974 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 774 time to evaluate : 6.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 299 ILE Chi-restraints excluded: chain W residue 322 GLU Chi-restraints excluded: chain W residue 436 MET Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 173 CYS Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 251 ILE Chi-restraints excluded: chain d residue 349 ILE Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 375 SER Chi-restraints excluded: chain f residue 397 LYS Chi-restraints excluded: chain f residue 422 VAL Chi-restraints excluded: chain f residue 517 VAL Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 686 LEU Chi-restraints excluded: chain f residue 797 LEU Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain g residue 86 GLU Chi-restraints excluded: chain g residue 93 LEU Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 157 GLU Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 186 LYS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 277 MET Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 15 GLU Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 174 MET Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 30 SER Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain J residue 199 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain L residue 45 VAL Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 130 LEU Chi-restraints excluded: chain U residue 217 CYS Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 431 THR Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 474 ARG Chi-restraints excluded: chain U residue 538 GLU Chi-restraints excluded: chain U residue 560 MET Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 699 THR Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 759 SER Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain V residue 169 LEU Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 237 THR Chi-restraints excluded: chain V residue 301 GLU Chi-restraints excluded: chain V residue 378 VAL Chi-restraints excluded: chain V residue 489 MET Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 106 GLU Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 227 GLU Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 65 ILE Chi-restraints excluded: chain Y residue 122 THR Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Z residue 44 GLN Chi-restraints excluded: chain Z residue 106 ILE Chi-restraints excluded: chain Z residue 119 SER Chi-restraints excluded: chain Z residue 121 LEU Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 253 THR Chi-restraints excluded: chain a residue 303 THR Chi-restraints excluded: chain X residue 28 HIS Chi-restraints excluded: chain X residue 48 GLN Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 218 HIS Chi-restraints excluded: chain X residue 223 LYS Chi-restraints excluded: chain X residue 246 LYS Chi-restraints excluded: chain X residue 249 THR Chi-restraints excluded: chain X residue 393 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 873 random chunks: chunk 208 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 405 optimal weight: 4.9990 chunk 330 optimal weight: 4.9990 chunk 235 optimal weight: 8.9990 chunk 559 optimal weight: 0.9980 chunk 309 optimal weight: 0.9990 chunk 172 optimal weight: 0.0040 chunk 603 optimal weight: 0.9980 chunk 230 optimal weight: 9.9990 chunk 165 optimal weight: 0.8980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 ASN d 234 GLN ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 452 ASN A 88 GLN D 65 GLN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 ASN I 51 ASN I 155 ASN J 239 ASN L 68 ASN M 221 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 685 GLN V 318 GLN ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN Z 243 GLN X 329 ASN X 334 ASN X 416 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.082880 restraints weight = 121119.764| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.13 r_work: 0.2942 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 71318 Z= 0.160 Angle : 0.522 9.812 96349 Z= 0.265 Chirality : 0.039 0.275 10984 Planarity : 0.004 0.075 12396 Dihedral : 6.260 87.408 9816 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 3.21 % Allowed : 23.36 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.61 (0.09), residues: 8771 helix: 1.75 (0.07), residues: 5025 sheet: -0.34 (0.17), residues: 901 loop : 0.50 (0.13), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP d 154 HIS 0.009 0.001 HIS C 90 PHE 0.015 0.001 PHE U 250 TYR 0.018 0.001 TYR a 156 ARG 0.010 0.000 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 879 time to evaluate : 6.227 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: W 76 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: W 85 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8501 (mm-30) REVERT: W 112 VAL cc_start: 0.8499 (t) cc_final: 0.8228 (t) REVERT: W 118 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8195 (tp) REVERT: W 130 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8826 (ttt) REVERT: W 201 ARG cc_start: 0.8225 (tpp80) cc_final: 0.8000 (tpp80) REVERT: W 216 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: W 322 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8342 (mp0) REVERT: W 326 MET cc_start: 0.8882 (mmp) cc_final: 0.8000 (tmt) REVERT: W 375 MET cc_start: 0.9026 (mmm) cc_final: 0.8792 (tpp) REVERT: b 48 ASN cc_start: 0.8518 (m-40) cc_final: 0.8147 (t0) REVERT: b 64 LEU cc_start: 0.8598 (mp) cc_final: 0.8397 (mt) REVERT: d 168 MET cc_start: 0.9050 (mmm) cc_final: 0.8758 (mmm) REVERT: d 265 ASP cc_start: 0.9024 (m-30) cc_final: 0.8562 (m-30) REVERT: d 266 THR cc_start: 0.8873 (p) cc_final: 0.8483 (t) REVERT: d 269 ASP cc_start: 0.8551 (t0) cc_final: 0.8199 (p0) REVERT: f 196 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8130 (mtm) REVERT: f 341 GLU cc_start: 0.8349 (pp20) cc_final: 0.8007 (pp20) REVERT: f 392 THR cc_start: 0.8830 (m) cc_final: 0.8566 (p) REVERT: f 571 GLU cc_start: 0.8654 (pt0) cc_final: 0.8403 (pm20) REVERT: f 759 LEU cc_start: 0.9436 (tp) cc_final: 0.9210 (tm) REVERT: f 815 HIS cc_start: 0.9335 (OUTLIER) cc_final: 0.9003 (p90) REVERT: f 829 MET cc_start: 0.8113 (tpp) cc_final: 0.7905 (tpt) REVERT: g 87 VAL cc_start: 0.8937 (t) cc_final: 0.8732 (p) REVERT: g 104 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.7163 (mmm160) REVERT: g 110 ARG cc_start: 0.8904 (tpp80) cc_final: 0.8115 (mmm160) REVERT: g 113 ARG cc_start: 0.9183 (OUTLIER) cc_final: 0.8829 (tmt90) REVERT: B 35 LYS cc_start: 0.8328 (mmtt) cc_final: 0.8082 (mmtm) REVERT: B 63 LEU cc_start: 0.9027 (mt) cc_final: 0.8807 (mp) REVERT: B 76 GLU cc_start: 0.8621 (tp30) cc_final: 0.8231 (tp30) REVERT: B 94 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8269 (mm-30) REVERT: B 286 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8832 (mt-10) REVERT: B 349 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8946 (mtt-85) REVERT: B 371 ARG cc_start: 0.8690 (mmm160) cc_final: 0.8048 (mmp80) REVERT: B 405 MET cc_start: 0.8588 (mmp) cc_final: 0.8310 (mmt) REVERT: A 46 LYS cc_start: 0.8066 (mmmm) cc_final: 0.7617 (tppp) REVERT: A 111 TYR cc_start: 0.8927 (m-80) cc_final: 0.8552 (m-80) REVERT: A 168 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8140 (tm-30) REVERT: A 204 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7778 (tt) REVERT: D 52 GLU cc_start: 0.8996 (tt0) cc_final: 0.8715 (tt0) REVERT: D 60 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8569 (t80) REVERT: E 48 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8281 (mmmt) REVERT: E 62 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8744 (ttmm) REVERT: E 122 MET cc_start: 0.9211 (mtt) cc_final: 0.8905 (mtt) REVERT: E 157 GLU cc_start: 0.8900 (pm20) cc_final: 0.8655 (pm20) REVERT: E 195 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8340 (m-80) REVERT: E 232 MET cc_start: 0.9311 (mtp) cc_final: 0.9063 (mtp) REVERT: F 183 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8558 (mp0) REVERT: F 321 GLN cc_start: 0.9098 (mm110) cc_final: 0.8765 (mm-40) REVERT: G 11 ARG cc_start: 0.9111 (mmt180) cc_final: 0.8886 (mmt180) REVERT: G 19 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: H 183 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: I 178 ASP cc_start: 0.8777 (t0) cc_final: 0.8439 (t0) REVERT: I 235 GLN cc_start: 0.8742 (tp40) cc_final: 0.8328 (tp-100) REVERT: J 113 SER cc_start: 0.8941 (p) cc_final: 0.8655 (m) REVERT: K 69 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: L 6 TYR cc_start: 0.9128 (m-80) cc_final: 0.8604 (m-80) REVERT: L 143 HIS cc_start: 0.8390 (m-70) cc_final: 0.7985 (m170) REVERT: M 187 ARG cc_start: 0.8553 (mmm160) cc_final: 0.7884 (mmt-90) REVERT: U 188 MET cc_start: 0.8676 (mmm) cc_final: 0.8350 (mmp) REVERT: U 235 LYS cc_start: 0.8979 (mmmm) cc_final: 0.8770 (mmmm) REVERT: U 474 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8069 (mtm-85) REVERT: U 759 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8786 (m) REVERT: V 132 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8492 (mm) REVERT: V 145 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6489 (pt) REVERT: V 221 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8592 (mm) REVERT: V 489 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8946 (mmp) REVERT: V 515 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7866 (mt-10) REVERT: c 211 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7893 (tp30) REVERT: c 227 GLU cc_start: 0.8674 (pt0) cc_final: 0.8189 (pp20) REVERT: c 233 ASP cc_start: 0.9213 (t0) cc_final: 0.8934 (t0) REVERT: e 21 GLU cc_start: 0.7861 (pt0) cc_final: 0.7556 (pm20) REVERT: Y 215 ASP cc_start: 0.8588 (t0) cc_final: 0.8372 (t0) REVERT: Y 248 GLU cc_start: 0.8488 (tp30) cc_final: 0.8125 (tp30) REVERT: Y 282 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8797 (mtp) REVERT: Y 364 TRP cc_start: 0.8781 (t60) cc_final: 0.8467 (t60) REVERT: Z 90 ARG cc_start: 0.8125 (mtp85) cc_final: 0.7815 (mmm160) REVERT: Z 112 MET cc_start: 0.9094 (mmm) cc_final: 0.8697 (mmm) REVERT: Z 255 ASP cc_start: 0.9100 (m-30) cc_final: 0.8883 (m-30) REVERT: a 137 ASP cc_start: 0.8670 (t0) cc_final: 0.8408 (t70) REVERT: a 166 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8593 (pt) REVERT: a 175 ASP cc_start: 0.8660 (m-30) cc_final: 0.7812 (t0) REVERT: X 223 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8699 (mmmm) REVERT: X 297 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7534 (mtp180) REVERT: X 395 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8265 (mtpp) REVERT: X 416 ASN cc_start: 0.8640 (m-40) cc_final: 0.8278 (m-40) outliers start: 246 outliers final: 102 residues processed: 1060 average time/residue: 1.4681 time to fit residues: 2070.2507 Evaluate side-chains 941 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 810 time to evaluate : 6.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 322 GLU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 177 ASP Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 237 MET Chi-restraints excluded: chain d residue 251 ILE Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 397 LYS Chi-restraints excluded: chain f residue 422 VAL Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain g residue 86 GLU Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain g residue 164 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 130 LEU Chi-restraints excluded: chain U residue 217 CYS Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 431 THR Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 474 ARG Chi-restraints excluded: chain U residue 538 GLU Chi-restraints excluded: chain U residue 560 MET Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 759 SER Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 169 LEU Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 237 THR Chi-restraints excluded: chain V residue 301 GLU Chi-restraints excluded: chain V residue 489 MET Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Z residue 44 GLN Chi-restraints excluded: chain Z residue 106 ILE Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 243 GLN Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 303 THR Chi-restraints excluded: chain X residue 28 HIS Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 218 HIS Chi-restraints excluded: chain X residue 223 LYS Chi-restraints excluded: chain X residue 297 ARG Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 395 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 873 random chunks: chunk 755 optimal weight: 0.9980 chunk 400 optimal weight: 5.9990 chunk 391 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 329 optimal weight: 0.9980 chunk 68 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 chunk 296 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 ASN ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 198 HIS f 452 ASN B 425 ASN D 65 GLN D 127 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 51 ASN I 155 ASN J 239 ASN L 68 ASN M 221 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 266 GLN V 318 GLN ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 42 ASN e 47 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 243 GLN X 367 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.113288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081608 restraints weight = 121877.911| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.16 r_work: 0.2932 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 71318 Z= 0.200 Angle : 0.539 14.852 96349 Z= 0.271 Chirality : 0.040 0.260 10984 Planarity : 0.004 0.078 12396 Dihedral : 6.180 89.996 9809 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.58 % Favored : 97.39 % Rotamer: Outliers : 3.13 % Allowed : 23.82 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.64 (0.09), residues: 8771 helix: 1.77 (0.07), residues: 5037 sheet: -0.32 (0.16), residues: 910 loop : 0.52 (0.13), residues: 2824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP d 154 HIS 0.010 0.001 HIS C 90 PHE 0.019 0.001 PHE g 120 TYR 0.035 0.001 TYR f 142 ARG 0.011 0.000 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 841 time to evaluate : 6.534 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: W 76 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7972 (mp0) REVERT: W 85 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8545 (mm-30) REVERT: W 112 VAL cc_start: 0.8508 (t) cc_final: 0.8227 (t) REVERT: W 118 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8192 (tp) REVERT: W 130 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8826 (ttt) REVERT: W 216 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: W 322 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: W 375 MET cc_start: 0.9049 (mmm) cc_final: 0.8804 (tpp) REVERT: b 42 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7859 (mtm-85) REVERT: b 48 ASN cc_start: 0.8577 (m-40) cc_final: 0.8205 (t0) REVERT: d 168 MET cc_start: 0.9038 (mmm) cc_final: 0.8724 (mmm) REVERT: d 265 ASP cc_start: 0.9031 (m-30) cc_final: 0.8558 (m-30) REVERT: d 266 THR cc_start: 0.8870 (p) cc_final: 0.8464 (t) REVERT: d 269 ASP cc_start: 0.8553 (t0) cc_final: 0.8197 (p0) REVERT: f 196 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8091 (mtm) REVERT: f 341 GLU cc_start: 0.8346 (pp20) cc_final: 0.7994 (pp20) REVERT: f 392 THR cc_start: 0.8818 (m) cc_final: 0.8543 (p) REVERT: f 397 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8645 (mtmm) REVERT: f 407 MET cc_start: 0.9171 (mtp) cc_final: 0.8311 (mmm) REVERT: f 571 GLU cc_start: 0.8664 (pt0) cc_final: 0.8428 (pm20) REVERT: f 759 LEU cc_start: 0.9422 (tp) cc_final: 0.9182 (tm) REVERT: f 815 HIS cc_start: 0.9377 (OUTLIER) cc_final: 0.9053 (p90) REVERT: g 89 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8752 (mm) REVERT: g 104 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.7193 (mmm160) REVERT: g 110 ARG cc_start: 0.8920 (tpp80) cc_final: 0.8142 (mmm160) REVERT: g 113 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8806 (tmt90) REVERT: B 32 ARG cc_start: 0.7721 (ptm160) cc_final: 0.7467 (ptt90) REVERT: B 63 LEU cc_start: 0.9017 (mt) cc_final: 0.8805 (mp) REVERT: B 76 GLU cc_start: 0.8608 (tp30) cc_final: 0.8194 (tp30) REVERT: B 94 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8282 (mm-30) REVERT: B 286 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8845 (mt-10) REVERT: B 349 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8968 (mtt-85) REVERT: B 371 ARG cc_start: 0.8695 (mmm160) cc_final: 0.8045 (mmp80) REVERT: B 405 MET cc_start: 0.8611 (mmp) cc_final: 0.8320 (mmt) REVERT: B 420 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7578 (mtmm) REVERT: A 46 LYS cc_start: 0.8091 (mmmm) cc_final: 0.7631 (tppp) REVERT: A 111 TYR cc_start: 0.8764 (m-80) cc_final: 0.8492 (m-80) REVERT: A 168 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8187 (tm-30) REVERT: A 204 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7797 (tt) REVERT: A 232 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8154 (mmm160) REVERT: D 52 GLU cc_start: 0.8985 (tt0) cc_final: 0.8698 (tt0) REVERT: D 60 TYR cc_start: 0.9117 (OUTLIER) cc_final: 0.8572 (t80) REVERT: D 163 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8537 (mtm) REVERT: D 351 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8537 (ttmm) REVERT: E 48 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8290 (mmmt) REVERT: E 62 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8740 (ttmm) REVERT: E 100 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8828 (mt) REVERT: E 122 MET cc_start: 0.9222 (mtt) cc_final: 0.8914 (mtt) REVERT: E 157 GLU cc_start: 0.8903 (pm20) cc_final: 0.8670 (pm20) REVERT: E 195 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8407 (m-80) REVERT: E 232 MET cc_start: 0.9272 (mtp) cc_final: 0.9068 (mtp) REVERT: E 384 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8226 (mt) REVERT: F 183 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8566 (mp0) REVERT: F 321 GLN cc_start: 0.9102 (mm110) cc_final: 0.8758 (mm-40) REVERT: G 19 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8324 (pm20) REVERT: G 182 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8536 (mptm) REVERT: H 183 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7392 (tm-30) REVERT: I 178 ASP cc_start: 0.8789 (t0) cc_final: 0.8470 (t0) REVERT: I 235 GLN cc_start: 0.8748 (tp40) cc_final: 0.8331 (tp-100) REVERT: J 113 SER cc_start: 0.8961 (p) cc_final: 0.8664 (m) REVERT: K 69 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: L 6 TYR cc_start: 0.9125 (m-80) cc_final: 0.8565 (m-80) REVERT: L 143 HIS cc_start: 0.8389 (m-70) cc_final: 0.8096 (m170) REVERT: L 220 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8103 (tp30) REVERT: M 71 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7541 (ptt180) REVERT: M 187 ARG cc_start: 0.8563 (mmm160) cc_final: 0.7932 (mmt90) REVERT: U 188 MET cc_start: 0.8615 (mmm) cc_final: 0.8304 (mmp) REVERT: U 474 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8070 (mtm-85) REVERT: U 759 SER cc_start: 0.9179 (OUTLIER) cc_final: 0.8796 (m) REVERT: V 132 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8480 (mm) REVERT: V 145 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6491 (pt) REVERT: V 221 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8645 (mm) REVERT: V 489 MET cc_start: 0.9286 (OUTLIER) cc_final: 0.8960 (mmp) REVERT: c 207 TYR cc_start: 0.9041 (m-80) cc_final: 0.8690 (m-80) REVERT: c 211 GLU cc_start: 0.8521 (mm-30) cc_final: 0.7819 (tp30) REVERT: c 227 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8192 (pp20) REVERT: c 233 ASP cc_start: 0.9208 (t0) cc_final: 0.8870 (t0) REVERT: c 236 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8575 (mt-10) REVERT: e 21 GLU cc_start: 0.7919 (pt0) cc_final: 0.7583 (pm20) REVERT: Y 165 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8888 (mtpp) REVERT: Y 215 ASP cc_start: 0.8590 (t0) cc_final: 0.8380 (t0) REVERT: Y 248 GLU cc_start: 0.8478 (tp30) cc_final: 0.8108 (tp30) REVERT: Y 282 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8794 (mtp) REVERT: Y 364 TRP cc_start: 0.8799 (t60) cc_final: 0.8471 (t60) REVERT: Z 79 TYR cc_start: 0.8231 (t80) cc_final: 0.8007 (t80) REVERT: Z 90 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7778 (mmm160) REVERT: Z 105 ASP cc_start: 0.8853 (m-30) cc_final: 0.8617 (m-30) REVERT: Z 112 MET cc_start: 0.9111 (mmm) cc_final: 0.8700 (mmm) REVERT: a 26 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8045 (pp20) REVERT: a 139 GLU cc_start: 0.8204 (tp30) cc_final: 0.7899 (tp30) REVERT: a 140 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8028 (tm-30) REVERT: a 166 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8596 (pt) REVERT: a 175 ASP cc_start: 0.8638 (m-30) cc_final: 0.7795 (t0) REVERT: X 223 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8689 (mmmm) REVERT: X 297 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7614 (mtp180) REVERT: X 395 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8264 (mtpp) REVERT: X 416 ASN cc_start: 0.8620 (m-40) cc_final: 0.8318 (m-40) outliers start: 240 outliers final: 118 residues processed: 1015 average time/residue: 1.4973 time to fit residues: 2005.3830 Evaluate side-chains 955 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 796 time to evaluate : 6.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 322 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 233 GLU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 173 CYS Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 251 ILE Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 397 LYS Chi-restraints excluded: chain f residue 422 VAL Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain f residue 861 THR Chi-restraints excluded: chain g residue 86 GLU Chi-restraints excluded: chain g residue 89 LEU Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain J residue 53 LEU Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 220 GLU Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 130 LEU Chi-restraints excluded: chain U residue 141 CYS Chi-restraints excluded: chain U residue 217 CYS Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 431 THR Chi-restraints excluded: chain U residue 474 ARG Chi-restraints excluded: chain U residue 538 GLU Chi-restraints excluded: chain U residue 560 MET Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 759 SER Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 169 LEU Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 237 THR Chi-restraints excluded: chain V residue 301 GLU Chi-restraints excluded: chain V residue 489 MET Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 227 GLU Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 65 ILE Chi-restraints excluded: chain Y residue 165 LYS Chi-restraints excluded: chain Y residue 214 MET Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Z residue 44 GLN Chi-restraints excluded: chain Z residue 106 ILE Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 212 LEU Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 244 GLU Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 303 THR Chi-restraints excluded: chain X residue 28 HIS Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 218 HIS Chi-restraints excluded: chain X residue 223 LYS Chi-restraints excluded: chain X residue 246 LYS Chi-restraints excluded: chain X residue 297 ARG Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 395 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 873 random chunks: chunk 759 optimal weight: 7.9990 chunk 533 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 308 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 548 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 740 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 90 HIS ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 452 ASN A 88 GLN D 65 GLN D 127 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 GLN I 51 ASN I 155 ASN I 240 HIS J 239 ASN L 68 ASN M 221 ASN U 373 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 318 GLN ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN Z 243 GLN Z 256 GLN X 329 ASN X 367 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.111777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.079893 restraints weight = 122219.224| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.33 r_work: 0.2894 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 71318 Z= 0.298 Angle : 0.573 13.383 96349 Z= 0.287 Chirality : 0.041 0.211 10984 Planarity : 0.004 0.089 12396 Dihedral : 6.337 88.698 9809 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 3.12 % Allowed : 24.07 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: 1.60 (0.09), residues: 8771 helix: 1.73 (0.07), residues: 5040 sheet: -0.35 (0.16), residues: 917 loop : 0.52 (0.13), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP d 154 HIS 0.010 0.001 HIS C 90 PHE 0.018 0.001 PHE c 73 TYR 0.022 0.001 TYR f 103 ARG 0.012 0.000 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 811 time to evaluate : 6.219 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: W 76 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: W 85 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8572 (mm-30) REVERT: W 118 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8289 (tp) REVERT: W 130 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8875 (ttt) REVERT: W 212 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8734 (mmmt) REVERT: W 216 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: W 322 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8408 (mp0) REVERT: W 375 MET cc_start: 0.9042 (mmm) cc_final: 0.8834 (tpp) REVERT: C 166 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: d 168 MET cc_start: 0.9051 (mmm) cc_final: 0.8834 (mmm) REVERT: d 265 ASP cc_start: 0.9012 (m-30) cc_final: 0.8548 (m-30) REVERT: d 266 THR cc_start: 0.8891 (p) cc_final: 0.8512 (t) REVERT: d 269 ASP cc_start: 0.8556 (t0) cc_final: 0.8206 (p0) REVERT: f 196 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8046 (mtm) REVERT: f 341 GLU cc_start: 0.8351 (pp20) cc_final: 0.7995 (pp20) REVERT: f 392 THR cc_start: 0.8790 (m) cc_final: 0.8519 (p) REVERT: f 397 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8507 (mppt) REVERT: g 104 ARG cc_start: 0.7632 (mmm-85) cc_final: 0.7248 (mmm160) REVERT: g 110 ARG cc_start: 0.8917 (tpp80) cc_final: 0.8161 (mmm160) REVERT: g 113 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8919 (tmt90) REVERT: g 137 GLN cc_start: 0.8454 (pm20) cc_final: 0.8136 (pm20) REVERT: B 32 ARG cc_start: 0.7748 (ptm160) cc_final: 0.7477 (ptt90) REVERT: B 63 LEU cc_start: 0.9133 (mt) cc_final: 0.8888 (mp) REVERT: B 76 GLU cc_start: 0.8679 (tp30) cc_final: 0.8266 (tp30) REVERT: B 94 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8309 (mm-30) REVERT: B 286 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8858 (mt-10) REVERT: B 293 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8745 (mtpp) REVERT: B 349 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.9008 (mtt-85) REVERT: B 371 ARG cc_start: 0.8729 (mmm160) cc_final: 0.8101 (mmp80) REVERT: B 385 MET cc_start: 0.7913 (mmm) cc_final: 0.7684 (tpt) REVERT: B 412 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8340 (mtm) REVERT: A 46 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7800 (tppt) REVERT: A 88 GLN cc_start: 0.8889 (mt0) cc_final: 0.8486 (mp10) REVERT: A 168 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8171 (tm-30) REVERT: A 204 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8040 (tt) REVERT: A 232 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8238 (mmm160) REVERT: D 52 GLU cc_start: 0.9032 (tt0) cc_final: 0.8714 (tt0) REVERT: D 60 TYR cc_start: 0.9182 (OUTLIER) cc_final: 0.8789 (t80) REVERT: D 163 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8621 (mtm) REVERT: E 62 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8700 (ttmm) REVERT: E 100 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8872 (mt) REVERT: E 157 GLU cc_start: 0.8950 (pm20) cc_final: 0.8732 (pm20) REVERT: E 195 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8479 (m-80) REVERT: E 232 MET cc_start: 0.9349 (mtp) cc_final: 0.9102 (mtp) REVERT: E 384 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8311 (mt) REVERT: F 69 MET cc_start: 0.5159 (OUTLIER) cc_final: 0.4748 (ppp) REVERT: F 183 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8534 (mp0) REVERT: F 321 GLN cc_start: 0.9090 (mm110) cc_final: 0.8764 (mm-40) REVERT: G 182 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8538 (mptm) REVERT: H 183 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: I 178 ASP cc_start: 0.8838 (t0) cc_final: 0.8501 (t0) REVERT: I 235 GLN cc_start: 0.8782 (tp40) cc_final: 0.8373 (tp-100) REVERT: L 6 TYR cc_start: 0.9152 (m-80) cc_final: 0.8611 (m-80) REVERT: L 143 HIS cc_start: 0.8511 (m-70) cc_final: 0.8255 (m170) REVERT: M 71 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7586 (ptt180) REVERT: U 188 MET cc_start: 0.8639 (mmm) cc_final: 0.8351 (mmp) REVERT: U 474 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8232 (mtm-85) REVERT: U 759 SER cc_start: 0.9236 (OUTLIER) cc_final: 0.8856 (m) REVERT: V 132 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8476 (mm) REVERT: V 145 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6462 (pt) REVERT: V 489 MET cc_start: 0.9318 (tpp) cc_final: 0.9004 (mmp) REVERT: c 211 GLU cc_start: 0.8536 (mm-30) cc_final: 0.7927 (tp30) REVERT: c 227 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8264 (pp20) REVERT: c 233 ASP cc_start: 0.9237 (t0) cc_final: 0.8889 (t0) REVERT: c 236 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8606 (mt-10) REVERT: e 26 ASP cc_start: 0.8608 (t0) cc_final: 0.8394 (p0) REVERT: Y 165 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.9026 (mtpp) REVERT: Y 248 GLU cc_start: 0.8513 (tp30) cc_final: 0.8152 (tp30) REVERT: Y 282 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8807 (mtp) REVERT: Y 364 TRP cc_start: 0.8862 (t60) cc_final: 0.8514 (t60) REVERT: Z 81 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8085 (mmt) REVERT: Z 105 ASP cc_start: 0.8913 (m-30) cc_final: 0.8703 (m-30) REVERT: a 26 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8038 (pp20) REVERT: a 139 GLU cc_start: 0.8232 (tp30) cc_final: 0.7911 (tp30) REVERT: a 166 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8628 (pt) REVERT: X 223 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8706 (mmmm) REVERT: X 246 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7489 (mmpt) REVERT: X 297 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.7687 (mtp180) REVERT: X 395 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8337 (mtpp) REVERT: X 416 ASN cc_start: 0.8679 (m-40) cc_final: 0.8399 (m-40) outliers start: 239 outliers final: 127 residues processed: 985 average time/residue: 1.5156 time to fit residues: 1966.6849 Evaluate side-chains 954 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 786 time to evaluate : 6.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 322 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 173 CYS Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 251 ILE Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 397 LYS Chi-restraints excluded: chain f residue 422 VAL Chi-restraints excluded: chain f residue 517 VAL Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 797 LEU Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain g residue 86 GLU Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 165 GLN Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 130 LEU Chi-restraints excluded: chain U residue 141 CYS Chi-restraints excluded: chain U residue 217 CYS Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 335 ILE Chi-restraints excluded: chain U residue 431 THR Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 474 ARG Chi-restraints excluded: chain U residue 538 GLU Chi-restraints excluded: chain U residue 593 SER Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 639 LEU Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 759 SER Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 169 LEU Chi-restraints excluded: chain V residue 237 THR Chi-restraints excluded: chain V residue 301 GLU Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 227 GLU Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 165 LYS Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Z residue 44 GLN Chi-restraints excluded: chain Z residue 81 MET Chi-restraints excluded: chain Z residue 106 ILE Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 303 THR Chi-restraints excluded: chain X residue 28 HIS Chi-restraints excluded: chain X residue 48 GLN Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 218 HIS Chi-restraints excluded: chain X residue 223 LYS Chi-restraints excluded: chain X residue 246 LYS Chi-restraints excluded: chain X residue 297 ARG Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 395 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 873 random chunks: chunk 205 optimal weight: 4.9990 chunk 586 optimal weight: 8.9990 chunk 669 optimal weight: 7.9990 chunk 332 optimal weight: 9.9990 chunk 650 optimal weight: 5.9990 chunk 431 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 521 optimal weight: 0.7980 chunk 580 optimal weight: 0.8980 chunk 751 optimal weight: 2.9990 chunk 699 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 ASN ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 452 ASN D 65 GLN D 127 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN I 51 ASN I 155 ASN J 239 ASN L 68 ASN M 221 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 318 GLN ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 GLN e 47 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 243 GLN X 44 GLN X 329 ASN X 367 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.111954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.079936 restraints weight = 122365.314| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.11 r_work: 0.2910 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 71318 Z= 0.283 Angle : 0.581 13.262 96349 Z= 0.292 Chirality : 0.041 0.227 10984 Planarity : 0.004 0.092 12396 Dihedral : 6.380 89.952 9809 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 2.88 % Allowed : 24.28 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.09), residues: 8771 helix: 1.71 (0.07), residues: 5041 sheet: -0.35 (0.16), residues: 915 loop : 0.51 (0.13), residues: 2815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP d 154 HIS 0.008 0.001 HIS f 161 PHE 0.017 0.001 PHE U 903 TYR 0.040 0.001 TYR f 142 ARG 0.014 0.000 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1025 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 804 time to evaluate : 6.155 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: W 76 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: W 85 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8559 (mm-30) REVERT: W 130 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8856 (ttt) REVERT: W 212 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8727 (mmmt) REVERT: W 216 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: W 322 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8359 (mp0) REVERT: W 375 MET cc_start: 0.9040 (mmm) cc_final: 0.8827 (tpp) REVERT: C 166 GLU cc_start: 0.9180 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: d 168 MET cc_start: 0.9054 (mmm) cc_final: 0.8796 (mmm) REVERT: d 188 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7844 (tmm) REVERT: d 265 ASP cc_start: 0.9001 (m-30) cc_final: 0.8541 (m-30) REVERT: d 266 THR cc_start: 0.8900 (p) cc_final: 0.8505 (t) REVERT: d 269 ASP cc_start: 0.8545 (t0) cc_final: 0.8198 (p0) REVERT: f 196 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8004 (mtm) REVERT: f 341 GLU cc_start: 0.8336 (pp20) cc_final: 0.7978 (pp20) REVERT: f 392 THR cc_start: 0.8758 (m) cc_final: 0.8485 (p) REVERT: f 397 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8485 (mppt) REVERT: g 89 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8491 (mm) REVERT: g 104 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7259 (mmm160) REVERT: g 110 ARG cc_start: 0.8905 (tpp80) cc_final: 0.8126 (mmm160) REVERT: g 113 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8917 (tmt90) REVERT: g 137 GLN cc_start: 0.8504 (pm20) cc_final: 0.8183 (pm20) REVERT: B 32 ARG cc_start: 0.7744 (ptm160) cc_final: 0.7449 (ptt90) REVERT: B 63 LEU cc_start: 0.9115 (mt) cc_final: 0.8871 (mp) REVERT: B 76 GLU cc_start: 0.8643 (tp30) cc_final: 0.8268 (tp30) REVERT: B 94 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8324 (mm-30) REVERT: B 286 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8868 (mt-10) REVERT: B 293 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8719 (mtpp) REVERT: B 349 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.8989 (mtt-85) REVERT: B 371 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8115 (mmp80) REVERT: B 385 MET cc_start: 0.8026 (mmm) cc_final: 0.7748 (tpt) REVERT: B 412 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8324 (mtm) REVERT: A 46 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7807 (tppt) REVERT: A 88 GLN cc_start: 0.8892 (mt0) cc_final: 0.8593 (mp10) REVERT: A 168 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 204 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8079 (tt) REVERT: A 232 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8170 (mmm160) REVERT: D 52 GLU cc_start: 0.9008 (tt0) cc_final: 0.8706 (tt0) REVERT: D 55 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8141 (tm-30) REVERT: D 60 TYR cc_start: 0.9191 (OUTLIER) cc_final: 0.8801 (t80) REVERT: D 163 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8567 (mtm) REVERT: E 48 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8341 (mmmt) REVERT: E 62 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8701 (ttmm) REVERT: E 100 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8851 (mt) REVERT: E 157 GLU cc_start: 0.8926 (pm20) cc_final: 0.8714 (pm20) REVERT: E 195 PHE cc_start: 0.9046 (OUTLIER) cc_final: 0.8468 (m-80) REVERT: E 384 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8311 (mt) REVERT: F 69 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4760 (ppp) REVERT: F 183 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: F 321 GLN cc_start: 0.9076 (mm110) cc_final: 0.8762 (mm-40) REVERT: G 19 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8344 (pm20) REVERT: G 182 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8541 (mptm) REVERT: H 183 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: I 178 ASP cc_start: 0.8799 (t0) cc_final: 0.8455 (t0) REVERT: I 235 GLN cc_start: 0.8766 (tp40) cc_final: 0.8358 (tp-100) REVERT: L 6 TYR cc_start: 0.9128 (m-80) cc_final: 0.8596 (m-80) REVERT: L 143 HIS cc_start: 0.8512 (m-70) cc_final: 0.8298 (m170) REVERT: M 71 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7563 (ptt180) REVERT: M 187 ARG cc_start: 0.8459 (mmm160) cc_final: 0.7967 (mmt-90) REVERT: U 55 ARG cc_start: 0.8120 (tpt90) cc_final: 0.7631 (tmm-80) REVERT: U 188 MET cc_start: 0.8609 (mmm) cc_final: 0.8353 (mmp) REVERT: U 474 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8242 (mtm-85) REVERT: U 759 SER cc_start: 0.9233 (OUTLIER) cc_final: 0.8844 (m) REVERT: V 132 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8463 (mm) REVERT: V 145 LEU cc_start: 0.6751 (OUTLIER) cc_final: 0.6469 (pt) REVERT: V 404 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8364 (ttmt) REVERT: V 489 MET cc_start: 0.9307 (tpp) cc_final: 0.9003 (mmp) REVERT: c 207 TYR cc_start: 0.9102 (m-80) cc_final: 0.8784 (m-80) REVERT: c 211 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7901 (tp30) REVERT: c 227 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8133 (pp20) REVERT: c 233 ASP cc_start: 0.9219 (t0) cc_final: 0.8861 (t0) REVERT: c 236 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8551 (mt-10) REVERT: e 21 GLU cc_start: 0.8142 (pt0) cc_final: 0.7642 (pm20) REVERT: Y 248 GLU cc_start: 0.8490 (tp30) cc_final: 0.8131 (tp30) REVERT: Y 282 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8232 (mtp) REVERT: Y 364 TRP cc_start: 0.8882 (t60) cc_final: 0.8527 (t60) REVERT: Z 81 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8082 (mmt) REVERT: Z 90 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7967 (mmm160) REVERT: a 26 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8027 (pp20) REVERT: a 139 GLU cc_start: 0.8204 (tp30) cc_final: 0.7881 (tp30) REVERT: a 166 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8632 (pt) REVERT: X 223 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8722 (mmmm) REVERT: X 297 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.7706 (mtp180) REVERT: X 395 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8325 (mtpp) REVERT: X 416 ASN cc_start: 0.8675 (m-40) cc_final: 0.8399 (m-40) outliers start: 221 outliers final: 137 residues processed: 969 average time/residue: 1.4933 time to fit residues: 1903.5771 Evaluate side-chains 969 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 789 time to evaluate : 6.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 212 LYS Chi-restraints excluded: chain W residue 216 GLU Chi-restraints excluded: chain W residue 322 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 173 CYS Chi-restraints excluded: chain d residue 177 ASP Chi-restraints excluded: chain d residue 188 MET Chi-restraints excluded: chain d residue 194 LEU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 251 ILE Chi-restraints excluded: chain f residue 58 MET Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 321 MET Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 397 LYS Chi-restraints excluded: chain f residue 422 VAL Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 686 LEU Chi-restraints excluded: chain f residue 797 LEU Chi-restraints excluded: chain f residue 817 VAL Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain g residue 89 LEU Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 158 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 293 LYS Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 268 ASP Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain E residue 384 LEU Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 112 ILE Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain L residue 206 THR Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain M residue 35 THR Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain U residue 42 VAL Chi-restraints excluded: chain U residue 130 LEU Chi-restraints excluded: chain U residue 141 CYS Chi-restraints excluded: chain U residue 217 CYS Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 335 ILE Chi-restraints excluded: chain U residue 431 THR Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 474 ARG Chi-restraints excluded: chain U residue 538 GLU Chi-restraints excluded: chain U residue 593 SER Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 639 LEU Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 759 SER Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 169 LEU Chi-restraints excluded: chain V residue 237 THR Chi-restraints excluded: chain V residue 301 GLU Chi-restraints excluded: chain V residue 404 LYS Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 227 GLU Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Z residue 44 GLN Chi-restraints excluded: chain Z residue 81 MET Chi-restraints excluded: chain Z residue 106 ILE Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 303 THR Chi-restraints excluded: chain X residue 28 HIS Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 218 HIS Chi-restraints excluded: chain X residue 223 LYS Chi-restraints excluded: chain X residue 246 LYS Chi-restraints excluded: chain X residue 297 ARG Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 395 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 873 random chunks: chunk 159 optimal weight: 1.9990 chunk 715 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 850 optimal weight: 0.8980 chunk 755 optimal weight: 0.8980 chunk 311 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 760 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 260 optimal weight: 1.9990 chunk 648 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 452 ASN D 65 GLN D 127 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN I 51 ASN I 155 ASN J 239 ASN K 225 ASN L 68 ASN M 221 ASN U 373 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 318 GLN ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 GLN e 47 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 194 GLN Z 243 GLN Z 256 GLN a 36 GLN X 329 ASN X 367 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.113452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.081122 restraints weight = 121942.500| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.34 r_work: 0.2907 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 71318 Z= 0.190 Angle : 0.565 13.274 96349 Z= 0.282 Chirality : 0.040 0.257 10984 Planarity : 0.004 0.079 12396 Dihedral : 6.188 84.672 9806 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 2.44 % Allowed : 24.78 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.09), residues: 8771 helix: 1.77 (0.07), residues: 5033 sheet: -0.28 (0.17), residues: 891 loop : 0.51 (0.13), residues: 2847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP d 154 HIS 0.009 0.001 HIS f 161 PHE 0.026 0.001 PHE g 120 TYR 0.024 0.001 TYR H 83 ARG 0.016 0.000 ARG H 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17542 Ramachandran restraints generated. 8771 Oldfield, 0 Emsley, 8771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1011 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 824 time to evaluate : 6.078 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: W 76 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: W 85 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8532 (mm-30) REVERT: W 112 VAL cc_start: 0.8487 (t) cc_final: 0.8205 (t) REVERT: W 118 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8160 (tp) REVERT: W 130 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8846 (ttt) REVERT: W 322 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8350 (mp0) REVERT: W 375 MET cc_start: 0.9049 (mmm) cc_final: 0.8805 (tpp) REVERT: C 166 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: b 108 ARG cc_start: 0.7054 (tpp80) cc_final: 0.6564 (tpp80) REVERT: d 168 MET cc_start: 0.9025 (mmm) cc_final: 0.8660 (mmm) REVERT: d 188 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7764 (tmm) REVERT: d 265 ASP cc_start: 0.9048 (m-30) cc_final: 0.8650 (m-30) REVERT: d 266 THR cc_start: 0.8910 (p) cc_final: 0.8438 (t) REVERT: d 269 ASP cc_start: 0.8547 (t0) cc_final: 0.8173 (p0) REVERT: f 196 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8076 (mtm) REVERT: f 341 GLU cc_start: 0.8340 (pp20) cc_final: 0.7966 (pp20) REVERT: f 392 THR cc_start: 0.8736 (m) cc_final: 0.8452 (p) REVERT: f 397 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8502 (mppt) REVERT: f 759 LEU cc_start: 0.9418 (tp) cc_final: 0.9172 (tm) REVERT: f 815 HIS cc_start: 0.9380 (OUTLIER) cc_final: 0.9036 (p90) REVERT: g 86 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7380 (pm20) REVERT: g 87 VAL cc_start: 0.9197 (t) cc_final: 0.8972 (p) REVERT: g 110 ARG cc_start: 0.8923 (tpp80) cc_final: 0.8133 (mmm160) REVERT: g 113 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8955 (tmt90) REVERT: g 137 GLN cc_start: 0.8496 (pm20) cc_final: 0.8201 (pm20) REVERT: B 32 ARG cc_start: 0.7683 (ptm160) cc_final: 0.7410 (ptt90) REVERT: B 63 LEU cc_start: 0.9004 (mt) cc_final: 0.8772 (mp) REVERT: B 76 GLU cc_start: 0.8567 (tp30) cc_final: 0.8246 (tp30) REVERT: B 84 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7869 (tp40) REVERT: B 85 MET cc_start: 0.8056 (ptp) cc_final: 0.7693 (ptp) REVERT: B 94 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 286 GLU cc_start: 0.9259 (OUTLIER) cc_final: 0.8839 (mt-10) REVERT: B 295 TYR cc_start: 0.9115 (m-80) cc_final: 0.8901 (m-80) REVERT: B 349 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8940 (mtt-85) REVERT: B 371 ARG cc_start: 0.8691 (mmm160) cc_final: 0.8032 (mmp80) REVERT: B 412 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8289 (mtm) REVERT: B 420 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7592 (mtmm) REVERT: A 46 LYS cc_start: 0.8059 (mmmm) cc_final: 0.7602 (tppp) REVERT: A 47 GLN cc_start: 0.8766 (tp40) cc_final: 0.8385 (tp40) REVERT: A 88 GLN cc_start: 0.8903 (mt0) cc_final: 0.8574 (mp10) REVERT: A 111 TYR cc_start: 0.8950 (m-80) cc_final: 0.8515 (m-80) REVERT: A 168 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8135 (tm-30) REVERT: A 204 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7930 (tt) REVERT: A 232 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8110 (mmm160) REVERT: D 52 GLU cc_start: 0.8993 (tt0) cc_final: 0.8677 (tt0) REVERT: D 55 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: D 60 TYR cc_start: 0.9089 (OUTLIER) cc_final: 0.8533 (t80) REVERT: D 163 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8558 (mtm) REVERT: E 48 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8348 (mmmt) REVERT: E 62 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8723 (ttmm) REVERT: E 100 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8795 (mt) REVERT: E 122 MET cc_start: 0.9209 (mtt) cc_final: 0.8928 (mtt) REVERT: E 157 GLU cc_start: 0.8924 (pm20) cc_final: 0.8682 (pm20) REVERT: E 195 PHE cc_start: 0.9005 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: F 69 MET cc_start: 0.5164 (OUTLIER) cc_final: 0.4829 (ppp) REVERT: F 79 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7982 (mttt) REVERT: F 183 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8475 (mp0) REVERT: F 321 GLN cc_start: 0.9098 (mm110) cc_final: 0.8749 (mm-40) REVERT: G 19 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8282 (pm20) REVERT: G 182 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8511 (mptm) REVERT: H 183 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: I 178 ASP cc_start: 0.8806 (t0) cc_final: 0.8489 (t0) REVERT: I 235 GLN cc_start: 0.8807 (tp40) cc_final: 0.8393 (tp-100) REVERT: J 141 THR cc_start: 0.8453 (m) cc_final: 0.8247 (t) REVERT: J 179 GLU cc_start: 0.8958 (mp0) cc_final: 0.8662 (pm20) REVERT: L 6 TYR cc_start: 0.9101 (m-80) cc_final: 0.8896 (m-80) REVERT: L 143 HIS cc_start: 0.8386 (m-70) cc_final: 0.8154 (m90) REVERT: M 71 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7514 (ptt180) REVERT: M 187 ARG cc_start: 0.8378 (mmm160) cc_final: 0.7847 (mmt-90) REVERT: U 188 MET cc_start: 0.8635 (mmm) cc_final: 0.8387 (mmp) REVERT: U 474 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8024 (mtm-85) REVERT: U 759 SER cc_start: 0.9104 (OUTLIER) cc_final: 0.8755 (m) REVERT: V 132 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8389 (mm) REVERT: V 145 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6497 (pt) REVERT: V 404 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8269 (ttmt) REVERT: V 489 MET cc_start: 0.9277 (tpp) cc_final: 0.8960 (mmp) REVERT: c 207 TYR cc_start: 0.8963 (m-80) cc_final: 0.8602 (m-80) REVERT: c 211 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7816 (tp30) REVERT: c 227 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8135 (pp20) REVERT: c 233 ASP cc_start: 0.9197 (t0) cc_final: 0.8850 (t0) REVERT: c 236 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8560 (mt-10) REVERT: e 21 GLU cc_start: 0.8000 (pt0) cc_final: 0.7467 (pm20) REVERT: Y 248 GLU cc_start: 0.8483 (tp30) cc_final: 0.8117 (tp30) REVERT: Y 282 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8743 (mtp) REVERT: Y 364 TRP cc_start: 0.8871 (t60) cc_final: 0.8507 (t60) REVERT: Z 90 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7798 (mmm160) REVERT: Z 112 MET cc_start: 0.9095 (mmm) cc_final: 0.8671 (mmm) REVERT: a 26 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8056 (pp20) REVERT: a 33 LEU cc_start: 0.8377 (mt) cc_final: 0.8069 (pp) REVERT: a 139 GLU cc_start: 0.8177 (tp30) cc_final: 0.7963 (tp30) REVERT: a 166 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8586 (pt) REVERT: X 214 SER cc_start: 0.9169 (t) cc_final: 0.8929 (p) REVERT: X 223 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8673 (mmmm) REVERT: X 297 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7573 (mtp180) REVERT: X 395 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8268 (mtpp) REVERT: X 416 ASN cc_start: 0.8592 (m-40) cc_final: 0.8287 (m-40) outliers start: 187 outliers final: 114 residues processed: 959 average time/residue: 1.4691 time to fit residues: 1861.5580 Evaluate side-chains 949 residues out of total 7661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 794 time to evaluate : 6.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 76 GLU Chi-restraints excluded: chain W residue 118 LEU Chi-restraints excluded: chain W residue 130 MET Chi-restraints excluded: chain W residue 322 GLU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 166 GLU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain b residue 43 SER Chi-restraints excluded: chain b residue 52 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 62 THR Chi-restraints excluded: chain b residue 77 THR Chi-restraints excluded: chain b residue 138 VAL Chi-restraints excluded: chain b residue 160 LEU Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 173 CYS Chi-restraints excluded: chain d residue 188 MET Chi-restraints excluded: chain d residue 212 LEU Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 251 ILE Chi-restraints excluded: chain f residue 58 MET Chi-restraints excluded: chain f residue 68 THR Chi-restraints excluded: chain f residue 94 LYS Chi-restraints excluded: chain f residue 196 MET Chi-restraints excluded: chain f residue 240 VAL Chi-restraints excluded: chain f residue 277 LEU Chi-restraints excluded: chain f residue 370 MET Chi-restraints excluded: chain f residue 397 LYS Chi-restraints excluded: chain f residue 517 VAL Chi-restraints excluded: chain f residue 582 VAL Chi-restraints excluded: chain f residue 815 HIS Chi-restraints excluded: chain f residue 844 VAL Chi-restraints excluded: chain f residue 852 VAL Chi-restraints excluded: chain g residue 86 GLU Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 116 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 286 GLU Chi-restraints excluded: chain B residue 349 ARG Chi-restraints excluded: chain B residue 384 ILE Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 412 MET Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 232 ARG Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 229 ARG Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 148 VAL Chi-restraints excluded: chain E residue 170 CYS Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 195 PHE Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain E residue 322 LYS Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 183 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 116 SER Chi-restraints excluded: chain H residue 183 GLU Chi-restraints excluded: chain H residue 202 GLN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain I residue 43 VAL Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 225 ILE Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 147 THR Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 56 SER Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain L residue 106 SER Chi-restraints excluded: chain L residue 156 CYS Chi-restraints excluded: chain L residue 167 SER Chi-restraints excluded: chain M residue 71 ARG Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 207 LYS Chi-restraints excluded: chain U residue 130 LEU Chi-restraints excluded: chain U residue 141 CYS Chi-restraints excluded: chain U residue 217 CYS Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 431 THR Chi-restraints excluded: chain U residue 459 ASP Chi-restraints excluded: chain U residue 474 ARG Chi-restraints excluded: chain U residue 538 GLU Chi-restraints excluded: chain U residue 610 VAL Chi-restraints excluded: chain U residue 637 VAL Chi-restraints excluded: chain U residue 639 LEU Chi-restraints excluded: chain U residue 685 GLN Chi-restraints excluded: chain U residue 714 SER Chi-restraints excluded: chain U residue 759 SER Chi-restraints excluded: chain V residue 79 VAL Chi-restraints excluded: chain V residue 113 LEU Chi-restraints excluded: chain V residue 132 LEU Chi-restraints excluded: chain V residue 145 LEU Chi-restraints excluded: chain V residue 169 LEU Chi-restraints excluded: chain V residue 237 THR Chi-restraints excluded: chain V residue 301 GLU Chi-restraints excluded: chain V residue 404 LYS Chi-restraints excluded: chain c residue 84 VAL Chi-restraints excluded: chain c residue 132 SER Chi-restraints excluded: chain c residue 227 GLU Chi-restraints excluded: chain Y residue 50 MET Chi-restraints excluded: chain Y residue 282 MET Chi-restraints excluded: chain Z residue 44 GLN Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 229 GLN Chi-restraints excluded: chain Z residue 243 GLN Chi-restraints excluded: chain a residue 26 GLU Chi-restraints excluded: chain a residue 50 PHE Chi-restraints excluded: chain a residue 88 THR Chi-restraints excluded: chain a residue 166 ILE Chi-restraints excluded: chain a residue 183 VAL Chi-restraints excluded: chain a residue 303 THR Chi-restraints excluded: chain X residue 28 HIS Chi-restraints excluded: chain X residue 48 GLN Chi-restraints excluded: chain X residue 53 LEU Chi-restraints excluded: chain X residue 66 LEU Chi-restraints excluded: chain X residue 154 LEU Chi-restraints excluded: chain X residue 223 LYS Chi-restraints excluded: chain X residue 246 LYS Chi-restraints excluded: chain X residue 297 ARG Chi-restraints excluded: chain X residue 326 LEU Chi-restraints excluded: chain X residue 393 VAL Chi-restraints excluded: chain X residue 395 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 873 random chunks: chunk 400 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 852 optimal weight: 0.9990 chunk 415 optimal weight: 0.9990 chunk 376 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 676 optimal weight: 0.0870 chunk 596 optimal weight: 9.9990 chunk 594 optimal weight: 10.0000 chunk 625 optimal weight: 0.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 195 ASN ** d 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 452 ASN ** g 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 ASN D 65 GLN D 127 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 GLN G 172 GLN I 51 ASN I 155 ASN J 239 ASN L 68 ASN M 221 ASN ** U 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 805 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 318 GLN ** V 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN ** Y 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 329 ASN X 367 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.113432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.081221 restraints weight = 121931.479| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.31 r_work: 0.2905 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.199 71318 Z= 0.219 Angle : 0.613 59.198 96349 Z= 0.320 Chirality : 0.041 0.399 10984 Planarity : 0.004 0.077 12396 Dihedral : 6.141 84.710 9803 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 2.40 % Allowed : 24.98 % Favored : 72.62 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.09), residues: 8771 helix: 1.77 (0.07), residues: 5033 sheet: -0.28 (0.17), residues: 891 loop : 0.51 (0.13), residues: 2847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP d 154 HIS 0.009 0.001 HIS f 161 PHE 0.026 0.001 PHE a 155 TYR 0.020 0.001 TYR H 83 ARG 0.014 0.000 ARG g 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57741.87 seconds wall clock time: 984 minutes 57.53 seconds (59097.53 seconds total)