Starting phenix.real_space_refine on Mon Apr 8 21:30:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osg_17152/04_2024/8osg_17152_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osg_17152/04_2024/8osg_17152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osg_17152/04_2024/8osg_17152.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osg_17152/04_2024/8osg_17152.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osg_17152/04_2024/8osg_17152_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osg_17152/04_2024/8osg_17152_updated.pdb" } resolution = 3.8 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= 0.001 sd= 0.019 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 51 5.16 5 C 9147 2.51 5 N 2517 2.21 5 O 2801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ASP 332": "OD1" <-> "OD2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B GLU 88": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "D ASP 332": "OD1" <-> "OD2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 48": "OD1" <-> "OD2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ASP 159": "OD1" <-> "OD2" Residue "F ASP 160": "OD1" <-> "OD2" Residue "F PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 344": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14536 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2214 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 15, 'TRANS': 267} Chain breaks: 4 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2529 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 19, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2529 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 19, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2529 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 19, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2529 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 19, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 2024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2024 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 11, 'TRANS': 246} Chain breaks: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.77, per 1000 atoms: 0.53 Number of scatterers: 14536 At special positions: 0 Unit cell: (130.284, 138.6, 79.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 16 15.00 Mg 4 11.99 O 2801 8.00 N 2517 7.00 C 9147 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 - 3.50 Amino acid : False - 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: 5.94 Conformation dependent library (CDL) restraints added in 2.6 seconds 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 83 helices and 14 sheets defined 42.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.968A pdb=" N ILE A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASP A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 162 through 169 Processing helix chain 'A' and resid 207 through 210 removed outlier: 3.887A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 210' Processing helix chain 'A' and resid 223 through 238 removed outlier: 3.608A pdb=" N GLN A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 267 removed outlier: 3.587A pdb=" N LEU A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS A 263 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Proline residue: A 266 - end of helix Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 296 through 306 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.688A pdb=" N VAL A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.525A pdb=" N ARG A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N HIS A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG A 328 " --> pdb=" O CYS A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 328' Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.864A pdb=" N VAL A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 27 through 36 Processing helix chain 'B' and resid 53 through 61 removed outlier: 4.175A pdb=" N ILE B 57 " --> pdb=" O LYS B 53 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 61 " --> pdb=" O ILE B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 141 through 144 No H-bonds generated for 'chain 'B' and resid 141 through 144' Processing helix chain 'B' and resid 165 through 169 removed outlier: 3.663A pdb=" N ASP B 168 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER B 169 " --> pdb=" O LEU B 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 165 through 169' Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.688A pdb=" N ASP B 209 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ARG B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 205 through 210' Processing helix chain 'B' and resid 223 through 238 removed outlier: 4.534A pdb=" N VAL B 227 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 267 Proline residue: B 249 - end of helix removed outlier: 3.804A pdb=" N ALA B 253 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LYS B 256 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Proline residue: B 266 - end of helix Processing helix chain 'B' and resid 272 through 285 removed outlier: 3.504A pdb=" N VAL B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.827A pdb=" N VAL B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 328 removed outlier: 3.673A pdb=" N VAL B 320 " --> pdb=" O ASP B 316 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR B 322 " --> pdb=" O ARG B 318 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 325 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 326 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N HIS B 327 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ARG B 328 " --> pdb=" O CYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 350 Processing helix chain 'C' and resid 25 through 36 removed outlier: 3.709A pdb=" N ALA C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU C 31 " --> pdb=" O MET C 27 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 32 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 62 removed outlier: 3.833A pdb=" N ILE C 57 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU C 60 " --> pdb=" O THR C 56 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA C 61 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP C 62 " --> pdb=" O ARG C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.675A pdb=" N VAL C 120 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N CYS C 121 " --> pdb=" O ASP C 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 117 through 121' Processing helix chain 'C' and resid 141 through 145 Processing helix chain 'C' and resid 207 through 210 No H-bonds generated for 'chain 'C' and resid 207 through 210' Processing helix chain 'C' and resid 223 through 238 Processing helix chain 'C' and resid 249 through 261 removed outlier: 3.617A pdb=" N ALA C 253 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 267 No H-bonds generated for 'chain 'C' and resid 265 through 267' Processing helix chain 'C' and resid 272 through 285 removed outlier: 3.726A pdb=" N VAL C 276 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 4.161A pdb=" N LYS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 351 removed outlier: 3.541A pdb=" N GLU C 344 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 27 through 36 removed outlier: 4.085A pdb=" N LEU D 31 " --> pdb=" O MET D 27 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 59 removed outlier: 4.021A pdb=" N ILE D 57 " --> pdb=" O LYS D 53 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 92 No H-bonds generated for 'chain 'D' and resid 89 through 92' Processing helix chain 'D' and resid 117 through 120 No H-bonds generated for 'chain 'D' and resid 117 through 120' Processing helix chain 'D' and resid 142 through 145 Processing helix chain 'D' and resid 162 through 169 removed outlier: 3.765A pdb=" N LEU D 166 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP D 168 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER D 169 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 223 through 238 Processing helix chain 'D' and resid 240 through 246 removed outlier: 3.791A pdb=" N LEU D 244 " --> pdb=" O PRO D 240 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS D 246 " --> pdb=" O THR D 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 240 through 246' Processing helix chain 'D' and resid 248 through 261 removed outlier: 3.739A pdb=" N VAL D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 272 through 284 removed outlier: 3.599A pdb=" N VAL D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N CYS D 282 " --> pdb=" O ILE D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 307 removed outlier: 3.719A pdb=" N LYS D 301 " --> pdb=" O ASN D 297 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 321 No H-bonds generated for 'chain 'D' and resid 318 through 321' Processing helix chain 'D' and resid 341 through 350 Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 25 through 36 Processing helix chain 'E' and resid 53 through 60 removed outlier: 4.133A pdb=" N ILE E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU E 60 " --> pdb=" O THR E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 87 through 90 No H-bonds generated for 'chain 'E' and resid 87 through 90' Processing helix chain 'E' and resid 117 through 120 No H-bonds generated for 'chain 'E' and resid 117 through 120' Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 160 through 169 removed outlier: 4.269A pdb=" N VAL E 165 " --> pdb=" O HIS E 161 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU E 167 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP E 168 " --> pdb=" O ASP E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 223 through 238 Processing helix chain 'E' and resid 240 through 256 removed outlier: 3.526A pdb=" N GLU E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS E 246 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR E 247 " --> pdb=" O PHE E 243 " (cutoff:3.500A) Proline residue: E 249 - end of helix removed outlier: 3.902A pdb=" N ALA E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 254 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 267 Proline residue: E 266 - end of helix Processing helix chain 'E' and resid 272 through 284 removed outlier: 3.567A pdb=" N LYS E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 307 removed outlier: 3.665A pdb=" N ALA E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS E 301 " --> pdb=" O ASN E 297 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA E 302 " --> pdb=" O ARG E 298 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR E 304 " --> pdb=" O ALA E 300 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA E 305 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR E 306 " --> pdb=" O ALA E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 318 removed outlier: 3.547A pdb=" N ARG E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 314 through 318' Processing helix chain 'E' and resid 321 through 324 No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 339 through 351 Processing helix chain 'F' and resid 26 through 36 removed outlier: 3.578A pdb=" N ALA F 30 " --> pdb=" O GLU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 61 removed outlier: 3.637A pdb=" N ILE F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 58 " --> pdb=" O SER F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 169 Processing helix chain 'F' and resid 205 through 208 No H-bonds generated for 'chain 'F' and resid 205 through 208' Processing helix chain 'F' and resid 223 through 238 Processing helix chain 'F' and resid 241 through 262 removed outlier: 3.797A pdb=" N GLU F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS F 246 " --> pdb=" O THR F 242 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR F 247 " --> pdb=" O PHE F 243 " (cutoff:3.500A) Proline residue: F 249 - end of helix removed outlier: 4.007A pdb=" N THR F 252 " --> pdb=" O ASN F 248 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA F 253 " --> pdb=" O PRO F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 284 Processing helix chain 'F' and resid 291 through 307 removed outlier: 4.048A pdb=" N LYS F 301 " --> pdb=" O ASN F 297 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA F 302 " --> pdb=" O ARG F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 324 removed outlier: 3.709A pdb=" N ARG F 319 " --> pdb=" O ASP F 315 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL F 320 " --> pdb=" O ASP F 316 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR F 322 " --> pdb=" O ARG F 318 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU F 323 " --> pdb=" O ARG F 319 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS F 324 " --> pdb=" O VAL F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 351 Processing sheet with id= A, first strand: chain 'A' and resid 108 through 110 removed outlier: 6.329A pdb=" N ILE A 149 " --> pdb=" O VAL A 109 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.250A pdb=" N ILE B 149 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU B 111 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N TYR B 151 " --> pdb=" O LEU B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 174 through 179 removed outlier: 3.862A pdb=" N VAL B 177 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 184 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 179 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 43 through 46 removed outlier: 6.668A pdb=" N MET C 213 " --> pdb=" O MET C 44 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N MET C 46 " --> pdb=" O MET C 213 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA C 215 " --> pdb=" O MET C 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 108 through 110 removed outlier: 6.147A pdb=" N ILE C 149 " --> pdb=" O VAL C 109 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 175 through 177 removed outlier: 3.650A pdb=" N ILE C 184 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 213 through 217 removed outlier: 3.508A pdb=" N ALA D 215 " --> pdb=" O MET D 44 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET D 46 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 217 " --> pdb=" O MET D 46 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLY D 194 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N GLY D 47 " --> pdb=" O GLY D 194 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY D 196 " --> pdb=" O GLY D 47 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 66 through 70 Processing sheet with id= I, first strand: chain 'D' and resid 108 through 111 removed outlier: 6.223A pdb=" N ILE D 149 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU D 111 " --> pdb=" O ILE D 149 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N TYR D 151 " --> pdb=" O LEU D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 174 through 177 removed outlier: 3.700A pdb=" N VAL D 177 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 184 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 43 through 47 removed outlier: 6.873A pdb=" N MET E 213 " --> pdb=" O MET E 44 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N MET E 46 " --> pdb=" O MET E 213 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA E 215 " --> pdb=" O MET E 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 66 through 70 removed outlier: 3.728A pdb=" N LYS E 104 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL E 69 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU E 102 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 108 through 111 removed outlier: 6.139A pdb=" N ILE E 149 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU E 111 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR E 151 " --> pdb=" O LEU E 111 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'F' and resid 192 through 196 removed outlier: 3.831A pdb=" N ILE F 45 " --> pdb=" O GLY F 194 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET F 213 " --> pdb=" O MET F 44 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N MET F 46 " --> pdb=" O MET F 213 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA F 215 " --> pdb=" O MET F 46 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 984 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: 3.56 Time building geometry restraints manager: 6.36 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: 3953 1.33 - 1.45: 2068 1.45 - 1.57: 8624 1.57 - 1.69: 26 1.69 - 1.81: 85 Bond restraints: 14756 Sorted by residual: bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" C5 ADP F 401 " pdb=" C6 ADP F 401 " ideal model delta sigma weight residual 1.490 1.404 0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.66e+01 bond pdb=" N ASP E 78 " pdb=" CA ASP E 78 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.64e+01 bond pdb=" N ASN A 197 " pdb=" CA ASN A 197 " ideal model delta sigma weight residual 1.457 1.488 -0.031 9.10e-03 1.21e+04 1.19e+01 ... (remaining 14751 not shown) Histogram of bond angle deviations from ideal: 100.45 - 108.31: 682 108.31 - 116.18: 9452 116.18 - 124.04: 9468 124.04 - 131.91: 383 131.91 - 139.77: 18 Bond angle restraints: 20003 Sorted by residual: angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 128.57 11.30 1.00e+00 1.00e+00 1.28e+02 angle pdb=" PA ATP E 401 " pdb=" O3A ATP E 401 " pdb=" PB ATP E 401 " ideal model delta sigma weight residual 136.83 129.97 6.86 1.00e+00 1.00e+00 4.71e+01 angle pdb=" CA GLY E 42 " pdb=" C GLY E 42 " pdb=" O GLY E 42 " ideal model delta sigma weight residual 122.52 118.27 4.25 7.90e-01 1.60e+00 2.90e+01 angle pdb=" C LEU E 203 " pdb=" CA LEU E 203 " pdb=" CB LEU E 203 " ideal model delta sigma weight residual 116.54 110.49 6.05 1.15e+00 7.56e-01 2.77e+01 angle pdb=" CA MET B 44 " pdb=" CB MET B 44 " pdb=" CG MET B 44 " ideal model delta sigma weight residual 114.10 123.39 -9.29 2.00e+00 2.50e-01 2.16e+01 ... (remaining 19998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.32: 8539 30.32 - 60.64: 591 60.64 - 90.96: 41 90.96 - 121.28: 3 121.28 - 151.60: 2 Dihedral angle restraints: 9176 sinusoidal: 3911 harmonic: 5265 Sorted by residual: dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 148.40 151.60 1 2.00e+01 2.50e-03 4.51e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.34 -145.34 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O2A ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PA ADP F 401 " pdb=" PB ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 56.39 -116.39 1 2.00e+01 2.50e-03 3.47e+01 ... (remaining 9173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1714 0.043 - 0.086: 446 0.086 - 0.129: 158 0.129 - 0.173: 16 0.173 - 0.216: 4 Chirality restraints: 2338 Sorted by residual: chirality pdb=" CA MET D 44 " pdb=" N MET D 44 " pdb=" C MET D 44 " pdb=" CB MET D 44 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LEU F 167 " pdb=" N LEU F 167 " pdb=" C LEU F 167 " pdb=" CB LEU F 167 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.78e-01 chirality pdb=" CA ILE D 337 " pdb=" N ILE D 337 " pdb=" C ILE D 337 " pdb=" CB ILE D 337 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 2335 not shown) Planarity restraints: 2579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 208 " -0.016 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C LEU F 208 " 0.057 2.00e-02 2.50e+03 pdb=" O LEU F 208 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP F 209 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 240 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO A 241 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 241 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 241 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 239 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO F 240 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO F 240 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 240 " 0.022 5.00e-02 4.00e+02 ... (remaining 2576 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 151 2.59 - 3.17: 12037 3.17 - 3.74: 21337 3.74 - 4.32: 26644 4.32 - 4.90: 43717 Nonbonded interactions: 103886 Sorted by model distance: nonbonded pdb=" O2B ATP D 401 " pdb="MG MG D 402 " model vdw 2.009 2.170 nonbonded pdb=" OD1 ASP B 87 " pdb=" N GLU B 88 " model vdw 2.115 2.520 nonbonded pdb=" CB SER B 54 " pdb="MG MG B 401 " model vdw 2.131 2.570 nonbonded pdb=" O SER E 279 " pdb=" OG SER E 283 " model vdw 2.161 2.440 nonbonded pdb=" O VAL F 165 " pdb=" OG SER F 169 " model vdw 2.198 2.440 ... (remaining 103881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 65 or resid 103 through 104 or resid 108 throug \ h 111 or resid 142 through 173 or resid 188 through 353)) selection = (chain 'B' and (resid 14 through 65 or resid 103 through 104 or resid 108 throug \ h 111 or resid 142 through 173 or resid 188 through 353)) selection = (chain 'C' and (resid 14 through 65 or resid 103 through 104 or resid 108 throug \ h 111 or resid 142 through 173 or resid 188 through 353)) selection = (chain 'D' and (resid 14 through 65 or resid 103 through 104 or resid 108 throug \ h 111 or resid 142 through 173 or resid 188 through 353)) selection = (chain 'E' and (resid 14 through 65 or resid 103 through 104 or resid 108 throug \ h 111 or resid 142 through 173 or resid 188 through 353)) selection = (chain 'F' and (resid 14 through 65 or resid 103 through 353)) } 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=1.00 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: 1.630 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: 5.750 Check model and map are aligned: 0.230 Set scattering table: 0.160 Process input model: 39.520 Find NCS groups from input model: 1.100 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.004 0.110 14756 Z= 0.250 Angle : 0.743 13.306 20003 Z= 0.420 Chirality : 0.044 0.216 2338 Planarity : 0.004 0.044 2579 Dihedral : 18.748 151.600 5752 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.11 % Favored : 91.84 % Rotamer: Outliers : 0.19 % Allowed : 35.80 % Favored : 64.01 % 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: -1.30 (0.20), residues: 1789 helix: 0.55 (0.21), residues: 659 sheet: -1.02 (0.50), residues: 116 loop : -1.90 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.005 0.001 HIS B 214 PHE 0.011 0.001 PHE A 351 TYR 0.014 0.001 TYR D 341 ARG 0.003 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 148 time to evaluate : 1.598 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 149 average time/residue: 0.2402 time to fit residues: 55.1836 Evaluate side-chains 138 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 146 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 152 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14756 Z= 0.217 Angle : 0.603 11.784 20003 Z= 0.289 Chirality : 0.042 0.155 2338 Planarity : 0.004 0.044 2579 Dihedral : 11.177 153.897 2126 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.61 % Favored : 91.34 % Rotamer: Outliers : 5.45 % Allowed : 32.73 % Favored : 61.82 % 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: -1.16 (0.20), residues: 1789 helix: 0.74 (0.21), residues: 687 sheet: -1.12 (0.44), residues: 136 loop : -1.93 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 174 HIS 0.005 0.001 HIS C 214 PHE 0.015 0.001 PHE F 16 TYR 0.015 0.001 TYR D 341 ARG 0.003 0.000 ARG F 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 140 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8265 (p0) REVERT: B 44 MET cc_start: 0.7704 (tmt) cc_final: 0.7367 (tmt) REVERT: C 40 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8779 (mm) REVERT: C 110 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7920 (p0) REVERT: E 113 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9195 (tt) REVERT: F 24 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7338 (pp30) REVERT: F 190 PHE cc_start: 0.8822 (p90) cc_final: 0.8606 (p90) REVERT: F 210 ARG cc_start: 0.7390 (tpm170) cc_final: 0.6934 (tpm170) REVERT: F 270 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7224 (tt) outliers start: 87 outliers final: 47 residues processed: 215 average time/residue: 0.2186 time to fit residues: 74.1190 Evaluate side-chains 186 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 133 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 316 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 91 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 136 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 164 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 132 optimal weight: 7.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14756 Z= 0.219 Angle : 0.582 11.214 20003 Z= 0.279 Chirality : 0.042 0.141 2338 Planarity : 0.004 0.042 2579 Dihedral : 10.743 156.113 2124 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 6.83 % Allowed : 32.23 % Favored : 60.94 % 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: -1.07 (0.20), residues: 1789 helix: 0.88 (0.21), residues: 680 sheet: -1.19 (0.42), residues: 155 loop : -1.89 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 174 HIS 0.005 0.001 HIS C 214 PHE 0.011 0.001 PHE F 236 TYR 0.014 0.001 TYR D 341 ARG 0.004 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 137 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7731 (tmt) cc_final: 0.7178 (tmt) REVERT: C 40 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8763 (mm) REVERT: C 110 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7924 (p0) REVERT: D 213 MET cc_start: 0.8867 (mtm) cc_final: 0.8638 (mtm) REVERT: D 331 LYS cc_start: 0.8230 (ptmm) cc_final: 0.7842 (pttp) REVERT: E 27 MET cc_start: 0.7383 (tmm) cc_final: 0.6927 (tmm) REVERT: E 113 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9202 (tt) REVERT: F 190 PHE cc_start: 0.8863 (p90) cc_final: 0.8616 (p90) REVERT: F 210 ARG cc_start: 0.7137 (tpm170) cc_final: 0.6652 (tpm170) REVERT: F 270 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7269 (tt) outliers start: 109 outliers final: 73 residues processed: 228 average time/residue: 0.2162 time to fit residues: 78.5635 Evaluate side-chains 208 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 131 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 339 SER Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 110 ASP Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 296 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 85 MET Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 282 CYS Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 316 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 162 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 47 optimal weight: 0.0270 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS F 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14756 Z= 0.157 Angle : 0.561 10.497 20003 Z= 0.264 Chirality : 0.041 0.149 2338 Planarity : 0.004 0.043 2579 Dihedral : 10.438 156.994 2124 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 5.27 % Allowed : 34.17 % Favored : 60.56 % 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: -1.03 (0.20), residues: 1789 helix: 0.92 (0.21), residues: 693 sheet: -1.25 (0.43), residues: 145 loop : -1.90 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 174 HIS 0.004 0.001 HIS C 214 PHE 0.013 0.001 PHE E 347 TYR 0.015 0.001 TYR D 341 ARG 0.002 0.000 ARG C 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 144 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8282 (p0) REVERT: B 44 MET cc_start: 0.7699 (tmt) cc_final: 0.7070 (tmt) REVERT: C 40 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8705 (mm) REVERT: D 331 LYS cc_start: 0.8197 (ptmm) cc_final: 0.7800 (pttp) REVERT: E 27 MET cc_start: 0.7401 (tmm) cc_final: 0.6897 (tmm) REVERT: E 144 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8224 (tmmt) REVERT: E 179 ARG cc_start: 0.8511 (mmp80) cc_final: 0.8265 (mmp80) REVERT: F 190 PHE cc_start: 0.8855 (p90) cc_final: 0.8519 (p90) REVERT: F 210 ARG cc_start: 0.7017 (tpm170) cc_final: 0.6519 (tpm170) REVERT: F 229 ILE cc_start: 0.8904 (mt) cc_final: 0.8374 (tp) REVERT: F 270 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7209 (tt) REVERT: F 323 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8570 (tt) outliers start: 84 outliers final: 57 residues processed: 214 average time/residue: 0.2438 time to fit residues: 79.7676 Evaluate side-chains 199 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 137 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 324 CYS Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 145 optimal weight: 0.8980 chunk 99 optimal weight: 0.0030 chunk 2 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS F 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14756 Z= 0.159 Angle : 0.550 9.926 20003 Z= 0.259 Chirality : 0.041 0.147 2338 Planarity : 0.004 0.043 2579 Dihedral : 10.250 157.567 2124 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 6.14 % Allowed : 33.98 % Favored : 59.87 % 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: -0.97 (0.21), residues: 1789 helix: 1.08 (0.22), residues: 685 sheet: -1.18 (0.44), residues: 134 loop : -1.94 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 174 HIS 0.004 0.001 HIS C 214 PHE 0.015 0.001 PHE F 236 TYR 0.014 0.001 TYR D 341 ARG 0.002 0.000 ARG C 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 140 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7586 (tmt) cc_final: 0.6994 (tmt) REVERT: B 91 GLN cc_start: 0.8984 (pp30) cc_final: 0.8710 (pm20) REVERT: C 40 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8697 (mm) REVERT: D 331 LYS cc_start: 0.8222 (ptmm) cc_final: 0.7815 (pttp) REVERT: E 27 MET cc_start: 0.7362 (tmm) cc_final: 0.6825 (tmm) REVERT: E 144 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8213 (tmmt) REVERT: F 190 PHE cc_start: 0.8877 (p90) cc_final: 0.8517 (p90) REVERT: F 210 ARG cc_start: 0.6907 (tpm170) cc_final: 0.6423 (tpm170) REVERT: F 229 ILE cc_start: 0.8924 (mt) cc_final: 0.8415 (tp) REVERT: F 323 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8565 (tt) outliers start: 98 outliers final: 73 residues processed: 224 average time/residue: 0.2195 time to fit residues: 78.2119 Evaluate side-chains 213 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 137 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 58 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 14 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS B 72 ASN F 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14756 Z= 0.158 Angle : 0.551 9.650 20003 Z= 0.259 Chirality : 0.041 0.148 2338 Planarity : 0.004 0.044 2579 Dihedral : 10.133 158.152 2124 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 5.89 % Allowed : 34.86 % Favored : 59.25 % 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: -0.90 (0.21), residues: 1789 helix: 1.10 (0.22), residues: 690 sheet: -1.11 (0.42), residues: 156 loop : -1.89 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 174 HIS 0.004 0.001 HIS C 214 PHE 0.014 0.001 PHE F 236 TYR 0.017 0.001 TYR B 341 ARG 0.005 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 137 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6998 (tmt) REVERT: B 64 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8265 (mp) REVERT: C 40 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8676 (mm) REVERT: D 138 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6651 (pp20) REVERT: D 331 LYS cc_start: 0.8233 (ptmm) cc_final: 0.7817 (pttp) REVERT: E 27 MET cc_start: 0.7386 (tmm) cc_final: 0.6834 (tmm) REVERT: E 144 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8204 (tmmt) REVERT: F 190 PHE cc_start: 0.8877 (p90) cc_final: 0.8496 (p90) REVERT: F 210 ARG cc_start: 0.6789 (tpm170) cc_final: 0.6328 (tpm170) REVERT: F 229 ILE cc_start: 0.8914 (mt) cc_final: 0.8410 (tp) REVERT: F 323 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8562 (tt) outliers start: 94 outliers final: 74 residues processed: 217 average time/residue: 0.2247 time to fit residues: 77.0584 Evaluate side-chains 216 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 136 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 168 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 chunk 99 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS ** F 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14756 Z= 0.221 Angle : 0.586 10.679 20003 Z= 0.276 Chirality : 0.042 0.140 2338 Planarity : 0.004 0.043 2579 Dihedral : 10.156 157.989 2124 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 6.27 % Allowed : 33.92 % Favored : 59.81 % 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: -0.92 (0.21), residues: 1789 helix: 1.06 (0.22), residues: 693 sheet: -1.08 (0.42), residues: 167 loop : -1.91 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 174 HIS 0.004 0.001 HIS C 214 PHE 0.015 0.001 PHE F 16 TYR 0.016 0.001 TYR B 341 ARG 0.005 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 136 time to evaluate : 1.879 Fit side-chains revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8374 (mm-30) REVERT: B 44 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7006 (tmt) REVERT: B 64 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8296 (mp) REVERT: B 91 GLN cc_start: 0.8950 (pp30) cc_final: 0.8660 (pm20) REVERT: C 40 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8724 (mm) REVERT: D 331 LYS cc_start: 0.8245 (ptmm) cc_final: 0.7823 (pttp) REVERT: E 27 MET cc_start: 0.7503 (tmm) cc_final: 0.6968 (tmm) REVERT: E 144 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8219 (tmmt) REVERT: F 151 TYR cc_start: 0.8208 (t80) cc_final: 0.7979 (t80) REVERT: F 190 PHE cc_start: 0.8916 (p90) cc_final: 0.8555 (p90) REVERT: F 210 ARG cc_start: 0.6819 (tpm170) cc_final: 0.6297 (tpm170) REVERT: F 229 ILE cc_start: 0.8953 (mt) cc_final: 0.8445 (tp) REVERT: F 323 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8641 (tt) outliers start: 100 outliers final: 80 residues processed: 224 average time/residue: 0.2190 time to fit residues: 77.3559 Evaluate side-chains 219 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 133 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 81 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 107 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 291 ARG Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.0570 chunk 33 optimal weight: 0.9990 chunk 110 optimal weight: 0.0570 chunk 118 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 chunk 16 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 158 optimal weight: 4.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS F 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14756 Z= 0.149 Angle : 0.574 12.026 20003 Z= 0.265 Chirality : 0.041 0.143 2338 Planarity : 0.004 0.044 2579 Dihedral : 10.021 159.409 2124 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 4.89 % Allowed : 35.24 % Favored : 59.87 % 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: -0.86 (0.21), residues: 1789 helix: 1.18 (0.22), residues: 684 sheet: -1.17 (0.46), residues: 131 loop : -1.87 (0.19), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 174 HIS 0.003 0.001 HIS C 214 PHE 0.015 0.001 PHE F 16 TYR 0.022 0.001 TYR B 341 ARG 0.005 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 141 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7562 (OUTLIER) cc_final: 0.6946 (tmt) REVERT: B 64 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8266 (mp) REVERT: B 91 GLN cc_start: 0.8910 (pp30) cc_final: 0.8612 (pm20) REVERT: D 138 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6636 (pp20) REVERT: D 331 LYS cc_start: 0.8211 (ptmm) cc_final: 0.7858 (pttp) REVERT: E 27 MET cc_start: 0.7412 (tmm) cc_final: 0.6850 (tmm) REVERT: E 144 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8203 (tmmt) REVERT: F 24 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7954 (pp30) REVERT: F 190 PHE cc_start: 0.8748 (p90) cc_final: 0.8470 (p90) REVERT: F 210 ARG cc_start: 0.6714 (tpm170) cc_final: 0.6242 (tpm170) REVERT: F 229 ILE cc_start: 0.8893 (mt) cc_final: 0.8404 (tp) REVERT: F 323 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8553 (tt) outliers start: 78 outliers final: 61 residues processed: 206 average time/residue: 0.2376 time to fit residues: 77.0666 Evaluate side-chains 202 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 135 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 237 ASP Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 209 ASP Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 232 GLN Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 144 LYS Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 167 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 97 optimal weight: 0.0970 chunk 70 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 153 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS F 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14756 Z= 0.314 Angle : 0.658 10.975 20003 Z= 0.311 Chirality : 0.044 0.155 2338 Planarity : 0.004 0.043 2579 Dihedral : 10.305 157.996 2124 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 5.77 % Allowed : 34.55 % Favored : 59.69 % 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: -1.25 (0.20), residues: 1789 helix: 0.63 (0.21), residues: 712 sheet: -1.51 (0.48), residues: 125 loop : -1.96 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.005 0.001 HIS C 214 PHE 0.014 0.001 PHE F 16 TYR 0.022 0.001 TYR B 341 ARG 0.003 0.000 ARG E 179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 132 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8448 (mm-30) REVERT: B 44 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7122 (tmt) REVERT: B 64 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8343 (mp) REVERT: D 331 LYS cc_start: 0.8223 (ptmm) cc_final: 0.7811 (pttp) REVERT: E 27 MET cc_start: 0.7579 (tmm) cc_final: 0.7010 (tmm) REVERT: F 210 ARG cc_start: 0.6731 (tpm170) cc_final: 0.6168 (tpm170) REVERT: F 323 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8748 (tt) outliers start: 92 outliers final: 75 residues processed: 212 average time/residue: 0.2223 time to fit residues: 75.2459 Evaluate side-chains 207 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 128 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 351 PHE Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 183 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain F residue 317 ILE Chi-restraints excluded: chain F residue 323 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 165 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 110 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 152 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 161 HIS F 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14756 Z= 0.153 Angle : 0.596 11.556 20003 Z= 0.277 Chirality : 0.041 0.144 2338 Planarity : 0.004 0.043 2579 Dihedral : 10.163 160.293 2124 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.08 % Allowed : 36.30 % Favored : 59.62 % 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: -0.95 (0.20), residues: 1789 helix: 1.04 (0.21), residues: 690 sheet: -1.34 (0.45), residues: 137 loop : -1.86 (0.19), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 174 HIS 0.003 0.001 HIS C 214 PHE 0.015 0.001 PHE F 16 TYR 0.020 0.001 TYR F 151 ARG 0.004 0.000 ARG E 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 134 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6952 (tmt) REVERT: B 91 GLN cc_start: 0.8937 (pp30) cc_final: 0.8603 (pm20) REVERT: D 331 LYS cc_start: 0.8237 (ptmm) cc_final: 0.7842 (pttp) REVERT: E 27 MET cc_start: 0.7423 (tmm) cc_final: 0.6857 (tmm) REVERT: F 210 ARG cc_start: 0.6579 (tpm170) cc_final: 0.6136 (tpm170) outliers start: 65 outliers final: 58 residues processed: 188 average time/residue: 0.2317 time to fit residues: 69.3598 Evaluate side-chains 192 residues out of total 1595 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 133 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 48 ASP Chi-restraints excluded: chain C residue 117 GLU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 343 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 48 ASP Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 51 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 287 VAL Chi-restraints excluded: chain F residue 316 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 43 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 143 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.0040 chunk 126 optimal weight: 0.0030 chunk 8 optimal weight: 20.0000 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.116370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089548 restraints weight = 35877.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.092012 restraints weight = 20520.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093721 restraints weight = 14560.907| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14756 Z= 0.148 Angle : 0.592 11.824 20003 Z= 0.274 Chirality : 0.041 0.135 2338 Planarity : 0.004 0.045 2579 Dihedral : 9.974 161.103 2124 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.95 % Allowed : 36.55 % Favored : 59.50 % 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: -0.92 (0.21), residues: 1789 helix: 1.03 (0.21), residues: 705 sheet: -1.51 (0.46), residues: 116 loop : -1.83 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 174 HIS 0.003 0.001 HIS C 214 PHE 0.018 0.001 PHE F 236 TYR 0.019 0.001 TYR B 341 ARG 0.006 0.000 ARG E 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2620.09 seconds wall clock time: 48 minutes 51.42 seconds (2931.42 seconds total)