Starting phenix.real_space_refine on Sat Nov 16 23:53:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvu_17972/11_2024/8pvu_17972.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvu_17972/11_2024/8pvu_17972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvu_17972/11_2024/8pvu_17972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvu_17972/11_2024/8pvu_17972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvu_17972/11_2024/8pvu_17972.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvu_17972/11_2024/8pvu_17972.cif" } resolution = 3.5 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= 0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 7887 2.51 5 N 2101 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12336 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 2480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2480 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 16, 'TRANS': 284} Chain breaks: 5 Chain: "A" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2586 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 1 Chain: "B" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2487 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2409 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 11, 'TRANS': 295} Chain breaks: 3 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2374 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 13, 'TRANS': 289} Chain breaks: 3 Time building chain proxies: 7.98, per 1000 atoms: 0.65 Number of scatterers: 12336 At special positions: 0 Unit cell: (91.16, 97.18, 137.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2280 8.00 N 2101 7.00 C 7887 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.7 seconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2902 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 10 sheets defined 54.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'E' and resid 61 through 78 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 122 through 143 Processing helix chain 'E' and resid 151 through 153 No H-bonds generated for 'chain 'E' and resid 151 through 153' Processing helix chain 'E' and resid 195 through 200 Processing helix chain 'E' and resid 207 through 223 removed outlier: 4.170A pdb=" N ILE E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 245 Processing helix chain 'E' and resid 257 through 266 Processing helix chain 'E' and resid 274 through 279 removed outlier: 3.617A pdb=" N LEU E 278 " --> pdb=" O PRO E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 294 Processing helix chain 'E' and resid 303 through 309 Processing helix chain 'E' and resid 340 through 352 Processing helix chain 'A' and resid 41 through 46 Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.803A pdb=" N GLY A 50 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR A 52 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 74 removed outlier: 3.951A pdb=" N ASN A 58 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS A 73 " --> pdb=" O MET A 69 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.788A pdb=" N ILE A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 109' Processing helix chain 'A' and resid 112 through 122 removed outlier: 3.988A pdb=" N HIS A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.516A pdb=" N VAL A 135 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.872A pdb=" N GLU A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 197 removed outlier: 4.035A pdb=" N PHE A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 180 " --> pdb=" O TYR A 176 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP A 181 " --> pdb=" O CYS A 177 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N MET A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.554A pdb=" N ILE A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 208 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU A 213 " --> pdb=" O ARG A 209 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 227 removed outlier: 3.798A pdb=" N TRP A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN A 225 " --> pdb=" O TYR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 250 removed outlier: 3.635A pdb=" N ASP A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 3.851A pdb=" N LEU A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 removed outlier: 3.505A pdb=" N HIS A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N MET A 296 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.804A pdb=" N ALA A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL A 325 " --> pdb=" O PRO A 321 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A 326 " --> pdb=" O ASP A 322 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 345 Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.874A pdb=" N GLU A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.709A pdb=" N ARG B 38 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 49 removed outlier: 3.635A pdb=" N PHE B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 53 removed outlier: 4.681A pdb=" N GLY B 53 " --> pdb=" O GLY B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 53' Processing helix chain 'B' and resid 54 through 74 removed outlier: 3.696A pdb=" N ASN B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 74 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 110 removed outlier: 4.116A pdb=" N ILE B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 removed outlier: 3.925A pdb=" N HIS B 122 " --> pdb=" O TYR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 141 removed outlier: 4.185A pdb=" N GLU B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 Processing helix chain 'B' and resid 173 through 196 removed outlier: 3.883A pdb=" N CYS B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE B 179 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU B 180 " --> pdb=" O TYR B 176 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP B 181 " --> pdb=" O CYS B 177 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TRP B 182 " --> pdb=" O LYS B 178 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.649A pdb=" N GLN B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 215 removed outlier: 3.672A pdb=" N GLU B 213 " --> pdb=" O ARG B 209 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 227 removed outlier: 3.907A pdb=" N TRP B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 225 " --> pdb=" O TYR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 removed outlier: 4.068A pdb=" N GLY B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 removed outlier: 3.811A pdb=" N ALA B 270 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 Processing helix chain 'B' and resid 295 through 298 Processing helix chain 'B' and resid 321 through 328 Processing helix chain 'B' and resid 342 through 353 removed outlier: 3.715A pdb=" N VAL B 346 " --> pdb=" O ASP B 342 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 347 " --> pdb=" O ALA B 343 " (cutoff:3.500A) Proline residue: B 348 - end of helix removed outlier: 3.544A pdb=" N GLU B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.584A pdb=" N ARG C 38 " --> pdb=" O ASP C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 49 removed outlier: 3.506A pdb=" N GLU C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE C 49 " --> pdb=" O LEU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 55 No H-bonds generated for 'chain 'C' and resid 53 through 55' Processing helix chain 'C' and resid 56 through 74 Processing helix chain 'C' and resid 104 through 109 removed outlier: 3.923A pdb=" N ILE C 108 " --> pdb=" O THR C 104 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 109' Processing helix chain 'C' and resid 112 through 122 removed outlier: 3.843A pdb=" N HIS C 122 " --> pdb=" O TYR C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 142 removed outlier: 3.589A pdb=" N VAL C 135 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C 138 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU C 139 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 3.799A pdb=" N GLU C 160 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN C 161 " --> pdb=" O GLU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 197 removed outlier: 4.162A pdb=" N LYS C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 179 " --> pdb=" O ASN C 175 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 3.898A pdb=" N ASP C 188 " --> pdb=" O MET C 184 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 removed outlier: 3.697A pdb=" N GLU C 213 " --> pdb=" O ARG C 209 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASN C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.673A pdb=" N GLN C 225 " --> pdb=" O TYR C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 248 removed outlier: 3.773A pdb=" N ASP C 243 " --> pdb=" O GLY C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 removed outlier: 3.767A pdb=" N LEU C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE C 272 " --> pdb=" O THR C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 296 removed outlier: 3.661A pdb=" N HIS C 288 " --> pdb=" O GLY C 284 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N MET C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 342 through 354 removed outlier: 3.510A pdb=" N VAL C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) Proline residue: C 348 - end of helix removed outlier: 3.571A pdb=" N GLU C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 41 through 49 removed outlier: 3.761A pdb=" N PHE D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 56 through 75 removed outlier: 3.554A pdb=" N GLU D 75 " --> pdb=" O GLU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 110 removed outlier: 4.118A pdb=" N ILE D 108 " --> pdb=" O THR D 104 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 122 removed outlier: 4.415A pdb=" N THR D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS D 122 " --> pdb=" O TYR D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 142 removed outlier: 3.944A pdb=" N GLU D 136 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 198 removed outlier: 3.860A pdb=" N LYS D 178 " --> pdb=" O GLU D 174 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE D 179 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU D 180 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP D 182 " --> pdb=" O LYS D 178 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Proline residue: D 185 - end of helix removed outlier: 3.554A pdb=" N GLN D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.844A pdb=" N LYS D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 213 " --> pdb=" O ARG D 209 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 226 removed outlier: 3.579A pdb=" N TRP D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS D 226 " --> pdb=" O TYR D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 252 removed outlier: 4.130A pdb=" N GLY D 242 " --> pdb=" O ASP D 238 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N HIS D 248 " --> pdb=" O MET D 244 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR D 250 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 251 " --> pdb=" O PHE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 272 removed outlier: 3.661A pdb=" N LEU D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 294 removed outlier: 3.790A pdb=" N HIS D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 327 removed outlier: 4.093A pdb=" N ALA D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL D 325 " --> pdb=" O PRO D 321 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N TRP D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 320 through 327' Processing helix chain 'D' and resid 346 through 354 Processing sheet with id=AA1, first strand: chain 'E' and resid 25 through 26 removed outlier: 3.677A pdb=" N VAL E 49 " --> pdb=" O ASP E 44 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP E 88 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 110 through 111 Processing sheet with id=AA3, first strand: chain 'E' and resid 145 through 146 Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 232 removed outlier: 6.576A pdb=" N LEU A 128 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL A 127 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 302 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA A 303 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N VAL A 339 " --> pdb=" O ALA A 303 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR A 305 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 163 through 166 Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 232 removed outlier: 6.588A pdb=" N LEU B 128 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 99 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N VAL B 129 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 101 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 98 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE B 279 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N PHE B 100 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N LEU B 281 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY B 102 " --> pdb=" O LEU B 281 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B 302 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA B 303 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N VAL B 339 " --> pdb=" O ALA B 303 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYR B 305 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 147 through 148 Processing sheet with id=AA8, first strand: chain 'C' and resid 231 through 232 removed outlier: 6.533A pdb=" N LEU C 128 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 99 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N VAL C 129 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 101 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR C 302 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA C 303 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL C 339 " --> pdb=" O ALA C 303 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR C 305 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 163 through 166 Processing sheet with id=AB1, first strand: chain 'D' and resid 231 through 232 removed outlier: 6.864A pdb=" N LEU D 128 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N VAL D 127 " --> pdb=" O CYS D 97 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE D 99 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N VAL D 129 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU D 101 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR D 302 " --> pdb=" O THR D 276 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1302 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: 3.37 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2882 1.33 - 1.45: 2535 1.45 - 1.57: 7056 1.57 - 1.69: 0 1.69 - 1.81: 113 Bond restraints: 12586 Sorted by residual: bond pdb=" N ILE D 330 " pdb=" CA ILE D 330 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.18e+01 bond pdb=" N ILE E 324 " pdb=" CA ILE E 324 " ideal model delta sigma weight residual 1.456 1.492 -0.037 1.15e-02 7.56e+03 1.02e+01 bond pdb=" N GLY D 299 " pdb=" CA GLY D 299 " ideal model delta sigma weight residual 1.446 1.477 -0.032 1.02e-02 9.61e+03 9.54e+00 bond pdb=" N ILE E 255 " pdb=" CA ILE E 255 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.27e-02 6.20e+03 9.04e+00 bond pdb=" C SER E 246 " pdb=" N PRO E 247 " ideal model delta sigma weight residual 1.335 1.361 -0.026 8.70e-03 1.32e+04 8.77e+00 ... (remaining 12581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 16604 2.09 - 4.18: 401 4.18 - 6.27: 36 6.27 - 8.36: 4 8.36 - 10.45: 2 Bond angle restraints: 17047 Sorted by residual: angle pdb=" CA GLY D 299 " pdb=" C GLY D 299 " pdb=" O GLY D 299 " ideal model delta sigma weight residual 122.23 118.51 3.72 6.90e-01 2.10e+00 2.91e+01 angle pdb=" N ALA E 143 " pdb=" CA ALA E 143 " pdb=" C ALA E 143 " ideal model delta sigma weight residual 113.01 107.81 5.20 1.20e+00 6.94e-01 1.88e+01 angle pdb=" CA PRO E 196 " pdb=" N PRO E 196 " pdb=" CD PRO E 196 " ideal model delta sigma weight residual 112.00 106.32 5.68 1.40e+00 5.10e-01 1.64e+01 angle pdb=" CA LEU E 252 " pdb=" C LEU E 252 " pdb=" O LEU E 252 " ideal model delta sigma weight residual 122.64 117.83 4.81 1.25e+00 6.40e-01 1.48e+01 angle pdb=" N GLN E 66 " pdb=" CA GLN E 66 " pdb=" C GLN E 66 " ideal model delta sigma weight residual 111.28 107.17 4.11 1.09e+00 8.42e-01 1.42e+01 ... (remaining 17042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6369 17.96 - 35.92: 829 35.92 - 53.88: 275 53.88 - 71.84: 44 71.84 - 89.80: 12 Dihedral angle restraints: 7529 sinusoidal: 3023 harmonic: 4506 Sorted by residual: dihedral pdb=" CA LEU E 338 " pdb=" C LEU E 338 " pdb=" N PRO E 339 " pdb=" CA PRO E 339 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CG ARG C 38 " pdb=" CD ARG C 38 " pdb=" NE ARG C 38 " pdb=" CZ ARG C 38 " ideal model delta sinusoidal sigma weight residual 90.00 42.56 47.44 2 1.50e+01 4.44e-03 1.16e+01 dihedral pdb=" CB GLU E 71 " pdb=" CG GLU E 71 " pdb=" CD GLU E 71 " pdb=" OE1 GLU E 71 " ideal model delta sinusoidal sigma weight residual 0.00 -89.77 89.77 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 7526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1378 0.046 - 0.092: 371 0.092 - 0.138: 144 0.138 - 0.183: 15 0.183 - 0.229: 8 Chirality restraints: 1916 Sorted by residual: chirality pdb=" CB THR D 268 " pdb=" CA THR D 268 " pdb=" OG1 THR D 268 " pdb=" CG2 THR D 268 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO E 196 " pdb=" N PRO E 196 " pdb=" C PRO E 196 " pdb=" CB PRO E 196 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE E 72 " pdb=" N ILE E 72 " pdb=" C ILE E 72 " pdb=" CB ILE E 72 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1913 not shown) Planarity restraints: 2192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 195 " -0.064 5.00e-02 4.00e+02 9.42e-02 1.42e+01 pdb=" N PRO E 196 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO E 196 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO E 196 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 338 " -0.045 5.00e-02 4.00e+02 6.94e-02 7.71e+00 pdb=" N PRO E 339 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO E 339 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 339 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 201 " 0.013 2.00e-02 2.50e+03 1.56e-02 6.08e+00 pdb=" CG TRP C 201 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP C 201 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP C 201 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 201 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 201 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 201 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 201 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 201 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 201 " 0.003 2.00e-02 2.50e+03 ... (remaining 2189 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2335 2.77 - 3.30: 11593 3.30 - 3.83: 18844 3.83 - 4.37: 21072 4.37 - 4.90: 35967 Nonbonded interactions: 89811 Sorted by model distance: nonbonded pdb=" O GLU A 323 " pdb=" OG SER A 326 " model vdw 2.234 3.040 nonbonded pdb=" O GLU A 174 " pdb=" NZ LYS A 178 " model vdw 2.244 3.120 nonbonded pdb=" O GLY B 50 " pdb=" OG1 THR B 57 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASP C 258 " pdb=" N ILE C 259 " model vdw 2.273 3.120 nonbonded pdb=" O LYS C 200 " pdb=" NZ LYS C 205 " model vdw 2.283 3.120 ... (remaining 89806 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 29 through 74 or resid 93 through 148 or resid 164 through \ 314 or resid 323 through 359)) selection = (chain 'B' and (resid 29 through 74 or resid 93 through 148 or resid 164 through \ 314 or resid 323 through 359)) selection = (chain 'C' and (resid 29 through 148 or resid 164 through 314 or resid 323 throu \ gh 359)) selection = (chain 'D' and (resid 29 through 74 or resid 93 through 314 or resid 323 through \ 359)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.540 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 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 : 0.005 0.063 12586 Z= 0.301 Angle : 0.705 10.455 17047 Z= 0.449 Chirality : 0.049 0.229 1916 Planarity : 0.005 0.094 2192 Dihedral : 18.071 89.799 4627 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.09 % Allowed : 32.16 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1520 helix: 0.44 (0.21), residues: 616 sheet: 0.97 (0.44), residues: 157 loop : -0.64 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 201 HIS 0.004 0.001 HIS E 80 PHE 0.017 0.002 PHE C 246 TYR 0.034 0.001 TYR E 193 ARG 0.008 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 556 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 135 ARG cc_start: 0.7752 (ttt180) cc_final: 0.7544 (ttt90) REVERT: E 138 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8266 (ttpt) REVERT: E 194 ARG cc_start: 0.7203 (mtp-110) cc_final: 0.6770 (mtp-110) REVERT: E 308 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8246 (mt) REVERT: E 316 TYR cc_start: 0.7769 (m-10) cc_final: 0.7455 (m-10) REVERT: E 322 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: E 324 ILE cc_start: 0.7065 (OUTLIER) cc_final: 0.6771 (pp) REVERT: A 124 MET cc_start: 0.7692 (mmt) cc_final: 0.7442 (mmt) REVERT: A 175 ASN cc_start: 0.8018 (m-40) cc_final: 0.7748 (m-40) REVERT: A 187 LEU cc_start: 0.8341 (mm) cc_final: 0.8031 (mp) REVERT: A 212 LYS cc_start: 0.8368 (mmmm) cc_final: 0.8145 (mtpp) REVERT: A 246 PHE cc_start: 0.8442 (t80) cc_final: 0.8091 (t80) REVERT: A 248 HIS cc_start: 0.8690 (t-90) cc_final: 0.8392 (t-170) REVERT: A 353 GLU cc_start: 0.7351 (mp0) cc_final: 0.7144 (mp0) REVERT: B 157 GLU cc_start: 0.7473 (tt0) cc_final: 0.7157 (tp30) REVERT: B 193 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7334 (mt-10) REVERT: B 200 LYS cc_start: 0.8530 (mptt) cc_final: 0.8321 (mptt) REVERT: C 338 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.7392 (tmmt) REVERT: D 184 MET cc_start: 0.7774 (mpp) cc_final: 0.7406 (mpp) REVERT: D 353 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6958 (tm-30) outliers start: 28 outliers final: 11 residues processed: 572 average time/residue: 0.2924 time to fit residues: 226.1453 Evaluate side-chains 567 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 551 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 303 GLU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain D residue 331 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 139 optimal weight: 0.1980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 GLN E 253 ASN A 67 ASN ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN C 121 GLN C 123 ASN D 37 ASN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12586 Z= 0.152 Angle : 0.506 8.784 17047 Z= 0.266 Chirality : 0.041 0.149 1916 Planarity : 0.004 0.054 2192 Dihedral : 6.472 71.229 1721 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.56 % Allowed : 27.97 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.22), residues: 1520 helix: 0.62 (0.20), residues: 677 sheet: 1.51 (0.45), residues: 153 loop : -0.71 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.003 0.001 HIS A 84 PHE 0.016 0.001 PHE C 246 TYR 0.014 0.001 TYR E 233 ARG 0.010 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 556 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.3895 (OUTLIER) cc_final: 0.1464 (p90) REVERT: E 60 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6546 (pm20) REVERT: E 146 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7130 (tt) REVERT: E 297 ASN cc_start: 0.8324 (t0) cc_final: 0.7285 (t0) REVERT: E 300 LYS cc_start: 0.8000 (mttt) cc_final: 0.7682 (mttt) REVERT: E 308 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7844 (tt) REVERT: E 316 TYR cc_start: 0.7776 (m-10) cc_final: 0.7504 (m-10) REVERT: E 324 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6704 (pp) REVERT: A 103 TYR cc_start: 0.8706 (p90) cc_final: 0.8468 (p90) REVERT: A 124 MET cc_start: 0.7630 (mmt) cc_final: 0.7297 (mmt) REVERT: A 175 ASN cc_start: 0.8090 (m-40) cc_final: 0.7710 (m-40) REVERT: A 178 LYS cc_start: 0.7858 (mtmm) cc_final: 0.7425 (mtmm) REVERT: A 246 PHE cc_start: 0.8700 (t80) cc_final: 0.8428 (t80) REVERT: A 248 HIS cc_start: 0.8696 (t-90) cc_final: 0.8477 (t-170) REVERT: A 329 LYS cc_start: 0.6773 (mttt) cc_final: 0.6335 (mttt) REVERT: A 353 GLU cc_start: 0.7542 (mp0) cc_final: 0.7243 (mp0) REVERT: B 32 ARG cc_start: 0.7226 (ttp80) cc_final: 0.6974 (ttp80) REVERT: B 157 GLU cc_start: 0.7453 (tt0) cc_final: 0.7139 (tp30) REVERT: B 200 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8240 (mptt) REVERT: B 218 GLU cc_start: 0.7250 (mm-30) cc_final: 0.7017 (mm-30) REVERT: B 265 LEU cc_start: 0.8526 (mt) cc_final: 0.8324 (mp) REVERT: C 43 ARG cc_start: 0.7474 (tmm160) cc_final: 0.7080 (tmm160) REVERT: C 103 TYR cc_start: 0.8400 (p90) cc_final: 0.7935 (p90) REVERT: C 206 MET cc_start: 0.7757 (ttp) cc_final: 0.7501 (ttp) REVERT: C 215 ASN cc_start: 0.8210 (t0) cc_final: 0.7969 (t0) REVERT: C 354 THR cc_start: 0.7601 (p) cc_final: 0.7365 (p) REVERT: D 99 ILE cc_start: 0.7735 (tt) cc_final: 0.7419 (tp) REVERT: D 114 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6692 (mm-30) REVERT: D 116 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8419 (tt) REVERT: D 166 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5753 (mp) REVERT: D 179 PHE cc_start: 0.8625 (t80) cc_final: 0.8359 (t80) REVERT: D 192 MET cc_start: 0.7706 (ttm) cc_final: 0.7501 (ttm) REVERT: D 226 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8046 (tppp) REVERT: D 338 LYS cc_start: 0.7269 (pttm) cc_final: 0.7043 (pttm) outliers start: 61 outliers final: 27 residues processed: 582 average time/residue: 0.2777 time to fit residues: 221.1940 Evaluate side-chains 582 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 547 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 285 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 140 optimal weight: 0.4980 chunk 151 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 138 optimal weight: 0.0670 chunk 47 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 227 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 HIS C 123 ASN C 227 ASN C 292 ASN D 30 GLN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12586 Z= 0.173 Angle : 0.498 8.968 17047 Z= 0.260 Chirality : 0.042 0.168 1916 Planarity : 0.004 0.055 2192 Dihedral : 4.763 59.152 1689 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 5.39 % Allowed : 28.42 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1520 helix: 0.80 (0.20), residues: 676 sheet: 1.76 (0.44), residues: 153 loop : -0.76 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.006 0.001 HIS B 248 PHE 0.015 0.001 PHE B 246 TYR 0.019 0.001 TYR A 118 ARG 0.006 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 537 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.3985 (OUTLIER) cc_final: 0.1602 (p90) REVERT: E 60 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6454 (pm20) REVERT: E 231 LYS cc_start: 0.8204 (mtmm) cc_final: 0.7962 (mtmm) REVERT: E 297 ASN cc_start: 0.8382 (t0) cc_final: 0.7384 (t0) REVERT: E 300 LYS cc_start: 0.7951 (mttt) cc_final: 0.7625 (mttt) REVERT: E 308 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7811 (tt) REVERT: E 316 TYR cc_start: 0.7771 (m-10) cc_final: 0.7485 (m-10) REVERT: E 324 ILE cc_start: 0.7025 (OUTLIER) cc_final: 0.6728 (pp) REVERT: A 103 TYR cc_start: 0.8695 (p90) cc_final: 0.8475 (p90) REVERT: A 124 MET cc_start: 0.7664 (mmt) cc_final: 0.7361 (mmt) REVERT: A 175 ASN cc_start: 0.8049 (m-40) cc_final: 0.7739 (m-40) REVERT: A 178 LYS cc_start: 0.7911 (mtmm) cc_final: 0.7407 (mtmm) REVERT: A 184 MET cc_start: 0.7590 (mmm) cc_final: 0.7174 (mmt) REVERT: A 248 HIS cc_start: 0.8736 (t-90) cc_final: 0.8483 (t-170) REVERT: A 329 LYS cc_start: 0.6749 (mttt) cc_final: 0.6378 (mttt) REVERT: B 157 GLU cc_start: 0.7464 (tt0) cc_final: 0.7163 (tp30) REVERT: B 200 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8273 (mptt) REVERT: C 34 TYR cc_start: 0.7831 (t80) cc_final: 0.7414 (t80) REVERT: C 43 ARG cc_start: 0.7514 (tmm160) cc_final: 0.7018 (tmm160) REVERT: C 64 GLN cc_start: 0.7988 (tp40) cc_final: 0.7658 (tp40) REVERT: C 103 TYR cc_start: 0.8476 (p90) cc_final: 0.8033 (p90) REVERT: C 190 MET cc_start: 0.8389 (tpt) cc_final: 0.7662 (tpt) REVERT: C 199 VAL cc_start: 0.8892 (p) cc_final: 0.7955 (t) REVERT: C 201 TRP cc_start: 0.7181 (m-10) cc_final: 0.5970 (m-10) REVERT: C 206 MET cc_start: 0.7968 (ttt) cc_final: 0.7651 (ttp) REVERT: C 215 ASN cc_start: 0.8375 (t0) cc_final: 0.7945 (t0) REVERT: C 338 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7341 (tmmt) REVERT: C 354 THR cc_start: 0.7638 (p) cc_final: 0.7398 (p) REVERT: D 38 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7772 (mtp180) REVERT: D 99 ILE cc_start: 0.7826 (tt) cc_final: 0.7431 (tp) REVERT: D 114 GLU cc_start: 0.7396 (mm-30) cc_final: 0.6753 (mm-30) REVERT: D 116 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8481 (tt) REVERT: D 179 PHE cc_start: 0.8725 (t80) cc_final: 0.8456 (t80) REVERT: D 184 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7494 (mpp) REVERT: D 302 TYR cc_start: 0.8421 (m-80) cc_final: 0.7985 (m-10) REVERT: D 338 LYS cc_start: 0.7251 (pttm) cc_final: 0.6876 (pttm) outliers start: 72 outliers final: 38 residues processed: 558 average time/residue: 0.2863 time to fit residues: 218.2234 Evaluate side-chains 573 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 527 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 292 ASN Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 184 MET Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.2980 chunk 105 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 140 optimal weight: 0.0970 chunk 148 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN A 227 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12586 Z= 0.252 Angle : 0.530 9.652 17047 Z= 0.281 Chirality : 0.044 0.188 1916 Planarity : 0.004 0.063 2192 Dihedral : 4.865 58.438 1689 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.91 % Allowed : 28.65 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1520 helix: 0.85 (0.21), residues: 671 sheet: 1.63 (0.43), residues: 155 loop : -0.77 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 201 HIS 0.004 0.001 HIS E 310 PHE 0.016 0.002 PHE D 100 TYR 0.021 0.001 TYR E 233 ARG 0.005 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 551 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4161 (OUTLIER) cc_final: 0.1872 (p90) REVERT: E 194 ARG cc_start: 0.7206 (mtp-110) cc_final: 0.6707 (mtp-110) REVERT: E 197 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6798 (pm20) REVERT: E 241 LEU cc_start: 0.8470 (mm) cc_final: 0.8177 (mt) REVERT: E 297 ASN cc_start: 0.8448 (t0) cc_final: 0.8237 (t0) REVERT: E 308 LEU cc_start: 0.8227 (tp) cc_final: 0.7926 (tt) REVERT: E 316 TYR cc_start: 0.7729 (m-10) cc_final: 0.7388 (m-10) REVERT: E 322 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: E 324 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6806 (pp) REVERT: A 67 ASN cc_start: 0.8463 (t0) cc_final: 0.8104 (t0) REVERT: A 124 MET cc_start: 0.7707 (mmt) cc_final: 0.7425 (mmt) REVERT: A 175 ASN cc_start: 0.8087 (m-40) cc_final: 0.7750 (m-40) REVERT: A 178 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7435 (mtmm) REVERT: A 237 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8341 (t) REVERT: A 248 HIS cc_start: 0.8761 (t-90) cc_final: 0.8547 (t-170) REVERT: A 329 LYS cc_start: 0.6754 (mttt) cc_final: 0.6364 (mttt) REVERT: A 353 GLU cc_start: 0.7428 (mp0) cc_final: 0.7205 (mp0) REVERT: B 157 GLU cc_start: 0.7472 (tt0) cc_final: 0.7170 (tp30) REVERT: B 200 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8301 (mptt) REVERT: B 218 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7072 (mm-30) REVERT: C 34 TYR cc_start: 0.7834 (t80) cc_final: 0.7325 (t80) REVERT: C 43 ARG cc_start: 0.7480 (tmm160) cc_final: 0.6955 (tmm160) REVERT: C 64 GLN cc_start: 0.8004 (tp40) cc_final: 0.7653 (tp40) REVERT: C 215 ASN cc_start: 0.8438 (t0) cc_final: 0.8104 (t0) REVERT: C 338 LYS cc_start: 0.7702 (OUTLIER) cc_final: 0.7498 (tmmt) REVERT: C 354 THR cc_start: 0.7670 (p) cc_final: 0.7434 (p) REVERT: D 99 ILE cc_start: 0.7889 (tt) cc_final: 0.7518 (tp) REVERT: D 114 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6823 (mm-30) REVERT: D 116 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8512 (tt) REVERT: D 166 ILE cc_start: 0.6072 (OUTLIER) cc_final: 0.5793 (mp) REVERT: D 179 PHE cc_start: 0.8749 (t80) cc_final: 0.8252 (t80) REVERT: D 180 GLU cc_start: 0.8008 (tt0) cc_final: 0.7797 (tt0) REVERT: D 338 LYS cc_start: 0.7384 (pttm) cc_final: 0.6944 (pttm) outliers start: 79 outliers final: 44 residues processed: 579 average time/residue: 0.2828 time to fit residues: 222.9294 Evaluate side-chains 592 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 539 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 70 ILE Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 20.0000 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 127 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 141 HIS ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN D 37 ASN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12586 Z= 0.295 Angle : 0.554 7.659 17047 Z= 0.295 Chirality : 0.045 0.205 1916 Planarity : 0.004 0.062 2192 Dihedral : 4.445 49.702 1680 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.91 % Allowed : 28.95 % Favored : 65.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1520 helix: 0.81 (0.21), residues: 668 sheet: 1.20 (0.43), residues: 161 loop : -0.74 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 201 HIS 0.004 0.001 HIS D 122 PHE 0.017 0.002 PHE D 100 TYR 0.022 0.001 TYR E 233 ARG 0.004 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 555 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4126 (OUTLIER) cc_final: 0.2001 (p90) REVERT: E 60 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: E 194 ARG cc_start: 0.7205 (mtp-110) cc_final: 0.6753 (mtp-110) REVERT: E 197 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6834 (pm20) REVERT: E 241 LEU cc_start: 0.8456 (mm) cc_final: 0.8167 (mt) REVERT: E 297 ASN cc_start: 0.8498 (t0) cc_final: 0.8267 (t0) REVERT: E 308 LEU cc_start: 0.8219 (tp) cc_final: 0.7903 (tt) REVERT: E 316 TYR cc_start: 0.7756 (m-10) cc_final: 0.7365 (m-10) REVERT: E 324 ILE cc_start: 0.7162 (OUTLIER) cc_final: 0.6863 (pp) REVERT: A 124 MET cc_start: 0.7806 (mmt) cc_final: 0.7384 (mmt) REVERT: A 175 ASN cc_start: 0.8112 (m-40) cc_final: 0.7875 (m-40) REVERT: A 178 LYS cc_start: 0.8073 (mtmm) cc_final: 0.7490 (mtmm) REVERT: A 191 VAL cc_start: 0.8674 (t) cc_final: 0.8433 (p) REVERT: A 248 HIS cc_start: 0.8784 (t-90) cc_final: 0.8567 (t-170) REVERT: A 329 LYS cc_start: 0.6740 (mttt) cc_final: 0.6285 (mttt) REVERT: B 47 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 157 GLU cc_start: 0.7460 (tt0) cc_final: 0.7158 (tp30) REVERT: B 200 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8309 (mptt) REVERT: B 218 GLU cc_start: 0.7380 (mm-30) cc_final: 0.7103 (mm-30) REVERT: C 34 TYR cc_start: 0.7754 (t80) cc_final: 0.7366 (t80) REVERT: C 43 ARG cc_start: 0.7498 (tmm160) cc_final: 0.7014 (tmm160) REVERT: C 64 GLN cc_start: 0.7999 (tp40) cc_final: 0.7634 (tp40) REVERT: C 107 LEU cc_start: 0.8108 (mm) cc_final: 0.7768 (mp) REVERT: C 190 MET cc_start: 0.8794 (tpp) cc_final: 0.7879 (tpp) REVERT: C 201 TRP cc_start: 0.8184 (OUTLIER) cc_final: 0.7074 (m-10) REVERT: C 215 ASN cc_start: 0.8479 (t0) cc_final: 0.8061 (t0) REVERT: C 338 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7559 (tmmt) REVERT: C 354 THR cc_start: 0.7749 (p) cc_final: 0.7513 (p) REVERT: D 74 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8149 (mm) REVERT: D 114 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6827 (mm-30) REVERT: D 116 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8515 (tt) REVERT: D 166 ILE cc_start: 0.6089 (OUTLIER) cc_final: 0.5777 (mp) REVERT: D 179 PHE cc_start: 0.8686 (t80) cc_final: 0.8178 (t80) REVERT: D 213 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: D 338 LYS cc_start: 0.7473 (pttm) cc_final: 0.6980 (pttm) outliers start: 79 outliers final: 48 residues processed: 584 average time/residue: 0.2820 time to fit residues: 224.3421 Evaluate side-chains 615 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 556 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 251 LYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 75 GLU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 2.9990 chunk 134 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.0470 chunk 149 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 0.0030 overall best weight: 0.3488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 55 GLN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12586 Z= 0.130 Angle : 0.494 9.366 17047 Z= 0.252 Chirality : 0.041 0.198 1916 Planarity : 0.004 0.062 2192 Dihedral : 3.953 43.866 1680 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.64 % Allowed : 31.41 % Favored : 63.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.22), residues: 1520 helix: 0.90 (0.21), residues: 670 sheet: 1.87 (0.45), residues: 147 loop : -0.79 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 201 HIS 0.003 0.000 HIS B 248 PHE 0.012 0.001 PHE D 312 TYR 0.025 0.001 TYR A 118 ARG 0.004 0.000 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 542 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4106 (OUTLIER) cc_final: 0.1908 (p90) REVERT: E 60 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6160 (pm20) REVERT: E 194 ARG cc_start: 0.7210 (mtp-110) cc_final: 0.6718 (mtp-110) REVERT: E 197 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6759 (pm20) REVERT: E 308 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7855 (tt) REVERT: E 316 TYR cc_start: 0.7727 (m-10) cc_final: 0.7376 (m-10) REVERT: E 322 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7440 (mt-10) REVERT: E 324 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6839 (pp) REVERT: A 46 LEU cc_start: 0.8561 (mt) cc_final: 0.8299 (mp) REVERT: A 124 MET cc_start: 0.7681 (mmt) cc_final: 0.7337 (mmt) REVERT: A 175 ASN cc_start: 0.8049 (m-40) cc_final: 0.7764 (m-40) REVERT: A 178 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7477 (mtmm) REVERT: A 191 VAL cc_start: 0.8588 (t) cc_final: 0.8340 (p) REVERT: A 213 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 248 HIS cc_start: 0.8690 (t-90) cc_final: 0.8448 (t-170) REVERT: A 329 LYS cc_start: 0.6698 (mttt) cc_final: 0.6219 (mttt) REVERT: A 353 GLU cc_start: 0.7261 (mp0) cc_final: 0.7032 (mp0) REVERT: B 47 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7829 (tm-30) REVERT: B 157 GLU cc_start: 0.7451 (tt0) cc_final: 0.7124 (tp30) REVERT: B 212 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.8080 (tttp) REVERT: C 43 ARG cc_start: 0.7422 (tmm160) cc_final: 0.7003 (tmm160) REVERT: C 103 TYR cc_start: 0.8446 (p90) cc_final: 0.8139 (p90) REVERT: C 107 LEU cc_start: 0.8141 (mm) cc_final: 0.7805 (mp) REVERT: C 215 ASN cc_start: 0.8490 (t0) cc_final: 0.8077 (t0) REVERT: C 338 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7471 (tmmt) REVERT: C 345 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8495 (mp) REVERT: C 354 THR cc_start: 0.7596 (p) cc_final: 0.7353 (p) REVERT: D 38 ARG cc_start: 0.7999 (mtp180) cc_final: 0.7762 (mtp180) REVERT: D 103 TYR cc_start: 0.8396 (p90) cc_final: 0.7806 (p90) REVERT: D 114 GLU cc_start: 0.7427 (mm-30) cc_final: 0.6796 (mm-30) REVERT: D 166 ILE cc_start: 0.6105 (OUTLIER) cc_final: 0.5803 (mp) REVERT: D 174 GLU cc_start: 0.8164 (tt0) cc_final: 0.7716 (tt0) REVERT: D 179 PHE cc_start: 0.8657 (t80) cc_final: 0.8399 (t80) REVERT: D 180 GLU cc_start: 0.7958 (tt0) cc_final: 0.7748 (tt0) REVERT: D 213 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: D 226 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7982 (tppp) REVERT: D 302 TYR cc_start: 0.8332 (m-80) cc_final: 0.8020 (m-80) REVERT: D 338 LYS cc_start: 0.7387 (pttm) cc_final: 0.6950 (pttm) outliers start: 62 outliers final: 36 residues processed: 569 average time/residue: 0.2779 time to fit residues: 217.0330 Evaluate side-chains 585 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 538 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 138 LYS Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 285 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN C 121 GLN C 123 ASN D 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12586 Z= 0.356 Angle : 0.593 6.561 17047 Z= 0.317 Chirality : 0.046 0.235 1916 Planarity : 0.004 0.063 2192 Dihedral : 4.421 32.557 1680 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.94 % Allowed : 30.67 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1520 helix: 0.79 (0.21), residues: 674 sheet: 1.59 (0.44), residues: 151 loop : -0.81 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 201 HIS 0.005 0.001 HIS D 122 PHE 0.019 0.002 PHE B 232 TYR 0.025 0.002 TYR E 233 ARG 0.006 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 574 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 25 TYR cc_start: 0.4075 (OUTLIER) cc_final: 0.2096 (p90) REVERT: E 60 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6356 (pm20) REVERT: E 150 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8590 (tt) REVERT: E 194 ARG cc_start: 0.7218 (mtp-110) cc_final: 0.6762 (mtp-110) REVERT: E 197 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: E 308 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7901 (tt) REVERT: E 316 TYR cc_start: 0.7771 (m-10) cc_final: 0.7445 (m-10) REVERT: E 322 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: E 324 ILE cc_start: 0.7165 (OUTLIER) cc_final: 0.6866 (pp) REVERT: A 67 ASN cc_start: 0.8573 (t0) cc_final: 0.8175 (t0) REVERT: A 121 GLN cc_start: 0.7820 (tt0) cc_final: 0.7539 (tt0) REVERT: A 124 MET cc_start: 0.7869 (mmt) cc_final: 0.7396 (mmt) REVERT: A 175 ASN cc_start: 0.8114 (m-40) cc_final: 0.7899 (m-40) REVERT: A 178 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7583 (mtmm) REVERT: A 191 VAL cc_start: 0.8645 (t) cc_final: 0.8410 (p) REVERT: A 248 HIS cc_start: 0.8803 (t-90) cc_final: 0.8602 (t-170) REVERT: A 281 LEU cc_start: 0.8147 (mp) cc_final: 0.7897 (mt) REVERT: A 312 PHE cc_start: 0.8758 (p90) cc_final: 0.8519 (p90) REVERT: A 329 LYS cc_start: 0.6645 (mttt) cc_final: 0.6291 (mttt) REVERT: B 47 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7897 (tm-30) REVERT: B 157 GLU cc_start: 0.7458 (tt0) cc_final: 0.7151 (tp30) REVERT: C 43 ARG cc_start: 0.7519 (tmm160) cc_final: 0.7076 (tmm160) REVERT: C 64 GLN cc_start: 0.8009 (tp40) cc_final: 0.7649 (tp40) REVERT: C 107 LEU cc_start: 0.8096 (mm) cc_final: 0.7758 (mp) REVERT: C 136 GLU cc_start: 0.7491 (tm-30) cc_final: 0.6970 (tm-30) REVERT: C 160 GLU cc_start: 0.8070 (tp30) cc_final: 0.7665 (tp30) REVERT: C 190 MET cc_start: 0.8735 (tpp) cc_final: 0.7802 (tpp) REVERT: C 201 TRP cc_start: 0.8099 (OUTLIER) cc_final: 0.7209 (m-10) REVERT: C 215 ASN cc_start: 0.8524 (t0) cc_final: 0.8075 (t0) REVERT: C 225 GLN cc_start: 0.8115 (pp30) cc_final: 0.7870 (pp30) REVERT: C 256 VAL cc_start: 0.8620 (t) cc_final: 0.8359 (p) REVERT: C 338 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7574 (tmmt) REVERT: C 345 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8516 (mp) REVERT: D 114 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6841 (mm-30) REVERT: D 116 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8527 (tt) REVERT: D 166 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5770 (mp) REVERT: D 180 GLU cc_start: 0.8096 (tt0) cc_final: 0.7858 (tt0) REVERT: D 213 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6759 (mp0) REVERT: D 338 LYS cc_start: 0.7526 (pttm) cc_final: 0.7019 (pttm) outliers start: 66 outliers final: 42 residues processed: 603 average time/residue: 0.2787 time to fit residues: 229.4369 Evaluate side-chains 627 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 572 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 295 THR Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 237 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 212 LYS Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 123 ASN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 310 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12586 Z= 0.213 Angle : 0.544 8.826 17047 Z= 0.283 Chirality : 0.043 0.213 1916 Planarity : 0.004 0.062 2192 Dihedral : 4.157 24.775 1680 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.56 % Allowed : 32.09 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1520 helix: 0.81 (0.21), residues: 662 sheet: 1.61 (0.44), residues: 151 loop : -0.85 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 201 HIS 0.003 0.001 HIS B 248 PHE 0.014 0.001 PHE D 312 TYR 0.023 0.001 TYR A 118 ARG 0.006 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 563 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6152 (pm20) REVERT: E 194 ARG cc_start: 0.7202 (mtp-110) cc_final: 0.6747 (mtp-110) REVERT: E 197 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6810 (pm20) REVERT: E 308 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7907 (tt) REVERT: E 316 TYR cc_start: 0.7757 (m-10) cc_final: 0.7416 (m-10) REVERT: E 322 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7388 (mt-10) REVERT: A 67 ASN cc_start: 0.8487 (t0) cc_final: 0.8088 (t0) REVERT: A 121 GLN cc_start: 0.7772 (tt0) cc_final: 0.7457 (tt0) REVERT: A 124 MET cc_start: 0.7835 (mmt) cc_final: 0.7364 (mmt) REVERT: A 147 TYR cc_start: 0.7720 (m-10) cc_final: 0.7473 (m-10) REVERT: A 156 LYS cc_start: 0.7729 (tttm) cc_final: 0.7353 (tttm) REVERT: A 175 ASN cc_start: 0.8078 (m-40) cc_final: 0.7868 (m-40) REVERT: A 178 LYS cc_start: 0.8112 (mtmm) cc_final: 0.7550 (mtmm) REVERT: A 191 VAL cc_start: 0.8612 (t) cc_final: 0.8378 (p) REVERT: A 213 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7561 (mm-30) REVERT: A 248 HIS cc_start: 0.8754 (t-90) cc_final: 0.8542 (t-170) REVERT: A 281 LEU cc_start: 0.8100 (mp) cc_final: 0.7862 (mt) REVERT: A 329 LYS cc_start: 0.6600 (mttt) cc_final: 0.6156 (mttt) REVERT: A 353 GLU cc_start: 0.7398 (mp0) cc_final: 0.6863 (mp0) REVERT: B 47 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7854 (tm-30) REVERT: B 157 GLU cc_start: 0.7438 (tt0) cc_final: 0.7134 (tp30) REVERT: C 43 ARG cc_start: 0.7481 (tmm160) cc_final: 0.7025 (tmm160) REVERT: C 64 GLN cc_start: 0.8008 (tp40) cc_final: 0.7683 (tp40) REVERT: C 107 LEU cc_start: 0.8116 (mm) cc_final: 0.7786 (mp) REVERT: C 136 GLU cc_start: 0.7458 (tm-30) cc_final: 0.6971 (tm-30) REVERT: C 160 GLU cc_start: 0.8059 (tp30) cc_final: 0.7653 (tp30) REVERT: C 190 MET cc_start: 0.8724 (tpp) cc_final: 0.7747 (tpp) REVERT: C 201 TRP cc_start: 0.7958 (OUTLIER) cc_final: 0.6788 (m-10) REVERT: C 215 ASN cc_start: 0.8510 (t0) cc_final: 0.8066 (t0) REVERT: C 256 VAL cc_start: 0.8587 (t) cc_final: 0.8332 (p) REVERT: C 338 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7545 (tmmt) REVERT: C 345 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8524 (mp) REVERT: C 354 THR cc_start: 0.7622 (p) cc_final: 0.7400 (p) REVERT: D 109 SER cc_start: 0.7807 (p) cc_final: 0.7310 (t) REVERT: D 114 GLU cc_start: 0.7472 (mm-30) cc_final: 0.6814 (mm-30) REVERT: D 124 MET cc_start: 0.7471 (mmm) cc_final: 0.7269 (mmm) REVERT: D 137 GLU cc_start: 0.7694 (tp30) cc_final: 0.7233 (tt0) REVERT: D 166 ILE cc_start: 0.6099 (OUTLIER) cc_final: 0.5765 (mp) REVERT: D 180 GLU cc_start: 0.7985 (tt0) cc_final: 0.7718 (tt0) REVERT: D 213 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: D 338 LYS cc_start: 0.7492 (pttm) cc_final: 0.6957 (pttm) outliers start: 61 outliers final: 42 residues processed: 586 average time/residue: 0.2779 time to fit residues: 224.2760 Evaluate side-chains 609 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 558 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12586 Z= 0.220 Angle : 0.540 7.431 17047 Z= 0.283 Chirality : 0.043 0.238 1916 Planarity : 0.004 0.061 2192 Dihedral : 4.099 25.333 1679 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.64 % Allowed : 31.56 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1520 helix: 0.83 (0.21), residues: 665 sheet: 1.58 (0.44), residues: 151 loop : -0.85 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 201 HIS 0.004 0.001 HIS B 248 PHE 0.013 0.001 PHE D 312 TYR 0.025 0.001 TYR A 118 ARG 0.005 0.000 ARG A 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 562 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 GLU cc_start: 0.6678 (OUTLIER) cc_final: 0.6256 (pm20) REVERT: E 194 ARG cc_start: 0.7209 (mtp-110) cc_final: 0.6730 (mtp-110) REVERT: E 197 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6820 (pm20) REVERT: E 308 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7903 (tt) REVERT: E 316 TYR cc_start: 0.7758 (m-10) cc_final: 0.7425 (m-10) REVERT: E 322 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: A 67 ASN cc_start: 0.8492 (t0) cc_final: 0.8109 (t0) REVERT: A 124 MET cc_start: 0.7853 (mmt) cc_final: 0.7371 (mmt) REVERT: A 147 TYR cc_start: 0.7727 (m-10) cc_final: 0.7480 (m-10) REVERT: A 156 LYS cc_start: 0.7731 (tttm) cc_final: 0.7359 (tttm) REVERT: A 175 ASN cc_start: 0.8092 (m-40) cc_final: 0.7886 (m-40) REVERT: A 178 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7566 (mtmm) REVERT: A 213 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7581 (mm-30) REVERT: A 248 HIS cc_start: 0.8744 (t-90) cc_final: 0.8542 (t-170) REVERT: A 281 LEU cc_start: 0.8119 (mp) cc_final: 0.7878 (mt) REVERT: A 329 LYS cc_start: 0.6593 (mttt) cc_final: 0.6146 (mttt) REVERT: A 353 GLU cc_start: 0.7390 (mp0) cc_final: 0.6861 (mp0) REVERT: B 47 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7837 (tm-30) REVERT: B 157 GLU cc_start: 0.7443 (tt0) cc_final: 0.7140 (tp30) REVERT: C 43 ARG cc_start: 0.7473 (tmm160) cc_final: 0.7024 (tmm160) REVERT: C 64 GLN cc_start: 0.8012 (tp40) cc_final: 0.7686 (tp40) REVERT: C 107 LEU cc_start: 0.8106 (mm) cc_final: 0.7789 (mp) REVERT: C 160 GLU cc_start: 0.8064 (tp30) cc_final: 0.7663 (tp30) REVERT: C 190 MET cc_start: 0.8754 (tpp) cc_final: 0.7823 (tpp) REVERT: C 201 TRP cc_start: 0.7956 (OUTLIER) cc_final: 0.6800 (m-10) REVERT: C 215 ASN cc_start: 0.8506 (t0) cc_final: 0.8054 (t0) REVERT: C 256 VAL cc_start: 0.8594 (t) cc_final: 0.8332 (p) REVERT: C 338 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7558 (tmmt) REVERT: C 354 THR cc_start: 0.7591 (p) cc_final: 0.7370 (p) REVERT: D 109 SER cc_start: 0.7843 (p) cc_final: 0.7321 (t) REVERT: D 114 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6808 (mm-30) REVERT: D 116 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8461 (tt) REVERT: D 137 GLU cc_start: 0.7706 (tp30) cc_final: 0.7216 (tt0) REVERT: D 166 ILE cc_start: 0.6098 (OUTLIER) cc_final: 0.5775 (mp) REVERT: D 174 GLU cc_start: 0.8206 (tt0) cc_final: 0.7758 (tt0) REVERT: D 180 GLU cc_start: 0.8021 (tt0) cc_final: 0.7728 (tt0) REVERT: D 213 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: D 338 LYS cc_start: 0.7487 (pttm) cc_final: 0.6930 (pttm) outliers start: 62 outliers final: 46 residues processed: 586 average time/residue: 0.2809 time to fit residues: 224.8947 Evaluate side-chains 616 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 561 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 296 MET Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 153 optimal weight: 0.6980 chunk 141 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 97 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN D 194 GLN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 ASN D 310 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12586 Z= 0.272 Angle : 0.568 8.303 17047 Z= 0.298 Chirality : 0.044 0.248 1916 Planarity : 0.004 0.063 2192 Dihedral : 4.206 25.658 1679 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.94 % Allowed : 31.71 % Favored : 63.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1520 helix: 0.73 (0.21), residues: 665 sheet: 1.52 (0.44), residues: 151 loop : -0.87 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 201 HIS 0.004 0.001 HIS B 248 PHE 0.014 0.002 PHE C 179 TYR 0.022 0.001 TYR A 118 ARG 0.005 0.000 ARG A 117 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 560 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 60 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6275 (pm20) REVERT: E 150 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8580 (tt) REVERT: E 308 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7917 (tt) REVERT: E 316 TYR cc_start: 0.7758 (m-10) cc_final: 0.7434 (m-10) REVERT: E 322 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7355 (mt-10) REVERT: A 67 ASN cc_start: 0.8526 (t0) cc_final: 0.8130 (t0) REVERT: A 124 MET cc_start: 0.7882 (mmt) cc_final: 0.7404 (mmt) REVERT: A 147 TYR cc_start: 0.7731 (m-10) cc_final: 0.7485 (m-10) REVERT: A 156 LYS cc_start: 0.7791 (tttm) cc_final: 0.7420 (tttm) REVERT: A 175 ASN cc_start: 0.8106 (m-40) cc_final: 0.7896 (m-40) REVERT: A 178 LYS cc_start: 0.8128 (mtmm) cc_final: 0.7570 (mtmm) REVERT: A 191 VAL cc_start: 0.8618 (t) cc_final: 0.8390 (p) REVERT: A 213 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 248 HIS cc_start: 0.8784 (t-90) cc_final: 0.8571 (t-170) REVERT: A 281 LEU cc_start: 0.8147 (mp) cc_final: 0.7901 (mt) REVERT: A 329 LYS cc_start: 0.6583 (mttt) cc_final: 0.6139 (mttt) REVERT: A 353 GLU cc_start: 0.7396 (mp0) cc_final: 0.6889 (mp0) REVERT: B 47 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7828 (tm-30) REVERT: B 157 GLU cc_start: 0.7440 (tt0) cc_final: 0.7139 (tp30) REVERT: B 201 TRP cc_start: 0.8227 (m100) cc_final: 0.7628 (m-10) REVERT: B 247 PHE cc_start: 0.8914 (m-80) cc_final: 0.8638 (m-80) REVERT: B 264 ARG cc_start: 0.7946 (mtp-110) cc_final: 0.7553 (mtp85) REVERT: C 43 ARG cc_start: 0.7495 (tmm160) cc_final: 0.7035 (tmm160) REVERT: C 64 GLN cc_start: 0.8019 (tp40) cc_final: 0.7666 (tp40) REVERT: C 107 LEU cc_start: 0.8110 (mm) cc_final: 0.7783 (mp) REVERT: C 160 GLU cc_start: 0.8068 (tp30) cc_final: 0.7667 (tp30) REVERT: C 190 MET cc_start: 0.8769 (tpp) cc_final: 0.7816 (tpp) REVERT: C 201 TRP cc_start: 0.7992 (OUTLIER) cc_final: 0.6967 (m-10) REVERT: C 215 ASN cc_start: 0.8509 (t0) cc_final: 0.8054 (t0) REVERT: C 256 VAL cc_start: 0.8607 (t) cc_final: 0.8331 (p) REVERT: C 308 THR cc_start: 0.8440 (t) cc_final: 0.8181 (m) REVERT: C 338 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7567 (tmmt) REVERT: D 109 SER cc_start: 0.7844 (p) cc_final: 0.7337 (t) REVERT: D 114 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6818 (mm-30) REVERT: D 116 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8473 (tt) REVERT: D 137 GLU cc_start: 0.7726 (tp30) cc_final: 0.7237 (tt0) REVERT: D 166 ILE cc_start: 0.6101 (OUTLIER) cc_final: 0.5771 (mp) REVERT: D 174 GLU cc_start: 0.8194 (tt0) cc_final: 0.7752 (tt0) REVERT: D 180 GLU cc_start: 0.8012 (tt0) cc_final: 0.7733 (tt0) REVERT: D 213 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: D 338 LYS cc_start: 0.7514 (pttm) cc_final: 0.6942 (pttm) outliers start: 66 outliers final: 52 residues processed: 583 average time/residue: 0.2900 time to fit residues: 231.7984 Evaluate side-chains 622 residues out of total 1337 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 561 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 73 LYS Chi-restraints excluded: chain E residue 115 LEU Chi-restraints excluded: chain E residue 150 LEU Chi-restraints excluded: chain E residue 221 MET Chi-restraints excluded: chain E residue 236 GLN Chi-restraints excluded: chain E residue 239 HIS Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 212 LYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 69 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 194 GLN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 201 TRP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain C residue 338 LYS Chi-restraints excluded: chain C residue 344 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 178 LYS Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 245 ILE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 296 MET Chi-restraints excluded: chain D residue 358 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 GLN C 123 ASN ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 ASN D 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.108103 restraints weight = 19687.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.112303 restraints weight = 8912.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.115090 restraints weight = 5039.882| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12586 Z= 0.191 Angle : 0.544 12.811 17047 Z= 0.280 Chirality : 0.043 0.220 1916 Planarity : 0.004 0.061 2192 Dihedral : 4.051 25.933 1679 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.56 % Allowed : 32.16 % Favored : 63.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1520 helix: 0.82 (0.21), residues: 660 sheet: 1.54 (0.44), residues: 151 loop : -0.84 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 201 HIS 0.004 0.001 HIS B 248 PHE 0.014 0.001 PHE D 312 TYR 0.024 0.001 TYR A 118 ARG 0.004 0.000 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3930.67 seconds wall clock time: 71 minutes 31.32 seconds (4291.32 seconds total)